[Chimera-users] Chimera 1.6 officially released

[Eric Pettersen]

Hello everybody,
A new production release of UCSF Chimera (version 1.6) is available:
<http://www.cgl.ucsf.edu/chimera/download.html>

Download is free for noncommercial use.
Platforms: Windows, Mac, Linux, including 64-bit versions (recommended
for working with large datasets on machines with at least 4GB memory).
This will be the last Chimera release supporting Mac PowerPC platforms
and OS X 10.5 (Leopard).

New features include a Rapid Access interface to frequently used data
and tools, new ribbon spline options, improved transparency rendering,
new fetch type: Uniprot protein sequence and annotations, and several
options for fitting atomic structures into density maps: global search,
iterative sequential fitting, symmetric fitting, etc.

More details are given below; see release notes for the full list:
<http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html>

Graphics, Depiction:
* new spline options for ribbon closer to backbone atom positions
* new initial model colors, pastel rather than saturated
* improved transparency rendering (global single-layer on by default)
* 3D labels drawn on top by default
* fancy backgrounds: images from files, color gradients from Palette  
Editor
* options for cleaner pocket/tunnel surface display (see "sop" command)

Structure Analysis and Modeling:
* AddH allows specifying less common states of Asp, Glu, Lys, Cys
* FindHBond can label H-bonds with distances
* Blast Protein shows more info for PDB hits (ligands, resolution, etc.)
* Build Structure improvements for joining peptides, swapping  
substituents
* tools to change chain IDs, renumber residues
* minimization:
  - can be conjugate gradient (previously steepest descent only)
  - parts of structures can be ignored
* distance and angle plotting for trajectories
* Cage Builder tool for generating polyhedral cage models
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html 
 >
* interface to MultiFit web service (simultaneous rigid fitting of
   multiple structures to density, developed by the Sali Lab, UCSF)
* "fitmap" command:
  - global search with random initial placement
  - iterative sequential fitting
  - symmetric fitting
* "measure" command options:
  - map symmetry
  - surface contact area
  - center of mass

User Interface and I/O:
* Rapid Access interface to frequently used data and tools shown at  
startup,
   can be hidden/shown at any time by clicking the lightning-bolt icon
<http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html>
* caching fetched data is turned on by default
* scaling with mouse/touchpad scrolling can be turned off (Mouse prefs)
* Model Panel:
  - group/ungroup function, such as for NMR ensembles
  - functions reorganized into favorites/all
* new input types: SPHGEN spheres, Maestro/Glide docking output  
(ViewDock)
* WebGL export (experimental feature)

Sequence-related:
* new fetch type UniProt: protein sequence and feature annotations
* Multalign Viewer:
  - UniProt features can be mapped onto already open sequences
  - Region Browser improvements for handling feature annotation regions
  - calculation of region overall RMSD
  - interface to Modeller homology modeling allows including water,  
other HET

Enjoy! On behalf of the Chimera team,

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

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