CMView 1.1 User`s Manual
Contents
1. CMView 1 1 User s Manual Table of Contents OVERVIEW 5253s ccc scealieyateigsssteaseea see ditecs tend deh cel da cesaaeazereiei ens tenga ystebiade oSsaeds Seosevibesataegssssteads 1 Contact map definiti n scssi cesta sconces eceessdseevees sien eccsasneeuessbuuedesdeueeesssanbesossaveensesiuees 1 Contact ypes riem tot eiae a a sss bates E E E a ed aaa E E EE RES 1 Screen CLEMENS sesto aieri eero Eer EEEE ceeds eee Palast eta on EE te REEE 2 Function Reference s ssssscssass efsedes ade scoes ap nE TE EEEE nE S AAR ON EEEE EEEE SEESE PEE SEERE 3 Fle r be estat sis occas EE EE ETS EEE NEE EEE EE EEEE EE EESE 3 Select espri eaa a a E E Dotan EE E A E E E a a S 5 COOK seasan E E Sen EE E EE asus EINE ET ESES 7 aCA COS n PEE E E E E E sons edeeadlsr ses 7 C mpare ienie Kas EEE E EE EEE E S debe EE E EEE EES EEE EEEE 8 Help eie t i ea ee tha E a a a T E a E E aa a eE ESERE 10 Context MENU seepe Foes e aE TEE ESE EOV ETE EEE TEET es i 10 Experimental features unsupported ss ssessserrssrerrsresrrrrsrrrressrerrsrrerrrresrrererreerere 10 Overlays er EE O EE A EEEIEE AET EEEE EREE EE SEE EEEE EEES 11 Command line parameters sss sinsin ika Seta pos ba E E E has OE eaa Es 12 Configuration oi sesscesssstsye EESE EEE EEEREN ESN o EE E E ETE ENE 12 OVERVIEW oni aora votes dics REE EEE A OESTE O dase REOS EEE ATE OVRE E OTTEET EESTE SEES 12 Available configuration parameters cscceecseceecceeeeaeeeeceeeeeaeeeeaeeeeaeeeeeaeeeeaees 12. e Click on white space to reset selection In ruler e Same behavior as in rectangular selection mode Diagonal selection mode In contact map e Click to select contacts on current diagonal e Drag to select contacts in several diagonals e Ctrl click to add to current selection CMView 1 1 User s Manual Click on white space to reset selection In ruler Same behavior as in rectangular selection mode Neighborhood selection mode In contact map Click on residue pair i j to select the neighborhoods of i and j i e all contacts made by residue i or residue j Click on diagonal to select neighborhood of single residue This can also be done by clicking in the ruler See below Ctrl click to add to current selection Click on lower left half to reset selection In ruler Click on residue to select its neighborhood Ctrl click to add to current selection Color selection mode Select contacts which have been previously marked with the color function In contact map Click on contact to select all contacts having the same color Ctrl click to add to current selection Click on white space to reset selection In ruler Same behavior as in rectangular selection mode Add remove contacts mode Add or remove individual contacts Note that this will modify the contact map and possibly make it inconsistent with the loaded 3D structure To exit this mode choose one of the other selection modes In contact map
3. PYMOL_SHUTDOWN_ON_EXIT PYMOL_LOAD_ON_START PYMOL_CONN_TIMEOUT Whether residue numbers in the alignment are shown in the lower left corner of the contact map in brackets after the default residue numbers Default false Whether PyMol specific features should be shown in the menus See also PYMOL_EXECUTABLE Default true Whether DSSP is used for secondary structure assigment from 3D coordinates See also DSSP_EXECUTABLE Default true The path to the local DSSP executable Parameters passed to DSSP when called by CMView Default The path to the locally installed DALI executable to be used for structural alignments The path to the local PyMol executable Whether PyMol will be shutdown when CMView is closed Default true Whether CMView will try to start PyMol on startup Default true The time in milliseconds that CMView will wait for PyMol to startup before reporting a time out error Default 15000 SHOW_CONTACTS_IN_REALTIME Whether currently selected contacts will be shown in PyMol in real time This can be switched off to increase performance In this case contacts can be shown in PyMol manually Default true Parameters affecting experimental features USE_EXPERIMENTAL_ FEATURES Whether experimental features will be enabled Experimental SHOW_WEIGHTED_CONTACTS features are unsupported probably not tested and are to be used on your own risk Default false Whether contacts with weigh
4. Reset contact colors to black Resets all contacts to the default color black Action Toggle Real Time Displaying of Contacts Toggles the real time mode on and off In real time mode the current position in the contact map as well as the currently selected contacts are immediately shown as edges in the 3D viewer This can be switched off to increase performance Show selected contacts in 3D Visualizes the currently selected contacts as edges in the 3D viewer The edges are drawn between the C alpha atoms of the residues in contact In single contact map mode two selection objects are created in the 3D viewer CMView 1 1 User s Manual 1 The set of contacts drawn as solid yellow lines 2 The set of residues participating in one of the contacts These selection objects can be manipulated directly in the 3D viewer for example to change colors or to display side chain atoms In comparison mode six contact objects and the corresponding residue selections are created 1 Contacts in structure A which are present in both structures drawn as solid yellow lines 2 Contacts in structure B which are present in both structures drawn as solid yellow lines 3 Contacts in structure A which are present only in structure A drawn as solid pink lines 4 Contacts in structure B which are present only in structure B drawn as solid green lines 5 Pseudo contacts in structure A present in B but absent in A drawn as dashed p
5. e Click on an existing contact to remove it from the contact map e Click on a white cell to add the respective contact to the contact map In ruler Same behavior as in rectangular selection mode Select all contacts Selects all currently visible contacts CMView 1 1 User s Manual Select by residue number Selects all contacts between elements from a user selected set of residues The residue set is specified by a selection string A selection string is a comma separated list of residue numbers and or residue ranges where a residue range rl r2 specifies all residues between and including r1 and r2 Example 1 3 5 7 10 12 Select helix helix contacts Selects all contacts between distinct alpha helices Select sheet sheet contacts Selects all contacts between distinct beta strands Select contacts between secondary structure elements Selects all contacts between distinct secondary structure elements Select contacts within secondary structure elements Selects all contacts between two residues from the same secondary structure element Color Different regions of interest in the contact map can be assigned user defined colors e g to highlight different domains or a particular functional site See also Select by color Choose color Chooses the active color for coloring contacts using the Paint selection contacts function Color selected contacts Assigns the active color to the currently selected contacts
6. for more information This will modify the current contact map and show the minimal subset and the original contact map in compare mode Compare Load second contact map Loads a second contact map in the following called B to compare it to the currently open one A For the different input options see Load from After a second contact map has been loaded contacts are shown with the following color coding 1 Black contacts present in both structure A and structure B CMView 1 1 User s Manual 2 Pink contacts present in contact map A but absent in B 3 Green contacts present in structure B but absent in A To overlay the contact maps an alignment between the residue of A and B needs to be defined CMView offers the following options to obtain an alignment 1 Needleman Wunsch sequence alignment Calculates a global sequence alignment using the classic Needleman Wunsch Gotoh algorithm with standard parameters Matrix BLOSSUM5S0 Gap open 10 Gap extend 0 5 The JAligner package 1 is used for the calculation Use this for sequence identical structures e g different conformations of the same protein Maximum contact map overlap structural alignment Calculates a structure based alignment using the SADP algorithm 2 It applies a very fast heuristic to maximize the contact map overlap between two structures The algorithm is particularly well suited for aligning contact maps since it can be applied even if no e
7. 2 Overview Contact map definition CMView is a software tool for visualizing and analyzing the network of contacts between amino acid residues in a protein structure Formally this network is a graph where each residue corresponds to a node and two nodes are connected by an edge if and only if the two residues are in contact Two residues are considered to be in contact if they are spatially close in the three dimensional structure In CMView the definition of contact is specified by two paremeters the contact type and the distance cutoff The contact type defines a subset of atoms of the residue Two residues i and j are then in contact if two atoms out of this subset one from i and one from j are not further apart than the distance cutoff The depiction of the contact network as a matrix formally the adjacency matrix of the contact graph is called a contact map Contact types The supported contact types are AL BB All atoms All backbone atoms SC All side chain atoms C The C atom of the backbone Ca Cb The C alpha atom of the backbone The C beta atom of the side chain C alpha for glycine CMView 1 1 User s Manual Screen elements Contact map window CMView shows the contact map of a single polypeptide chain in its main window A position i j in the contact map corresponds to residues i and j in the sequence of the displayed chain The contact map is symmetrical with re
8. act type gt the contact type for the contact map to be loaded in CM View See contact types e d lt distance cutoff gt the contact distance cutoff in Angstrom for the contact map to be loaded in CMView o lt config file gt a file to read configuration parameters from See Configuration e v print version and exit h print help on command line parameters and exit Configuration Overview CMvView can be customized using key value pairs in a configuration file cmview cfg The example file contains some commonly used settings CMView is looking for configuration files 1 In the current directory 2 In the user s home directory 3 At the location specified with the command line parameter o If the same variable is set in more than one file the latest value takes precedence according to the above order Available configuration parameters DEFAULT_CONTACT_TYPE The contact type shown in the load dialog by default and used for graph generation when loading structures with command line parameters p or f Default Cb CMView 1 1 User s Manual DEFAULT_DISTANCE_CUTOFF DEFAULT_MIN_SEQSEP DEFAULT_MAX_SEQSEP CONF IG_FILE_NAME DIST_MAP_CONTACT_TYPE PDB_FTP_URL TEMP_DIR INITIAL_SCREEN_SIZE LOUPE_WINDOW_SIZE LOUPE_CONTACT_SIZE SHOW_ICON_BAR SHOW_PDB_RES_NUMS SHOW_RULERS The distance cutoff shown in the load dialog by default and used for graph generation when loading structures w
9. d is the shortest distance Distances are calculated between C alpha atoms The distance map can only be calculated if 3D coordinates for the structure are available Common neighbours Displays hides common neighbor relationships CMView 1 1 User s Manual If two residues i and j are each in contact with a third residue k they are said to share the common neihgbour k Then by the triangle inequality one can infer that i and j can be no further apart than twice the contact distance cutoff even if i and j are not in contact themselves For predicted or incomplete contact maps this gives information that is not immediately visible in the raw contact map For example short range contacts those close to the diagonal can often be infered from long range contacts by common neighbor relationships The darker the shade of green in the overlay the more common neighbours the particular residues share Command line parameters The following command line parameters are available when calling CM View from the command line help can be obtained by calling emview h e p lt pdb code gt a 4 letter PDB code to be loaded in CMView from Online PDB Internet connection required e f lt pdb file gt a local PDB file to be loaded in CMView e c lt chain code gt a PDB chain code This will be the chain selected either from the PDB file or for the given PDB code If none is given the first chain in the file will be loaded t lt cont
10. esent in structure B but absent in A displayed in green Show difference map Displays hides the difference distance map of the two structures CMView 1 1 User s Manual The difference distance map is a powerful tool to visualize conformational changes between two protein structures For a pair of residues i j the distance map visualizes how much the distance between i and j has changed from one structure to the other This highlights regions of conformational change as red hotspots while regions which remain unchanged appear in blue For each pair of residues the absolute difference between the distance in structure A and the distance in structure B The difference map can only be shown if 3D coordinates for both structures are available Superimpose from selection Superimposes the structures in the 3D viewer based on the currently selected contacts When two structure are loaded for comparison they are initially superimposed using an all residue C alpha minimum RMSD fit In such a rigid body superimposition some regions may not align well in 3D This feature allows to select a region of interest and to perform a minimum RMSD fit only based on the residues participating in the contact selection Note When changing the orientation of structures in PyMol e g using the custom superposition function earlier contact objects are not moved with the original structure There is currently no workaround for this Show corres
11. etters or use click the Show sequence button at the bottom The number of residues in the full protein sequence The number of residues for which no 3D coordinates are available The source of the secondary structure annotation author DSSP or none The number of contacts in the contact map The number of contacts currently selected The number of contacts unique to this structure The number of contacts present in both structures The overlap between the two contact maps measured by the Tanimoto coefficient 1 T A B common contacts contacts A contacts B common contacts 1 Tanimoto T T 1957 IBM Internal Report 17th Nov 1957 Opens a window with a magnified view of the contact map around the current mouse position This is helpful when working with large contact maps The size of the loupe window and magnification can be set with the variables LOUPE_WINDOW_SITZEand LOUPE_CONTACT_SIZEin the config file CMView 1 1 User s Manual Load from CMView can import two general classes of data files 1 Tertiary structure files 3D coordinates 2 Contact map files For tertiary structure files e g PDB files a contact map will be calculated from the 3D coordinates using the user specified contact type and distance cutoff the structure will be automatically loaded into PyMol and the 3D visualization features will be available For contact map files e g Casp RR files only the main contact map window w
12. ill be available Contact map files saved by CMView in its native text format are special in the sense that they store the PDB code of the structure they were derived from if applicable When opening such a cm file the application tries to retrieve the 3D coordinates from the online PDB Load from online PDB Loads a structure from the PDB ftp site The file is downloaded in mmCIF format and cached locally Load from PDB file Load from Casp TS file Loads a structure from a local PDB file The file needs to contain an initial HEADER line and one or more ATOM lines following the PDB file specification 1 Alternatively files may also follow the CASP tertiary structure prediction format 2 1 http www wwpdb org docs html 2 http predictioncenter org casp7 doc casp7 format html TS Load from contact map file Loads a file in the native CMView contact map file format A file saved in this format contains some metadata including the PDB four letter code of the structure it was derived from if applicable The corresponding structure will then be retrieved from the PDB when the file is loaded again Load from CASP RR file Loads a contact map in CASP residue residue contact prediction format See http predictioncenter org casp7 doc casp7 format html RR for the format specification Save to Save to contact map file Saves the current contact map in CMView contact map file format The sequence the residue residue contacts and so
13. ink lines 6 Pseudo contacts in structure B present in A but absent in B drawn as dashed green lines Pseudo contacts means that the distance between the two residues is above the defined distance cutoff They are shown to allow easier analysis of conformational changes where contacts have been lost or new contacts have been established Note In PyMol 1 00 and above above selections will be grouped together for a better overview Earlier versions of PyMol do not support this feature Show threshold spheres for selected contacts in 3D For selected contacts i j draws spheres around residues i and j in the 3D viewer where the sphere radius is the current contact threshold This shows the sphere of influence of the individual residues under the chosen contact definition Threshold spheres can also be drawn for residue pairs not in contact by right clicking on the residue pair in the contact map and choosing Show Threshold Spheres For Residue Pair from the context menu Delete selected contacts Permanently deletes the currently selected contacts from the contact map Run Cone Peeling Algorithm Runs the Cone Peeling algorithm described in Sathyapriya et al Defining an Essence of Structure Determining Residue Contacts in Proteins PLoS Computational Biology 5 12 e1000584 2009 This algorithm attempts to calculate a minimal subset of contacts which are sufficient to reconstruct the fold with distance geometry See the reference
14. ith command line parameters p or f Default 8 0 The minimum sequence separation shown in the load dialog by default negative values meaning no restraint Default 1 The maximum sequence separation shown in the load dialog by default negative values meaning no restraint Default 1 The name of the configuration file Default cmview cfg The contact type being used to calculate the distance map Allowed values Ca Cb Default Ca A URL where PDB structures are being loaded from See Load from Online PDB This can be used to load structures from a local mirrored copy of the PDB Default mmCIF ftp ftp wwpdb org pub pdb data structures all The directory for storing temporary files Default The default system temp dir e g Windows Temp tmp or C The initial size in pixels of the main window on startup Default 650 The initial size in pixels of the loupe window Default 200 The size of each contact in the loupe window Default 15 Whether the toolbar with command shortcut icons is shown Default true Whether legacy PDB residue numbers are shown in the lower left corner of the contact map below the secondary structure Default true Whether secondary structure rulers are shown above and to the left of the contact map Default true CMView 1 1 User s Manual SHOW_ALIGNMENT_COORDS USE_PYMOL USE_DSSP DSSP_EXECUTABLE DSSP_PARAMETERS DALI_EXECUTABLE PYMOL_EXECUTABLE
15. me meta data original PDB four letter code and chain code contact type distance cutoff will be stored in the file Save to CASP RR file Saves the current contact map in CASP residue residue contact prediction format See http predictioncenter org casp7 doc casp7 format html RR for the format specification Save to PNG file Exports the current contents of the main contact map window as a PNG image file CMView 1 1 User s Manual Save Alignment to file Saves the current alignment to a text file in FASTA alignment format This function is only available in comparison mode Quit Closes all windows and exits CMView Select Selection modes The selection mode defines the mouse behavior for selecting contacts in the main contact map window and in the secondary structure rulers at the left and at the top of the contact map window Rectangular selection mode In contact map e Drag to select rectangular region of contacts e Drag to select rectangular region of contacts e Click on contact to select single contact e Ctrl click to add to current selection e Click on white space to reset selection In ruler e Click on secondary structure element to select the corresponding residues e Drag to select range of residues e Intersection of horizontal and vertical residue selections selects contacts Fill selection mode In contact map e Click on contact to select cluster of contacts e Ctrl click to add to current selection
16. or triangles in contact map Shows the common neighborhood for a pair of residues as triangles in the contact map Show common neighbor triangles in 3D Shows the common neighborhood for a pair of residues as triangles in the 3D viewer Show common neighborhood size map Shows the common neighborhood sizes for all residue pairs as colors in the contact map Overlays Overlays can be selected from the overlay menu in the side bar on the right They display additional information in the contact map windows Contact density Displays hides the contact density map The contact density map shows for every residue pair i j the density of contacts within the backbone fragment ranging from i to j The density is defined as the number of contacts within the fragment normalized by the average number of contacts over all fragments of the same size High densities are shown in red low densities are shown in blue High density regions often coincide with structural units like domains secondary and super secondary structure elements Distance map Displays hides a distance map showing all pairwise distances between residues Distances are visualized as colors The color coding depends on the distance cutoff of the current contact map Distances above the cutoff are shown in blue distances around the cutoff are shown in green and distances below the cutoff are shown in red where the darkest blue is the longest distance and the darkest re
17. ponding residues from selection Visualizes aligned residues in the 3D viewer To highlights the correspondence between residues in structure A and structure B lines are drawn between corresponding residues This gives a visual three dimensional impression of the underlying alignment Help Help Shows the inline help About Shows version and licensing information Context menu Available by right clicking on the main contact map window Show residue pair as edge in 3D Draws a line in the 3D viewer labeled with the distance between the respective residues in Angstroms This feature is independent of whether the two residues are in contact or not Show threshold spheres for residue pair in 3D Draws the threshold spheres for the selected pair of residues in the 3D viewer This feature is independent of whether the two residues are in contact or not Experimental features unsupported Experimental features can be enabled by setting USE_EXPERIMENTAL_FEATURES true in the config file CMView 1 1 User s Manual Load structure from relational database Loads PDB structures from a relational database in PDBase 1 or MSD 2 format 1 http openmms sdsc edu OpenMMS 1 5 1_Std openmms docs guides PDBase html 2 http www ebi ac uk msd srv docs dbdoc Load from save to graph database Loads and saves contact maps from to a simple relational database with tables for graphs nodes and edges Show common neighb
