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Hex 6.3 User Manual - bioweb: molecular modelling group

1. 17 Docking Molecules 19 5 L Rotational Search erien ene v uve eu exe ebbe tos 20 5 2 Distance Sub Stepping 22 5 8 Docking Examples 22 DA Disc Cache ms bs pe xU dns is 25 5 5 Calculating Bumps 25 5 6 Molecular Mechanics Refinement 25 5 7 Clustering Docking Results 25 5 8 Saving Docking Results 26 5 9 Docking Multiple Structures 27 5 10 Docking Very Large Molecules Macro Docking 27 5 11 Additional Docking Parameters 28 5 12 Molecular Matching 28 6 Miscellaneous 2o rd o RXDEe 30 CLS MATOS cr eren a ne buds mte echt EP hA tr eus 30 6 2 Hetero Atoms uu lee ues VOS i Ee Rex es 32 6 3 Hardcopy Output i2 c me og eee anpra dn 33 6 4 Compressed Files 33 6 5 Environment Variables 33 6 6 Command Line Options 34 6 6 1 Loading Three Structures Together 35 6 6 2 Loading and Superposing Two Structures 35 6 6 3 Docking with Macro File And Log File 35 6 6 4 Docking with File I O Redirection
2. 47 C 4 New Features in Hex Version 5 0 47 C 5 New Features in Version 4 5 48 C 6 New Features in Version 4 2 48 C 7 New Features in Version 4 1 49 C 8 New Features in Version 4 0 49 C 9 New Features in Version 3 4 49 C 10 New Features in Version 3 3 49 C 11 New Features in Version 3 2 49 C 12 New Features in Version 3 1 C 13 New Features in Version 3 0 Appendix D nVidia CUDA Configuration Appendix E nVidia Stereo Configuration Appendix F Frequently Asked Questions Subject Index ccr Sawa de ie be IRE ORE 50 50 52 54 57 iii Chapter 1 Introduction 1 1 Introduction hex heks v amp n US v 1 practise witchcraft 2 bewitch n 1 a magic spell 2 a witch GK hez six The Concise Oxford Dictionary Why sometimes I ve believed as many as six impossible things before breakfast Lewis Carroll 1 1 What the Heck is Hez Hex is an interactive molecular graphics program for calculating and displaying feasible docking modes of pairs of protein and DNA molecules Hex can also calculate protein ligand docking assuming the ligand is rigid and it c
3. 35 6 6 5 Serialising Several Batch Jobs 35 6 6 6 Using Hex as a Web Browser 35 6 7 Examples Directory 36 6 8 Bugs and Known Limitations 36 6 8 1 MACOS i tese eh ree X REESE RU E 36 6 8 2 Non Standard Residues 36 0 8 3 Postscript Honts 11 144 424 bang BEE Ae E 36 6 9 The Test Functions 37 6 10 Technical Information 38 li Contacten seen esce ERE NRA nt ne me a 38 6 12 Acknowledgements 38 6 13 Referentes ices s oce e Ec le dca droites E EI 39 6 4 Citing Hex ead paaa lon abe eue meer med ue ede AO Appendix A Licences 41 A Hex TiG nCe 22 476 tye ld vs REIR EMI 41 Az2 Stride Licences suu ere ep aen au eid caer Rs 43 AS Tess FRET Ficenc meet brates hese sl de eye ere ruidos 43 Appendix B Installation Guide 44 B 1 Microsoft Windows Installation 44 B gt Mac OS X Installation 12x nies eos bb v mienne 44 B 3 Linux Installation 44 Appendix C Feature History AT C 1 New Features in Hex Version 6 1 47 C 2 New Features in Hex Version 6 0 47 C 3 New Features in Hex Version 5 1
4. 38 Mn GWe ge cue eine ne Wee foie 39 Missing Ligand HETATM bug 62 MK sise simenmtenseseipemie AEIMUE 21 39 Molecular Centroids 13 Molecular Graphics 7 Molecular Matching 28 Molecular Mechanics Refinement 25 Molecular Similarity 2 Molecule Control Panel 8 9 Mol Mol sac site we VE ERE UDLPS ES 5T Molscript able Bien MN DRUMS 33 Mouse Buttons 5 Movie Typeac i I peRestecagDUPPRt Benet 14 MPD 5 He Se e ERR DEM Eds 62 MS Windows ses ie adeb pens 38 N Near Platie sue EE Dir 15 NMR Docking 27 NMR Models ie nie us ni ed Geb 27 No Docking Solutions FAQ 61 Non Standard Residues Bug 36 Non Standard Residues FAQ 59 Nvidia 3D Vision 55 nVidia CUDA Configuration 51 nVidia Drivers 15 nVidia Graphics Cards 15 nVidia Stereo Configuration 53 Subject Index O Orientation Control Panel 13 17 18 24 Orientation Editing T Origin Editing ele ETE oraa stef 7 Origin Editing Button 7 Orthographic Projection 7 15 P P Key onon dear Tat rd Ra b EE e te 7 Page Down
5. 5 Home View srl erg OPUS TEE a 6 HEVS Paper queer teme RE sah 39 Hydrogen Atoms 8 I Icosahedral Tessellation 37 1 Button reatet e RAR Sr AM ELVIS 6 Impossible Things 1 Installation Guide 43 Intel Linux Version 38 Intel Mac Version 38 Intermolecular Axis 5 18 Intermolecular Distance 6 Internal Energies 61 64 K Keyboard Keys rer Rp EY Y 7 14 Killing Jobs ru neret pent 7 Kis FR Date Phd SA Ne deem oe a om 21 39 Kiss FFT Licence 43 L Laguerre Polynomials 57 Licences 5 24 ed mulet ie Ahh hea a heeds 40 Ligand ket EVI ere Sets 4 19 Ligand Models 14 Linux 1586 1686 FAQ 59 Linux Install FAQ 57 M Mac OS X Version 38 Macro Docking so ipe RIRs 27 Macro Sampling Control Panel 27 Macross Ls nl Se salue de ae i de 30 Macros Bug iei ooh hee ve 36 Manoeuvring Molecules 16 Marching Tetragons 10 Matching Control Panel 28 Menu Buttons 5 6 Mesa saone nt Nr Pere ua 39 MicroSoft Windows Version
6. orientation is likely to be reduced because Hex will find more low energy false positive orientations during its search This effect can largely be alleviated by ensuring you cluster the generated solutions using the Clustering Control panel In general its better to over sample the search space and then cluster the solutions rather than risk missing good solutions by under sampling in order to make the program run faster The default value of the Distance Range in the Docking Control panel may be too small for large protein protein complexes Hence if you find that increasing the distance range gives a completely different set of docking orientations its likely that you were seriously under sampling the search space in the earlier run In other words if the distance range is too small the program is not going to explore all possible surface surface contacts as one molecule is rotated against the other Appendix F Frequently Asked Questions 61 Hex samples radial distances symmetrically from the starting orientation according to Starting Distance Distance Range 2 in equal steps of Step Size One way to work out what distance range to specify for a global search is to sketch each protein as a plane cross section in such a way that the plane chosen for each protein includes its centroid and the largest and smallest radial rays from the centroid to the surface Then set the initial inter centroid distance the starting dista
7. splitters often come included with stereo glasses kits For best performance use nVidia s AGP driver part of NVidia s driver distribution and Appendix E nVidia Stereo Configuration 55 NOT the Linux AGP driver dev agpgart etc Also use a kernel built with the MTRR option memory type range registers if your machine supports this Provided you have suitable hardware stereographics on flat panel displays using Nvidia s recent 3D Vision kit should work directly on Windows Vista and Windows 7 For Linux you will need to download and install a recent version 195 36 15 19 march 2010 or later of the driver Nvidia drivers http www nvidia com Download index5 aspx lang en us and set Option Stereo 10 in the etc X11 xorg conf file In order to let the nvidia driver detect the USB infra red emitter it is necessary to map USB devices to a pseudo file system which is not done automatically in Ubuntu Linux Here is an extract from my etc fstab file etc fstab static file system information mount the usb device pseudo file system none proc bus usb usbfs defaults 0 0 Here is a reduced extract from var log Xorg 0 log on my 64 bit FX 5800 workstation Cx Ce C II NVIDIA O Option Stereo 10 NVIDIA O Option TwinView O NVIDIA O Option MetaModes 1680x1050 120 4040 1680x1050 0 0 NVIDIA O USB IR emitter stereo requested NVIDIA O Enabling RENDER acc
8. 5 4 Disc Cache If you plan to use Hex more than once enabling a disc cache will speed up the trans lational part of each calculation When disc caching is enabled the large translation matrices are calculated only when necessary and are saved in the cache directory for re use Disc caching controls can be found under the File menu The default cache directory is HEX ROOT cache although it is recommended to set a cache directory explicitly using the HEX_CACHE environment variable The cache directory should be specially created for this purpose i e it contains nothing else and a distinct directory should be used by each user because there s no synchronisation between multiple invocations of Hex With typical usage the disc cache will occupy up to about 200 Mb of disc space 5 5 Calculating Bumps Following the basic docking correlation algorithm candidate docking orientations may be filtered and refined using one of the Post Processing options Post processing is applied to the top scoring 1 000 solutions from the correlation search or the user selected number of orientations to retain if larger than 1 000 The simplest option is to enable a bumps counter in which the number of steric clashes between non bonded pairs of heavy atoms in each solution is calculated An option in the Clustering Control panel may then be used to filter out solutions with a specified number of steric clashes 5 6 Molecular Mechanics Refinement In addit
9. Automated installation script hex configure bin Existing Her 2 4 users Please note that some of the parameter names used in macro files have changed from version 2 4 Therefore some of your existing macro files may no longer work as expected This was unavoidable given the many changes in the new version Apologies for any inconvenience Appendix D nVidia CUDA Configuration 52 Appendix D nVidia CUDA Configuration In order to use one or more Nvidia GPU devices in a docking calculation it is necessary to download a version of Hex wich was compiled with CUDA support and to install a CUDA enabled device driver and the cuFFT run time library which is part of the CUDA developer Toolkit http www nvidia com object cuda get html Get CUDA On Windows systems Hex plus CUDA should just work Some Linux systems e g Ubuntu provide a convenient way to download the Nvidia driver as a proprietary hardware driver However I recommend that you do NOT use this feature as it could cause problems when downloading the developer Toolkit I recommend downloading both driver and toolkit directly from the Nvidia web site However if you upgrade the Linux kernel you will need to re install the Nvidia drivers In order to let the Hex executable find the CUDA run time libraries you will need either to set the LD_LIBRARY_PATH environment variable to point to the folder containing the CUDA libraries or you will need to edit the system file etc ld
10. ligand S3hfl ly pdb open complex 3hfl pdb fit ligand When using a complex reference structure you should find that on loading the molecules the complex is drawn in grey and the complex molecule is superposed onto the receptor it is the complex that physically moves here If the ligand molecule originated from an Chapter 5 Docking Molecules 20 edited complex file then it will also be superposed over the complex because its coordinates are relative to the same coordinate frame as the receptor molecule Otherwise the ligand can be transformed into the receptor complex frame using the Fit Ligand button in the Orientation Control panel Note If you wish to superpose one or more proteins onto another the above behaviour may be exploited by treating the stationary molecule as the receptor and by treating each moving molecule as the complex Saving the fitted complex to a new PDB file will effectively write it out its fitted orientation in the coordinate frame of the receptor 5 1 Rotational Search Docking calculations are controlled by the options in the Docking Control panel Generally the docking search proceeds by rotating the receptor and ligand about their centroids at each of a range of intermolecular distances The receptor and ligand are each assigned two Euler rotation angles and the final rotation is defined as a twist of the ligand about the intermolecular axis The default behaviour is then to perform a ful
11. of each icosahedral tessellation vertex and by setting the radial distance for each angular sample to that of the function value You can control the number of sample points with the Mesh Order slider above and you can control the display style of the functions using the Display Mode selector of the Harmonic Surface control panel Try Graphics Harmonic Surface Display Mode Polyframe Note that when you rotate or translate the scene using the mouse buttons the display reverts to wire frame rendering until you release the button This is usually faster than re rendering polygons during the motion The Solid Motion button right hand border last button can be used to toggle this behaviour The three sliders in the Harmonics Control panel labelled Alpha Beta and Gamma are used to test Euler angle rotations of the spherical harmonics Changing these values will cause the rotated function R a 3 7 Yim 0 to be calculated and displayed Visually this should be identical to drawing the unrotated figure and then manually rotating it with the mouse by R y about the zaxis R B about the y axis followed by R a about the zaxis This is an important visual test because ensuring that the spherical harmonic functions can be rotated computationally is fundamental to Hez s shape superposition and docking calculations Chapter 6 Miscellaneous 38 Finally using spherical harmonics to parametrise the surface shape of a cube provides a furt
12. 10 Technical Information 38 Tessellation Mesh Order 12 Test Functions ss terenem ie sr Lo RR 37 TexInto 4 ue ute emt inet en epis 39 49 The Gimp ets dome e oH gap 39 Translation Matrices 11 25 Translation Matrices Paper 40 Twist Samples 24 V van der Waals Spheres 9 Viewing Large Molecules 8 VMD ns pecia BERLINE REA 57 W Windows XP 4 saute aye SO pi 38 Z zlib Za ci ble et Ee Ba aie bs 39 ZOO sem ae Ue ge net etwa Ne eee Ni 5
13. 3hfl mac 2ptc mac or hfl mac ptc mac This will open the files that contain the atom coordinates of either the crystallographically determined complex first pair or the coordinates of the separately determined protein subunits second pair superposed on the corresponding complex structure In both cases the structure of the complex should appear as a thin grey skeleton The examples directory also contains sample colour files col and a few other macro files mac which you might wish to examine In particular the startup mac file explains how to select an initial colour scheme for example It also shows how to switch off the initial logo display if you prefer to start with a blank screen and how to change the type of browser Netscape by default used to display this User Manual on line Please note the example docking scripts dock mac will only work correctly if Hex can find the relevant PDB files and related macros Once you ve defined the HEX PDB and HEX MACRO environment variables to point to your own directories you should copy the appropriate files from the examples directory into these new directories if you still want to use these scripts Optionally you can also download a more extensive set of docking examples from the Hex download page A much more extensive set of docking test cases can be obtained from Zhiping Weng group s Docking Benchmark http zlab bu edu zdock benchmark shtml 6 8 Bugs and Known Limitati
14. I think its hard to assess how good the predicted orientations might be and which of them might correspond to the actual solution It is certainly hard to devise a scoring function which can reliably eliminate false positives Camacho amp Vajda Curr Op Struct Biol 2002 12 36 40 Camacho amp Va jda and others have proposed using a combination of algorithms and to look for consensus orientations but I have doubts Personally I think the surest approach is to use whatever experimental or bioinformatics evidence e g correlated mutations might be available to help suggest the location of the binding sites and then to use a docking algorithm to create some feasible models which can subsequently be challenged by lab based experiments e How can I perform a purely electrostatic correlation Its not possible to do a pure electrostatic correlation in Hex However it should be possible to increase the weight of the electrostatic correlation in a shape electrostatic calculation For example if you create a small macro file containing factor g 7000 and then run this macro using the Macros Run menu all subsequent docking calcula tions will have electrostatic energies scaled up by a factor of 10 Thus electrostatics should dominate Generally I would say that shape complementarity is more important that elec trostatics but if you know electrostatics are important for a given system then this may be worth trying e When I en
15. LICENSOR the applicable LICENCE FEE within 30 days of receipt of an appropriate invoice prepared by the LICENSOR b For Academic and Governmental SITES the LICENCE FEE is waived 4 Iransfer of Licence a The LICENSEE shall not in any way sublicense rent assign or transfer this LICENCE or the computer program Hez 6 X 5 Copyright a The LICENSOR owns the copyright and all and any other intellectual and industrial property rights in Hex 6 X and its associated documentation You must therefore treat Hex 6 X and its associated documentation like any other copyrighted material e g a book b Hex 6 X and the associated documentation is protected by United Kingdom copyright laws international treaty provisions and all other applicable national laws c The LICENSEE acknowledges that it does not and shall not acquire any title copyright or any other intellectual property rights in Hex 6 X or the associated documentation 6 Limited Warranty and Disclaimer of Warranty a The LICENSEE acknowledges that software in general is not error free and that the existence of such errors shall not constitute a breach of this LICENCE Appendix A Licences 42 b Save as expressly provided under this LICENCE no warranty or conditions express or implied statutory or otherwise as to condition quality performance merchantability or fitness for purpose is given or assumed by the LICENSOR in respect of Hex 6 X and its associated documentation
16. be saved to disc The most com pact method is to write a docking summary file using the File Save Transform menu item This writes a file that lists the docking energies for all predicted orientations along with the rotation and translation parameters which should be applied to the ligand coordinates in the original ligand PDB file in order to produce the corresponding dock ing orientation in the coordinate frame of the recptor PDB file The actual file format is descibed in the first few comment lines of the output file similar but more detailed output file format is given by File Save Matrix This lists the transformations in a more verbose format using keywords to label each piece of data For rigid body docking both formats are quite compact but you will need to write your own code to process the docking summary file Its not possible to read these files back into Hex they are purely for output to external software Chapter 5 Docking Molecules 27 The second less compact output method is to write a separate PDB file for each docking orientation The current docking orientation can be written to a single PDB file by selecting File Save Both Alternatively a range of docking solutions may be saved using File Save Range This opens a new Save Docking Range panel in which a range of docking solutions may be specified along with a a file name pattern to be used for the output files The default i
17. correlation code is accelerated using a real fast Hartley transform FHT The number of solutions that are retained after a docking run is now user definable formerly hard coded at 512 Added a user definable cluster window size useful when the list of docking solutions is large Added support for one button mouse pointer using Ctrl and Meta keys Fixed Missing Ligand HETATM bug Fixed various minor bugs Added new environment variable HEX MESSAGES to control use of text message window C 6 New Features in Version 4 2 Hex Version 4 2 The coordinate origin for multiple model structures is now taken from the first model not the average of all models Fixed bug for PDB files containing one structure with one MODEL keyword Fixed silly bug in picking ID mode Text output to Message Window now much faster There are several undocumented features currently under development Appendix C Feature History 49 C 7 New Features in Version 4 1 Hex 4 1 is a bug fix release e Double clicking a directory in the file browser no longer crashes the program e Cartoons are now drawn correctly for chains with blank labels e Fixed start up crash up on some SGI systems JPEG lib version fault C 8 New Features in Version 4 0 e Microsoft Windows version now available thanks to e New Graphical User Interface GUI made with FLTK http www f1tk org e New Message Window for text output and session logging e New Progre
