RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps.

ABSTRACT

MOTIVATION Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. binding-site residues) and global (e.g. hinge motion), between unbound and bound proteins through distance patterns. Users can target residue pairs in RRDistMaps for further navigation in Chimera. The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps. AVAILABILITY AND IMPLEMENTATION RRDistMaps was developed as part of UCSF Chimera release 1.10, which is freely available at http//rbvi.ucsf.edu/chimera/download.html, and operates on Linux, Windows, and Mac OS. CONTACT conrad@cgl.ucsf.edu.