[Chimera-users] new release of UCSF Chimera

[Elaine Meng]

Hello everybody,
A new production release of UCSF Chimera (version 1.11) is available:
http://www.rbvi.ucsf.edu/chimera/download.html

Download is free for noncommercial use.
Platforms: Windows, Mac OS X, Linux.
64-bit builds are recommended for all capable platforms;
this will be the last release to support 32-bit builds.

New since version 1.10:
Molecular Dynamics Simulation tool, more Add Ions types,
residue interaction networks (RINs) from trajectories shown in 
Cytoscape, protein contact/distance map data export, 
Segment Map updated to new version of Segger, volume contour
levels can be specified in RMSDs from zero or SDs from mean,
"flat ribbon" publication preset, Ribbon Styles tutorial, 
"set showCofR" to show crosshairs at center of rotation.

More details are given below; see release notes for the full list:
http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.11.html

General I/O, Display:
* standard shortcuts for File menu (Ctrl/Cmd-q for Quit, etc.)
* "wall-eye stereo pair" option in Save Image dialog
* PubChem fetch uses PubChem3D instead of Pub3D
* "set showCofR" command to show "+" at center of rotation
* "pipes" command-line implementation of PipesAndPlanks
* reduced triangles in STL output for atoms/bonds

Structure Analysis and Modeling:
* Molecular Dynamics Simulation tool (thanks to V Munoz Robles
  and JD Marechal, Universitat Autonoma de Barcelona)
* many more ion types in Add Ions tool
* axes can be defined normal to previously defined planes
* RR Distance Maps can show distance differences for a pair of
  structures (means, std devs already available), export data
* MD Movie calculation of trajectory RINs, display in Cytoscape
* PDB2PQR updated to use new web service URL

Volume Data (density maps, electrostatic potential):
* new input map format: IMAGIC density
* Segment Map updated to new version of Segger
* "volume" command options "rmsLevel" and "sdLevel" to specify
  thresholds in units of RMSD from zero and SD from the mean
* "vop" options to sharpen map, create new zero-valued map

Enjoy!  On behalf of the Chimera team,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco