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Hex 4.5 User Manual - bioweb: molecular modelling group

1. 25 Docking Parameters FAQ Lsssss 54 Docking Beeultes onno annsannnrnnnrnnn renn 24 Docking Samples iced a 21 Docking Summary Hie 24 Docking Transformations File 24 Dot Surface Control Panel 11 Dot Surfacesosi ac seis ee asia 7 11 E Edit Origin Mode 17 ng ria AE eee 5 Editing Centroides 17 Editing Molecules n n unanuunrunnrnuernna 16 Editing Orientations 16 Electrostatic Correlations FAQ 53 54 Electrostatic Potential 9 Electrostatics 0 02 00 cece cece eee eee 1 Environment Variables 31 44 ESCAPES aot panies e ed EA 6 Euler Angie 16 Examples Director 34 45 F A A Stee awa CR dee 14 False Doetives eee eee 23 FAQS 20 23 stavo stie a a es ae 49 F r Elan 4 2 to ER 15 Fast Fourier Transform ssssesusurunes 1 Feature History 0o oooooooooonooooo 45 Subject Index A toe AS A EUN ax UE O 1 File Selection Panel lusus 4 Final Search E See eR dps 19 21 EEK Ds et aet oit e io 38 BOR eco eh rH RR Ur BU e T Font s bl eR a EE UNE E US 5 Frame Hate issii seen cee ii i ee eed oe uds 13 Full Rotational Search 20 Full Screen Mode 6 G LS Key ashe lt A M E aE 14 Gaussian DensitiesS ooooooooooooooo 9 Gaussian Surfaces 00 c cece cece eens 9 Getting btarted 26 dr Retos 3 Global Gearch annan 22 GMP ini a dd es 38 E EE 38 Graphics Ment r
2. Appendix E Frequently Asked Questions 53 the message Or add a null function entry that matches the Mesa version in the message into etc mesa conf to suppress it e I noticed you only provide an i586 executable for Linux I have an i686 i786 system so could you supply a binary for my machine It might run faster I compared the docking performance of Hex compiled for a 686 processor on my 686 sys tem 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 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 SHEX_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 ato
3. 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 to be evaluated might be skipped e 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 and 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 orientation
4. Otherwise browse it on line as HTML using Herz 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 18 and Superposition see Section 5 13 Molecular Matching page 26 If you want to try more than just one or two docking calculations Chapter 1 Introduction 3 you should also look at the section on using macros see Section 6 1 Macros page 28 and the contents of the examples directory see Section 6 7 Examples Directory page 34 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 publications see Section 6 14 References page 39 1 3 New Features In Version 4 5 Hex Version 4 5 e Executables now avalable for Mac OSX and Linux PowerPC machines e Added small distance sub stepping for high order correlations for better coverage of search space e The low level correlation code is accelerated using a
5. 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 Support for compressed files is thanks to the zlib http www gzip org zlib gzip http www gzip org and bzip2 http sources redhat com bzip2 projects The Linux version would have been impossible without the Mesa http www mesa3d org graphics library Much of the OpenGL http www opengl org support from Mesa has been incorporated into XFree86 http www xfree86 org via the DRI Project http dri sourceforge net The MS Windows version of Hex was built entirely under the MinGW http www mingw org environment Hex has never been anywhere near a Microsoft compiler This manual was produced using texinfo http www gnu org software texinfo So its thanks to all these excellent Open Source projects for making Hex possible Hex uses the Stride ftp ftp ebi ac uk pub software unix stride program to assign protein secondary structures for cartoon displays See Section A 2 Stride Licence page 42 if you have any doubts about whether you are entitled to use Stride I would also like to thank the following people for making significant programming contributions to Hex 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 col
6. bottom left slider to get a better view TIP 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 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 unro
7. 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 Appendix E Frequently Asked Questions 54 e When I enable electrostatics I only get one docking solution What is going on Its likely that your structures contain unrecognised residues and or unrecognised atoms Her 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 Hex might assign 0 5e to each hydrogen to give a highly positively charge protein A 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 Her 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 user
8. just uses the explicit atoms coordinates as usual Note that atom coordinates are only replicated at dis play 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 es pecially 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 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 repre sentations 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 Chapter 3 Molecul
9. method using the Orientation Control panel a molecule may selected using the Apply to selector and then rotated using the Euler angle Alpha Beta and Gamma sliders The inter molecular 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 In the second method editing can be performed by manually manipulating the scene with the mouse by pressing the Edit Mode button which looks like a lightning bolt in the left border This method can also be used in conjunction with the Orientation Control panel In both editing modes picking a molecule ties its motion to the mouse and to the rotation sliders in the Orientation Control panel The bonds of the picked molecule are 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 When editing molecular orientations it may help to activate the Intermolecular Axis 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
10. stereo in a window untested on SGI and Sun 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 D nVidia Stereo Configuration page 49 for more details However if you are upgrading an nVidia driver on Windows ensure you de install any earlier drivers first I caused myself significant grief by not doing this 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 nostereo Alternatively set the HEX_STEREO environment variable to a false value ie 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
11. the Surface Type selector provides the op tion to draw contoured density functions of the Sigma and Tau surface functions as 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 Chapter 3 Molecular Graphics 10 orders N the Tau density can be seen to give a remarkably good representation of the initial 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 The Sigma Tau Shift slider controls how the shape and electrostatic expansion coef ficients are computationally translated using the T R translation matrices prior to recon structing the surface from translated expansion coefficients Thus it is possible to view graphically how the representation used in the docking correlation degrades with increasing distance from the orig
12. 5 7 Molecular Mechanics Refinement oocoooooccocccoccco 23 5 8 Clustering Docking Beaultz eee eee 23 5 9 Saving Docking Heaults c eee eee eee ee 24 5 10 Docking Multiple Structures 25 5 11 Docking Very Large Molecules Macro Docking 25 5 12 Additional Docking Parameters 000 26 5 13 Molecular Matchs 26 6 Miscellaneous eere ooo 28 Orly MacrOS ici ei t totae epe ree tate ad ert 28 6 2 Hetero A OS mirra da ERR EI EP enne 30 6 3 Hardcopy Output zen repr ee a app ses 31 6 4 Compressed les 31 6 5 Environment Variables 0 0 cece esses 31 6 6 Command Line Option 32 6 6 1 Loading Three Structures Together 33 6 6 2 Loading And Superposing Two Structures 33 6 6 3 Docking With Macro File And Log File 33 6 6 4 Docking With File I O Redirection 33 6 6 5 Serialising Several Batch Jobs 33 6 6 6 Using Her As a Web Browser 33 6 7 Examples Director 34 6 8 Bugs and Known Limitations 0oooooccccococcoooo 34 6 8 1 No Multi Processing on MS Windows 34 6 8 2 GUI and Graphics Freeze During Docking 35 6 83 Matos i4 eade a Wee Dee al e Je VH eas 35 6 8 4 Non Standard Residues e 35 6 8 5 Hardcopy Fonts 0 cece eee eee eee 35 6 8 6 Colouring Multiple Models 35 6 9 The Test Functions 0 0 0 0 cece cece cence eens 35 6 10 Technical Informa
13. Both of these nVidia drivers are buggy If you can live with the 3123 SIGSEG problem I d suggest using that version The 4191 driver is faster but drawing surfaces is broken This is because something changed in the g1X interface causing Hex to get no depth buffer This has been fixed in Hez 3 3 I think nVidia are making a good effort to support Linux but they do seem to be over optimising their driver code at the expense of breaking certain basic operations Or maybe its because I was writing poor code and just got lucky with the earlier versions Hopefully such problems will be fixed in future Hex and or driver releases e l mrunning Hez version 4 on a Linux system with an nVidia graphics card I installed the 4191 nVidia driver but I still get a SIGSEG fault when Hez starts I m not sure but this seems to be related to the first call to XCreatePixmap to make the buttons for the GUI borders the actual fault happens in XGContextFromGC and is trapped by _dlopen What s this got to do with nVidia I don t know but it doesn t happen with the Mesa OpenGL driver Update This graphics driver problem seems to have been finally fixed in Fedora Core 4 June 2005 Appendix E Frequently Asked Questions 57 e I can t get the whole manual to print on my printer What s the problem Well it prints OK on our A4 laser printer However both the PDF and HTML versions of the manual use quite a few different fonts and it may be that yo
14. Hex 4 1 is a bug fix release Double clicking a directory in the file browser no longer crashes the program Cartoons are now drawn correctly for chains with blank labels Fixed start up crash up on some SGI systems JPEG lib version fault 3 New Features In Version 4 0 Microsoft Windows version now available thanks to New Graphical User Interface GUI made with FLTK http www f1tk org New Message Window for text output and session logging New Progress Panel for docking calculations New Cartoon display mode see Section 3 3 Cartoons page 9 Shape matching now uses a Carbo like similarity index see Section 5 13 Molecular Matching page 26 GUI controls now available in full screen mode see Section 3 10 Full Screen Model page 14 GUI controls and graphics window now stay responsive during docking SGI mips3 version dropped the O2 mips4 is now the minimum SGI platform for Hex Appendix C Feature History 47 C 4 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 31 e New 3D density superposition algorithm see Section 5 13 Molecular Matching page 26 e New User Manual made with texinfo http www gnu org software texinfo C 5 New Features In Version 3 3 H
