[Chimera-users] new Chimera release (v1.10)

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 6 09:39:02 PST 2014

Hello everybody,
A new production release of UCSF Chimera (version 1.10) is available:

Download is free for noncommercial use.  
Platforms: Windows, Mac OS X (including Yosemite), Linux.
This will be the last release to support OS X 10.6 and 10.7.

New since version 1.9:
Protein contact maps color-coded by distance, PDB biounit and
CATH domain web fetch, plotting all-atom and backbone RMSDs
along sequence alignments (previously only alpha-carbon RMSDs), 
update to AmberTools 14, "vop scale" density map normalization,
Modeller dialog allows specifying distance restraints, further
implementation of the MultiDomain Assembler homology-modeling 

More details are given below; see release notes for the full list:

I/O, Display:
* new web fetch options: PDB biounit, CATH domain
* improved New Molecules preferences (initial structure display)
* protein SSE (secondary structure element) inserted into 
   up/down-arrow selection cascade
* shortcuts rn, rp, ri to shift the selection to the next, 
   previous, and intervening residues in a chain
* "rainbow" command can assign a unique color to each SSE
* green-magenta (trioscopic) stereo mode
* new input format: COLLADA (.dae)

Structure Analysis and Modeling:
* new RR Distance Maps tool: protein contact maps color-coded 
  by distance (and/or std dev, if comparing structures)
* update to AmberTools 14 (new force field options)
* Multalign Viewer sequence alignment window:
 - can plot backbone and all-atom RMSDs, not just CA-RMSDs 
 - show feature annotations from NCBI Conserved Domain Database 
 - search by full or partial sequence name
* structure-derived amino acid substitution matrices SDM, HSDM
  (more choices for sequence alignment and conservation calcs)
* Modeller options: thorough optimization, distance restraints
* "mda" command (MultiDomain Assembler):
 - shows BLAST alignment in Multalign Viewer
 - provides more options for template selection
 - calls Modeller dialog

Volume Data (density maps, electrostatic potential):
* "vop" command new options: take pointwise minimum of two or
   more maps, skeletonize, normalize density maps
* "vseries measure" to track isosurface area, enclosed volume,
   and centroid position across time series

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

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