18. far as any calculations are concerned Enabled solvent atoms are displayed in light blue disabled atoms are displayed in grey The Hetero toggles have a similar function Similarly the Enable ARG LYS toggle allows the status of any arginine and lysine side chain atoms to be changed Disabling these side chains during a predictive docking run generally reduces the sensitivity of the docking correlation but is often highly beneficial in the following molecular mechanics refinement step This part of the program is still under development The Solvent Colour button activates a simple colour chart which may be used to select an alternative colour with which to display enabled solvent atoms Chapter 6 Miscellaneous 33 The Cull Solvent button calculates which water molecules are completely buried within a protein and disables those that are not The culling calculation uses the dot surface algorithm to determine the accessibility of each water molecule The van der Waals surface of each atom in the structure is covered with dots those dots which are occluded by neighbouring atoms are deleted in a recursive search so that any atom with no surviving dots must be completely inaccessible to a probe sphere Any water molecule that has surviving surface dots must therefore be accessible to the probe and is culled i e removed from the surface atom list The algorithm is repeated automatically until no more waters can be removed Usually this takes f
19. in the PDB data file Some further editing of the output file e g to rename duplicated chains may be required if the chains are to be individually coloured for example 3 2 Solid Models The Graphics Solid Models control panel contains several options for drawing lit solid models of molecular scenes including van der Waals spheres licorice and tube represen tations Aromatic rings may be drawn as hexagonal or pentagonal blocks which can produce some interesting displays especially when viewing DNA molecules The position and colour of the light may be controlled using the controls in the Graphics Lighting control panel 3 3 Cartoons The Graphics Cartoons control panel contains several options for drawing proteins as ribbon cartoons The default behaviour is to draw a cartoon over the molecular skeleton To view only the cartoon you can disable the molecular skeleton using the Display Molecule button in the Controls Molecule panel There are several options on the Cartoon Con trol panel which allow the colour width and thickness of ribbon cartoons to be controlled Chapter 3 Molecular Graphics 10 Different parts of the ribbon can also be coloured according to secondary structure type i e helix sheet turn The type of secondary structure is currently calculated using Frishman and Argos Stride program ftp ftp ebi ac uk pub software unix stride 3 4 Solid Surfaces Solid molecular surfaces may be
20. is normally used to display two molecules at once Go to the F ile menu and click on File Open Ligand to open another molecule You could open the same molecule for the ligand as you have opened for the receptor in which case the two molecules will be superposed Figure 2 below shows the result of loading the example lysozyme structure 3hfl ly pdb which is the natural antigen ligand of the HyHel 5 antobody In this example the R slider bar on the bottom border was used to separate the molecules and the van der Waals display mode and intermolecular axis were enabled using the right hand border short cut buttons Try experimenting with the other short cut buttons You should now find that the mouse buttons translate and rotate both molecules in the scene BAIE File Controls Graphics Macros Help Messages f 2 3hflfv Ligand 3hfl_ly l Ig s IN ER IS lrir 2 S 64 hs Z amp DI Dil Ea 2 Figure 2 Hex scene showing the HyHel 5 antibody Fv domain and lysozyme in van der Waals mode and with the intermolecular axis drawn in white 2 2 Function Buttons The column of buttons on the left hand border of the main window implement various picking and editing functions These operations differ from the short cut buttons in that they generally involve changing the operating mode of the mouse The inset icon in the top left border displays the current mouse mode The default Pointer
21. molecules respectively and optionally a complex file which contains both molecules in the docked orientation When using a complex structure you should ensure that the chain names and residue numbers are consistent with those of the receptor and ligand because Hex uses this information to identify and hence superpose corresponding pairs of alpha carbon atoms from each chain in order to calculate RMS deviations between the docked position of the ligand and its position in the known complex If necessary you can use the Linux utility hex_chain in Hez s bin directory to rename a chain in a PDB file Similarly the hex delta utility may be used to renumber the residues of a given chain Up to three protein structures can be loaded into Hex directly from the command line For example to load three of the PDB files from the examples directory for the HyHel 5 lysozyme complex you could type at the Linux command prompt hex 3hfl fv pdb 3hfl ly pdb 3hfl pdb If you are studying a particular system and you find you are continually repeating the same sequence of actions to get things set up you may find it to be more convenient to load all three molecules together using a short macro file similar to those in the examples directory For example the macro file 3hfl mac can be executed by selecting Macros Run 3hfl mac This macro file contains the following 3hfl mac close all set colour file 3hfl col open receptor S3hfl fv pdb open
22. or arrow keys Home Starting orientation Page Down Next solution Page Up Previous solution End 500 th or last solution You should find in the above example that Her generates several orientations with low RMS deviations from the correct starting orientation However you might object that the calculation was biased to find the right answer by restricting the search to the known binding sites If so you could try a global docking search about 1079 trial orientations using Controls Docking Receptor Range 180 Controls Docking Ligand Range 180 This calculation will take about 30 minutes on a single 1GHz Pentium III processor This is substantially faster than an equivalent calculation using a conventional FF T approach In this particular case Hex should still identify the correct docking orientation to within about 1 5 Angstrom RMS but its often useful to use restricted searches when starting with unbound subunits When viewing docking solutions it is helpful to keep either the receptor or the ligand in a fixed orientation in the display so that only one molecule moves when stepping through the docking solutions The default is to transfer any receptor motion onto the ligand so Chapter 5 Docking Molecules 25 that the ligand appears to translate and rotate about a fixed receptor This behaviour can be changed using the Orientation Control panel Controls Orientation Centre Ligand
23. or rds tanta 1 FEETSpeed8 sog 5 bum hee Eie 21 EFEW Eust dont eec iu ete o ehe 21 File Selection Panel 4 Final Search cir rep xni iR 21 24 ELDER ox deu nested deae eese enirn cw 39 POg nn ei Eb LEN IMBUE Eis 8 FONS e 2 gd on te x deo Do meer e 6 Frame R8t6 han enbiueTeck bed bate 14 Full Screen Mode 7 G ONMN PME 15 Gaussian Densities 10 Gaussian Surfaces 10 Getting Started 3 Global Search e pese en ami Rede ge 24 GMP serres den iU Mu demie dui 39 GPU Pap r see Ic EI ERU 39 Graphics Menu 8 GRASP Beaten seedy debes ei eiii 33 Grid Dimensions 23 GUT een se ne me MS 3 GUI Control Toggle 15 CPAS 33 39 49 Gzipped Files 33 H Hammer Button 6 18 Hardcopy Output 33 Harmonic Surface Control Panel 12 37 Harmonics Button 5 Harmonics Control Panel 27 37 Hbonds SI Tz erres 2 icde Re RISE inst 62 HETATM record bug 62 Hetero Atoms 32 Hetero Control Panel 19 32 Hex Lic nce iut d eda eye 41 Hex Dictionary Definition 1 Home Position
24. remnant in Hex They used to be used as an approximate but fast way to calculate the molecular surface the solvent accessible surface and the van der Waals surface for docking However docking and superposition calculations now use a much more accurate method based on contouring Gaussian density functions to Chapter 3 Molecular Graphics 13 calculate these two surfaces Nonetheless it is still sometimes useful to be able to draw a dot surface because Hex uses all the atoms from an input PDB or SDF file to draw the surfaces Hence dot surfaces may be used to verify the presence of atoms that might not be recognised or drawn properly in other drawing modes Like the SH surfaces dot surfaces are now calculated directly from the marching tetragons surface as described above 3 7 Changing the Scene Origin Normally rotation and scale zoom operations are applied relative to the scene origin When just one molecule is loaded the scene origin coincides with the centroid of the molecule However when two molecules are loaded the scene origin is taken as the mid point between the two molecular centroids This behaviour can be changed by using the first selector in the Orientation Control panel to select a given molecular centroid or a specific atom to act as the origin The Select Origin button a circle with a diagonal cross through it on the left hand border may also be used to select the zoom rotation centre Although docking calculations nor
25. running If using these controls changes the graphical complexity of the scene Hex will take a second or two to adjust the drawing speed back to the requested frame rate 3 10 Full Screen Mode Personally I think full screen mode is the best way to view molecular graphics scenes You can press F to switch back and forth between full screen and window manager modes By default Hex starts in window manager mode You can also press G at any time to toggle the display of the GUI controls when in full screen mode G only toggles the setting not the display So you won t see the effect until you enter full screen mode In both the Linux and Windows versions you should always use F to get full screen mode because this forces the window border off Conversely don t use the window manager s maximise control because this forces the window to keep a border and F won t then work In Windows XP you will probably still see the Windows Taskbar in full screen mode To get rid of this open the Taskbar and Start Menu in the Windows XP Control Panel and uncheck the Keep the taskbar on top of other windows item I don t know whether this feature is available on earlier versions of Windows In Mac OS X full screen mode does not override the Mac Taskbar and Dock panels Hence it is best not to use Hez s full screen mode but instead use the window manager s maximise button to ensure the graphics window is well behaved In Linux full screen G
26. sene eue Rech ne Rea 7 Page Up suites eU nee ace Le set 7 Papers Citing Hex 62 Parametric Functions 1 PIB sun en Sais tos IEEE Te RETE 4 P oplezc hdd x qe ee edP EE 39 Perspective Projection 7 15 Picking 5 i Et Eus 6 Pipe Output ss veo ict axxo aedi 33 Pipes Directory oves ds prs bah 45 Pointer Mode cipe nine 18 Pointer Mode Button 6 Polar Hydrogens RERUMS 8 Post Processing Options 25 Postscript Fonts Bug 36 PowerPC Version 38 Projection Control Panel 15 PVM ner CUP p ibd eae Eo Pd prey 62 R R 5lidersz2i ee RER he ere eH ets 6 Radial Cutoths yl ul ERROR ERR 8 Receptorzssllil1zilee leebpeueee ety Eve 6 pe 4 19 Receptor Models 14 Reference Energy FAQ 60 Reference Orientation 19 References 222v de dima ane seen 39 Refine Docking FAQ 59 Relative Permittivity 10 Reloading Docking Conformations 62 Ribbon Cartoons 9 Rotational Search 20 S S Keys selon a Turno i RR e E T den if Saving Docking Ranges 27 Saving Docking Results 26 Scene Centre er AM chery ee ER E 2 13 SGL Version sh
27. should be straight forward Just download the latest driver from http www nvidia com view asp PAGE linux and follow the instructions However as mentioned above make sure to de install any earlier nVidia drivers first Here s what the Device Section of my etc X11 xorg conf file looks like after editing nVidia s supplied template Stereo is not compatible with the compositing feature Section Extensions Option Composite Disable EndSection If you have multiple graphics cards use usr bin lspci to find the PCI bus ID of the specific device to use Section Device Identifier NV AGP VendorName nvidia Driver nvidia BusID PCI 1 0 0 Option Stereo 0 O off Option Stereo sh 1 DCC with cable splitter Option Stereo 3 3 3 pin DIN connector Option Stereo 10 10 USB IR emitter for 3D Vision kit Option metamodes DFP 1680x1050_120 0 0 DFP 1680x1050 0 0 Option NoLogo true Option Overlay false Option UseEdidFreqs true Option NvAgp 1 O off 1 nvidia 2 AGPGART 3 try 2 1 EndSection I verified these settings and that stereo was enabled by running the glxinfo program Although my old XGL700 has an on board stereo DIN 3 pin socket I couldn t get a signal off this with the 3123 4191 drivers Currently stereo synching only seems to work in DCC Data Control Channel mode This requires a monitor cable splitter to which the stereo glasses are connected Such
28. the script hex in the bin directory which then launches the appropriate executable from the exe directory As of version 6 0 there are normally two separate executables for each type of system one build with CUDA and one built without CUDA By default the launch script will run the CUDA executable if it has been installed You can give the option nocuda on the command line to select explicitly the non CUDA executable The examples directory contains several PDB files and example Hez macro files Unless you set the above environment variables Hex will first look in the examples directory for any macro and PDB files you want to use The data directory contains the runtime data files necessary to colour and charge protein and DNA molecules for example The pipes directory contains Linux scripts which allow the molecular structures in the current Hex scene to be written directly to external programs such as GRASP or Molscript The cache directory is the default location in which Hex will store its translation matrix files for docking runs You may wish to use a different location for the cache by defining the HEX CACHE environment variable to point to an alternative directory Appendix C Feature History 4T Appendix C Feature History Hex has been on going work for around 12 years although most of the basic functionality was implemented in the first three years This section summarises the development history There are no entries here for ver
29. wish to define the HEX STEREO and HEX CACHE variables By default Hex will use a stereographics window if a suitable graphics card is detected However this gives a slower drawing rate than non stereo mode even when viewing a non stereo zero parallax scene Setting HEX STEREO no causes a non stereographic window to be selected at start up time and hence should give faster graphics performance During a docking calculation Hex will write translation matrix files to the HEX_ROOT cache directory However you can define HEX CACHE to point to another directory possibly on another disc with more space to over ride the default In Windows XP environment variables are defined using the Advanced option in the System control panel B 2 Mac OS X Installation For Mac OS X just download and double click the hex 6a osx pkg package file This will install Hez as an application bundle in the Applications directory Double clicking the Hex icon will run the program The bundle automatically assigns the correct value of the HEX ROOT environment variable You may wish to edit the hex launch script within the bundle to assign non default values to the other environment variables mentioned in this section B 3 Linux Installation You will need to download the installation script hex_setup bin and either the hex 6a Inx tgz tar file for an Intel PC or hex 6a ppc tgz for Linux on a PowerPC machine i e not running Mac OS X The distribution fil
30. within the body of the larger molecule The shape matching algorithm re uses much of the docking code and the Matching Control panel works in almost exactly the same way as for docking see Section 5 3 Docking Exam ples page 22 One noticeable difference however is that similarity scores are calculated using a Carbo like overlap score This is essentially a normalised overlap volume scaled onto 1000 0 for compatibility with the existing clustering ranking and summary output code used by the docking module In other words Hex always thinks negative is good Chapter 6 Miscellaneous 30 6 Miscellaneous 6 1 Macros In Her macros or scripts are command files which contain a sequence of instructions equivalent to the commands that you might issue from the graphical user interface To create a macro file go to the Macros menu and select Learn All subsequent operations that you perform including opening files editing molecules changing colours etc will be recorded When you have completed the sequence of commands that you want to record select the Save command in the Macros menu This will produce a small window prompting you for a file name in which to save the command sequence The convention is to use a file name of the form filename mac although you could adopt your own convention Here is an example Lets open an antibody structure colour it according to the residue identities of the framework and hypervariable lo
31. Control panel The default settings are for the program to perform an initial Steric Scan at N 16 followed by a Final Search at N 25 using just the steric contribution to the docking energy In this mode about all but the top 30 000 orientations are discarded after the Steric Scan The Steric Scan may be toggled off in which case every orientation is evaluated using a steric correlation and optionally an electrostatic correlation to order N as given the Final Search slider However this can significantly increase total docking times Using the two step search with N 16 and N 25 is found to work well in practically all cases The electrostatic contribution to the docking correlation may be enabled using the Electrostatics toggle Electrostatics are only ever calculated in the Final Search phase You can get a feeling for how well each correlation order N recognises a given complex by running the program on known complexes and by observing how highly the correct solution is ranked in each case Chapter 5 Docking Molecules 22 Docking Control Correlation Type EEE FFT Mode 3D Fast Lite bd Post Processing None s Grid Dimenson o e Solutions soo Receptor Range 1s0 w stepSize 75 v Ligand Rangefiso StepSize 75 x TwistRange 360 v StepSize ss x Distance Range ao x ScanStep o 75 w substeps x r stericscan 1 T T Final Search 25 son s Activate Dismiss Figure 7 Screen shot of the Docking Control p
32. Hex 6 3 User Manual Protein Docking Using Spherical Polar Fourier Correlations Copyright c 1996 2010 David W Ritchie Dave Ritchie Team Orpailleur INRIA Nancy Grand Est LORIA 54506 Vavdoeuvre les Nancy France Table of Contents 1 Introduction 2s os 19222 RUDI ERE RI G45 Ss 1 1 1 What the Heck is Hex 1 1 2 New Features in Hex Version 6 8 2 1 3 How to Read this Manual 3 Getting Started 222 222 Lo onore 4 2 1 Short Cut Buttons 4 4 4 44 e y er ad 5 2 2 HUN CHON BUttONS sse lime cc DOLI EN Re e E e 6 2 3 Keyboard Keys nup Ee RARI Tu IEEE 7 Molecular Graphics 8 3 1 Basic Display Styles 8 3 27 Doud Models rda te RID REA Saye dee E te UAE I dg 9 3 93 QartoonS Le nc uxeviv eR sw o ue n ERU ede UY 9 3 4 SolidoSurfaces i eoi eroe EBD Ide tutam aque xu 10 3 5 Spherical Harmonic Surfaces 11 3 6 Dot Surfaces oec y LH ERU REP eS 12 3 7 Changing the Scene Origin 13 3 8 Clipping the Scene 13 3 9 SA nabloIbu erre M d PIDE LC dc RR E 14 3 10 Full Screen Mode 15 3 11 Stereo Displays psi d deiren en eed e Ra ve 15 Manoeuvring Molecules 17 4 1 Editing Origins and Orientations
33. Hex Licence This is a legal agreement between you the LICENSEE and the LICENSOR for use of the computer program Hex 6 X where 6 X is a version number This licence does not apply to versions of Hex with version numbers less than 6 0 By installing copying or otherwise using Hex 6 X you agree to be bound by the terms of this licence agreement If you do not agree to the terms of this licence agreement the licensor is unwilling to license the software to you In such circumstances you may not use or copy the software and you should return the unused product within 7 days 1 Definitions a LICENCE means the terms and conditions contained herein b LICENSOR means the Institut National de Recherche en Informatique et en Automa tique INRIA of Domaine de Voluceau Rocquencourt Le Chesnay France as owner of the software comprising the computer program Hex 6 X c SITE means a single computer or internal computer network operated by the LICENSEE at the premises of the LICENSEE specified when Her 6 X was ordered or installed 2 Grant of Licence a The LICENSOR grants the LICENSEE a non transferable and non exclusive licence to use Hex 6 X in connection with computers only on the SITE to which the LICENCE applies b The LICENSEE will not under any circumstances reverse engineer decompile or dis assemble Hex 6 X 3 Licence Fee a In consideration of the LICENCE granted pursuant to Section 2 the LICENSEE shall pay to the