18. rical contact map See Overlays e Further context dependent tools for experimental features if enabled e At the bottom the coordinates display information about the residue pair at the current mouse position in the contact map The following overlays can be selected from the overlay menu e Distance map shows distances between C alpha atoms if 3D coordinates are available e Contact density helps to identify domain and subdomain structures e Common neighbours triangle inequality relationships CMView 1 1 User s Manual Function Reference File Info Shows information about the currently loaded contact map or contact maps in compare mode Name Contact type Distance cutoff Min Seq Sep Max Seq Sep Sequence Sequence length Unobserved residues Secondary structure source Number of contacts Number of selected contacts Only in compare mode Loupe Number of unique contacts Number of common contacts Contact map overlap An identifier for the contact map usually the PDB four letter plus chain code if applicable The contact type used when creating the contact map e g Ca Cb SC BB The distance cutoff in angstroms used when creating the contact map The minimum sequence separation filter used when creating the contact map The maximum sequence separation filter used when creating the contact map The protein sequence To see the full sequence hover mouse over the first few l
19. spect to the main diagonal In the lower right corner information is displayed about the residue pair or pairs in compare mode at the current mouse position e The residue numbers of i and j in the sequence e The residue types in three letter notation e The secondary structure types alpha beta or none e The PDB residue numbers These are shown only if a tertiary structure file was loaded By default CMView numbers residues by their position in the sequence This does not necessarily match the numbers assigned to residues in the ATOM lines of PDB files To compare with other data where the PDB residue numbering is used the residue numbers as found in the PDB file are printed here Note This function has to be enabled with SHOW_PDB_RES_NUMSs true in the config file Secondary structure rulers The rulers shown above and to the left of the contact map are used for e Displaying secondary structure elements e Selecting residues see selection modes e Selecting secondary structure elements see selection modes The color scheme for secondary structure elements is e Blue Alpha helix e Red Beta sheet e Green Turn Side bar To the right of the contact map is the side bar which contains further elements e The overlay menu Different background overlays can be selected which display additional information in the contact map window The overlays can be selected seperately for the upper left and lower right half of the symmet
20. ts between 0 and are shown as shades of grey in the contact map Default true CMView 1 1 User s Manual USE_DATABASE Whether database specific features should appear in the menus Default true DB_HOST The database server for structure graph databases DB_PWD The password for accessing the database DB_USER The username for accessing the database DEFAULT _PDB_DB The default database for loading structures in PDBASE format DEFAULT_GRAPH_DB The default database for loading contact maps 15
21. xact 3D coordinates are available DALI structural alignment Computes a structural alignment using DALI 3 DALI needs to be installed locally and the parameter DALI_EXECUTABLE has to be setinthe cmview cfg config file See installation for instructions on how to install DALI This feature can only be selected if 3D coordinates for both structures to be compared are available Load alignment from FASTA file Loads an alignment from a text file in FASTA alignment format This format can be exported by many standard sequence alignment programs e g Muscle T Coffee EMBOSS Bioperl The sequences in the alignment file have to match the ones of the structures to be compared References 1 Ahmed Moustafa JAligner Open source Java implementation of Smith Waterman http jaligner sourceforge net 2006 03 23 2 Jain B J and M Lappe 2007 Joining Softassign and Dynamic Programming for the Contact Map Overlap Problem Springer Lecture Notes in Computer Science S Hochreiter and R Wagner Eds BIRD 2007 LNBI 4414 pp 410 423 3 Holm L and Park J 1999 DaliLite workbench for protein structure comparison Bioinformatics 16 566 567 Show common contacts Shows hides contacts present in both structure A and structure B Show contacts unique to first structure Shows hides contacts present in contact map A but absent in B displayed in pink Show contacts unique to second structure Shows hides contacts pr
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