[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:
http://www.rbvi.ucsf.edu/chimera/download.html

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 
pipeline. 

More details are given below; see release notes for the full list:
http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.10.html

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
----------
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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