UCSF Chimera

UCSF Chimera

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UCSF Chimera

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Description:
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality and can be created. Chimera includes complete and can be free of charge for noncommercial use.

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is funded by the NIH National Center for Research Resources (grant P41-RR001081).

General Structure Analysis

  • automatic atom type identification
  • hydrogen addition and partial charge assignment
  • high-quality hydrogen bond, contact, and clash detection
  • distance and angle measurements, rotatable bonds, including Ramachandran plot visualization
  • amino acid rotamer libraries (backbone-dependent and -independent)
  • analysis of metal coordination geometry
  • molecular dynamics trajectory playback (many formats)
  • clustering of conformational ensembles
  • morphing between conformations of a protein or even different proteins
  • calculation of theoretical SAXS profiles
  • display of attributes (B-factor, hydrophobicity, etc.) with colors, radii, "worms"
  • easy creation of new attributes with simple text file inputs
  • rich set of commands, powerful specification syntax
  • many formats read, PDB and Mol2 written
  • web fetch from Protein Data Bank, EDS......
  • ...

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