From owner-chemistry@ccl.net Tue Jun 26 16:15:00 2007
From: "Elaine Meng meng#cgl.ucsf.edu" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: new Chimera release
Message-Id: <-34578-070626144831-28065-IsH6p8pmmCic0hgdCNXfpw/a\server.ccl.net>
X-Original-From: "Elaine  Meng" <meng ~ cgl.ucsf.edu>
Date: Tue, 26 Jun 2007 14:48:28 -0400


Sent to CCL by: "Elaine  Meng" [meng^cgl.ucsf.edu]
Hello everyone,
A new production release of UCSF Chimera (1.2422) is available from
http://www.cgl.ucsf.edu/chimera/download.html

Chimera is free for noncommercial use, includes full documentation,
and is available for several platforms including Windows, Mac, and Linux.

Here are just a few of the changes in the last year or so:

- embedded POV-Ray for making glossy, shadowed images; labels included
- ability to supersample or raytrace when recording movies
- presets for interactive use and publication image scenarios
- more input formats: MDL MOL/SDF, CIF/mmCIF, Gromacs trajectories
- more Fetch by ID types: 
        EDS (fo-fc) electron density difference map
        PQS predicted biological unit
        VIPERdb viral capsid structures
- can morph between homologs as well as different conformations
- interactive clash/contact detection
- partial charge assignment:
        Amber (Cornell et al.) for standard residues
        embedded Antechamber to calculate charges for nonstandard residues
- sequence alignment viewer allows sequence addition, deletion, reordering
- can optimize overlay of density maps
- Side View includes "top view" for adjusting stereo params interactively
- session files smaller, restore faster
- improved preferences handling
- updates to handle new atom/res naming conventions in remediated PDB

For more details on recent changes, see:
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2422.html
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2417.html
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2304.html

Best Regards,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng^cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html