Shows information about the currently loaded contact map (or contact maps in compare mode):
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 letters, or use click the 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.
CMView can import two general classes of data files:
Tertiary structure files (3D coordinates)
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, only the main contact map window will be available.
CMView contact map files are special in the sense that they store the PDB code of the structure they were derived from (if applicable). When opening a .cm file, the application then tries to retrieve the 3D coordinates from the online PDB.
Loads a structure from the PDB ftp site. The file is downloaded in mmCIF format and cached locally.
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
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.
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.
Saves the current contact map in CMView contact map file format. The sequence, the residue-residue contacts and some meta data (original PDB four-letter code and chain code, contact type, distance cutoff) will be stored in the 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.
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.
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 red 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.
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.
In contact map
Drag to select rectangular region of contacts
Drag to select rectangular region of contacts
Click on contact to select single contact
Ctrl+click to add to current selection
Click on white space to reset selection
In ruler
Click on secondary structure element to select the corresponding residues
Drag to select range of residues
Intersection of horizontal and vertical residue selections selects contacts
In contact map
Click on contact to select cluster of contacts
Ctrl+click to add to current selection
Click on white space to reset selection
In ruler
Same behavior as in rectangular selection mode
In contact map
Click to select contacts on current diagonal
Drag to select contacts in several diagonals
Ctrl+click to add to current selection
Click on white space to reset selection
In ruler
Same behavior as in rectangular 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
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
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 r1-r2 specifies all residues between and including r1 and r2.
Example: 1,3,5-7,10-12
Selects all contacts between distinct secondary structure elements.
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
Chooses the active color for coloring contacts using the Paint selection contacts function.
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 object are created in the 3D viewer:
The set of contacts (drawn as solid yellow lines)
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:
Contacts in structure A which are present in both structures – drawn as solid yellow lines
Contacts in structure B which are present in both structures – drawn as solid yellow lines
Contacts in structure A which are present only in structure A – drawn as solid pink lines
Contacts in structure B which are present only in structure B – drawn as solid green lines
Pseudo-contacts in structure A (present in B but absent in A) – drawn as dashed pink lines
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.
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:
Black: contacts present in both structure A and structure B
Pink: contacts present in contact map A but absent in B
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:
Needleman-Wunsch sequence alignment
Calculates a global sequence alignment using the classic Needleman-Wunsch-Gotoh algorithm with standard parameters (Matrix: BLOSSUM50, Gap-open: 10, Gap-extend: 0.5). The JAligner package [1] is used for the calculation.
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 exact 3D coordinates 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).
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.
Shows/hides contacts present in contact map A but absent in B (displayed in pink).
Shows/hides contacts present in structure B but absent in A (displayed in green).
Displays/hides the difference distance map of the two structures.
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.
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.
Available by right-clicking on the main contact map window.
Experimental features can be enabled by setting
USE_EXPERIMENTAL_FEATURES = true in the
config file.
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
Loads and saves contact maps from/to a simple relational database with tables for graphs, nodes and edges.
Shows the common neighborhood for a pair of residues as triangles in the contact map.
Shows the common neighborhood for a pair of residues as triangles in the 3D viewer.