34. Hex was written mostly in C but also uses some C for the GUI The graphical user interface was built with FLTK http www fltk org The Hex logo and icons were created with The Gimp http www gimp org The translation matrices used in Hex are calculated using the GMP library http www swox com gmp The 3D and 5D FFTs were implemented on Linux using the Intel MKL http www intel com library and on other platforms using Kiss FFT http sourceforge net projects kissfft Copyright c 2003 2004 Mark Borgerding Support for compressed files is thanks to zlib http www gzip org zlib gzip http www gzip org and bzip2 http sources redhat com bzip2 The initial Linux version of Hex would have been impossible without the Mesa http www mesa3d org graphics library The Windows version of Hex was built entirely under the MinGW http www mingw org environment Her has never been anywhere near a Microsoft compiler This manual was produced using texinfo http www gnu org software texinfo Hex uses the Stride ftp ftp ebi ac uk pub software unix stride program to as sign protein secondary structures for cartoon displays See Section A 2 Stride Licence page 43 if you have any doubts about whether you are entitled to use Stride Vishwesh Venkatraman helped to re write the CPU and GPU correlation calculations to use multi threading The following people for making significant programming contributions to Hez as p
35. Mode a left arrow represents the basic scene manipulation mode described above You can revert to this mode by pressing the Left Arrow button which is the first button in the left hand border Chapter 2 Getting Started T The next JD button selects atom picking mode In this mode picking an atom i e pressing and releasing Button 1 over an atom will identify the atom by displaying its chain residue and atom numbers The atom coordinates and charge Q will also be displayed in the Messages window The Graphics Fonts menu can be used to select the font in which atom labels are displayed In stereo displays picking uses the right eye object coordinates since most people are right eye dominant Picking the same atom again will remove the atom ID label The Hammer button the last button in this border will clear all picked ID s This button generally acts to undo or kill the previous operation s depending on the current mouse mode Below the ID button is the Manoeuvring Molecules button which looks like a lightning bolt and below this is the Origin Editing button a line with two crosses This is followed by the Clipping Mode button three faces of a cube which controls scene clipping see Section 3 8 Clipping the Scene page 13 Manoeuvring molecules also called editing is something you may need to do before run ning a docking calculation For example before docking you should always ensure that the molecules are located
36. PRI Blind Trial 22 27 CAPRI Papers acc beet ep enm 40 Carbo Iudex sete eoe ene 29 Cartoon Button 5 Cartoon Control Panel 9 Cartos dns rb Re PIC HB e E 9 GCavities fines nant tet ak ete N 10 Changing the Scene Origin 13 Charge Density 10 Checkerboard 7 Cit mex yoy seu Bed ne pU URDU ED Lt ts 40 Clipping recie teet ILES MEER ETE 13 Clipping Button 7 Clipping Clipping the Scene T Clipping Slider 14 Clustering Control Panel 25 26 Clustering Docking Results 25 Colour Files BD eee an ee Vei ed 8 Colour Ranps ae ate ee ech ba tne er ER 10 Colour Schemes 8 63 Command Line Options 34 Commercial Licence FAQ 60 Complex utn TR ane dde Da 4 19 Compressed Files 33 eonnect ETTO sss aioi che ds eine demie done 58 Contacts nerga dete te se mele ating Ete n to 38 Control Q i dou xoc d tym alee 7 Contxol Q 5e nias Sea sate hae te ng an iE res 7 Correlation ille il rir UE 1 Crystal Symmetry 9 CUBE BAI o iren E UD EUR SE NE 21 52 D Data Directory oed ERU et 45 DCC Stereo Mode 54 Disc Cache entes tn EH Ra 25 Dis
37. S and HEX FIRST GPUJ have been added to allow close control over which GPUs to use during a calculation C 3 New Features in Hex Version 5 1 5D and 3D FFT grids are scaled to match user defined search range angles This allows localised 5D FFTs to fit in much less memory and requires less post filtering Added Box remarks to PDB docking output to help set up MD refinements C 4 New Features in Hez Version 5 0 3D and 5D FFT docking correlations have been implemented Linux version uses Intel MKL code for better FFT docking performance Appendix C Feature History 48 Simpler set up of docking search parameters Added the ability to read SDF files as well as PDB files Added the ability to recognise and draw spherical harmonic surfaces and surface prop erties calculated by the ParaSurf program from Cepos Insilico Ltd Simpler single file installation tar file for Linux Executables for Silicon Graphics and SunOS are no longer provided Molecular surfaces may now be drawn in a new alpha blending transparency mode Added the ability to set up initial docking orientations by specifying named interface residues Added screen shots and illustrations to the User Manual Various minor bug fixes C 5 New Features in Version 4 5 Hex Version 4 5 Executables now avalable for Mac OSX and Linux PowerPC machines Added small distance sub stepping for high order correlations for better coverage of search space The low level
38. The plane is now drawn in white either as a filled shape or as an outline depending on which face you happen to be viewing The mouse buttons now move only this plane relative to the scene or if you have hit the Space Bar the mouse moves the plane and the scene together The filled face will become the clipping face of that plane Button 2 may be used to activate the selected plane just press Button 2 anywhere in the scene That is every part of the scene above the filled face should become clipped Pressing Button 2 again toggles clipping Try moving the clipping plane though the scene using the right slider or by using the mouse and the Space Bar to control the movement Iry using the Delete Key keyboard backspace to toggle the sense of the clipping plane Once you are happy with the position of the clipping plane you can revert to Pointer Mode select the Left Arrow button or you can proceed to pick and activate further clipping planes Chapter 3 Molecular Graphics 14 In pointer mode the right hand slider continues to operate the most recently activated clipping plane It is also possible to make the slider move two planes simultaneously Having activated a clipping plane now try picking it with Button 3 This draws the plane in yellow and ties its motion to the slider Now pick and activate the clipping plane using Buttons 1 and 2 on the opposite face of the clipping skeleton The right slider should now move both planes toget
39. UI mode with the Gnome window manager is quirky Everything works as it should except that Hex control panels can t be re raised over the full screen window after the control panel loses mouse focus i e when the cursor leaves the panel You will need to revert to window manager mode F to see everything again These problems seem to be due to a strange interaction between the Gnome window manager and the FLTK interface toolkit 3 11 Stereo Displays Stereo is known to work on Windows XP and RedHat Linux 8 0 kernel version 2 4 18 14 XFree86 version 4 0 0 or later with an nVidia Quadro4 XGL700 card and using a recent nVidia driver 1 0 3123 or later For best results with Hex and nVidia cards please use the latest versions of both driver software service packs and operating systems The recent nVidia drivers give Hex both stereo in a window and full screen stereo on both Windows XP and Linux nVidia s 4351 driver May 2003 is excellent and is very easy to install See Appendix E nVidia Stereo Configuration page 54 for more details However if you are upgrading an nVidia driver on Windows ensure you de install amy earlier drivers first The type of graphics visual that Hex uses is determined when the program first starts up By default Hex tries to use a stereographics window However this nearly halves the drawing rate compared to non stereo drawing So if you don t like want stereo you can force stereo off by using hex noste
40. Waals steric density model whereas the electrostatic model is derived from classical electrostatic theory By writing expressions for the overlap of pairs of parametric functions one can obtain an over all docking score as a function of the six degrees of freedom in a rigid body docking search With suitable scaling factors this docking score can be interpreted as an interaction energy which we seek to minimise Due to the special orthogonality property of the basis functions the correlation or overlap as a function of translation rotation operations between a pair of 3D functions can be calculated using expressions which involve only the original expansion coefficients In many respects this approach is similar to conventional fast Fourier transform FFT docking methods which use Cartesian grid representations of protein shape and other properties and which then use translational FFTs to perform the docking correlations However the Cartesian grid approach only accelerates a docking search in three translational degrees of freedom whereas the SPF approach allows the effect of rotations and translations to be calculated directly from the original expansion coefficients Even though the FFT part of a docking search may be fast the overall speed of calculation still depends very much on the initial set up costs and the final post processing costs of Chapter 1 Introduction 2 filtering and perhaps clustering the results Hex is fast bec
41. able electrostatics I only get one docking solution What is going on Appendix F Frequently Asked Questions 60 Its likely that your structures contain unrecognised residues and or unrecognised atoms Hez assigns a default charge and radius to any unrecognised atoms normally based on the first letter of each atom name These defaults are usually reasonable but if a structure has a large number of unrecognised hydrogens Her might assign 0 5e to each hydrogen to give a highly positively charge protein pair of such proteins will have a very unfavourable electrostatic interaction and docking such a pair will give a total of zero low energy orien tations In order to avoid having zero length arrays within the program Hex forces at least one solution to be reported e What is the licensing fee for commercial user There is currently no licence fee for commercial users But this does not mean the software is free When you download or otherwise obtain a copy of Hex you are agreeing to be bound by the Hex Licence Agreement You are also asked to obtain prior agreement with the author if the program is to be used for profit This might seem to be unnecessarily complicated but the intention is to make the software available and to publicise the algorithms used without compromising the possibility of potential future commercialisation These days universities like to protect their assets and I want to protect my assetc e What is th
42. an superpose pairs of molecules using only knowledge of their 3D shapes Hex has been available for about 12 years now but as far as I know it is still the only docking and superpostion program to use spherical polar Fourier SPF correlations to accelerate the calculations and its still one of the few docking programs which has built in graphics to view the results Also as far as I know it is the first protein docking program to be able to use modern graphics processor units GPUs to accelerate the calculations The graphical nature of Hex came about largely because I wanted to visualise the results of such docking calculations in a natural and seamless way without having to export unman ageably many and usually quite big coordinate files to one of the many existing molecular graphics programs For this reason the graphical capabilities in Hez are generally relatively primitive compared to professional molecular graphics packages but the main aim here is to do docking not to make publication quality images In Hex s docking calculations each molecule is modelled using 3D expansions of real orthog onal spherical polar basis functions to encode both surface shape and electrostatic charge and potential distributions Essentially this allows each property to be represented by a vector of coefficients which are the components of the basis functions Hex represents the surface shapes of proteins using a two term surface skin plus van der
43. and all such warranties and conditions are hereby excluded save to the extent that this exclusion is prohibited by law 7 Limitations of Liability a Except to the extent that such liability may not lawfully be excluded the LICENSOR shall not be liable for damages arising out of or in conjunction with the LICENCE of Hex 6 X or its use or performance b In no event shall the LICENSOR be liable for any loss of profits business interruption loss of business information or other special consequential damages even if the LICENSOR has been advised of the possibility of such damages or for any claim against the LICENSEE by any other party 8 Termination a This LICENCE agreement is effective from the date of purchase or installation which ever is earlier of the computer program Hez 6 X b The LICENSEE can terminate the LICENCE at any time by notifying the LICENSOR of its intention in writing c The LICENSOR can terminate the LICENCE after providing the LICENSEE with 14 days prior notice and an opportunity to remedy the situation if the LICENSEE fails to pay any amount due to the LICENSOR d The LICENCE shall terminate 30 days after written notice by either party in the event of any material or persistent breach by the other party of any of the terms of this LICENCE which is either incapable of remedy or remains unremedied at the end of the said period of 30 days e Upon termination of this LICENCE the LICENSEE shall i disc
44. anel Although the default is to use correlations to N 25 in Rounds 3 5 of the CAPRI blind trial http capri ebi ac uk I found that better results are obtained using N 30 correlations see Section 6 13 References page 39 Generally N 30 is recommended when docking high resolution crystal structures for which the conformational change on binding is expected to be small N 25 should be used when docking model built structures or structures which are expected to be more flexible As rule of thumb I would use N 16 for the scan stage with final scoring at N 30 and I would use scans using N 20 when scoring with N 30 In some cases a good solution can be missed with the N 16 scan It is safer but obviously slower always to use N 20 for the initial scan 5 2 Distance Sub Stepping As of version 4 5 Hex performs the high resolution Final Search correlation using smaller distance incerements than are used for the fast low resolution Steric Scan phase This allows the search space to be covered more rapidly coarsely in the first phase but more finely in the final phase This behaviour is controlled by the Distance Range Scan Step and SubSteps parameters in the Docking Control panel The default values are Distance Range 40 Scan Step 0 75 SubSteps 2 This means that the Steric Scan phase will search over 55 distance increments of 0 75 A from the starting separation plus the starting separation itself These orientations are sorted
45. aneous 31 Here is a more complicated example using several macro files starting with the top level macro dock ptc mac which is provided in the examples directory dock ptc mac docking_receptor_samples 492 docking_ligand_samples 492 docking_alpha_samples 128 receptor_range_angle 180 ligand_range_angle 30 twist_range_angle 360 ri2_range 21 ri2 step 0 75 grid size 0 6 docking main scan 16 docking main search 25 run macro ptc mac run macro randomise ligand mac activate docking ptc mac loads unbound protein subunits in standard orientation close_all open receptor 2ptn_e pdb open ligand 4pti_i pdb open complex 2ptc pdb fit ligand randomise ligand mac moving thing 1 edit O receptor 1 ligand 2 complex Chapter 6 Miscellaneous 32 randomise molecule i e randomise the ligand orientation commit view commit changes moving thing 1 done editing Sa ae A a mn nn SS ee One could run this macro sequence interactively and then use the Page Up and Page Down keys to step through displayed solutions However when testing the docking algorithm or when performing multiple docking runs its probably easier and of more interest to examine the calculated energies and ranks of each predicted docking orientation Since these values are printed as the calculations proceed its often convenient to run the whole thing in batch and to capture the results in a log file For example at th
46. art of their Honours or MSc projects Ryan Cairns BSc FLTK port Ewan Lyle BSc ribbon cartoons Ioannis Zaferopoulos BSc solid models Russell Hamilton MSc macro docking displays Guillaume Valadon BSc surface colouring Gary MacIndoe wrote a nice web interface http www loria fr ritchied hex server This is useful if you wish to try out Hex without having to in stall it However for best results please download the program from Hex http www loria fr ritchied hex and run it locally 6 13 References e Last FFT Protein Protein Docking on Graphics Processors D W Ritchie and V Venkatraman 2010 Manuscript in preparation e Accelerating Protein Protein Docking Correlations Using A Six Dimensional Analytic FFT Generating Function D W Ritchie D Kozakov and S Vajda 2008 Bioinfor matics 24 17 1865 1873 e Recent Progress and Future Directions in Protein Protein Docking D W Ritchie 2008 Curr Prot Pep Sci 9 1 1 15 http www loria fr ritchied papers ritchie cpps 2008 pdf e Toward High Throughput 3D Virtual Screening using Spherical Harmonic Molecular Surface Representations L Mavridis and D W Ritchie 2007 J Chem Inf Model Chapter 6 Miscellaneous 40 47 5 1787 1796 http pubs acs org cgi bin abstract cgi jcisd8 2007 47 i05 abs ci7001507 htmlf e High Order Analytic Translation Matrix Elements for Real Space Sir Dimensional Polar Fourier Correlations D W Ritchie 2005 J Ap
47. ation Controls Docking Activate You have just started an example docking search restricted to the known binding sites so the calculation should only take a few minutes The program will take a few seconds to calculate the surface skin coefficients and then proceed to calculate docking correlation scores at each of the specified angular and intermolecular increments A Cartesian grid is used to sample the molecular skins numerically but this grid plays no further role in the calculation once the surface skin expansion coefficients have been determined Most conventional FFT docking algorithms have to use rather large grids e g 1 ngstrom cubes because the grid must accommodate all possible translations of the ligand about a Chapter 5 Docking Molecules 24 stationary receptor Here the grid only needs to contain the larger of the two molecules so that much finer sampling grids are feasible In Hez a 0 6 Angstrom grid seems to work well and is still reasonably fast to calculate The sampling grid size may be varied using the Grid Dimension selection box The calculation of the surface skins used in the docking correlation is controlled by the parameters in the Surface Control panel The default values do not normally need to be changed The search in the above example is restricted because setting the ligand and receptor range angles to 45 degrees means that only a small fraction of the total possible rotational increments the Recep
48. ause it uses FF T correlations as much as possible and because the set up costs are much lower in the SPF approach than in Cartesian grid based approaches It also turns out that the FFT part of the calculation maps very well to the GPU hardware Thus further speed ups can be expected if you have a suitable graphics card Although it is not always easy to compare the performance of different docking algorithms because a lot depends on the size of the translational or rotation steps used for example I would still claim that Hex is at least 10 times faster than conventional FFT docking algorithms Hex is also very easy to use However to use Hez most effectively it can sometimes require some thought when setting up the calculation especially when setting up the starting orientations of the proteins to be docked In the spherical polar approach it is natural to assign the six rigid body degrees of freedom as five Euler rotation angles and an intermolecular separation Thus in complete contrast to Cartesian based FFT approaches the rotational part of a docking search is the easy bit and modelling translations becomes the hard part Fortunately however only a few translations typically about 40 steps of 0 75 Angstrom are required to complete a six dimensional docking search One advantage of the spherical polar approach is that it is easy to constrain the docking search to one or both binding sites when this knowledge is available
49. by calculated energy and a new set of trial orientations are generated for the top scoring 10 000 20 000 orientations using the Scan Step and SubSteps parameters to construct new distance samples in steps of Scan Step Substeps from the initial orientations In other words the default behaviour is essentially to scan the search space at 1A resolution but to perform the high resolution scoring at 0 5A resolution Setting SubSteps 0 gives the old behaviour of earlier versions in which a constant distance step is used for both resolution levels Chapter 5 Docking Molecules 23 5 3 Docking Examples OK lets start docking Open the Docking Control panel and select the following mostly default values from the selection boxes Controls Docking Correlation Type Shape Only Controls Docking FFT Mode 3D Fast Lite Controls Docking Post Processing None Controls Docking Grid Dimension 0 6 Controls Docking Solutions 500 Controls Docking Receptor Range 45 Controls Docking Receptor Step Size 7 5 Controls Docking Ligand Range 45 Controls Docking Ligand Step Size 7 5 Controls Docking Twist Range 360 Controls Docking Twist Step Size 5 5 Controls Docking Distance Range 40 Controls Docking Scan Step 0 75 Controls Docking Substeps 2 Controls Docking Steric Scan 16 Controls Do
50. can then use the Clustering control panel to put solutions with more than a given number of bumps to the end of the list if you wish Requesting molecular mechanics MM energies also causes backbone bumps checking to be turned on Similarly Hbonds 1 means no hydrogen bonds were calculated You need to enable the Show H bonds toggle in the Molecule Control panel Subject Index Subject Index 5 SD BET Paper e iom ELEVATA 39 A Acknowledgements 38 Additional Docking Parameters 28 Animation 2 402 a xe MUSS E Le 14 Animation Control Panel 14 Arrow Keyvscosi d LIRE hay ae Sani 7 Ath OP suc sur de sante dea bas sets aad 2s 38 AXES AXIS rei ua need d ee e abel e e Cree ates 5 B B Rey ss ea ota dew teas cuite reds T Basic Display Styles 8 Batch Docking Example 32 BBSRG ssi fee lee de ee BES LS ces 39 Beowulf Parallelisation 62 pind errorae tk Na Ett xe en 58 Biological Symmetry 9 Bond Widths sereg eai eue riens nets 8 Broken Ribbons 57 B BSus cuis So x eee t eet e ate PED pr d 36 BUM pS vene ee et nr pere en 25 Bumps s 7 ewe dodo a deis 62 Buttons ssc eh se et sera ver E UMP 5 6 bzip2 t esee MERC EARIU MU RET 33 39 49 Bzipped Files 33 C Cant See the Ligand 62 CA
51. cking Final Search 25 This says that the Steric Scan N 16 phase of the docking calculation will be performed at 1 40 0 75 53 intermolecular separations in steps of 0 75 A starting from the current distance posted in the R slider in the bottom border of the main window The Final Search N 25 phase will be applied to the the highest scoring scan orientations in steps of 0 75 2 as described above The rotational search will use angular increments of about 7 5 degrees in each of the two ligand and receptor rotational angles and in steps of 5 5 degrees about the twist angle Internally the given step sizes will be adjusted to give computationally convenient numbers of samples For example a step size of 5 5 degrees will actually give 64 samples 360 64 5 625 Specifying a step size of 7 5 degrees will give 48 or 24 angular samples in the corresponding FFT grid or it will select an icosahedral tesselation with 812 vertices because that is the tesselation order which will give an average angular distance between neighbouring pairs of vertices of about 7 5 degrees Note This method specifying the angular resolution is new in version 5 0 Earlier versions required the user to specify the sampling density directly in terms of tesselation orders which was not very easy to understand Please also note that the default search step sizes are often somewhat finer than the search increments used in previous versions Now start the calcul
52. d by a separate subprocess so you will normally see two Hex processes running in your system s process or task monitor tool and Unix style sockets are used to communicate between the two processes The error messages referring to bind or connect indicate there was a problem creating the message window subprocess This could happen if networking is disabled on your machine unlikely if there is a problem with the machine s hostname possible or on very slow machines likely due to time outs Hez always assumes that the standard name localhost IP address 127 0 0 1 exists and that networking is enabled to the extent that ping localhost works On Unix Linux machines you can stop Hex from trying to create a message window by typing hex nomessages or by setting the environment variable HEX MESSAGES no in which case Hex will print Appendix F Frequently Asked Questions 59 all its messages to the terminal window Windows XP does not use terminal windows and Hez relies on the message window process to show all text messages e I noticed you only provide an i586 executable for Linux I have an 1686 1786 system so could you supply an executable for my machine It might run faster I compared the docking performance of Hex compiled for a 686 processor on my 686 system with a 585 compiled version and there was hardly any difference Docking performance depends almost entirely on the efficiency of a few floating point operations and
53. d with icc Removed limit of 65 535 atoms per molecule Fixed obscure bug with model numbers in multi model dockings Fixed bug where mis named gamma hydrogens were silently charged as mercury Hg Note there is still technically a PDB limit of 99 999 atoms per structure Fortran I5 format but Hex will try to read files that break this restriction As of version 3 1 the models in multi model structures are now numbered from 1 or use the actual model number given in the PDB MODEL record C 13 New Features in Version 3 0 Hex 3 0 contains several new features and a number of improvements compared to Hez 2 4 These are mostly concerned with the docking algorithm and the graphics displays although several bugs reported by users have also been fixed The main new features are Docking multiple models e g from NMR structures Docking very large molecules as in the CASP2 CAPRI docking challenges Clustering docking solutions Appendix C Feature History 51 Bumps filter for docking Molecular mechanics refinement of docking orientations still under development Docking twist search now accelerated by FFT Multi file output of docking results New molecular surface calculation Solid Models VDW spheres licorice tubes etc Lighting with movable light Screen shot output to JPEG PNG and Postscript files Special pipe option e g to pass a scene to Molscript or Grasp Better Linux support Improved command line options
54. drawn using the Graphics Solid Surfaces control panel These surfaces are calculated using a novel marching tetragons algorithm to contour a Gaussian density representation of the atoms of each molecule The surface skins used in the docking correlations are calculated using this Gaussian density approach The Colour Mode selector allows surfaces to be coloured by atom colour the default electrostatic potential or charge density or by using the classic blue red colour scheme used in earlier versions of Heg For electrostatic surfaces a colour ramp is calculated which initialy shows positive potentials charges in blue negative values in red and intermediate values in white The Surfaces Colour Ramp button may be used to activate a simple graphical controller for the colour ramp The electrostatic potential and charge density displays are calculated from the in vacuo global charge density expansion using the current speherical polar docking expansion order N The colours in a charge density display may appear somewhat washed out compared to perhaps more familiar potential displays This is because the potential is calculated directly from the charge density using Poisson s equation and the del squared form of this equation strongly emphasises any local variation in the charge density So if the potentials ook right then the charge density is also correct NB Hez uses a relative permittivity value of 8 instead of the mo
55. e don t put a batch run in the background force GUI mode even when stdin is not a terminal request a stereographic window same as stereo request a non stereographic window Chapter 6 Miscellaneous 35 nos same as nostereo messages write messages to a separate window the default nomessages write messages to standard output not separate window stdout same as nomessages log logfile or 1 write log of entire session to file 1 logfile same as log pdb pdbfiles load up to 3 PDB files to be displayed browse same as pdb but forces interactive mode for browser noligand treat two PDB files as receptor complex 2 short form of noligand superposes two molecules pos position ligand near receptor the default nopos don t mess with ligand coordinates e macfile s execute up to 3 macro files 6 6 1 Loading Three Structures Together Load three PDB files which contain a receptor a ligand and an existing complex structure to be used to calculate RMS deviations of the docking predictions and execute a macro file of docking commands writing the results to a named log file hex r pdb 1 pdb c pdb e docking job mac 1 docking job log 6 6 2 Loading and Superposing Two Structures Load a receptor and a complez i e no ligand and superpose the complex onto the receptor hex 2 r pdb c pdb 6 6 3 Docking with Macro File And Log File Run a docking calculation assumed to b
56. e fully specified in a macro file using 2 CPUs hex ncpu 2 e job mac 1 job log 6 6 4 Docking with File I O Redirection Run the previous example using I O redirection hex ncpu 2 lt job mac gt job log 6 6 5 Serialising Several Batch Jobs If both stdin and stdout are not terminal devices Hex automatically puts itself into the background When running a Unix script with a series of different jobs this behaviour should be suppressed using the noexec option hex ncpu 2 noexec lt jobi mac gt jobl log job2 starts after jobl hex ncpu 2 noexec lt job2 mac gt job2 log 6 6 6 Using Hex as a Web Browser On Unix systems Hex may be used as a web browser helper application for PDB files by specifying that Hex should be invoked when the browser receives a MIME type that corresponds to a PDB file e g chemical x pdb See the hex browser file in the HEX ROOT bin directory for details If anyone implements something similar for MS Windows please let me know Chapter 6 Miscellaneous 36 6 7 Examples Directory The examples directory under the main hex directory contains PDB data files of examples of two protein complexes HyHel 5 lysozyme and BPTI Inhibitor It also contains short macro files to load the subunits of these complexes Unless you have changed the values of the HEX PDB and HEX MACROS environment variables Hex will look in the examples directory by default Select Macros Run and then select one of
57. e reference energy for electrostatic calculations in Hex and in thermody namic terms are you working with G or U In Hex the reference zero energy point is for two proteins at infinite separation i e zero interaction Negative scores are favourable positive unfavourable i e the molecules interpenetrate or have poor surface contacts The electrostatic energy Hex calculates corresponds to the classical internal energy U of a system of point charges The shape complementarity score or hydrophobic energy is scaled to comparable units but forced to have more negative energies This pseudo energy is also closer to U than G but could easily be in error by 100 s of KJ mol compared to experimental measurements I have compared calculated Hex energies of complexes with equilibrium constants ie ignoring the difference between U and G due to entropy for some antibody antigen complexes and found no correlation So the calculated energies are pretty meaningless on an absolute scale But I m sure this is also true of most all other macromolecular docking software e When I change some of the parameters in the docking control panel such as the intermolecular distance I get different docking results What s going on The first few controls in the Docking Control panel define the search increments that Hex will use during a docking search If you increase the number of steps i e use more and smaller steps then the rank of the right
58. e unix prompt type hex lt dock_ptc mac gt dock_ptc log Hex goes into the background ps ef grep hex check background process running The various docking parameters are described in more detail in Chapter 5 Docking Molecules page 19 Please be aware that very little checking is done when reading a macro file Hence you should always use the GUI via Macros Learn and Macros Save to find legal values for the macro commands Using values which are not available in the GUI may crash the program or produce meaningless results 6 2 Hetero Atoms When Hex loads a protein or DNA structure it tries to draw all atoms including any water molecules or other hetero atoms such as ions and other small molecules that it finds in the PDB file The Hetero Control panel allows a certain degree of control over how such atoms are treated The Hetero Control panel is activated using Controls Hetero This panel allows you to modify the treatment of solvent and hetero atoms Display Solvent toggle Enable Solvent toggle Display Hetero toggle Enable Hetero toggle When Enable Solvent is selected all water molecules are treated as part of the structure when calculating dot surfaces or spherical harmonic surfaces for example Toggling this option excludes solvent from the surface calculation The Display Solvent toggle may be used to eliminate all waters from the graphics display but remember they still exist if enabled as
59. eleration NVIDIA O NVIDIA GPU Quadro FX 5800 GT200GL at PCI 2 0 0 GPU 0 E NVIDIA O Memory 4194304 kBytes NVIDIA O VideoBIOS 62 00 3a 00 03 NVIDIA O Detected PCI Express Link width 16X NVIDIA O Interlaced video modes are supported on this GPU NVIDIA O Connected display device s on Quadro FX 5800 at PCI 2 0 0 NVIDIA O Samsung SyncMaster DFP 1 NVIDIA O Samsung SyncMaster DFP 1 330 0 MHz maximum pixel clock NVIDIA O Samsung SyncMaster DFP 1 Internal Dual Link TMDS NVIDIA O Validated modes NVIDIA O DFP 1680x1050_120 0 0 NVIDIA O DFP 1680x1050 0 0 NVIDIA O Virtual screen size determined to be 1680 x 1050 NVIDIA O DPI set to 88 88 computed from UseEdidDpi X config NVIDIA O option NVIDIA O Disabling 32 bit ARGB GLX visuals NVIDIA O USB IR emitter Copyright c 2009 NVIDIA Corp NVIDIA O stereo controller NVIDIA O Initialized GPU GART NVIDIA O Setting mode DFP 1680x1050_120 0 0 Loading extension NV GLX NVIDIA O Initialized OpenGL Acceleration Appendix E nVidia Stereo Configuration 56 However for 3D vision to work on many Quadro models it is necessary to connect the IR emitter to the GPU using a mini DIN to 1 8 inch connector to get the synchronisation signal for the glasses This cable was missing in my 3D Vision shipment ordered in France but the Nvidia support team quickly mailed me the necessary part Appendix F Frequently Asked Questions 57 Appe
60. ems involve translating and rotating one or both molecules into the desired orientation How ever to a first approximation the similarity problem can be reduced to a three dimensional rotational search by initially placing both molecules in a common coordinate system Al though Hez will remain primarily a docking program the 3D superposition calculations implemented in Hex demonstrate the potential for performing fast 3D superpositions using the SPF correlation approach Work is in progress to develop this approach further as a separate program for high throughput ligand screening Chapter 1 Introduction 3 1 2 New Features in Hez Version 6 3 This is a bug fix release from version 6 1 e Fixed some memory leaks in the docking code e The CUDA version now comes with the run time libraries CUDA 3 1 included This should fix some compatibility issues between Hex and different versions of the CUDA run time libraries especially between CUDA versions 2 3 and 3 0 e The GUI has been built using FLTK version 1 3 1 3 How to Read this Manual This Manual attempts to describe the main features of Hex by a mentioning each feature at least once and b by giving some examples of how to use the program most effectively In the following sections italic text is used to refer to Menu Item and Button Names or other important concepts within the program Typewriter text is used to indicate a sequence of menu selections or button actions that are
61. es a directory of PDB files HEX_PIPE optional HEX_ROOT pipes locates a directory of Hex pipe scripts HEX_MESSAGES optional yes write messages to separate output window HEX ROOT required none locates the main Hez installation di rectory e g usr local hex HEX STARTUP optional none locates a start up macro script e g HEX ROOT data startup v4 mac HEX STEREO optional yes defines whether a stereographic visual is requested by default HEX VERSION optional 6a the default version of Hex to use Additionally you should ensure that your PATH contains the SHEX_ROOT bin directory On systems with multiple GPUs it may be desirable to reserve some GPUs for display or other compute purposes For example on a system with 3 GPUs you could force Hex to use only the last GPU by setting HEX FIRST GPU 2 and HEX GPUS 1 6 6 Command Line Options The general command line format to invoke Hex is hex options pdbfile s where options may be a combination of vit ncpu n ngpu n nice n cuda nocuda kill B2 debug noexec gui stereo s nostereo where is a version number string e g 4f 5a where n is the number of CPUs to use where n is the number of GPUs to use runs at lower priority n a nice value request program with CUDA support the default request program with no CUDA support try to kill any stuck Hex jobs run within a debugger such as gdb print debugging messages another debug adds mor
62. es should be installed using the shell script hex setup bin by typing sh hex setup bin This script can normally be trusted to install Hex correctly even if you have already installed an earlier version of the program The script will add any necessary environment variables to your default shell environment In cases where a central file server is used to serve files to different types of workstations several different executables may be installed into a single hex installation directory Note that in previous versions of Herz the installation script was called hex_install bin If you prefer to install the program manually you should create a hex directory cd to that directory and then uncompress the distribution files into it For example assuming you are installing the usual Linux PC version use zcat hex 6a 1nx tgz tar xvpf Appendix B Installation Guide 45 In order to make Hex work properly your login script login or profile or whatever should set the environment variable HEX ROOT to the hex installation directory You should also add Hez s bin directory to your PATH so that a you can run Hez and b Hex can find the files it needs under HEX ROOT These two steps are normally performed by the hex setup bin script Optionally you can also specify directories that specify where Hex should start looking for colour files macro files and PDB files and you can specify the location of a temporary cache directory all excep
63. f7000 libgcc s so 1 gt lib libgcc s so 1 0x00007f6b2abe0000 libc so 6 lib libc so 6 0x00007f6b2a871000 lib64 1d linux x86 64 s0 2 0x00007f6b31065000 libdl so 2 gt lib libdl so 2 0x00007f6b2a664000 libstdc so 6 gt usr lib libstdc s0o 6 0x00007f6b2a354000 Appendix D nVidia CUDA Configuration 53 librt so 1 gt lib librt so 1 0x00007 6b2a155000 libz so 1 gt lib libz so 1 0x00007f6b29f3e000 libGLcore so 1 gt usr lib libGLcore so 1 0x00007f6b282e7000 libnvidia tls so 1 gt usr lib tls libnvidia tls so 1 0x00007f 6b3115b000 B libXau so 6 gt usr lib libXau so 6 0x00007f 6b280e4000 libxcb so 1 gt usr lib libxcb so 1 0x00007f6b27ec8000 libXdmcp so 6 gt usr lib libXdmcp so 6 0x00007f6b27cc3000 Appendix E nVidia Stereo Configuration 54 Appendix E nVidia Stereo Configuration For OpenGL stereo in a window and full screen stereo you will need a Quadro FX 1800 graphics card or higher http www nvidia com object quadro pro graphics boards html Nvidia Quadro stereo For stereo on a flat panel display you will need a device with a refresh rate of 100Hz or higher Nvidia recommend the Samsung SyncMaster 2233RZ or the Viewsonic VX2265 http www nvidia com object 3D Vision Requirements html flat panel stereo If you have the right hardware and Windows Vista or Windows 7 stereographics should just work On Linux configuring your nVidia graphics card for stereo
64. g from the edited pose Hez can also read a list of ligands from a multi molecule SDF file However docking results are always written out in PDB format 5 10 Docking Very Large Molecules Macro Docking The radial shape functions used in Hex decay exponentially beyond about 35 Angstroms from the chosen origin This means that the shapes of proteins much larger than this are not represented well One example of such a large protein is the viral surface hemagglutinin molecule presented in the CASP II and CAPRI protein docking challenges In order to dock such large molecules Hex assigns multiple local coordinate systems to the larger molecule assumed to be the receptor and docks the ligand around each local coordinate frame on the receptor Setting up the receptor coordinate systems is controlled by the Controls Macro Sampling control panel The general approach is to construct a very low resolution spherical harmonic surface rep resentation of the receptor say setting L 5 in the Harmonics Control panel and then to cover this surface with a large number of spheres These spheres are placed using the surface normals of each triangular patch used to draw the harmonic surface The spheres are then iteratively culled where the sphere with the greatest overlap with its neighbours is culled at each iteration This is repeated until some pre set number of spheres default Chapter 5 Docking Molecules 28 25 remain these should still co
65. hange directory to the hex exe directory and type hex6a 1586 to start the program without the aid of the front end startup script it should give you a graphics window with the Hex logo on a black background The 5 part of the filename corresponds to version 5 0 if you have a different version of the program the executables will have slightly different names Anyway Appendix F Frequently Asked Questions 58 if that works the problem is definitely with HEX ROOT or PATH in which case check that HEX ROOT is set to the directory you installed hex in i e your stuff hex without anything after the hex bit also check that the PATH variable includes HEX_ROOT bin ie your stuff hex bin in amongst the other colon separated bits of the PATH sorry if this is all obvious but different people have different levels of knowledge You should be able to type which hex and get back your stuff hex bin if the PATH is properly set up If running stand alone hex5 1586 doesn t work the next thing to try is the 1dd utility This shows the dependency list of any shared libraries that a program was linked against ldd hex5d i586 The output on my Linux system looks like this linux gate so 1 gt 0x00b36000 libGLU so 1 gt usr X11R6 lib libGLU so 1 0x028f 3000 libGL so 1 gt usr lib libGL so 1 0x00a7d000 libXext so 6 gt usr X11R6 1ib libXext so 6 0x00d6a000 1ibX11 so 6 gt usr X11R6 1ib libXi1 s0o 6 0x00c94000 libp
66. her possibly perverse test of the method You could try File Open cube and then experiment with different display styles and surface resolutions Using L 16 gives a remarkably good spherical harmonic cube In addition to rotating the cube manually it can be rotated by rotating the harmonic basis functions above or equivalently by rotating the shape expansion coefficients by setting the Rotate Coefficients toggle in Harmonics Control 6 10 Technical Information In order to run Hez your system should have at least 64Mb main memory but preferably more 128 Mb or greater and about 4 MB of disc space for the program and data files The speed of the docking calculations can be increased by allocating an optional disc cache directory of up to about 100 MB For molecular docking and graphics applications I d recommend buying the highest spec Linux machine you can afford but be sure to select a graphics card that has Linux support I personally own a Pentium III Xeon system with a Quadro4 XGL700 graphics card currently running Redhat 9 and Fedora 4 and 8 Its great The latest Linux version was built on Pentium III Xeon system running Fedora Core 8 kernel 2 6 23 X org 7 1 gcc 4 1 Versions are also available for Fedora Core 4 kernel 2 6 21 X org 6 8 2 gcc 4 0 RedHat 9 0 kernel 2 4 20 8 XFree86 4 3 0 gcc 3 2 2 and RedHat 8 0 kernel 2 4 18 14 XFree86 4 2 0 gcc 3 2 7 Earlier versions of Hex are still available fo
67. her through the scene You can tie multiple planes to the slider although selecting two perpendicular planes is probably the most sensible option As you might expect picking a plane with Button 3 for a second time unties it from the slider At any time while in clipping mode you can undo the most recent operation using the Hammer button l hree successive clicks on the Hammer will clear all clipping settings and will return the display to an unclipped scene If necessary you can use the keyboard Plus and Minus keys to zoom the clipping skeleton independently of the scene If the scene contains molecular surfaces dots lines or polygons you can use the keyboard Equals key to toggle between clipping both the molecule and its surface the default and clipping just the surface leaving the molecular skeleton fully visible 3 9 Animation The Animation Control panel allows you to run a movie of either the results of a docking calculation or a sequence of models from an NMR structure for example and it controls how the scene spins if you perform a mouse drag release action After a docking run pressing Start in the Graphics Animation control panel will cause Hex to draw each docking solution in turn The rate at which orientations are drawn is controlled by the Frame Rate slider Similarly if you have loaded a PDB file that contains several NMR model structures setting the Movie Type to Receptor Models or Ligand Models as app
68. ial atomic Gaussian density The order of the 3D expansion default N 25 is taken from the Docking Final Search parameter in the Docking Control panel Both the Sigma and Tau surfaces are contoured using a hard wired density value of 0 25 However reconstructing each 3D density from the shape expansion coefficient vectors is a relatively expensive calculation This display mode is mainly intended to illustrate the internal rep resentations used in docking Figure 3 shows some example shape density isosurfaces In Chapter 3 Molecular Graphics 11 this figure the highest polynomial power in the SPF expansion L is related to the order N in the Docking Control panel by L N 1 Qo dodge Sa a he Figure 3 Illustration of the SPF steric density representations at various 3D expansion orders for the complex between the HyHel 5 antibody Fv domain left and quail lysozyme right From top left to bottom right steric density isosurfaces shown at expansion orders L 12 16 20 24 and 26 with the subunits separated by 15 A to give a full view of each domain The bottom right pair shows the van der Waals surfaces from which the SPF expansions are derived The Sigma Tau Shift slider controls how the shape and electrostatic expansion coefficients are computationally translated using the T R translation matrices prior to reconstructing the surface from translated expansion coefficients Thus it is possible to view graphically how the re
69. ibution Neither the author nor the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIB UTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DI RECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSEQUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTI TUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUDING NEGLI GENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE Appendix B Installation Guide 44 Appendix B Installation Guide B 1 Microsoft Windows Installation For Microsoft Windows just download and run the self installer program hex 6a win exe This adds a Hex icon to the Programs menu and adds the environment variable HEX ROOT to the registry That s all you should need to get started However there are several other environment variables which you can set to customise Hex s behaviour These have the same names as the Linux version described below In particular you may
70. ic density functions for each molecule It will then systematically search over the range of angular and intermolecular distance samples given in the Matching Control panel However unlike docking Hex first translates the ligand s centre of mass to coincide with that of the receptor If the molecules are similar this essentially reduces the search space to a rotational search to a first approximation Hence the default distance range and angular samples are set to much smaller values than are used in a typical docking correlation search Similarly good global overlaps can be found using much lower order correlations than needed for docking Therefore its usually sensible to leave all the superposition search parameters at their default values Nonetheless the defaults generally give a search which significantly over samples the search space and only one or two distinct superpositions are likely to remain after clustering By default superpositions are calculated using only the van der Waals density representation of each molecule However this can be changed with the Search Mode selector to match shapes using both the interior van der Waals and exterior surface skin density functions This doubles the computational cost but it can be useful when matching a small molecular fragment onto a surface patch of a larger molecule because the skin matching component ensures surface matches are favoured over trivial inclusion matches of the fragment
71. icitly using the syntax atom_name first atom last atom colour name The Molecule Control panel also contains toggles to display molecular centroids and average molecular ellipsoids The ellipsoids are calculated from low order L 2 spherical harmonic surfaces This control panel also allows the display of any crystallographically related molecules whose coordinates are not given explicitly in the PDB file Use the Symmetry Type selector to select these additional symmetry elements Selecting Crystal causes the scene to be generated using the SMTRY transformations from the PDB file Biological selects the transformations from the BIOMT records and None the default just uses the explicit atoms coordinates as usual Note that atom coordinates are only replicated at display time using OpenGL display lists so that even quite large molecules can be displayed reasonably quickly A fun one to try is the tobacco mosaic virus PDB code IRMV especially when low resolution harmonic surfaces are enabled Another nice structure is the viral coat protein of the phi X174 bacteriophage PDB code 1CD3 which just happens to be the 10 000th entry in the PDB By selecting the File Save Symmetry Biological option Hex will write out all the symmetry related atom coordinates when saving a structure to disc This is useful in cases where the biologically active molecule is a dimer or has some sort of symmetry but only the minimal coordinate set appears
72. in The Apply Radial Cutoff button may be used to enable this behaviour and the Radial Cutoff slider may be used to adjust the radial distance threshold Distances are relative to the current scene rotation centre which may be changed using Origin Editing button in the left hand border the crossed circle icon The Colour Scheme selector allows the molecular skeleton to be coloured from a fixed palette of colours or by using very simple commands in a text file to specify particular colours for specific residues Some examples of colour files can be found in the examples directory The general format for a colour file is chain first_residue last_residue colour_name where colour_name is any one of the X11 colour names The colour names may be found by listing the rgb_colours dat file in the data directory Alternatively each time a colour is picked from the Colour Chart its name is printed to the terminal window Shown below is an example colour file 3hfl col from the examples directory which specifies the colours to use when drawing an antibody antigen complex Subsets of the residues in each chain are assigned different colours to highlight the positions of the antibody hypervariable loops L1 214 grey L 25 33 red L 90 97 blue Chapter 3 Molecular Graphics 9 H1 225 RoyalBlue1 H 25 33 red H 52 56 yellow H 95 102 green Y 1 999 OrangeRed Y 41 53 yellow Y 67 70 red Y 84 84 blue Colour files may also be used to colour atoms expl
73. ion to the bumps counter a single rigid body molecular mechanics energy may be calculated for each docking solution MM Energies or a Newton like energy miminisation MM Minimisation can be applied to each docking solution These energies are calculated using soft Lennard Jones and hydrogen bond potentials adapted from the OPLS force field parameters along with an explicit charge charge electrostatic contribution When docking complexes where conformational changes are known to be small this gives an effective way to prune many false positive orientations and to enhance the energy of the right answer However this rigid body refinement procedure should not be used if conformational changes are expected to be large because despite using soft potentials it tends to eject ligands with incorrect conformations from the binding site This part of the program is still under development 5 7 Clustering Docking Results Because Hex uses essentially a brute force search approach to the docking problem it is advisable to over sample the search space rather than to risk missing a good solution by under sampling the space However this can cause multiple similar but incorrect orienta tions false positives to push good solutions down the list By default Hex uses a simple clustering algorithm to group spatially similar docking orientations Each docking solution is first ordered by energy and the lowest energy solution is made the seed
74. l six dimensional search over the full rotational ranges However more limited docking searches can be performed in which the allowed angular and distance ranges may be constrained by the user The docking coordinate system is illustrated in Figure 6 below See Chapter 4 Manoeuvring Molecules page 17 for details on setting up the initial docking orientation Intermolecular Axis Range Angles Receptor Origin Interface Residues Ligand Origin Figure 6 Illustration of spherical polar docking with respect to the intermolecular axis An initial docking orientation may be defined by specifying which residues should be located at the local coordinate origin for each molecule and by defining interface residues which will be located on the zaxis The docking search may be restricted by defining a range angle for the receptor and or ligand orientations If range angles are defined then the interface residues will always be constrained to appear within a spherical cone defined by the corresponding range angle This illustration shows two range angles each of 45 degrees The calculation is arranged so that the intermolecular twist angle search is in the innermost loop of the search The search around the twist angle may be accelerated using a 1D FFT Alternatively all three Euler angles assigned to the ligand can be searched together using a 3D FFT In the Linux version all five rotation angles may be searched together using a Chapte
75. le is highlighted dragging Button 1 will move the origin of the selected molecule In Edit Origins mode buttons 2 and 3 always rotate the entire scene When you revert to the default Pointer Mode the new origin will be activated Note that the new origin only applies to the current session It is not saved when you write an edited molecule to disc You can use virtually all of the other GUI functions while in edit mode although certain operations e g opening closing molecules cause Hez to revert to pointer mode You can also explicitly specify the location of the molecular origins using the Receptor Origin and Ligand Origin text entry boxes in the Orientation Control panel For example following the HyHel 5 lysozyme example you could enter Y 38 into the Ligand Origin text box and then press the return key in order to set the ligand origin to the the CA atom of PHE 38 in the lysozyme Y chain Similarly as of Hex version 5 0 the Receptor Interface and Ligand Interface text entry boxes may be used to specify the residues which should be located on the positive or negative z axis respectively Orienting each protein with respect Chapter 4 Manoeuvring Molecules 18 to the z axis in this way is equivalent to specifying initial values for five of the six rigid body degrees of freedom i e all but the twist angle Another way to control the molecular orientations is to use the Apply to selector in the Orientation Control panel to select eithe
76. mally move both the ligand and the receptor the default display behaviour is to keep the receptor fixed in space and to assign all the motion to the ligand as successive docking solutions are viewed This behaviour can be changed using the Docking Motion selector in the Orientation Control panel 3 8 Clipping the Scene The Clipping button three faces of a cube on the left hand border selects scene clipping mode You can define up to six clipping planes in the scene several of which may be moved together using a single slider However controlling clipping is probably the most difficult part of the program to master since this involves the use of all three mouse buttons and several keyboard keys in addition to the basic graphical widgets When scene clipping mode is selected you should see a wire frame drawing of six skeletal clipping planes centred in the scene A new slider control is also drawn in the bottom right border This new slider may be used to move selected clipping planes through the scene in plane perpendicular directions In clipping mode the mouse buttons may be used to translate and rotate the clipping skeleton in the usual way Note however that the rest of the scene remains fixed You can use the keyboard Space Bar to toggle between moving the skeleton about the scene and moving the scene about the skeleton Picking one of the skeletal planes using Button 1 for picking selects that plane and attaches it to the scene
77. nce to the average of the sums of the smallest and largest radii For example if the smallest radii sum to 28A and the largest radii sum to 46A you should set the starting separation to 28 46 2 37A and the Distance Range to 2 46 37 18A Using the default Step Size 0 75A Hex will then explore 18 0 75 25 trial distances i e 12 inward and 12 outward distance steps plus 1 for the initial distance In practice its often not possible to calculate the radii exactly and hence set an optimal initial intermolecular separation An alternative approach is to enable the Radial Envelope Filter and to set a large Distance Range When the radial filter is enabled Hex will use low resolution spherical harmonic surface approximations of each surface to select which intermolecular distances to evaluate at each angular pose of each molecule However be cause these surface representations are inexact they assume the proteins are globular or star like there is a possibility that some orientations that should be evaluated might be skipped e I loaded a receptor and a ligand into Hex ran a default docking calculation but nothing seemed to happen At the end of the run the ligand hadn t moved What s going on Hex should always place the ligand near the receptor in tightly fitting orientations You should get a ranked list of such orientations at the end of each run and you should be able to scroll through these interactively using the Page Down a
78. nd Page Up and Home and End keys on the keyboard Whether any of these orientientations actually represent the right answer is of course a completely separate matter In any case if you are not seeing this it is probably because you need to place the two molecules quite close together before starting the calculation Hex searches over the range of intermolecular separations and angular orientations as specified in the Docking Control panel If the molecules are initially too far apart Her will not search over relatively small separations unless you specify a large distance range in the docking search But this will add significantly to the execution time If you know the location of the ligand binding site you should manually move the ligand to be close to the binding site this can be done in Edit Molecule mode and then restrict the receptor rotation angle range to a small value say 45 degrees If you know or have a hunch about the binding mode of the ligand you can also use Edit Molecule mode to orient the binding surface of the ligand towards the receptor binding site and then also restrict the ligand rotation angle similarly When pre positioning the molecules it may help to enable the inter molecular axis display the double headed arrow on the right hand border This shows the current zaxis as a white line about which the docking is performed The end points of this line are the molecular origins which can also be changed using Edi
79. ndix F Frequently Asked Questions Actually the questions listed below aren t so frequently asked at all As of January 2010 the program has been downloaded by about 15 000 people I have had almost no prob lems complaints since version 5 1 But here are the main points people have raised e Why are ribbon cartoons sometimes not drawn properly Hex uses the Stride program to calculate secondary structure element types Stride needs at least 5 residues to work with Hence it cannot assign secordary structures shorter than this and Hex will therefore draw a red tube which normally represents a loop in such cases Additionally if a PDB file contains two chains with the same chain label Stride will skip the second chain and only the first chain will be drawn correctly in cartoon mode This can happen quite often if one uses Hex to view previously calculated complexes for example e I noticed you supply only binary executables Is there any chance of getting a copy of the source code In general the answer is no At least not yet Hex represents many years of work and it implements some ideas that have not been published yet I would also like to keep open the possibility of potential future commercialisation which might be difficult if the source is freely available If your main interest in the source is just to poke around to see how it works there are other OpenGL based molecular graphics packages which do provide source that you c