15. 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 42 f In the event that any 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 to 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 Appendix B Installation Guide 43 Appendix B Installation Guide When downloading Hex from the Internet files should be copied in binary mode and saved as source B 1 Microsoft Windows Installation For Microsoft Windows just download and run the self installer program hex 4e win exe T
16. Panel 12 16 22 Orientation dng 6 Origin Exditingixi an to 6 Origin Editing Button 6 Orthographic Projection 6 15 Other Search Modes annaasannrannrnnnene 19 P E Ke e mg en A UT Rie os 6 Page Downes gcse nee os gee ae da 6 Page Up i208 i Seine iboats 6 Papers Citing Hex 57 Parametric Functions 1 EWEG et derer oo eae SQ pedo 4 People rea gee tad 38 Perspective Projection 04 6 15 Picking mut S CREAR eg 5 Pipe Output te ein a eee eee ene 31 Pipes Directory scsscrerseerrrrererrre 45 Pointer Mode 16 17 Pointer Mode Button 5 Polar Hydrogens 2 ERR Dl T Post Processing Options ssusasunsenne 23 PowerPC Version 37 Printing Manual AO 57 Probe Radius eese Poe eg be ea EE 10 Projection Control Panel 15 PAM dc 57 R EGSlid6E uo mi EE ne 6 Radial Cutoff 23 nce cag oon ase ea ais 7 Radial Filters o oooooooocoooccommoo 20 Receptors rax lx tate ds ore See a ae 4 18 Receptor Model 13 Receptor Range 0 00 e eee ee eee 19 Reference Energy FAO 00000 eee 54 Reference Orientation 18 References cue eee eges ror aad ote s 38 Refine Docking AO 53 Relative Permittivity sssunssunrrrnrrne 9 Reloading Docking Conformations 97 Ribbon Cartoons ecrire ddp 9 Rotational Bearch 19 61 S Seis adds 6 Saving Docking Range 24 Saving Docking Results oooooooo o o 24 Scene
17. SGI executables should work on earlier versions of IRIX down to 6 1 at least The Sun version was built on an UltraSparc E450 running SunOS 5 8 and using the OpenWindows version of OpenGL It was compiled to make a generic SunOS executable which should run on other UltraSparc systems The Windows version was built on a Pentium III 686 system running Windows XP and using the MinGW http www mingw org development environment The binary should work on other Windows systems 6 11 Caveats Please remember that Her is essentially a research program and it is provided as is without any guarantee of updates or user support I always try to respond to problems Chapter 6 Miscellaneous 38 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 E FAQs page 50 and check Hex s Home Page http www csd abdn ac uk hex to make sure you re using the lastest version 6 12 Contacts Author Dave Ritchie http www csd abdn ac uk dritchie Before e mailing me with a problem or question please first check the FAQs see Appendix E FAQs page 50 6 13 Acknowledgements Much of Hex was developed during projects 1996 2000 funded by the BBSRC http www bbsrc ac uk Hex was written mostly in C but also uses some C for the GUI The new Her GUI version 4 0 was built with FLTK http www fltk org
18. Thus in the low resolution Steric Scan phase 642 x 642 distinct rotational orientations are produced although any orientations that fall outside the angular range cones are discarded At each of the surviving orientations the ligand is then rotated or twisted through 360 degrees about the axis in 64 steps of about 5 6 degree increments specified by the Twist Samples value In this constrained example Hex will evaluate the docking score at each of 46 x 46 x 64 135 424 distinct rotational orientations with the calculation being repeated at each of the 41 intermolecular distances implied by the distance range and step parameters In the high resolution Final Search phase the best 10 000 of the above orientations will be used to generate 25 529 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 no benefit in using finer steps in this phase It should be noted that such docking calculations never give a unique solution Rather Hex 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 Soln slider or you can step through the solutions using the keypad or arrow keys Home Starting orientation Page
19. 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 6 7 Examples Directory The examples directory under the main hex directory contains PDB data files of ex amples 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 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 lin
20. a constant distance step is used for both resolution levels 5 4 Radial Filters When performing a full 6D docking search the most expensive part of the calculation is normally the initial steric scan This phase can be accelerated by selecting a Radial Envelope Filter in order to avoid scanning orientations in which the molecules overlap sig nificantly or are too far apart for ther surfaces to interact There are two radial filtering modes which both use low resolution spherical harmonic surface envelopes to define an approximate radial envelope for each molecule The surfaces are constructed using the cur rent expansion order default L 12 from the Controls Harmonics Order selector The Re entrant filter assumes each molecule is fully contained within the harmonic surface and excludes trial distances at which the surfaces are too far apart The more aggressive Star like filter assumes the surfaces are single valued with respect to a ray from the origin and additionally excludes trial distances at which the surfaces are presumed to be too close together for docking to be feasible It is unwise to use these filters if either docking partner is non globular Chapter 5 Docking Molecules 21 5 5 Docking Examples OK lets start docking Open the Docking Control panel and select the following mostly default values from the selection boxes Controls Docking Grid Dimension 0 6 Controls Docking Solutions 500 C
21. a list of approximately evenly spaced angular sample points derived from the vertices of a tessellated icosahedron along with a radial distance from the origin to the surface at the corresponding angular sample Note that the surface envelope does not properly handle multi valued or re entrant surfaces That is if a ray from the origin cuts the molecular surface more than once only the most extreme cut point is recorded for the given angular sample Nonetheless this type of global envelope often gives a remarkably good low resolution representation of most protein surfaces By default the molecular envelope just described is not normally displayed Instead Hex uses the sample points of the envelope to calculate a parametric representation of the envelope using a spherical harmonic power series expansion You can view the molecular envelope by selecting Graphics Harmonic Surface Enable Surface toggle on Chapter 3 Molecular Graphics 11 The sampling resolution is controlled by the Dot Density selector and the Mesh Order slider The dot density is the number of dots originally assigned to each atom in the dot surface calculation The mesh order controls the number of vertices in the icosahedral angular mesh by defining the number of subdivisions along each edge in the original icosahedron The Probe Radius slider may be used to modify the size of the probe sphere used in the initial dot surface calculation Setting a probe radius o
22. assign non default values to the other environment variables mentioned in this section B 3 Unix Linux Installation You will need to download the installation script hex_configure bin the generic run time data file hex 4e rt tgz and one or more of the executables hex 4e sgi tgz hex 4e sun tgz hex 4e Inx tgz or hex 4e ppc tgz Here Inx refers to Linux on an Intel PC and ppc refers to Linux on a PowerPC machine not running Mac OS X The Inx executables may include shared or static in the filename please only take one such file It is safe to install a new version into the same directory structure as an earlier version unless you have changed any of the former scripts or data files The distribution files should be installed using the shell script hex configure bin by typing sh hex configure bin This script is intended to simplify the installation process and can normally be trusted to install Hex correctly even if you have already installed an earlier version of the program Appendix B Installation Guide 44 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 If you prefer to install the program manually you should create a hex directory cd to that directory and then uncompress the distribution fi
23. constitute a breach of this LICENCE Appendix A Licences 41 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 and its associated documentation 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 Herz 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 whichever is earlier of the computer program Hez 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
24. ee e e ees 8 Caveats sce ee ellen er me EE 37 Cavities eet ED P Eee ea bea RE 9 Changing The Scene Origin 12 Charge Density 00 eee eee 9 Checkerboard issue aca edere ER 6 Cb Hex JL lera denk epe ely gf seed 39 Clipping eu a a ER 12 Clipping Button 6 Clipping Clipping The Scene 6 Clipping Slider 0 cee eee eee eee 13 Clustering Control Panel 23 24 Clustering Docking Results 23 Colo r Eilesz ote tet ed ao Ret ile ek he ds 7 Colour Ramp At EEN AER NEEN 9 Colour Schemes cat ti 7 Colouring Multiple Models Bug 35 Command Line Options essssssuaure ea 32 Commercial Licence PAO 54 Complex idas tbh ate dia 4 18 59 Compressed Hiles 31 CONNECE GPEOL I 1 so e voe dur eee 52 Contacts cunis voee tunt ees eee beet 38 Control Give usura tet postera ss ele 6 Control Q ici o dE 6 Correlation 3 Aaner do dece mtt 1 Crystal Symmetry sss esses 8 D Data Directory cuota 45 DCC Stereo Mode 49 Density Model 2 Disc Cache dreni rempan Porristas 22 Display Styles cc da 7 Distance Range sscrssuererrrrerrreers 19 Distance Sub Stepping ococoocccoooocco o 20 Docking Control Panel 9 19 21 26 54 Docking Eaxamples 20 Docking Large Molecules 25 Docking Molecules oooooooccccccccco o 17 Docking Motion issis eener m9 his 12 Docking Multiple Structures
25. have plenty of physical memory its possible that you re running out of program stack space Some system admistrators set fairly aggressive ulimit values which limit the resources any individual process can use You should check and possibly increase the values reported by the ulimit command possibly using ulimit a to see them all e I always get a SIGFPE fault towards the end of a Hex docking run on my SGI work station IRIX 6 5 256Mb memory Can you fix this I would if I could replicate the problem on my O2 machine IRIX 6 5 320Mb memory Despite having IRIX 6 5 it could be that some of your system s run time libraries are not up to date I remember a similar strange problem on an SGI machine that didn t have all full set of low level string handling libraries and hence failed while reading data files If people are willing to send me their data files along with a description of what they re trying to calculate preferably as a Hex macro file Pll be happy to try debugging the problem I will promise not to divulge or otherwise exploit any structures I might receive But as this example shows I cannot guarantee a solution e I m running Hex on a Linux system with an nVidia graphics card When using nVidia s 3123 driver Hex gives a SIGSEG fault when I first run the program but on subsequent attempts it works fine With the 4191 driver Hex starts properly but solid surfaces seem broken up What s going on
