Manual


Table of Contents

Overview
Contact map definition
Contact types
Screen elements
Function Reference
File
View
Select
Color
Action
Compare
Help
Context menu
Experimental features (unsupported)
Command line parameters
Configuration
Overview
Available configuration parameters:

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 spacially close in the three dimensional structure. The exact definition of contact depends on two parameters which can be chosen interactively in the program: 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 is often called a contact map. CMView shows the contact map of a single polypeptide chain in its main window.

Contact types

The supported contact types are:

ALAll atoms
BBAll backbone atoms
SCAll side-chain atoms
CThe C atom of the backbone
CaThe C-alpha atom of the backbone
CbThe C-beta atom of the side-chain (C-alpha for glycine)

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. In the lower left corner information is displayed about the current residue pair (or pairs in compare mode):

  • The residue numbers of i and j in the sequence

  • The residue types (in three letter notation)

  • The secondary structure types (alpha, beta or none)

  • 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.

Secondary structure rulers

The rulers shown above and to the left of the contact map are used for:

The color scheme for secondary structure elements is:

  • Blue: Alpha-helix

  • Red: Beta-sheet

  • Green: Turn