80. nearby non null tesselation vertices Hex doesn t use spherical har monic surfaces in any of its calculations It only displays them However the commercial ParaFit program also written by Dave Ritchie can rapidly superpose and spherical har monic surfaces and surface properties calculated by the ParaSurf program Both ParaSurf and ParaFit are available from Cepos Insilico Ltd http www ceposinsilico com Hex can read ParaSurf SDF files and it can display the key ParaSurf spherical harmonic surface properties The Harmonic Surface control panel controls the way in which spherical harmonic molecular surfaces are calculated and displayed You can view the molecular envelope by selecting Graphics Harmonic Surface Enable Surface toggle on The icosahedral sampling resolution is controlled by the Mesh Order slider The order of the spherical harmonic expansion can be selected using the Order L slider in the Harmonics Control panel The SH envelope may be displayed in different styles and colours using the Display Mode and Line Colours selectors Figure 4 shows the SH surfaces for the antibody lysozyme example obtained by pressing the Harmonics short cut button on the right hand border Es 2 5 sl El zi i el Ed z E Figure 4 Illustration of spherical harmonic surfaces to order L 12 for the HyHel 5 antibody Fv domain left and lysozyme right 3 6 Dot Surfaces Dot surfaces are somewhat of a historical
81. ng OK You should now see a skeletal display of the molecule s from your chosen PDB file Figure 1 below shows the scene obtained after loading the example file 3hfl fv pdb which is the Fv fragment of the HyHel 5 antibody BAIE E Jax File Controls Graphics Macros Help Messages f al 2 64 is Pa DI Dil Ea 2 Figure 1 The initial Hex scene showing the HyHel 5 antibody Fv domain as a molecular skeleton Chapter 2 Getting Started 5 In Figure 1 you will also see a small graphic in the top left of the scene that represents the z y z coordinate axes Note that the zaxis points towards the right and the z axis points away from you into the scene Hex uses this convention because most displays have a greater width than height and when two molecules are loaded it is convenient to assign the z direction to the intermolecular axis Also looking at a pair of molecules side on somehow seems more natural Anyway you can translate and rotate the scene with the mouse buttons Assuming you have a three button mouse dragging with button 1 left button translates the scene and dragging with Button 2 middle button rotates it This rotation is always about an axis perpendicular to the direction of motion of Button 2 The right button also rotates the scene but about different axes A right left motion of this button gives an anticlockwise rotation You will probably find that Button 2 feels more natural for mo
82. ng the program For example F toggles between full screen and windowed mode G toggles the GUI border buttons and sliders in full screen mode S toggles stereographics on or off if stereo is available P toggles between perspective and orthographic projections and B toggles a checker board background which can help en hance perspective projections Hitting the escape key Esc or typing Ctr1 Q will exit the program Typing Ctr1 C will interrupt and exit the program even if it is in the middle of a calculation When viewing the calculated orientations from a docking run the keypad Page Down and Page Up keys may be used to scroll through the predicted orientations and the Home and End keys may be used to jump to the initial before docking and last docked orientations respectively The keyboard arrow keys are also mapped to these actions Down Up Left Right respectively Chapter 3 Molecular Graphics 8 3 Molecular Graphics Hez can display protein and DNA molecules in several ways The simplest display styles are controlled by the settings in the Molecule Control panel and some of the short cut buttons on the right hand border Molecules can also be displayed as solid models see Section 3 2 Solid Models page 9 solid surfaces see Section 3 4 Solid Surfaces page 10 spherical harmonic surfaces see Section 3 5 Spherical Harmonic Surfaces page 11 and dot surfaces see Section 3 6 Dot Surfaces page 12 panel These displa
83. of the provisions of this LICENCE are held to be invalid or unenforceable this agreement shall be construed without such provisions A 2 Stride Licence The following text is reproduced from the Stride Documentation All rights reserved whether the whole or part of the program is concerned Permission io use copy and modify this software and its documentation is granted for academic use provided that i this copyright notice appears in all copies of the software and related documentation ii the reference given below Frishman and Argos 1995 must be cited in any publication of scientific results based in part or completely on the use of this program iii bugs will be reported to the authors The use of the software in commercial activities is not allowed without a prior written commercial license agreement A 3 Kiss FFT Licence The following text is reproduced from the Kiss FFT source code Copyright c 2003 2004 Mark Borgerding All rights reserved Redistribution and use in source and binary forms with or without modification are per mitted provided that the following conditions are met Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer Redistributions in binary form must reproduce the above copyright notice this list of con ditions and the following disclaimer in the documentation and or other materials provided with the distr
84. oint in using multiple nodes for a single pair wise docking calculation If you wish to do multiple pair wise docking I would recommend using Unix scripts to spread the calculation over multiple nodes on a cluster and to collect the results e Can you recommend any papers that cite Hex I would like to learn more about how other people use it Quite a few journal articles cite Hex However they generally do not describe in detail how it was used and so would probably not help someone to get started If you do wish to look at articles that use Her you would need to use a bibliography service to search for papers that cite Ritchie amp Kemp e I have both my protein and ligand in PDB files The protein is seen on the screen but upon loading the ligand I can t see it This bug should have been fixed in Hez version 4 5 If you cannot upgrade to that version or later you probably need to edit the ligand PDB file to change HETATM to ATOM 6 characters Prior to version 4 5 Hex would not display a molecule that contains only HETATM data e What does Bumps 1 mean in the output table Similarly why do I always get Hbonds 1 The 1 means nothing was calculated You will always see this value unless you enable Backbone Bumps in the Postprocessing selector in the Docking Control panel In that case each orientation will be checked for steric clashes between backbone atoms the column will show the total count of bumps You
85. ons Please report any bugs suggestions to the author see Section 6 11 Contacts page 38 Described below are some known limitations some of which might never be fixed 6 8 1 Macros When Hez runs a macro it doesn t update the state of any toggles or any numerical values in the graphical user interface Thus the state of the display and the values shown in the user interface controls may become inconsistent after running a macro 6 8 2 Non Standard Residues Non standard or substituted amino acid residues may not be drawn properly because Hex requires an entry in the atom type dat and atom bonds dat files for each type of atom and bond respectively However Hex makes a reasonable attempt to draw the bonds of unrecognised molecules typically small ligands The sequence File Open Dataset is intended to allow user specific atom and bond data files to be loaded but this isn t properly implemented yet Chapter 6 Miscellaneous 37 6 8 3 Postscript Fonts The Graphics Font selected from the font menu panel is not propagated to Postscript All printed text always appears in Times Roman 6 9 The Test Functions Surface sampling using an icosahedral tessellation and surface parametrisation using spher ical harmonic functions are both central to the shape similarity and complementarity cal culations in Hex In Test Mode you can view the spherical harmonic basis functions and the icosahedral tessellations used in the calculati
86. ons Go to the File menu and select File Open Test You now should see a spherical grid plotted as a white mesh Each grid cell has approxi mately the same area Formerly this grid was used as a look up table to map an arbitrary spherical coordinate 0 9 onto the nearest vertex of an icosahedral tessellation but its no longer used in the current version You can change the number of grid cells using the Mesh Order slider in the Harmonic Surface control panel Select Graphics Harmonic Surface Mesh Order 10 The Mesh Order slider controls the number of vertices to be used in an icosahedral tessella tion by specifying the number of subdivisions made along each edge of a regular icosahedron It also indirectly controls the number of cells in the corresponding spherical grid You can view the icosahedral tessellation by selecting the L 0 spherical harmonic function Controls Harmonics Order 0 and by clicking the Enable Harmonics button You may need to adjust the zoom factor bottom left slider to get a better view The Harmonics button which looks like a balloon its supposed to represent the L 2 M 0 harmonic function on the right hand border of the main window also acts as a toggle equivalent to the Enable Harmonics button You can now display arbitrary spherical harmonic functions using the Order L and Degree M sliders Each function is plotted by evaluating the function at the angular coordinates
87. ontinue use of Hex 6 X ii deliver to the LICENSOR all the software furnished by the LICENSEE pursuant hereto together with all copies thereof and iii erase or destroy any of Hex 6 X contained in the computer memory or data storage systems under the control of the LICENSEE 9 Entire Agreement a This agreement constitutes the complete and exclusive statement of the agreement between the LICENSEE and the LICENSOR and supercedes all other oral or written pro posals prior agreements and other prior communications between the parties concerning the subject matter of this agreement 10 General a This agreement shall be governed by and construed in accordance with the laws of France and the parties prorogate the exclusive jurisdiction of the French Courts b No representation or promise relating to and no amendment of this agreement shall be binding unless it is in writing and signed by both parties c The terms and conditions of this agreement shall previal notwithstanding any variance with the terms and conditions of any order submitted by the LICENSEE d Except for the LICENSEE s obligation to pay the LICENSOR neither party shall be liable for any failure to perform due to cause beyond reasonable control e No waiver by a party of any breach of any provision of this agreement shall constitute a waiver of any other breach of that or any other provision of this agreement Appendix A Licences 43 f In the event that any
88. op regions and position the molecule using the mouse in a pleasing orientation The command sequence might be Macros Learn start recording File Open Receptor 3hfl pdb existing file Controls Molecule Colour File 3hfl col existing file Controls Hetero Display Solvent solvent display off Lock lock home view Macros Save test mac save commands Printing the file test mac should show a command sequence similar to open receptor 3hfl pdb set colour file 3hfl col display solvent 0 button active 3 cursor rotation 0 0161 0 0233 button active 0 button_active 2 cursor_rotation 0 0121 0 0295 button_active 0 lock_home_view 1 You can now re execute these commands using File Close All Macros Run test mac If you make a mistake while recording a macro and want to cancel the current recording select Macros Forget Note that running a macro does not update the state of any toggles or any numerical values in the graphical user interface Thus the state of the display and the values shown in the GUI controls may become inconsistent after running a macro Nonetheless macros are useful for running canned sequences of commands and for running batch jobs Since a macro file may invoke another macro it is quite easy to set up a sequence of docking calculations for example using the same docking parameters on a number of trial complexes Chapter 6 Miscell
89. orientation for the Chapter 5 Docking Molecules 26 first cluster The list is then searched down to a given depth for other similar orientations whose main chain alpha Carbon RMS deviation is within a given threshold default 3 RMS of the seed orientation and these orientations are then assigned to the first cluster The process is then repeated starting from the next lowest unassigned orientation until all solutions have been assigned to a cluster The Cluster Window parameter may be used to control the search depth when looking for cluster members Because clustering uses a simple but inefficient algorithm rather like a bubble sort it is advisable use this parameter to limit the search depth if the number of saved solutions is large The Controls Clustering control panel may be used to control the type of clustering and clustering parameters used and how cluster membership affects the displayed solu tions By default only the lowest energy member of each cluster is displayed or written to an output PDB file Display Clusters Best Alternatively you can choose to view or output all solutions Display Clusters All Similarly solutions may be viewed in cluster order best to worst or in order of calculated energy using the Sort Solutions selection op tion The RMS threshold for cluster membership may be changed using the RMS Threshold slider Displayed solutions may also be selected by the number of steric clashes or b
90. ote eoe er ALA Nee EA 38 Shape Matching Scores 29 Short Cut Buttons 5 Sidechains Button 5 8 65 Sigma Surface imite erem ere 10 Silicon Graphics Version 38 Sliders Sois sr EE PR TEE 5 Soft Potentials oni yn a etuim ea 25 Solid Model Button 5 Solid Model Control Panel 9 solid Models 22 1 dires ss Rm 8 9 Solid Motion Button 5 Solid Surface Button 5 Solid Surfaces o LIRE bei 8 10 Solvent Culling 32 Source Code FAQ 57 Spherical Harmonic cube 38 Spherical Harmonic Functions 37 Spherical Harmonic Rotation 37 Spherical Harmonic Surfaces 5 8 11 12 Spin Angles 3564 bees cele lues RNA Ve 14 Sta rtup crashz uo clp NM eee 58 Stereo Displays 7 15 Stereo Parallax 15 Serie SCANS dt snum Lee dE IN pete 21 24 RS 0 0 RE E IPReRA TRUM RIS Ree 9 39 57 Stride Licence 2222 uempent RE RR eee ee bre 43 SUD V TSION ove vere rex aen thaws 38 Superposing Molecules 28 Surface Control Panel 23 Surface Skins 1 Symmetry Types 9 T T u ourface ecu PSP Yr
91. ould take a look at instead e g VMD http www ks uiuc edu Research vmd MolMol http www mol biol ethz ch wuthrich software molmol If you re more interested in the computational parts spherical harmonics Laguerre polynomials etc these should be quite easy for any reasonably competent C or Fortran programmer to code up anyway In terms of lines of code this represents only a very small proportion of the program On the other hand I can see that putting it all together to make a new docking program or other application is not trivial I am considering making all the polar Fourier code available as a dynamic runtime library DLL or so Please let me know if you are interested in this idea e I downloaded the Linux version of Hex followed all the instructions but still nothing works What do I try next I m not aware of any recent Intel Linux systems it doesn t run on However I can t guaran tee that Hex will run on every Linux system because a lot depends on where the run time libraries are located eg usr lib libc so etc although I ve tried to minimise such depen dencies There are really two main reasons why Her might not work Assuming you have downloaded an appropriate executable the problem is probably due to incorrect file permissions or the executable search path If nothing happens when you type hex its probably a problem with the HEX ROOT and PATH variables check the README file If these look OK c
92. pl Cryst 38 808 818 http scripts iucr org cgi bin paper ea5040 e Docking Essential Dynamics Eigenstructures D Mustard and D W Ritchie 2005 PROTEINS Struct Funct Bioinf 60 2 269 274 http www loria fr ritchied papers ritchie_gaeta_2005 pdf e Evaluation of Protein Docking Predictions Using Hex 8 1 in CAPRI Rounds 1 and 2 D W Ritchie 2003 PROTEINS Struct Funct Genet 52 98 106 http www loria fr ritchied papers ritchie_capri_paper pdf e Protein Docking Using Spherical Polar Fourier Correlations D W Ritchie and G J L Kemp 2000 PROTEINS Struct Funct Genet 39 178 194 http www loria fr ritchied papers docking pdf e Fast Computation Rotation and Comparison of Low Resolution Spherical Harmonic Molecular Surfaces D W Ritchie and G J L Kemp 1999 J Comp Chem 20 383 395 http www loria fr ritchied papers matching pdf e Parametric Protein Shape Recognition D W Ritchie 1998 PhD Thesis University of Aberdeen http www loria fr ritchied papers dwr thesis pdf e Knowledge Based Protein Secondary Structure Assignment D Frishman and P Argos 1995 PROTEINS Struct Funct Genet 23 566 579 ftp ftp ebi ac uk pub software unix stride 6 14 Citing Hex When citing Hex in a publication please cite whichever of the above articles seems most appropriate and please also mention Hez s Home Page http www loria fr ritchied hex Appendix A Licences 41 Appendix A Licences A 1
93. play Styles Lb LER REDE 8 Distance Sub Stepping 22 Docking Control Panel 10 20 23 28 60 Docking Examples 22 Docking Large Molecules 27 Docking Molecules 18 Docking Motion 13 Docking Multiple Structures 27 Docking Parameters FAQ 60 Docking Res lts 5 0 3h mission 26 Docking Review Paper 39 Docking Samples 24 Docking Summary File 26 Docking Transformations File 26 Dot Surfaces lle le ELI peak eee et RUP 8 12 E BditiBg 4bewvebetedCUPD SYM eM 6 Editing Molecules 17 Editing Origins and Orientations 17 Electrostatic Correlations FAQ 59 Electrostatic Potential 10 Electrostatics 2 2 mte Irem RR EUR 1 Environment Variables 33 44 Escape end Re rennes amiante RS 7 Euler Angles 17 Examples Directory 35 45 F p Roy DR REN US ue dome 15 False Positives 25 FAQS araea e en Dallas testet etu a tM 56 Far Pl ne a he s er race e OS ok S 15 Fast Fourier Transform 1 Feature History 46 Subject Index EBD tene brem tea onn etes di
94. presentation used in the docking correlation degrades with increasing distance from the origin In this display mode the receptor surface is translated in the negative z direction and the ligand surface is translated in positive z for ease of viewing You should see a blurring of those portions of each molecule furthest from the origin although the shapes of the surface regions near the origin are very well preserved after translation NB In Hex s docking correlations all computational translations are applied entirely to the receptor Please be aware that drawing surfaces can use a lot of memory Drawing the surface of a large molecule using a fine 0 25 0 5 Angstrom grid can use hundreds of megabytes of memory Attempting to draw a complex surface on a machine with insufficient memory could cause the machine to hang 3 5 Spherical Harmonic Surfaces In Hex version 5 0 spherical harmonic SH molecular surfaces are generated from the marching tetragons surface described above Essentially all of the vertices from the tran gulated surface are first projected onto an icosahedral tesselation of the sphere If more than one surface point maps to the same tesselation vertex then the point with the largest radial distance from the origin is selected Hence a bounding envelope of sample points Chapter 3 Molecular Graphics 12 is constructed Any gaps in the tesselation which might remain are filled in by interpo lating from values of
95. r 5 Docking Molecules 21 5D FFT However this requires at least 1 gigabyte of memory to hold the very large 5D rotational grid Note The speed of the 3D and 5D FFT calculations depends very much on the quality of FFT code and whether it exploits any hardware acceleration For CPU based docking the Intel MKL http www intel com code is about twice as fast as FFTW http www fftw org which is about one and a half times as fast my own multi dimensional FFT code which is partly based on Kiss FFT http sourceforge net projects kissfft and which doesn t use any assembly or SSE instructions However only the Linux version of the MKL library is available for free to non profit organisations So docking is fastest with the Linux version of Hez I do not use the FF TW code because I do not agree with its GPL license conditions Hence 3D and 5D docking correlations on the Windows and Mac versions of Her is relatively slow For GPU based docking 1D correlations using cuFFT http www nvidia com object cuda l get html on a high end GeForce or Quadro card are much faster than on a high end CPU Compared to using a single high end CPU 3 2GHz i7 965 the same calculation on a high end GPU FX 5800 is about 45x faster Ritchie and Venkatraman manuscript in preparation There are several controls which specify the resolution and in particular the order N of the docking correlation Figure 7 below shows a screen shot of the Docking
