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UCSF Chimera updated

UCSF Chimera Version 1.5 has been released. Chimera is a highly 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.
The new tools include
  • Metal Geometry (Structure Analysis) — analyze metal coordination geometry
  • Modeller interface - graphical interface to the Modeller homology modeling program (Sali Lab, UCSF)
    • interface currently accessible from the Structure menu in MultAlign Viewer
    • the SaliLab Model Evaluation Server can be called to compute additional model scores
  • Ramachandran Plot (only accessible from Model Panel currently)
  • PDB/UniProt Info (Sequence) — retrieve annotations for PDB entries using a web service from the RCSB (tool is in early stage, may change significantly)
  • Segment Map, Fit to Segments (Volume Data) — these comprise the Segger package (thanks to Greg Pintilie, National Center for Macromolecular Imaging)
  • Small-Angle X-Ray Profile (Higher-Order Structure) — calculate theoretical SAXS profile, compare with experimental profile
  • In addition there are a number of other improvements and updates
  • Updated many of the bundled software packages, most notably: Python 2.7, ScientificPython 2.9.0, AmberTools 1.4
  • Actions... Color menu simplified, all options... opens separate dialog with target settings and full set of colors
  • Actions... Atoms/Bonds menu includes controls for ring fill, aromaticity display, nucleotide display
  • start-of-line aliases (defined with alias ^name) now available from top-level Aliases menu
  • selection broadening/narrowing cascades now include "nothing," one level narrower than the original selection
  • new coil selector specifies all non-helix, non-strand amino acid residues
  • default label offsets increased for better readability
  • appearance of small sticks improved
  • subdivision quality default (Effects, interactive presets) raised to 1.5
  • Focus (menu and command) and window command with specified targets now consider window height, not just width
  • for purposes of Focus (menu and command), ribbon display implies display of backbone atoms rather than all atoms of a residue
  • residue label position can be based on primary atom or backbone only rather than all displayed atoms
  • ModBase fetch shows additional model scores, where available
  • PDB fetching improvements — personal PDB directories can be flat or hierarchical, files compressed or not
  • saving to multiple PDB or Mol2 files allows file naming by model name
  • Mol2 files can be written with Amber/GAFF atom types (from Add Charge) instead of Sybyl atom types
  • can read PQR format as produced by PDB2PQR v1.6, assign atomic charge and radius attributes accordingly
  • can read Gromos87 format (single structure, not trajectory)
  • added VRML level-of-detail (LOD) support
  • added General preference, whether to try to place dialogs beside the main window instead of on top (on by default)
  • commands can be copied from the Command History for pasting into another application window
  • most histograms (e.g., Render by Attribute) now automatically adjust their displayed range when a value outside the range is entered
  • Selector Construction Panel removed
  • the --script option (used at startup from the system command-line) now uses quotes to delimit which arguments go to the script, behaves like the runscript command
  • the startup option --script and command runscript run scripts in Chimera's current directory instead of the directory containing the script
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