Function Reference

File

Info

Shows information about the currently loaded contact map (or contact maps in compare mode):

Name

An identifier for the contact map (usually the PDB four-letter plus chain code if applicable)

Contact type

The contact type used when creating the contact map, e.g. Ca, Cb, SC, BB

Distance cutoff

The distance cutoff in angstroms used when creating the contact map

Min Seq Sep

The minimum sequence separation filter used when creating the contact map

Max Seq Sep

The maximum sequence separation filter used when creating the contact map

Sequence

The protein sequence. To see the full sequence, hover mouse over the first few letters, or use click the Show sequence button at the bottom.

Sequence length

The number of residues in the full protein sequence

Unobserved residues

The number of residues for which no 3D coordinates are available

Secondary structure source

The source of the secondary structure annotation (author, DSSP or none)

Number of contacts

The number of contacts in the contact map

Number of selected contacts

The number of contacts currently selected

Only in compare mode:
Number of unique contacts

The number of contacts unique to this structure

Number of common contacts

The number of contacts present in both structures

Contact map overlap

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.

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, 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.

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

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 some 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 contents of the main contact map window as a PNG image file.

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.

View

Show 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.

Show 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 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.

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

  • 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

Fill selection mode

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

Diagonal 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

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

Select all contacts

Selects all currently visible contacts.

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 r1-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

Reset contact colors to black

Resets all contacts to the default color (black)

Action

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 object are created in the 3D viewer:

  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 pink 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.

Delete selected contacts

Permanently deletes the currently selected contacts from the contact map.

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

  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: BLOSSUM50, Gap-open: 10, Gap-extend: 0.5). The JAligner package [1] is used for the calculation.

  2. 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.

  3. 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. 

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 present in structure B but absent in A (displayed in green).

Show difference map

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.

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 corresponding 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.

Experimental features (unsupported)

Experimental features can be enabled by setting USE_EXPERIMENTAL_FEATURES = true in the config file.

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 neighbor 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.