96. r some older versions of RedHat As of Hez 4 5 PowerPC executables are now available for Mac OS X Tiger 10 4 and Linux Fedora Core 8 These were built on a G4 PowerBook but should work on other PowerPC systems An version for the Intel Mac will be made available soon The Windows version was built on a Pentium III 686 system running Windows XP and using the MinGW http www mingw org development environment As far as I know the Windows executable works on all recent Windows systems Due to lack of available hardware and rapidly falling demand executables for SGI IRIX and Sun sparc are now only available up to version 4 5 Sorry 6 11 Contacts Author Dave Ritchie http www loria fr ritchied Before e mailing me with a problem or question please first check the FAQs see Appendix F FAQs page 57 I always try to respond to problems and I welcome suggestions for future enhancements However if you do have a question suggestion or if you think you ve found a bug please check the FAQs first see Appendix F FAQs page 57 and check Hex s Home Page http www loria fr ritchied hex to make sure you re using the lastest version Please remember that Hez is essentially a research program and it is provided as is without any guarantee of updates or user support Chapter 6 Miscellaneous 39 6 12 Acknowledgements Much of Hex was developed during projects 1996 2000 funded by the BBSRC http www bbsrc ac uk
97. r the receptor or the ligand and then to rotate the selected molecule using the Euler angle Alpha Beta and Gamma sliders The intermolecular separation can be modified with the R slider at the bottom of the main window Select Commit when you re done editing in order to commit the new transformations into the molecules Orientation editing can also be performed manually clicking on the Edit Mode left border button which looks like a lightning bolt and then by picking and dragging molecules using the mouse In both editing modes picking a molecule ties its motion to the mouse and to the rotation sliders in the Orientation Control panel The covalent skeleton of the picked molecule is displayed as dashed lines as a visual reminder that this molecule has been activated for editing Picking the background i e a Button 1 pick that misses all atoms de selects the active molecule and makes the mouse move the whole scene The Hammer button can be used to undo the most recent sequence of editing movements Once you re happy with your edits revert to Pointer Mode to commit the new orientations You can now save the scene by going to the File menu and selecting File Save Both This causes a file selection widget to appear prompting you for the name of a file in which to save both molecules in the newly edited orientation You can confirm the new orientation has been created by loading the new file into another Hex session you may have to ro
98. re usual value of around 80 So in addition to Hez s in vacuo assumption the numerical values for the potential are likely to differ from other software Some molecules may have internal cavities and these can produce one or more contour surfaces in additional to the primary external surface Other molecular structures e g structures with many waters or well separated domains may also give multiple surfaces when contoured As the contouring algorithm implicitly produces positively oriented sur faces outward normals positive total volumes it is convenient to assign each calculated surface to one of two possible classes Primary positive volumes outward normals or Secondary negative volumes inward normals By default only Primary surfaces are dis played but this may be changed using the Draw Surface control In addition to the default Gaussian surface the Surface Type selector provides the option to draw contoured density functions of the Sigma and Tau surface functions which are used by the docking algorithm These two density functions allow the shape functions used in docking calculations to be visualised Sigma is the external skin density function typically calculated with a probe radius of 1 4A and Tau is the interior density function effectively the van der Waals volume For relatively small molecules and when using high expansion orders N the Tau density can be seen to give a remarkably good representation of the init
99. reasonably close to each other and that their centroids are a rea sonable distance e g 30 Angstroms apart The white intermolecular axis connects the default centroids of each molecule If you have a good idea about the binding epitopes of one or both proteins then it would be a good idea to rotate one or both proteins such that the intermolecular axis passes through the centre of the epitope Before you start a docking calculation you should always consider carefully the locations of the molecular centroids and the relative orientations of your proteins with respect to the intermolecular axis The Origin Editing button allows you to move these centroids and the Orientation Editing button allows you to rotate each molecule about its centroid and to translate each molecule individually relative to the scene These operations are described in more detail in See Chapter 4 Manoeuvring Molecules page 17 Note that the R slider bar can be used to change the intermolecular separation permanently as described above but it is recommended that you use this control only for temporary changes to the scene e g when viewing the result of docking or superposition calculations and that you make permanent changes only in editing mode 2 3 Keyboard Keys All of the features in Hex are controlled using the GUI components However when you place the mouse in the main graphics window several keyboard keys can be used as addi tional short cut ways of controlli
100. reo Alternatively set the HEX STEREO environment variable to a false value i e any one of no n false f or 0 in your login script If a stereo visual has been selected the display may be toggled between stereo and mono using the Stereo Parallax option in the Projection Control panel or simply by pressing the keyboard S key The Parallax slider may be used to adjust the stereographic effect Stereo Chapter 3 Molecular Graphics 16 parallax is the perceived separation between the left and right images in the viewing plane monitor screen The numerical values in the parallax slider correspond approximately to screen millimetres on an un zoomed display Positive parallax values make the scene appear inside the display whereas negative values cause the scene to appear through or in front of the plane of the display A better stereographic effect is achieved when the Perspective Projection toggle is enabled by default an orthographic projection is used The keyboard P key may also be used to toggle between perspective and orthographic projection modes When perspective is enabled a checker board background may also be enabled to enhance the perspective effect keyboard B Figure 5 shows the antibody lysozyme scene with perspective and background modes enabled The perspective effect can be increased by reducing the Far Plane and or increasing the Near Plane slider values For most people a small positive parallax and a moderate per
101. required to perform a particular function This type of text is also used when listing the contents of some of the example files provided with the program Bold face text is used to highlight file or directory names that refer to the installation and use of Herz If you really want to read the whole of the Manual print out the PDF version hex manual pdf Otherwise browse it on line as HTML using Hex s Help button The graphical user interface GUI in Hex is intended to be easy to use Generally most actions cause an immediate effect on the display so that once you ve loaded a protein or DNA molecule preferably two such molecules most of the program s features can be understood by experiment If you re comfortable with this approach go right ahead Much of this Manual can probably be skipped Just keep an eye on the Messages Window for any information messages The parts that everyone should read are the sections on Docking see Chapter 5 Docking Molecules page 19 and Superposition see Section 5 12 Molecular Matching page 28 If you want to try more than just one or two docking calculations you should also look at the section on using macros see Section 6 1 Macros page 30 and the contents of the examples directory see Section 6 7 Examples Directory page 36 It should be noted that algorithmic details of the docking and superposition calculations are not given here Its assumed that you have copies of the relevant publication
102. rom one to four cycles depending on how many shells of solvent surround the molecule As an alternative to this automatic calculation it is also possible to manually select water molecules or any other atoms to be culled Select ID picking mode and pick those atoms you wish to cull Pressing the Toggle Picked IDs button in Hetero Control will toggle the status of any picked atoms Finally using the Apply to selector you can choose to apply these operations to all molecules the default or only to a selected molecule If more sophisticated atom selections are required it will probably be necessary to edit PDB files manually before loading them into the program 6 3 Hardcopy Output Hex supports JPEG PNG and Postscript hardcopy output Just compose your scene and then use the appropriate File Print option to write the scene to an image file The File Print menu also contains a special Pipe option This causes the molecular coordinates for the current scene to be piped in the sense of a Unix pipe to a script in the HEX_ROOT pipes directory which can be used to load the current structures directly into an external program such as GRASP or Molscript The HEX ROOT pipes directory contains example scripts to run these programs 6 4 Compressed Files Hex has full support for gzip gz and bzip2 bz bz2 file compression formats If you specify an output file name with one of these file name extensions you will automaticall
103. ropriate and pressing Start wil show a movie of the sequence of models The orientations or frames of both types of movie may be shown just once or cycled forever The movie can be stopped at the current frame by pressing the Stop button The speed of the movie is controlled by the Frame Rate slider The maximum frame rate achievable will depend on the speed of the CPU and on whether your machine has hardware accelerated graphics The Frame Rate thus defines a requested rate Actual performance will vary But please note Hex never hogs the CPU in a tight loop on input events even during an animation as do many other programs which shall remain nameless Thus it should still be possible to perform other activities while a movie is running without things becoming sluggish You can spin the scene by dragging with Button 1 or Button 2 to start a rotation and by releasing the button while still moving the mouse to initiate a continuous rotation spinning When spinning the rotatation angle is incremented by the current value in the Spin Angle slider and new rotational increments are drawn at the current Frame Rate lf desired the mouse button action that initiates spinning can be enabled disabled with the Enable Spinning toggle Spinning is enabled by default and it is possible to spin a movie if thats what you really want to see Chapter 3 Molecular Graphics 15 Any of the usual user interface controls may be used while an animation is
104. s see Section 6 13 References page 39 Chapter 2 Getting Started 4 2 Getting Started If you haven t already done so please download and install Hex from Hex s Home Page http www loria fr ritchied hex See Appendix B Installation Guide page 44 for details It should be easier to follow this Manual if you have Hex up and running in front of you Been there done it Great Lets get started Hex reads protein and DNA molecular structures from PDB format files As of version 5 0 Hex can also read SDF format small molecule structure files PDB files can be downloaded from the main Protein Data Bank repository at Rutgers University http www rcsb org pdb Up to three input files can be loaded into Hez at any one time These are treated as a receptor a ligand and a reference complex Well ignore these distinctions for now and just load a single protein Go to the File menu and select File Open Receptor When you release the mouse button a new File Selection menu panel should appear Edit the Filter text area to specify the directory containing your PDB file s and press the Filter button Alternatively you could navigate to the hex examples directory and load one of the provided example PDB files You should now see one or more PDB files listed in the Files box if not use the File Selection controls to navigate to the hex examples directory Pick a PDB file by double clicking on it or by highlighting it and picki
105. s to save the first 100 solutions to separate PDB files of the form dock001 pdb etc in the current directory In both the PDB range and the summary output modes either a list of raw solutions sorted by energy are written or a range of clustered orientations are written depending on the current clustering option In other words the sequence of solutions written out is the same sequence that you would see when stepping through the orientations using the Page Down and Page Up or arrow keys 5 9 Docking Multiple Structures Docking multiple structures e g NMR structures with Hex is easy Just put all your ligand structures assumed to be in a common coordinate frame into a single PDB file and use the PDB convention of MODEL ENDMDL to distinguish each structure Hex will run its docking search for each ligand in turn Similarly multiple receptor model structures may be loaded and docked giving an M by N docking may take a while though The actual structures to be docked may be selected using the Receptor Docking and Ligand Docking selectors in the Controls Solid Models control panel default all v s all Individual structures may be selected for viewing using the Receptor Display and Ligand Display selectors in the same control panel This panel also contains some experimental controls for cloning and editing different models where each clone is treated as a new NMR type model structure to be docked with each docking run each startin
106. simply by constraining one or two of the angular degrees of freedom This can reduce docking times to a matter of minutes on a modern workstation As of Hex version 5 0 the rotational part of the search may be accelerated by one dimensional 1D three dimensional 3D or five dimensional 5D rotational correlations Earlier versions just used multiple 1D correlations The 1D correlations are fast but the 3D correlations in Hex 5 0 are about twice as fast However for basic shape based docking 3D is also counter intuitively faster than 5D largely due to the relatively high set up cost of the 5D correlation expression As of Hex version 6 0 the 1D and 3D calculations may optionally be performed on one or more GPUs which can give a considerable speed up compared to using conventional CPUs In this case also counter intuitively 1D correlations are much faster than 3D correlations on the GPU Additionally the CPU based calculations have also been re written to use multi threading in order to support parallelisation on both Windows and and Linux based multi core systems Thus significant performance improvements can be expected from version 6 0 if you have suitable hardware Closely related to the protein docking problem is the molecular similarity problem i e how to find the relative orientation of a pair of similar molecules such that some measure of the similarity difference between the molecules is maximised minimised Both probl
107. sions 4 3 and 4 4 these were internal development versions and were never released C 1 New Features in Hex Version 6 1 Macro docking now works correctly again Docking multi model PDB files caused a memory fault in version 6 0 This has been fixed In the refinement stage of a docking calculation re sampling distance sub steps has now been turned off as the default behavour The default correlation scan order has been changed from 16 to 18 this happened some time ago but I forgot to document it The distance heuristic for setting up the initial inter molecular separation has been improved This should normally give better starting orientations but it may change the results in some cases because it may cause a different range of orientations to be sampled C 2 New Features in Hez Version 6 0 The docking correlation code has been rewritten to be thread safe and to be able to use as many CPUs as are available The 1D and 3D calculations have been ported to the run on Nvidia GPUs using CUDA Docking calculations may now simultaneously use as may GPUs and CPUs as are available Switching between full screen and window manager modes finally works properly again Some old FAQs have been deleted from the manual this means anything before about 2005 or Redhat 9 Some command line arguments have been changed to allow more control over the num ber of CPUS and GPUs to use Similarly two new environment variables HEX GPU
108. so conf to mention the location of the CUDA libraries if they were not in a well known place such as usr lib On my 64 bit workstation I installed CUDA in usr local cuda I then edited etc ld so conf to make it look like include etc ld so conf d conf make CUDA run time stuff globally visible usr local cuda lib64 The usr bin ldd tool make be used to check that all run time libraries are visible to the Hex executable Here is the result on my system jordan ldd home ritchied hex exe hex6 cuda x64 linux vdso so 1 gt 0x00007fff013bf000 libpthread so 0 gt lib libpthread so 0 0x00007f6b30e49000 libcufft so 2 gt usr local cuda lib64 libcufft so 2 0x00007f6b303f4000 H libcudart so 2 gt usr local cuda lib64 libcudart so 2 0x00007f6b301b4000 H libcuda so 1 gt usr lib libcuda so 1 0x00007f6b2c532000 libGLU so 1 gt usr lib libGLU so 1 0x00007f6b2c2c1000 libGL so 1 usr lib libGL so 1 0x00007f6b2c0c2000 libXft so 2 gt usr lib libXft so 2 0x00007f6b2bead000 libXrender so 1 gt usr lib libXrender so 1 0x00007f6b2bca3000 libfontconfig so 1 gt usr lib libfontconfig so 1 0x00007f6b2ba71000 libexpat so 1 gt lib libexpat so 1 0x00007f6b2b848000 libfreetype so 6 gt usr lib libfreetype so 6 0x00007f6b2b5c3000 libXext so 6 gt usr lib libXext so 6 0x00007f6b2b3b1000 libX11 so 6 gt usr lib libX11 s0 6 0x00007f6b2b07b000 libm so 6 gt lib libm so 6 0x00007f6b2ad
109. spective gives a pleasing effect without straining the eyes File Controls Graphics Macros Help Messages x x 1D z 4 Figure 5 Illustration of the HyHel 5 Lysozyme complex shown as contoured Gaussian density surfaces and coloured by chain colour drawn using perspective keyboard P and background keyboard B modes enabled Chapter 4 Manoeuvring Molecules 17 4 Manoeuvring Molecules When Her reads in a molecule it uses its all atom centre of mass as its centroid This centroid is used as the local coordinate origin for docking and as the point about which any molecular rotations are applied However if one or both molecules are quite large i e too big to fit within about a 30 ngstrom radius ball you will probably want to change the centroids used for docking This is because Hez s radial functions fall off rapidly beyond about 30A from the origin Hence unless you move the origin s to be closer to the expected binding site s you are likely to get very poor docking results If you don t know or suspect where the binding site is on a very large molecule you should use Hez s macro docking mode for such cases See Section 5 10 Macro Docking page 27 In addition to rotating translating and scaling a molecular graphics scene Hez also al lows you to change the relative orientations of a pair of molecules Hex calls this editing because saving manoeuvred structures out to a file causes them to be wri
110. ss Panel for docking calculations e New Cartoon display mode see Section 3 3 Cartoons page 9 e Shape matching now uses a Carbo like similarity index see Section 5 12 Molecular Matching page 28 e GUI controls now available in full screen mode see Section 3 10 Full Screen Mode page 15 e GUI controls and graphics window now stay responsive during docking e SGI mips3 version dropped the O2 mips4 is now the minimum SGI platform for Hex C 9 New Features in Version 3 4 e Improved stereo support works with nVidia s 3123 and later drivers see Section 3 11 Stereo Displays page 15 e New compressed file support can read write gzip gz and bzip bz bz2 files see Section 6 4 Compressed Files page 33 e New 3D density superposition algorithm see Section 5 12 Molecular Matching page 28 e New User Manual made with texinfo http www gnu org software texinfo C 10 New Features in Version 3 3 Hex 3 3 is a bug fix release Running Hex in batch mode or when standard input was not a terminal device was broken The program would quickly crash with a SIGSEG error Fixed now C 11 New Features in Version 3 2 Hex 3 2 contains mostly minor bugfixes However stereo graphics is now available on Linux systems that have suitable hardware support e New stereo display option type hex stereo to request stereo see Section 3 11 Stereo Displays page 15 Appendix C Feature Histor