26. is recommended that you use this control only for a 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 additional short cut ways of controlling 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 enhance perspective projections Hitting the escape key Esc or typing Ctr1 Q will exit the program Rapidly typing Ctrl C twice in the terminal window will abort Hex even if its in the middle of a calculation However such an interrupt may be ignored at certain times during a docking calculation on multi CPU platforms If you really want to kill a long running or stuck Hex job type hex ki11 in another terminal window 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 ar
27. 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 2A 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 Chapter 5 Docking Molecules 24 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 clus tering and clustering parameters used and how cluster membership affects the displayed solutions 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 bumps detected Any solution containing a num
28. 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 4e the default version of Hex to use Additionally you should ensure that your PATH contains the HEX_ROOT bin directory 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 where is a version number string e g 3d 3c ncpu n where n is the number of CPUs to use nice n runs at lower priority n a nice value noexec don t put a batch run in the background gui force GUI mode even when stdin is not a terminal stereo request a stereographic window 8 same as stereo nostereo request a non stereographic window 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 Chapter 6 Miscellaneous 33 kill kill all your Hex processes 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 c
29. mechanics energy may be calculated for each docking solution MM Energies or a Newton like energy mi minisation 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 contribu tion 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 8 Clustering Docking Results Because Her 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 orientation for the first cluster The list
30. 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 Angstrom cubes because the grid must accommodate all possible translations of the ligand about a stationary receptor Here the grid only needs to contain the larger of the two molecules so that much finer sampling grids are feasible In Hex 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 30 degrees means that only a small fraction of the 642 rotational increments the Receptor Samples and Ligand Samples values will actually be used for the molecular rotations of each molecule These rotational samples are generated from an icosahedral tessellation of the sphere and in this case have an angular separation of about 8 5 degrees between each sample point Essentially each molecule is rotated incrementally so that Chapter 5 Docking Molecules 22 successive tessellation points are rotated onto the intermolecular axis the axis
31. 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 hex4e i586 UI try to figure out what needs to be done and if possible make up a new Linux release to fix it e I downloaded the Sun version of Hex followed all the instructions but still nothing works What do I try next Sun machines are probably the systems I know least about they don t seem to give quite the same transparency across different hardware and CPU configurations as does IRIX for example or is this just my ignorance Anyway similar comments to Linux apply as above Here s what Her was built on uname a SunOS trogon 5 9 Generic_118558 08 sun4u sparc SUNW Sun Fire 280R And here s what the Idd output looks like ldd hex4e sparc libGLU so 1 gt usr lib libGLU so 1 libGL so 1 gt usr lib libGL so 1 libsocket so 1 gt usr lib libsocket so 1 libnsl so 1 gt usr lib libnsl so 1 libXext so 0 gt usr lib libXext so 0 libX11 so 4 gt usr lib libX11 s0 4 Appendix E Frequently Asked Questions 52 libm so 1 gt usr lib libm so 1 libSM so 6 gt usr lib libSM so 6 libICE so 6 gt usr lib libICE
32. 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 anti body s binding site is known it is a good idea to orient the ligand antibody such that the binding 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 generated starting orientations and in each orientation the antibody will be trans formed 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 12 Additional Docking Parameters There exist a few further 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
33. toggle to control the display of summary text in the graphics window The Azes button two arrows at right angles toggles the display of the coordinate axes useful for screen dumps 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 8 The Solid Surface button toggles the calculation and display of solid surfaces see Section 3 4 Solid Surfaces page 9 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 10 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 final Solid Motion button the black square with an arrow can be used to toggle whether solid shapes or just b
34. 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 origin 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 d
35. 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 look right then the charge density is also correct NB Hex uses a relative permittivity value of 8 instead of the more usual value of around 80 So in addition to Hex 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 con tour 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 sur faces when contoured As the contouring algorithm implicitly produces positively oriented surfaces outward normals positive total volumes it is convenient to assign each calcu lated surface to one of two possible classes Primary positive volumes outward normals or Secondary negative volumes inward normals By default only Primary surfaces are displayed but this may be changed using the Draw Surface control In addition to the default Gaussian surface
36. works What do I try next Hmm Well Hex is known to run on all versions of Redhat Linux from version 6 0 onwards But RedHat 7 1 was a bit dodgy and I wouldn t recommend that I m not aware of any recent Intel Linux systems it doesn t run on However I can t guarantee 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 dependencies There are really two main reasons why Hex might not work Assuming you have down loaded an appropriate binary 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 change directory to the hex exe directory and type hex4e i586 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 4e part of the filename corresponds to version 4 5 if you have a different version of the program the executables will have slightly different names Anyway 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 bi
37. 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 13 Molecular Matching Hex superposes or matches pairs of molecular structures using the same 3D density representation 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 Controls Matching Activate Hez will take a few seconds to calculate the steric density functions for each molecule It will then systematically search over the range of angular and intermolecular distance samples Chapter 5 Docking Molecules 2T given in the Matching Control panel However unlike docking Her 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 distanc
38. 686 FAQ eee eee eee eee 53 Linux Install FAQ 0 0 22 50 M Mac OS X Version 0 eee eee 37 Macro Docking i cp eek bee the SEENEN ren 25 Macro Sampling Control Panel 25 MAGCrOSt slo I edente Rado atan toi putos 28 Macros Bugis cite 5 oi eer 35 Manoeuvring Molecules 15 Marching Teteagons 9 Matching Control Panel 26 Menu Buttons 4 5 Mesina da 38 Mesa Install FAQ oooooooocccccccccoo 52 MicroSoft Windows Version 37 Min A EE 38 Missing Ligand HETATM bug 57 Molecular Centroids o ooooooccoooccooooo 12 Molecular Graphie 6 Molecular Matching 26 Molecular Mechanics Refinement 23 Molecular Similarity 2 Molecule Control Panel 7 8 Maikel Hi HORE Aa cd 50 Molscript d oe deco Te eese od Exam 31 Mostly Hames 38 Mouse Buttons 4 Movie Type ER SU nei ts eat 13 MPBE 2713 tia Mes 57 MS Windows 37 N Near P O cui oR ek oe Lee als 15 NMR Docking vero e RE 25 NMR Models mre RETE 25 No Docking Solutions FAQ euausauaaneua 55 No Multi Processing on MS Windows 34 Non Standard Residues Bug 35 Non Standard Residues FAQ 53 nVidia Drivers is dre 15 nVidia Graphics Cards 15 nVidia Graphics AO 56 Subject Index nVidia Stereo Configuration 48 O Open Source Project 38 OpenGL Warnings EAO 54 Orientation Control
39. 7 Appendix C Feature History 48 Improved multi tasking up to 20 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 10 speed up Linux RedHat 7 3 version available also compiled 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 8 New Features In Version 3 0 2 4 Hex 3 0 contains several new features and a number of improvements compared to Her 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 C
40. CENSOR grants the LICENSEE a non transferable and non exclusive licence to use Hex 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 Hez 3 Licence Fee a In consideration of the LICENCE granted pursuant to Section 2 the LICENSEE shall pay to the 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 Transfer of Licence a The LICENSEE shall not in any way sublicense rent assign or transfer this LI CENCE or the computer program Hez 5 Copyright a The LICENSOR owns the copyright and all and any other intellectual and industrial property rights in Hex and its associated documentation You must therefore treat Her and its associated documentation like any other copyrighted material e g a book b Hex 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 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
41. Centre xke Sek Sel A tle RE E ax 12 SGI Install FAQ 52 Shape Matching Scores asunnssnrrnnns 27 Short Cut Buttons 4 Sidechains Button 5 7 SIGFPE Docking Fault FAQ 56 Sigma Surface 000s cece eee eee 9 SIGSEG Startup Fault Fedora Core 56 SIGSEG Startup Fault RedHat 9 56 SIGSEG Surface Fault FAQ 56 Silicon Graphics Version 3T Skin Factor zucca esi eene t AA 12 Slider aee eet belle nce p emi es 4 Soft BPotentials vule yet RAE 23 Solid Model Button 5 Solid Model Control Panel 8 Solid Models 0 0 cece cece eee eens 7 8 Solid Motion Button 5 Solid Surface Button 5 Solid Surfaces ic epi ree e ee 7 9 Solvent Cullng oo 31 Source Code AO 50 Spherical Harmonic cube 36 Spherical Harmonic Functions 36 Spherical Harmonic Rotation 36 Spherical Harmonic Surfaces 5 7 10 SpA la da 14 start p ctash neie tb Re ERR 52 Stereo Displays oo ooooooooo o 6 14 15 Stereo Parallax orent E Yr 15 Serie Deal a id E dI 19 21 bride s soient te ERAI pee 9 38 Stride Licence 42 Sun Graphics Version ooooococoooooooo 3T Sun Install FAO sites rete rus 51 Ni Em 3T Superposing Molecules lusus 26 Surface Control Panel 21 Surface Skins meenet cece eee eee eee eee 1 Symmetry Vy pesis ic 4n ele e e beta 8 T Tau age
42. Down Next solution Page Up Previous solution End 500 th or last solution You should find in the above example that Hex 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 trial 1079 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 FFT 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 TIP When viewing docking solutions its 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 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 Chapter 5 Docking Molecules 23 TIP If you plan to use Hex more than once
43. Hex 4 5 User Manual Macromolecular Docking Using Spherical Polar Fourier Correlations Copyright c 1996 2005 David W Ritchie Dave Ritchie Department of Computing Science University of Aberdeen Aberdeen AB24 3UE Scotland UK Table of Contents 1 Introd cion 2 1 ideal 1 11 What The Heck Is Her 1 1 2 How To Read This Manual 2 1 3 New Features In Version A5 3 2 Getting Started e is 4 2 1 Sh ort Cut Buttons siese tai a Aaa 4 2 2 F nction Puttes ute ae EA 5 2 3 Keyboard bes 6 3 Molecular GraphicS 7 3 1 Basic Display Styles 0 0 eee tenes fe 3 2 Solid Models cuca eet ned bid psit ake wd 8 A LANGUE M 8 39 4 Solid Surfacesus ep bi utt 9 3 5 Spherical Harmonic Surfaces o ooooooomoorroom 10 3 6 Dot Surfaces iss ease aed peace eher RE ERE oras 11 3 7 Changing The Scene Origin sssusesslssssssesn 12 3 8 Clipping The Scene 0 cece eee eee eens 12 3 01 A ee Kette E E 13 3 10 Full Screen Mode 14 3 11 Stereo Displays 14 4 Manoeuvring Molecules 16 4 1 Editing Orientation 16 4 2 Editing Centroids 22a vie who eek wh da dda aeons 17 5 Docking Molecules 18 5 1 Rotational Search 19 5 2 Other Search Modes iius 19 5 3 Distance Sub HBtenpimg 0 0 c eee eee eee eee ee 20 5 4 Radial A ETS 5e ti ns 20 5 5 Docking Examples 0oooooooocccocrccccc ro 20 5 6 Calculating Bumm 23
44. 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 discontinue use of Hex 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 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 Scotland and the parties prorogate the exclusive jurisdiction of the Scottish 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
45. 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 rotate the scene to see exactly the same view Alternatively you could write each molecule to a separate file using Chapter 4 Manoeuvring Molecules 17 File Save Receptor and File Save Ligand You could then open these new files to verify the new orientation You may want to try using these editing features to manually dock the ligand into the receptor binding site if appropriate or you might try to superpose the two molecules if they are similar Neither task is easy 4 2 Editing Centroids 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 Angstrom 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 large molecule you should use Hex s macro docking mode for such cases See Se
46. 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 representation 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 25 remain these should still cover the surface but be reasonably well dispersed The positions 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 Chapter 5 Docking Molecules 26 way
47. able 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 Chapter 6 Miscellaneous 31 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 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 from 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 molec
48. ar Graphics 9 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 should can disable the molecular skeleton using the Display Molecule button in the Controls Molecule panel The type of secondary structure within each protein chain is currently calculated us ing Frishman and Argos Stride ftp ftp ebi ac uk pub software unix stride pro gram 3 4 Solid Surfaces Solid molecular surfaces may be 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 Hex 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
49. are described in more detail in Chapter 5 Docking Molecules page 18 TIP 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 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 En
50. ata 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 Chapter 3 Molecular Graphics 8 L 90 97 blue 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 explicitly using the syntax atom_name first atom last_atom colour name More sophisticated colour selection schemes could be implemented but visualisation issues get a rather low priority in Hez 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 Sym metry 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
51. be used to adjust the stereographic effect Stereo 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 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 perspective gives a pleasing effect without straining the eyes For PC Linux stereo you should download the shared link executable see Section 6 10 Technical Information page 37 because hardware stereo support is currently only available in the vendor supplied GL GLX libraries Even if you don t have hardware stereo you may still get better graphics performance using the shared link executable if your graphics card has hardware accelerated OpenGL support Chapter 4 Manoeuvri
52. ber 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 generate good coverage of the search space and to distinguish different but similar solu tions 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 3A 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 2A threshold seems to work well for large ish ligands roughly 100 residues but should probably be reduced for smaller ligands 5 9 Saving Docking Results There are two main ways in which docking results may be saved to disc The most compact 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 wich should be applied to the li
53. by initially placing both molecules in a common coordinate system In fact much of the early development of Hex concentrated on displaying and superpos ing protein surface shapes using two dimensional spherical harmonic expansions to represent surface shapes parametrically This proved to be a fast and accurate way to superpose pairs of similar protein molecules but this type of 2D surface approach does not encode suff cient detail to give a viable docking algorithm It was this observation that prompted the development of our 3D density model of molecular shape 1 2 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 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 Hex At various points this Manual also contains tips like this TIP Some parts of this Manual are quite heavy going If you really want to read the whole thing print out the PDF version hex manual pdf
54. commercial sites resulting in about a dozen problems queries Here they are e I noticed you supply only binaries Is there any chance of getting a copy of the source code In general the answer is no At least not yet Hex represents over nine years of work and it implements some ideas that have not yet been published Gee research is pretty competitive these days I d 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 could 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 inter ested 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 pro gram On the other hand if you have any novel or interesting research projects you might want to collaborate on then I could probably be persuaded to cut a deal In any case if you have a genuine interest in some parts of the code please contact me personally e I downloaded the Linux version of Hex followed all the instructions but still nothing
55. ct until you enter full screen mode In both the Unix 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 Hex s full screen mode but instead use the window manager s maximise button to ensure the graphics window is well behaved On Linux Fedora RedHat full screen GUI 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 I don t know what other Linux window managers might do but it seems many window managers don t handle full screen windows very well Chapter 3 Molecular Graphics 15 3 11 Stereo Displays Stereographic displays should work on systems that support
56. ction 5 11 Macro Docking page 25 Molecular centroids may be edited using the Edit Origins button two crosses and a line on the left hand border Try changing to Edit Origins mode and pick a molecule to edit Once the picked molecule is highlighted dragging Button 1 will move the origin of the selected molecule As with editing orientations above it may help to activate the Intermolecular Axis in order to see the new and old positions of the centroid s 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 TIP You can use virtually all of the other GUI functions while in edit mode although certain operations e g opening closing molecules cause Hex to revert to pointer mode Chapter 5 Docking Molecules 18 5 Docking Molecules In order to run a docking calculation in Hex 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 complex 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 heter
57. d ie 7 GRASP wie ese cir di ane ee daa a 31 Grid Dimensions 000 cece ences 21 CEU Eae tnt E Beye A oe a 2 GUI and Graphics Freeze During Docking 35 GUI Control Iogele e eee eee 14 PAP A x xu EE 31 38 47 Gzipped Files 0 cece eee eee eee 31 H Hammer Button 5 16 Hardcopy Fonts Bue 35 Hardcopy Output 31 Harmonic Surface Control Panel 10 36 Harmonics Button 5 Harmonics Control Panel 11 25 36 37 Hbonds lt 1 72 52 ED tee ees th aes 57 HETATM record bg 57 Hetero Atom 30 Hetero Control Panel sess 18 30 Hee Humour 2221 I 0 wend doe ld abe en 38 Hex iGence ss rr td Ae 40 Hex Dictionary Definition 1 Home Position ess sornra terne en TE a 5 Home View node tra a ses 6 Hydrogen Atoms 0 0c cece eee eee eee 7 I Icosahedral Tessellation 10 35 ID ButtOn izienshenebetgeeIethbRIe RABAT 5 Impossible Things sese 1 Installation Guide 42 Intel Linux Version 37 Intermolecular Ais 5 16 Intermolecular Distance sesuuuunununne 6 Internal Energies 0oooooooccccccccco 57 TREX a EN bx ire 37 60 K Keyboard kees 6 13 Killing Jobs dcir dorada 6 L Laguerre Polynomials nas unssunnrnnnene 50 Licencia a EA Ae 39 Ligand 52 prada E ed 4 18 Ligand Model 13 Ligand Orbit licor reete Ge d A 19 Ligand Ranges SA PN fe as 19 Ligand Translation 19 Linux 1586 1
58. e 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 Limitations Please report any bugs suggestions to the author see Section 6 12 Contacts page 38 Described below are some known limitations some of which might never be fixed 6 8 1 No Multi Processing on MS Windows On Unix and Linux Her can exploit multiple processors in most of its calculations This has been implemented using the Unix fork feature which doesn t exist in the MS Windows operating system So currently the MS Windows version can only use one CPU Chapter 6 Miscellaneous 35 I haven t bothered to write a Windows threads version of the docking module because I assumed most MS Windows users would likely only have a single CPU anyway But I could be persuaded otherwise if there is sufficient demand 6 8 2 GUI and Graphics Freeze During Docking Although it was claimed i
