#Chimera tool for mac software
#Chimera tool for mac mac

As an extension to the molecular visualization application UCSF Chimera ( Pettersen etВ al., 2004), we developed RRDistMaps, a tool to interactively compute and display distance maps for individual proteins and to compare the distance maps of pairs of similar proteins. Instead of using a single cutoff threshold for contacts, displaying a color-coded distance map can help users visualize longer-range interactions. However, longer-range interactions may be used to identify larger-scale motions such as hinge movements. 2D contact maps provide a complementary view to 3D molecular visualization as they are unaffected by rotation or translation and can be easily compared and superimposed.Д¬ontact maps are typically shown as square plots with markers denoting interactions between residues residue pairs that fall outside of the interaction threshold are completely unmarked. pairs of amino acids with О±-carbons <8 Г… apart ( Wu etВ al., 2008). RR contact maps are powerful two-dimensional (2D) representations of protein 3D structure that plot patterns of spatial interactions, e.g. Recent applications such as CMView ( Vehlow etВ al., 2011) examine the nature of structural differences or changes in proteins through the use of residueвЂ“residue (RR) contact maps ( Holm and Sander, 1993).

#Chimera tool for mac software

The rapid improvement of technology in recent decades has enhanced our knowledge of protein structure, as visualization software has revolutionized our understanding of molecular mechanisms.

#Chimera tool for mac mac

The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.ДЄvailability and implementation: RRDistMaps was developed as part of UCSF Chimera release 1.10, which is freely available at, and operates on Linux, Windows, and Mac OS. Users can target residue pairs in RRDistMaps for further navigation in Chimera. hinge motion), between unbound and bound proteins through distance patterns. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges.

Motivation: Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification.