CMView Contact map visualization made easy.
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CMView Description

CMView is a handy, easy-to-use, Java-based, interactive contact map visualization and analysis application. 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. Main features: Combined contact map and 3D structure view (using PyMol) Various im- and export options: PDB files, Online PDB, Image export, CASP prediction format and others Calculation of contact maps with user-defined contact definitions Integration with PyMol for feature-rich 3D molecular visualization Structure and contact map comparison using built-in sequence or structural alignments Distance map, difference map, contact density analysis

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