59. e 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 repre sentation 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 den sity 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 within the body of the larger molecule The shape matching algorithm re uses much of the docking code and the Matching Con trol panel works in almost exactly the same way as for docking see Section 5 5 Docking Examples page 21 One noticeable difference however is that similarity scores are cal culated using a Carbo like overlap score This is essentially a normalised overlap volume scaled onto 1000 0 for compa
60. ecked for steric clashes between backbone atoms the column will show the total count of bumps You 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 A Acknowledgements cece eee eee 38 Additional Docking Parameters 26 Angular Envelope ssssrsussrrurrrrrrerss 10 Animation succi Ged ae he 13 Animation Control Panel 13 Arrow Reg ic c4 del eh ar RR E ee 6 AUS cia MEER uM EU rr ps 38 Axes AXIS siio Pop er ido Amy 5 B Bici idad 6 Basic Display Styles annnnaunneanrnnnrnne 7 Batch Docking Example 30 BBSROS as Saee t mx hp ders 38 Beowulf Parallelisation 57 bind errors 272 034 stele Rd PA 52 Biological Symmetry 0000000 8 Bond Widths ici ioe neta detona RR petu 7 ENEE 34 IER 23 BUMPS ila eue oed 5T Buttons i 3020 43 EE EE be 4 5 L sic ERO e elut 31 38 47 Beipped Piles 6d eg RR 31 C Cant See the Ligand uessusecesreesernns 97 CAPRI Blind Trial 19 25 39 Carbo Index sp e eee edd het 27 Cartoon Button 5 Cartoon Control Panel 9 Carts siria poe bpp
61. enabling a disc cache will speed up the translational 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 Her With typical usage the disc cache will occupy from 50 to 200 Mb of disc space 5 6 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 7 Molecular Mechanics Refinement In addition to the bumps counter a single rigid body molecular
62. ernal 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 i e 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 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 Appendix E Frequently Asked Questions 55 Control panel In general its better to over sample the search space and then cluster the solutions rather than risk missing good solutio
63. et nib A IER 9 Technical Information 3T Tessellation Mesh Order 10 Test Functions 2 2 mec re e EIER 35 Texcl tou 3er e abb ERI EUR 38 47 The CIP a RU 38 Translation Matrices suuuuuuueeenna 10 22 Twist Angle cia is dan 19 Twist Samples lesse eese 21 Subject Index 62 V X van der Waals Spheres ooooocooooroooomo mo IN n eee eee ee 38 Viewing Large Molecules 7 EMU E 50 Z d Dia ia rr is 38 Windows X Po cn 28 deed ida 37 LOMA a ls i sed 4
64. ex 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 6 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 C 7 New Features In Version 3 1 Hex 3 1 represents a fairly major upgrade relative to Hex 3 0 as follows e New Full Screen Display option type F to toggle see Section 3 10 Full Screen Mode page 14 e New Animation Mode to cycle over docked orientations or multi model structures see Section 3 9 Animation page 13 e New Save Docking option to write docking transformations to a disc file see Save Docking page 24 e New Solid Surface display modes to draw electrostatic and steric density functions see Section 3 4 Solid Surfaces page 9 e New Radial Filtering modes for docking scans up to 25 speed up see Section 5 4 Radial Filters page 20 e New Radial Cutoff option for viewing large molecules see Radial Cutoff Distance page 7 e New command hex kill to clean up stuck processes see Section 6 6 Command Line Options page 32 e New dynamically linked Linux executables for hardware graphics support see Sec tion 6 10 Technical Information page 3
65. f zero would give a van der Waals surface instead of the molecular surface The envelope may be displayed in different styles and colours using the Display Mode and Line Colours selectors By disabling the envelope display and by enabling spherical harmonics one can view the corresponding spherical harmonic molecular surface Graphics Harmonic Surface Enable Surface toggle off Controls Harmonics Enable Harmonics toggle on In fact these are Hez s default settings so that once a molecule has been loaded pressing the Harmonics button on the right hand border calculates and displays a spherical harmonic surface directly The order of the spherical harmonic expansion can be selected using the Order L slider in the Harmonics Control panel 3 6 Dot Surfaces These days dot surfaces are somewhat of a historical 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 calculate these two surfaces Nonetheless its still sometimes useful to be able to draw dot surfaces If nothing else dot surfaces give a fast way to verify that Hex is recognising all the atoms in a PDB file because sometimes unrecognised atoms may not be drawn in the other drawing modes whereas the dot surface ca
66. fault Full Rotation mode in which the receptor and ligand are effectively rotated about their own centroids and the ligand is twisted about the intermolecular axis at each of a range of intermolecular distances Thus the default behaviour is to perform a full 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 calculation is arranged so that the intermolecular twist angle search is in the innermost loop of the algorithm This innermost loop turns out to involve a sum over sines and cosines of the twist angle which may be accelerated using a one dimensional FFT There are several controls which specify the resolution and in particular the order N of the docking correlation 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 20 000 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 cont
67. ficult 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 Chapter 3 Molecular Graphics 13 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 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 T
68. gand coordinates in the original ligand PDB file in order to produce the corresponding docking 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 A 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 bot 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 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 Chapter 5 Docking Molecules 25 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 is 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 cu
69. he exact binding mode is not These modes are less efficient than the default rotational search mode since they can t exploit the fast FFT twist angle search on the innermost loop of a rotational docking search If in doubt use the default Full Rotational search mode 5 3 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 1 0 SubSteps 2 This means that the Steric Scan phase will search over 41 distance increments 20 steps of 1 A from the starting separation plus the starting separation itself These orientations are sorted 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 1 resolution but to perform the high resolution scoring at 0 5 resolution Setting SubSteps 0 gives the old behaviour of earlier versions in which
70. herical 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 the FFT approach the rotational part of a docking search is the easy bit Chapter 1 Introduction 2 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 A further 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 simply by constraining one or two of the angular degrees of freedom This can reduce docking times to a matter of minutes on modern workstations So depending on how well a particular FFT algorithm is implemented and on who you believe I claim that Hex is somewhere between 10 and 100 times faster than conventional FFT docking algorithms 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 problems involve translating and rotating one or both molecules into the desired orientation However to a first approximation the similarity problem can be reduced to a three dimensional rotational search
71. hesis 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 15 Citing Hex When citing Hex in a publication please cite whichever of the above articles seems most appropriate and please also mention Her s Home Page http www csd abdn ac uk hex Appendix A Licences 40 Appendix A Licences A 1 Hex Licence This is a legal agreement between you the LICENSEE and the LICENSOR for use of the computer program Hex It must be understood that by downloading or obtaining a copy of Hex by any other means you agree to be bound by the following licence agreement BY INSTALLING COPYING OR OTHERWISE USING Her 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 LICENCE THE SOFTWARE TO YOU IN SUCH AN EVENT 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 University of Aberdeen of Regent Walk Aberdeen Scotland UK as owner of the software comprising the computer program Hez c SITE means a single computer or internal computer network operated by the LICENSEE at the premises of the LICENSEE specified when Hex was ordered or installed 2 Grant of Licence a The LI
72. his adds a Her 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 Unix Linux version described below In particular you may 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 4e osx pkg package file This will install Hex 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
73. ie hex colours setenv HEX DATA home dritchie hex data setenv HEX CACHE mp dritchie hex cache setenv HEX STARTUP home dritchie hex examples my startup v4 mac setenv HEX CPUS 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 dritchie hex set HEX_PDB home dritchie pdb set HEX_MACROS home dritchie hex_macros set HEX_COLOUR home dritchie hex_colours set HEX_DATA home dritchie hex data set HEX_CACHE tmp dritchie hex_cache set HEX_STARTUP home dritchie hex examples my_startup_v4 mac Appendix B Installation Guide 45 set HEX_CPUS 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 Typing hex at the Unix command prompt should locate the script hex in the bin directory which then launches the appropriate executable from the exe directory The exe directory may contains several executables typically hex mips4 and hex sparc where is a version number The examples directory contains several PDB files and example Hex macro files Unless you set the above environment variable