111. st movements but that occasionally Button 3 is needed to complete a manoeuvre If you have a one button mouse e g on a Mac you can hold down the Ctrl or Meta Command Special keys with Button 1 which might be the only button to simulate buttons 2 and 3 respectively On Linux the Ctrl or Alt keys do the same thing Some window managers e g Gnome may interpret Alt drag as a window movement shortcut There should be a window manager option that allows this key binding to be changed to make the Alt available to Hex The Slider on the lower left border may be used to zoom the scene in and out The other borders around the graphics window contain various pull down menus and control buttons These are described in more detail below 2 1 Short Cut Buttons The column of buttons on the right hand border of the main window implement handy or frequently used operations For example Hez stores a Home Position for the scene Press ing the House button at the top right border resets the scene to the current home position If you have oriented the molecule into a view that you like you can make this orientation the Home Position position by pressing the Lock button below the Home button The Unlock button resets the Home Position to its the original setting z axis to the right etc The next button the 6 6 icon is a text toggle to control the display of summary text in the graphics window The Axes button two arrows at right angles toggles
112. t Origin mode Please also look at the answer given for the previous FAQ e What does Etot mean and how do I find the internal energies of the proteins Etot is the total calculated interaction energy of the system Hez doesn t calculate internal energies and so doesn t report separate individual molecular energies Appendix F Frequently Asked Questions 62 e If I wish to reload my docked conformations and visualise them sequentially then how can I do that If you select File Save Range from the File menu you can write out each pre diction of the complex to a separate PDB file these can then be read back into Hex in subsequent sessions However these are then treated as a single molecule in Hez rather than the seprate receptor ligand that you started with Alternatively you can select a docking prediction and then use File Save Receptor and File Save Ligand to save the separate components of the current orientation These can then be read back together from the Unix command line hex receptor pdb ligand pdb Unfortunately its not possible to reload together all the predictions from a previous session You would need to rerun the calculation from the beginning to get that behaviour e Can Hex use Beowulf style parallelisation such as MPI or PVM No Hex can exploit only the processors ot it can see on the motherboard Since the basic calculation now takes only a matter of seconds there is little p
113. t the hex installation directories are optional and must be created manually You can also specify the default number of CPUs to use on a multi processor system These parameters are described in Section 6 5 Environment Variables page 33 Here s a C shell example I have these lines in my cshrc file setenv HEX ROOT home ritchied hex Setenv HEX PDB setenv HEX MACROS setenv HEX COLOUR setenv HEX DATA home ritchied hex data setenv HEX CACHE tmp ritchied hex cache setenv HEX STARTUP home ritchied hex examples my startup vb mac Setenv HEX CPUS 8 setenv HEX GPUS 2 setenv HEX MESSAGES yes setenv HEX STEREO yes setenv PATH PATH HEX_ROOT bin For Bourne and Korn shell users the corresponding commands in the profile file would be set HEX_ROOT home ritchied hex set HEX_PDB set HEX_MACROS set HEX_COLOUR set HEX_DATA home ritchied hex data set HEX_CACHE tmp ritchied hex_cache set HEX_STARTUP home ritchied hex examples my_startup_v5 mac set HEX_CPUS 8 set HEX_GPUS 2 set HEX_MESSAGES yes set HEX STEREO yes set PATH PATH HEX_ROOT bin export PATH HEX_CACHE HEX_STARTUP HEX_CPUS HEX_STEREO export HEX_ROOT HEX_PDB HEX_MACROS HEX_COLOUR HEX_DATA In addition to the README and LICENCE files the hex directory should contain the following 7 directories bin exe doc data examples pipes cache Appendix B Installation Guide 46 Typing hex at the Linux command prompt should locate
114. tate the scene to see exactly the same view Alternatively you could write each molecule to a separate file using File Save Receptor and File Save Ligand You could then open these new files to verify the new orientation Chapter 5 Docking Molecules 19 5 Docking Molecules In order to run a docking calculation in Hez you will need to load a receptor and a ligand PDB structure using the File pull down menu If you want to test the docking algorithm by docking two separately determined sub units of a complex for which the crystal structure is also available you can also load the complez structure which will be used as a reference orientation to evaluate the accuracy of the docking prediction Generally you will have to remove water molecules and any other hetero molecules prior to docking You can do this globally using the Hetero Control menu panel If more detailed control is required you will probably have to edit each PDB file manually using a text editor It may also be necessary to remove other chains in the PDB file or to shorten a chain to the domain of interest in docking For example when docking an antigen to an antibody it is usually advisable to delete all but the Fv fragment of the antibody structure although the program has been used to dock a protein G molecule to a complete Fab fragment Having edited your PDB files you should have a receptor and a ligand file which contain only the receptor and ligand
115. the display of the coordinate axes useful for screen shots Below this is the Intermolecular Axis button a double headed arrow This draws a white line between the centroids of the receptor and ligand molecules If only one molecule has been loaded a short white line is still drawn along the z axis The Solid Models button toggles the display of solid models the default being van Der Waals spheres The type of solid model to display may be selected from the Solid Models control panel see Section 3 2 Solid Models page 9 The Solid Surface button toggles the calculation and display of solid surfaces see Section 3 4 Solid Surfaces page 10 Similarly the Harmonics button which looks like a balloon toggles the calculation and display of spherical harmonic molecular surfaces see Section 3 5 Spherical Harmonic Surfaces page 11 and the Cartoon button which is supposed to look like part of a protein ribbon toggles the cartoon displays The Sidechain button toggles the display of protein sidechains and DNA bases With large molecules rotating and translating the scene can be much faster if only the backbone trace is drawn This is especially true if solid models or surface meshes are being displayed The Chapter 2 Getting Started 6 final Solid Motion button the black square with an arrow can be used to toggle whether solid shapes or just bond skeletons are drawn when moving molecules within the scene As you might expect Hex
116. the larger 686 instruction set doesn t make floating point operations go any faster Having said that compiling with Intel s icc http www intel com software products compilers gives about a 10 speed up over GNU s gcc 2 96 http gcc gnu org and the release versions of Hex are compiled with icc whenever possible sorry GNU e I want to display and dock a protein with non standard residues What do I do The HEX ROOT data directory contains several files residue types dat atom bonds dat atom names dat atom types dat which define the atom connectivity charges and names of non standard residues You will need to define new entries in these files to define your new residues Probably the easiest approach is to identify the most similar existing amino acid and to copy rename edit the entries You may need to calculate guess some partial charges for the new atoms e How can I refine the results from a docking correlation It is possible to further refine results from the docking correlation in Hez version 3 This refinement applies a soft molecular mechanics energy evaluation and or minimisation to the top 1000 orientations However if the amount of conformational change on binding is large this refinement could eliminate what was a good solution On the other hand if the conformational change is small then the calculation should lower the energy of a good orientation and significantly raise the energy of other orientations
117. ther parameters which control the docking calculation but which are not accessible from the GUI These parameters must be set using keywords in a macro file For example the steric overlap penalty factor has a default value of 11 This can be adjusted by running the example macro factor q mac steric q mac change steric penalty factor Q default 11 this parameter can t be changed from the GUI yet factor_q 11 Similarly another example macro file is factor_g mac factor g mac change electrostatic scale factor def 700 J mol this parameter can t be changed from the GUI yet factor_g 700 5 12 Molecular Matching Hex superposes or matches pairs of molecular structures using the same 3D density repre sentation as for docking Superposition is very much like docking except now the search is for maximum similarity rather than maximum complementarity Superposition calculations can only be performed once you have opened a receptor and a ligand molecule If you want to superpose a pair of molecules that originate from the same PDB file you will have to manually edit the molecules into separate PDB format files Superposition calculations are controlled by the parameters in the Matching Control panel To calculate a superposition using the default settings which are usually reasonable use Chapter 5 Docking Molecules 29 Controls Matching Activate Hez will take a few seconds to calculate the ster
118. thread so 0 gt lib libpthread so 0 0x00d7b000 libstdc so 6 gt usr lib libstdc so 6 0x008e7000 libm so 6 gt lib libm so 6 0x00c53000 libgcc s so 1 gt lib libgcc s so 1 0x008db000 libc so 6 gt lib libc so 6 0x00112000 libGLcore so 1 gt usr lib libGLcore so 1 0x00d8d000 libnvidia tls so 1 gt usr lib tls libnvidia tls so 1 0x00b23000 libdl so 2 gt lib libdl so 2 0x00c79000 lib ld linux so 2 0x00b05000 If there are any blanks in the ldd output or if the version numbers of the libraries in your lib directory are hopelessly below the numbers here then this is probably the problem You would then need to try installing a version that was built for a more similar vintage of your operating system or better you should update your entire operating system Otherwise you re out of luck for the moment but I d appreciate it if you could send me some details of your system e g Linux vendor amp release output from uname a etc and particularly the exact message you get after typing hex5 1586 I ll try to figure out what needs to be done and if possible make up a new Linux release to fix it e When I try to start Hex it prints some brief messages about connect or bind and then just seems to get stuck it never shows the graphics window What should I do By default Hex writes all its information and warning messages to a dedicated text output window This window is is controlle
119. tor Samples and Ligand Samples values will actually be used for the molecular rotations of each molecule Essentially each molecule is rotated incrementally so that successive tessellation points are rotated onto the intermolecular axis the z axis Thus in the low resolution Steric Scan phase 812 x 812 distinct rotational orientations are produced although any orientations that fall outside the angular range cones are discarded Angular search ranges are illustrated in Figure 6 At each of the surviving orientations the ligand is then rotated or twisted through 360 degrees about the z axis in 64 steps of about 5 5 degree increments specified by the Twist Samples value In the high resolution Final Search phase the best 10 000 of the above orientations will be used to generate up to 25 000 new distinct trial orientations after distance sub sampling see above and re evaluated at N 25 using 128 samples for each twist angle search Note Hex is hard wired to use 64 twist steps in the initial steric scan phase because there is no benefit in using finer steps in this phase It should be noted that such docking calculations never give a unique solution Rather Hez sorts the generated orientations by docking energy and prints a summary of the 10 000 highest scoring lowest energy orientations The best 500 orientations are retained for viewing You can view the solutions using the Soin slider or you can step through the solutions using the keypad
120. tten using their transformed coordinates Note Edit Mode is only enabled when you have two molecules loaded Editing is often a necessary preparatory step before running a docking calcula tion For example when you load a pair of molecules Hex uses some heuristics to place the ligand near the receptor However you may have knowledge about one or both of the binding sites and hence you may want to manoeuvre the molecules into something that resembles the expected binding orientation If you do this you can then limit the search range of the docking correlation instead of performing a global search This should give fewer false positives and it will certainly make the docking calculation go faster It should be noted that although you can edit the scene by picking and moving both the receptor and the ligand orientations the coordinates of the receptor take priority when structures are written to an output file In other words any relative motion is always transferred entirely onto the ligand on output The receptor coordinates are always restored to their original values 4 1 Editing Origins and Orientations Molecular centroids may be edited using the Edit Origins button two crosses and a line on the left hand border When editing orientations it may help to activate the Intermolecular Axis in order to see the new and old positions of the centroid s Try changing to Edit Origins mode and pick a molecule to edit Once the picked molecu
121. umps detected Any solution containing a number of bumps which is less than or equal to the current Bumps Threshold default 0 is a candidate for cluster membership Solutions with a greater number of bumps may still be viewed or output but these always appear after any non bumping solutions in the sorted list of solutions i e have a larger cluster rank The default docking search range and clustering parameters are normally sufficient to gener ate good coverage of the search space and to distinguish different but similar solutions But you may wish to experiment Clustering is re calculated whenever a clustering parameter is changed without having to re run the docking search Here good coverage means that for each docking orientation there is about a 99 chance of generating at least one other solution within 3 RMS of the first one unpublished experiments Deciding whether or not two similar but different orientations ought to fall within the same cluster is somewhat subjective The 3 threshold seems to work well for large ish ligands roughly 100 residues but should probably be reduced for smaller ligands In the CAPRI blind docking experi ment I tend to use a large threshold of say 5 to try to improve the chances of finding at least one medium accuracy prediction within the first 10 predictions submitted But this doesn t always help 5 8 Saving Docking Results There are two main ways in which docking results may
122. ver the surface but be reasonably well dispersed The po sitions of these spheres are then used to generate initial docking orientations for the ligand over the receptor and an appropriate local coordinate frame is derived from the geometry For multi domain receptors each sphere can be assigned to a source chain and spheres that do not belong to a given chain may optionally be excluded The gives a simple but imperfect way to limit the docking search to one of several symmetry related domains as in the hemagglutinin case for example In order to set up such a calculation for an antibody antigen system where the antibody s binding site is known it is a good idea to orient the ligand antibody such that the bind ing site faces the receptor i e the principal intermolecular axis passes near the antibody hypervariable loops This can be achieved by manually editing the antibody into position Then the macro sampling algorithm will place the ligand antibody at each of the gener ated starting orientations and in each orientation the antibody will be transformed to face the receptor Using the main Docking Control panel a search range of 45 degrees should be set for both the ligand and receptor so that the docking search will gyrate each molecule about the local intermolecular coordinate system yet still keep each molecule roughly facing the other as defined by the starting pose 5 11 Additional Docking Parameters There exist a few fur
123. y get the corresponding type of compressed output Similarly if any input file has one of these extensions Hex will automatically decompress the file as it reads it If you have installed a copy of the PDB e g from the PDB CDROM disc set on your hard drive you can use Hex to view the structure files without first having to decompress them Just point Hez s file selection widget at the top level of your PDB directory and start visual browsing 6 5 Environment Variables Hex uses several environment variables to locate directories and data files Most of these are optional as described in the table below The non optional environment variables are defined automatically if you use the self installing bundles or the hex configure bin script to install Hez Chapter 6 Miscellaneous 34 Name HEX CACHE HEX COLOURS Status Default Description optional SHEX ROOT cache locates a cache directory for the trans lation matrices highly recommended optional SHEX ROOT examples locates a directory of Hex colour files HEX CPUS optional 1 the default number of CPUs to use HEX_GPUS optional 1 the default number of GPUs to use HEX_FIRST_GPUoptional 0 defines the first GPU to use for computations HEX_DATA optional HEX_ROOT data locates non standard Hex data files HEX_LOG optional hex log defines the name of the current log file HEX MACROS optional HEX ROOT examples locates a directory of Hex macro files HEX_PDB optional SHEX ROOT examples locat
124. y 50 C 12 New Features in Version 3 1 Hex 3 1 represents a fairly major upgrade relative to Hex 3 0 as follows New Full Screen Display option type F to toggle see Section 3 10 Full Screen Mode page 15 New Animation Mode to cycle over docked orientations or multi model structures see Section 3 9 Animation page 14 New Save Docking option to write docking transformations to a disc file see Save Docking page 27 New Solid Surface display modes to draw electrostatic and steric density functions see Section 3 4 Solid Surfaces page 10 New Radial Filtering modes for docking scans up to 2596 speed up New Radial Cutoff option for viewing large molecules see Radial Cutoff Distance page 8 New command hex kill to clean up stuck processes see Section 6 6 Command Line Options page 34 New dynamically linked Linux executables for hardware graphics support see Sec tion 6 10 Technical Information page 38 Improved multi tasking up to 2096 speed up on dual processor systems Improved accuracy for translation matrices some performance penalty when creating disc cache Correlation limit increased to N 32 for large memory machines not generally rec ommended Improved surface contouring slightly slower calculation but smoother surfaces and faster graphics Linux RedHat 7 2 version compiled with Intel icc compiler up to 1096 speed up Linux RedHat 7 3 version available also compile
125. y types are controlled by additional control panels under the main Graphics menu This menu also contains options to allow the foreground and background colours to be selected the position and colour of a directional light to be modified and a simple Fog effect to be applied 3 1 Basic Display Styles The basic appearance of protein and DNA molecules is controlled by the Molecule Control panel The default style is to draw all covalent bonds as a skeleton with each half bond colour coded by atom type Probably the two most useful controls in this panel are the Show Sidechains toggle which displays a protein in backbone only or backbone sidechain mode and the Colour Scheme selector which allows a limited degree of control over the colours used to draw each molecule Line widths may be changed using the Bond Widths control When a protein or DNA molecule is loaded Hex adds any missing polar hydrogen atoms using a set of templates from the atom_templates dat file in the data directory Polar hydrogens can be displayed using the Show Hydrogens toggle The Show Sidechains toggle has an equivalent short cut button on the right hand border of the main window which is supposed to look like a phenylalanine residue Setting Show Sidechains to off which also turns off hydrogen atom display makes manipulating complex scenes easier When viewing large molecules its sometimes useful to draw only those atoms within a given distance of the molecular orig

Hex 6.3 User Manual - bioweb: molecular modelling group

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