74. ighest 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 Fedora Core 4 and Redhat 9 Its great The latest Linux version was built on Pentium III Xeon system Fedora Core 4 kernel 2 6 11 X org 6 8 2 gcc 4 0 Versions are also available for 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 Hez are still available for some older versions of RedHat It is generally advisable to select a version which is no newer than your own system If you have difficulties installing the shared link executable you could try instead installing a static link executable if available This should work on all hardware because it does all the OpenGL graphics processing in software using the Mesa library However this cannot exploit any hardware acceleration your graphics card might offer A shared link executable will be required for PC Linux hardware stereo support As of Hex 4 5 PowerPC executables are now available for Mac OS X Tiger 10 4 and Linux Fedora Core 4 These were built on a G4 PowerBook but should work on other PowerPC systems The Silicon Graphics version was built on a MIPS R5000 O2 system running IRIX 6 5 and was compiled to give generic 32 bit code The SGI executable is known to run on R5000 and R10000 systems The
75. in In this display mode the receptor surface is translated in the neg ative 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 Hez s docking correlations all computational translations are applied entirely to the receptor 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 The Harmonic Surface control panel controls the way in which spherical harmonic molec ular surfaces are calculated and displayed Spherical harmonic molecular surfaces are gener ated from the dot surfaces calculated by Hez s internal dot surface algorithm according to the parameters set in the Harmonic Surface control panel These parameters are distinct from similar parameters in the Dot Surfaces control panel which generates dot surfaces purely for visualisation see Section 3 6 Dot Surfaces page 11 When Her calculates a spherical harmonic molecular surface it first finds the shape of an angular envelope which just enclosed all dots of the dot surface This envelope is made up of
76. 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 If 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 Any of the usual user interface controls may be used while an animation is 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 effe
77. l options Section Device Identifier NV AGP VendorName nvidia Driver nvidia BusID PCI 1 0 0 Option Stereo 1 O off 1 DCC 2 blueline 3 onboard DIN Option NoLogo true Option UBB true Option PageFlip true Option WindowFlip 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 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 splitters often come included with stereo glasses kits However nVidia s 4349 driver claims to support DIN stereo output but I haven t tested this yet For best performance use nVidia s AGP driver part of NVidia s driver distribution and 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 Appendix E Frequently Asked Questions 50 Appendix E Frequently Asked Questions Actually the questions listed below aren t so frequently asked at all As of July 2005 the program has been downloaded by about 2 000 people about 800 downloads were obviously from academic or
78. lculation always uses all atoms regardless of their type Spherical harmonic surface envelopes are also calculated from the sampled dot surface The calculation and display of dot surfaces is controlled by settings in the Dot Surface control panel The short cut Dots button on the right hand border of the main window provides a fast way to toggle the display of dot surfaces By default Hex displays a molecular surface calculated using a 1 4 Angstrom radius probe sphere Dot surfaces are calculated by covering the surface of each atom with a set of sample points generated from an icosahedral tessellation of the sphere The default dot density is 162 dots atom but this may be changed using the Dot Density selector Any dots which are occluded by neighbouring atoms are immediately discarded If the Probe Radius is zero then this gives the van der Waals surface Otherwise the program calculates the molecular surface and solvent accessible surface by rolling a probe sphere over the surface non occluded atoms of the molecule When Hez calculates a molecular surface non occluded atom dots are classified as one of convex accessible toroidal reentrant or singular reentrant These classifications correspond to the type of contact the dot should make with a probe sphere being rolled over the molecule The convez accessible dots are those which may be touched by the probe when the probe sphere is not simultaneously in contact with any other atom All othe
79. les into it For example assuming you are installing the SGI version use zcat hex 4e rt tgz tar xvpf zcat hex 4e sgi tgz tar xvpf If your zcat doesn t recognize gzip ed files use instead gunzip hex 4e rt tgz tar xvpf hex 4e rt tar gunzip hex 4e sgi tgz tar xvpf hex 4e sgi tar The tar p option is used to extract files with their original permission settings i e world read and execute as appropriate 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 BOOT These two steps are normally performed by the hex configure 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 except 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 32 Here s a C shell example I have these lines in my cshre file setenv HEX ROOT home dritchie hex setenv HEX PDB home dritchie pdb setenv HEX MACROS home dritchie hex macros setenv HEX COLOUR home dritch
80. lt 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 12 Manoeuvring molecules also called editing is something you might wish to do before running a docking calculation Hence editing only makes sense when you have two molecules loaded Go to the File 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 Use the R slider bar on the bottom border to separate the molecules Then use the Lock button to make this orientation the Home View In any case you should now find that the mouse buttons translate and rotate both molecules in the scene You can now use the Intermolecular Axis double headed arrow on the right border to enable the display of the intermolecular axis This axis connects the default centroids of each molecule 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 relative to the scene These operations are described in more detail in See Chapter 4 Manoeuvring Molecules page 16 TIP The R slider bar can be used to change the intermolecular separation permanently as described above but it
81. lustering docking solutions 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 Automated installation script hex configure bin Existing Hex 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 Stereo Configuration 49 Appendix D nVidia Stereo Configuration Configuring an nVidia graphics card for stereo should be straight forward Just down load 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 Anyway here s what the Device Section of my etc X11 xorg conf file or etc X11 XF86Config in RedHat 9 looks like after editing nVidia s supplied template Used lspci command to verify PCI bus ID Used NVidia README file for additiona
82. 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 r12_range 21 r12_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 Chapter 6 Miscellaneous 30 moving_thing 1 edit O receptor l ligand 2 complex randomise_molecule i e randomise the ligand orientation commit_view commit changes moving thing 1 done editing Sat I SS SS eS SS SS Se ee SS EEE 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 the unix prompt type hex dock ptc mac dock ptc log Hex goes into the background ps ef grep hex check background process running The various docking parameters
83. ms e How can I refine the results from a docking correlation It is possible to further refine results from the docking correlation in Hex 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 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
84. n in amongst the other colon separated bits of the PATH sorry if this is all obvious to you but different people have different levels of Unix knowledge You should be able to type which hex and get back your stuff hex bin if the PATH is properly set up Appendix E Frequently Asked Questions 51 If running stand alone hex4e 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 hex2d i586 The output on my Linux system looks like this linux gate so 1 gt 0x00b36000 libGLU so 1 gt usr X11R6 1ib 1ibGLU so 1 0x028f3000 libGL so 1 gt usr lib libGL so 1 0x00a7d000 libXext so 6 gt usr X11R6 lib libXext so 6 0x00d6a000 1ibX11 so 6 gt usr X11R6 1ib 1ibX11 s0 6 0x00c94000 libpthread so 0 gt lib libpthread so 0 0x00d7b000 libstdct so 6 gt usr lib libstdc s0 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
85. n t always work correctly for structures with multiple models 6 9 The Test Functions Surface sampling using an icosahedral tessellation and surface parametrisation using spherical harmonic functions are both central to the shape similarity and complementarity calculations in Hex In Test Mode you can view the spherical harmonic basis functions and the icosahedral tessellations used in the calculations Go to the File menu and select Chapter 6 Miscellaneous 36 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 func tion Controls Harmonics Order O and by clicking the Enable Harmonics button You may need to adjust the zoom factor
86. n the new features section that the GUI and graphics window remain responsive even during docking there are some stages in the calculations where its not possible to respond to user interaction This is especially true during multi processor docking runs because its too difficult to preempt the sub tasks Technical note If you re interested in this kind of thing despite appearances Her is a purely single threaded appli cation not counting fork and exec calls 6 8 3 Macros When Hex runs a macro it doesn t update the state of any toggles or any numerical values in the graphical user interface T hus the state of the display and the values shown in the user interface controls may become inconsistent after running a macro 6 8 4 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 Her 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 6 8 5 Hardcopy Fonts The Graphics Font selected from the font menu panel is not propagated to Postscript All printed text always appears in Times Roman 6 8 6 Colouring Multiple Models The molecule colouring options do
87. ne 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 appropriate and pressing Start will show a movie of the sequence of models The orientations or frames of both types of movie may be shown just once or Chapter 3 Molecular Graphics 14 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
88. ng Molecules 16 4 Manoeuvring Molecules In addition to rotating translating and scaling a molecular graphics scene Hex also allows 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 written 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 calculation 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 TIP In the graphics you can edit both the receptor and the ligand orientations but the coordinates of the receptor take priority when structures are saved to disc 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 Orientations There are two main ways to edit molecular orientations within the scene In the first
89. ns 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 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 distance 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
90. o 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 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 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 are consistent with those of the receptor and ligand because Hex uses the chain labels 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 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 Unix prompt hex 3hfl fv pdb 3hfl ly pdb 3hfl pdb However its often more convenient to load all three molecules together u
91. ockwise rotation You ll probably find that Button 2 feels more natural for most 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 or Unix 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 Hez 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 Chapter 2 Getting Started 5 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 Hex stores a Home Position for the scene Pressing 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 ori entation 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
92. onary Why sometimes I ve believed as many as six impossible things before breakfast Lewis Carroll 1 1 What The Heck Is Hex Hez is an interactive molecular graphics program for calculating and displaying feasible docking modes of pairs of protein and DNA molecules Her can also calculate small ligand protein docking provided the ligand is rigid and it can superpose pairs of molecules using only knowledge of their 3D shapes The main thing which distinguishes Hex from other macromolecular docking programs and molecular graphics packages is its use of spherical polar Fourier correlations to accel erate the docking and superposition calculations The graphical nature of Her came about largely because I wanted to visualise the results of such docking calculations in a natural and seamless way without having to export unmanageably many and usually quite big coordinate files to one of the many existing molecular graphics packages For this reason the graphical capabilities in Hex are relatively primitive compared to commercial packages although these days one can do quite a lot with a few calls to OpenGL Nonetheless if your main interest is in modelling macromolecular docking then please read on Hex may have something new to offer In Hex s docking calculations each molecule is modelled using 3D parametric functions which are used to encode both surface shape and electrostatic charge and potential dis tributions The pa
93. ond skeletons are drawn when moving molecules within the scene 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 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 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 Chapter 2 Getting Started 6 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 JD button is the Manoeuvring Molecules button which looks like a lightning bo
94. ontrols Docking Receptor Range 30 Controls Docking Ligand Range 30 Controls Docking Receptor Samples 642 Controls Docking Ligand Samples 642 Controls Docking Twist Range 360 Controls Docking Twist Samples 128 Controls Docking Distance Range 40 Controls Docking Distance Step 1 0 Controls Docking Substeps 2 Controls Docking Steric Scan 16 Controls Docking Final Search 25 This says that the Steric Scan N 16 phase of the docking calculation will be performed at 1 40 1 0 41 intermolecular separations in steps 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 1 2 A as described above The angular search will be restricted to 30 degree angular cones centred on the intermolecular axis and the best 500 solutions will be retained for viewing Now start the calculation Controls Docking Activate You ve 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
95. oordinates 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 struc ture 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 complex 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 be 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 Her 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 noxexec lt job1 mac gt jobl log job2 starts after jobl hex ncpu 2 noxexec lt job2 mac gt job2 log Chapter 6 Miscellaneous 34 6 6 6 Using Hex As a Web Browser On Unix systems Her may be used as a web browser helper application for PDB files by specifying that Hex should be invoked when the browser receives
96. or 3hf1 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 Chapter 6 Miscellaneous 29 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 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
97. ouring Over the last few years Hex has become quite a personal hobby of mine One day Hex might even become famous But obviously not yet according to the Hex Googlisms http www googlism com what_is h hex I quite like the one that says Hex is not a persistent environmental contaminant I hope Herz will eventually reach the more elevated status of Mostly Harmless http www bbc co uk cult hitchhikers guide earth shtml Chapter 6 Miscellaneous 39 6 14 References e Docking Essential Dynamics Eigenstructures D Mustard and D W Ritchie 2005 PROTEINS Struct Funct Bioinf 60 2 269 274 http www csd abdn ac uk dritchie papers ritchie gaeta 2005 pdf e Evaluation of Protein Docking Predictions Using Hex 3 1 in CAPRI Rounds 1 and 2 D W Ritchie 2003 PROTEINS Struct Funct Genet 52 98 106 http www csd abdn ac uk dritchie 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 csd abdn ac uk dritchie 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 csd abdn ac uk dritchie papers matching pdf e Parametric Protein Shape Recognition D W Ritchie 1998 PhD Thesis University of Aberdeen http www csd abdn ac uk dritchie papers dwr t
98. r dots Chapter 3 Molecular Graphics 12 are considered as reentrant Reentrant dots are then pushed out from the atom surface to meet the locus of the molecular surface The position of the reentrant surface can be calculated by a 2D analysis of the path of the probe sphere for toroidal dots and by a similar calculation using the 3D stationary probe positions for the singular points when the probe simultaneously touches 3 or more atoms Without going into more detail here the algorithm is exact when an infinitely small probe is used but the quality of the resulting surface degrades as the probe size increases This is because there is only a fixed number of dots with which to populate the re entrant surface regions However this degradation is hardly noticeable with probe radii up to about 1 5 Angstroms Since the dot surfaces produced here are primarily for computational rather than visualisation purposes a modest degree of inaccuracy is quite acceptable The type of dot surface which is actually displayed is controlled by the Skin Factor slider Setting the skin factor to zero causes the molecular surface to be displayed a skin factor of one draws the solvent accessible surface Intermediate values cause dots to be drawn at the corresponding fraction along each of the outward surface normals The Display Mode may be changed from dots to vectors in which case surface normals are drawn as lines of the length implied by the current skin fac
99. rametric functions are based on expansions of real orthogonal spherical polar basis functions Essentially this allow each property to be represented by a vector of coefficients Hez s surface shape representation uses a novel 3D surface skin model of pro tein topology whereas the electrostatic model is derived from classical electrostatic theory By writing an expression for the overlap of pairs of parametric functions one can derive an expression for a 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 opera tions 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 conven tional fast Fourier transform FFT docking methods which use a Cartesian grid to perform the Fourier transforms However the FFT approach only accelerates a docking search in three translational degrees of freedom whereas with a spherical polar approach we can both translate with some effort and rotate relatively easily the coefficient vectors to gen erate and evaluate candidate docking orientations in what is effectively a six dimensional Fourier correlation In the sp
100. real fast Hartley transform FHT e The number of solutions that are retained after a docking run is now user definable formerly hard coded at 512 e Added a user definable cluster window size useful when the list of docking solutions is large e Added support for one button mouse pointer using Ctrl and Meta keys e Fixed Missing Ligand HETATM bug e Fixed various minor bugs e Added new environment variable HEX_MESSAGES to control use of text message window 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 biochem abdn ac uk hex See Appendix B Installation Guide page 43 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 PDB files can be downloaded from the main Protein Data Bank repository at Rutgers University http www rcsb org pdb Up to three PDB files can be loaded into Hex at any one time These are treated as a receptor a ligand and a reference complex We ll 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 pre
101. ribution 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 NB 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 14 References page 39 5 2 Other Search Modes In addition to the basic rotational search Hex also supports a Ligand Translation and a Ligand Orbit search mode In Ligand Translation mode the receptor is held fixed and the ligand is translated about the receptor using the Ligand Range and Samples angular Chapter 5 Docking Molecules 20 parameters and the Distance Range and Step parameters to generate different ligand poses about the receptor A pure translation is achieved if the twist angle is set to zero In Ligand Orbit mode the ligand is translated as above but it is now also rotated about its own principle axis in fixed steps of 10 degrees A wobble may be added to the search by setting a small range say 30 degrees for the twist angle These search modes are largely experimental but may be useful if the relative orientation of a pair of molecules in a complex is known but t
102. row keys are also mapped to these actions Down Up Left Right respectively Down Chapter 3 Molecular Graphics 7 3 Molecular Graphics Her 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 8 solid surfaces see Section 3 4 Solid Surfaces page 9 spherical harmonic surfaces see Section 3 5 Spherical Harmonic Surfaces page 10 and dot surfaces see Section 3 6 Dot Surfaces page 11 panel These display types are con trolled 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
103. rrent 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 10 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 starting from the edited pose 5 11 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
104. ry moving the clipping plane though the scene using the right slider or by using the mouse and the Space Bar to control the movement Try 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 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 together 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 Three 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 sce
105. s But this does not mean the soft ware 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 algo rithms 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 Whenever I run Hex I get a whole bunch of messages saying Warning OpenGL says invalid enumerant What does this mean This only seems to happen on SGI machines There is internal diagnostic code within Hex to check on the status of the OpenGL engine after each screen refresh I can t see anything that s actually wrong in the generated graphics and there don t seem to be any adverse effects on hardware that show this message Just ignore it e What is the reference energy for electrostatic calculations in Hex and in thermody namic terms are you working with G or U In Hez 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 int
106. s 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 Unix 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 46 Appendix C Feature History Hex has been on going work for around nine years although most of the functionality was implemented in the first three years This section summarises the development history over the years There are no entries here for versions 4 3 and 4 4 these were internal development versions and were never released C C C 1 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 2 New Features In Version 4 1
107. s as specified in the Docking Control panel If the molecules are initially too far apart Hex 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 Appendix E Frequently Asked Questions 56 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 Edit Origin mode Please also look at the answer given for the previous FAQ e I get a segmentation fault when Hex samples protein surfaces prior to a docking run What s causing this I m using an Octane with 640Mb of memory Surface contouring in Hex uses quite a lot of memory and makes quite a few calls to low level functions So even if you
108. sing 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 This example macro file loads the antibody HyHel 5 lysozyme complex By default Hex will look in the HEX_ROOT examples directory for the PDB files and the colour file referenced here You may wish to change this behaviour by setting some environment variables in your login csh or profile sh ksh files dk HH dt dt dto OF close all set colour file 3hfl col Chapter 5 Docking Molecules 19 open_receptor Shfl fv pdb open ligand S3hfl ly pdb open complex 3hf1 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 receptor molecule is superposed onto the appropriate part of the complex If the ligand molecule originated from an edited complex file then it will 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 5 1 Rotational Search Hex currently supports three docking search modes which may be selected using the Search Mode selection box in the Docking Control panel Most docking problems require only the de
109. so 6 libdl so 1 gt usr lib libdl so 1 libCstd so 1 gt usr lib libCstd so 1 libCrun so 1 gt usr lib libCrun so 1 libw so 1 gt usr lib libw so 1 libc so 1 gt usr lib libc so 1 libintl so 1 gt usr lib libintl so 1 libXmu so 4 gt usr openwin lib libXmu so 4 libdga so 1 gt usr openwin lib libdga so 1 libmp so 2 gt usr lib libmp so 2 libXt so 4 gt usr openwin lib libXt so 4 usr lib cpu sparcv8plus libCstd isa so 1 usr platform SUNW Sun Fire 280R lib libc psr so 1 OpenGL for SunOS is available at http www sun com software graphics penGL e I downloaded the SGI IRIX version of Hex followed all the instructions but still nothing works What do I try next Hex should work out of the box for IRIX 6 1 or higher Apart from making a mistake with the HEX BOOT and PATH variables the only other reason things might not work is if you have a very reduced IRIX installation without all the necessary run time libraries or if your system is set up with an unusual locale Please complain to your system administrator If s he manages to fix the problem please let me know the story it might save other people some grief in the future 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 Hez writes all its information and warning messages to a dedicated text output
110. ss the Filter button 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 picking OK You should now see a skeletal display of the molecule s from your chosen PDB file TIP Keep all your PDB files in a single directory and set the environment variable HEX_PDB to point to this directory The other file selection panels in Hex work in a similar manner Congratulations You should now have your molecule in the centre of the scene You should 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 its convenient to assign the 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 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 anticl
111. such as MPI or PVM Not at the moment Her can exploit both processors on dual processor Linux Unix machines I had thought about using MPI to parallelise it further but I don t get much time to do programming these days Maybe I will try to get one of our students to work on that for a project e Can you recommend any papers the 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 Hez 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 Appendix E Frequently Asked Questions 58 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 ch
112. tated figure and then manually rotating it with the mouse by R y about the zaxis R 8 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 Finally using spherical harmonics to parametrise the surface shape of a cube provides a further 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 Chapter 6 Miscellaneous 37 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 for the order L should be kept at their default values except during the TIP Generally all parameters in the Harmonics Control panel except above tests 6 10 Technical Information In order to run Hex 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 h
113. tibility with the existing clustering ranking and summary output code used by the docking module In other words Hez always thinks negative is good NB Prior to version 4 0 Hex used un normalised overlap volumes for similarity scoring Using normalised scores makes it easier to compare and perhaps cluster multiple molecules Work on a more efficient 6D matching search algorithm is in progress Chapter 6 Miscellaneous 28 6 Miscellaneous 6 1 Macros In Hex 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 loop regions and position the molecule using the mouse in a pleasing orientation The command sequence might be Macros Learn start recording File Open Recept
114. tion 0 00 ccc eens 37 GAT v Cayeats ave iion abet ae td thts PD edel 37 0 12 r CONTAR cu doti po Ree e S E 38 6 13 Acknowledeementz 000 cece eee ee 38 6 14 Reterences soo odere ter e ee he 38 6 15 Citing Hexion ein tiie meee baad d 39 Appendix A Licences o oooooooooooo 40 AL Hex Licence a Bie ee sae aia ed art 40 A 2 Stride Licence ice daa a5 be EN o 42 Appendix B Installation Guide 43 B 1 Microsoft Windows Installation 43 B 2 Mac OS X Installatton 43 B 3 Unix Linux Installation cet is qutd 43 Appendix C Feature History 46 C 1 New Features In Version 4 2 00o oooooooommoooo 46 C 2 New Features In Version 4 1 00o oooooooocmmooo o 46 C 3 New Features In Version 4 0 oooooooooomooo o 46 C 4 New Features In Version 3 4 0oooooooooocmmoomo 46 Ch New Features In Version 3 3 ooooooooooommoooo 4T C 6 New Features In Version 3 2 00ooooooooocmmoooo 47 C 7 New Features In Version 3 1 0ooooooooomooom o 4T C 8 New Features In Version 3 D 0ooooooooomooomo 48 i Appendix D nVidia Stereo Configuration Appendix E Frequently Asked Questions Subject Index tana aaa 111 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 Dicti
115. tor Vectors are drawn as dots if the skin factor is zero Dots or vectors may be coloured according to atom type or a colour may be selected from the colour chart using the Dot Colours selector 3 7 Changing The Scene Origin Normally rotation and scale zoom operations are applied relative to the scene ori gin 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 midpoint 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 normally 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 dif
116. ules 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 3 4 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 automatically 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 TIP If you ha
117. ur printer has insufficient memory to handle the entire file Try printing a few pages at a time say 20 or try changing your printer settings to generate lower quality output Also ensure that you enable whatever shrink strech options are available if you are using a different paper size than A4 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 Hex doesn t calculate internal energies and so doesn t report separate individual molecular energies 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 prediction of the complex to a separate PDB file these can then be read back into Her 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
118. ve 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 Chapter 6 Miscellaneous 32 6 5 Environment Variables Her 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 Name Status Default Description HEX_CACHE optional SHEX_ROOT cache locates a cache directory for the trans lation matrices highly recommended HEX_COLOURS optional HEX ROOT examples locates a directory of Hex colour files HEX_CPUS optional 1 the default number of CPUs to use HEX_DATA optional SHEX_ROOT data locates non standard Hez data files HEX_LOG optional hex log defines the name of the current log file HEX_MACROS optional SHEX_ROOT examples locates a directory of Hex macro files HEX_PDB optional SHEX_ROOT examples locates a directory of PDB files HEX_PIPE optional SHEX_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 Hex installation di rectory e g usr local hex HEX STARTUP optional none locates a start up
119. window This window is is controlled 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 Hex 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 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 Why does Hex print a message about a Mesa configuration file Actually its the Mesa code that prints the message This can happen when Mesa is already installed on your system but the installed version as cited in the etc mesa conf file differs from the version that Hex was built with The Hex program is normally statically linked against Mesa so its not necessary to explicitly install Mesa to run Her Just ignore

Hex 4.5 User Manual - bioweb: molecular modelling group

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