[Chimera-users] 1.7 production release

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 30 17:25:39 PST 2013

Hello everybody,
The official 1.7 production release of UCSF Chimera is now available:

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).
Note: 1.6 was the last version to support Mac PPC and OS X 10.5.

New features include faster loading and graphics, improvements in
lighting and interactive shadows, "click-to-center" mouse mode,
map display as orthogonal planes, interface to Modeller for building
missing loops, Animation timeline, enhanced commands for animation,
interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking.

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

Graphics, Depiction: 
* faster loading of large molecules
* faster graphics on many systems; target frame rate raised to 60 fps
* interactive shadows: finer quality; available on more systems
* glossy default lighting, better control over contrast
* users can create custom presets
* 2D Labels can have backgrounds (colored rectangles beneath)
* PipesAndPlanks can color SSEs uniquely, show arrowheads
* Actions...Color menu works on axis, plane, and centroid objects
* CASTp pocket display omits small surface fragments
* "surface" and "sop" command options to hide small fragments

* Animation tool allows placing scenes and simple actions 
  (rock, roll) along a timeline to define a movie
* new output movie formats H.264, VP8/WebM, Theora
* "play" command to animate complex motions like radial explosion
* "transparency" command to set transparency of atoms, ribbons, etc.
  without otherwise changing their colors, can be applied gradually
* "movie" command usability improvements 
* "perframe" allows embedding other commands directly, substituting
  variables other than frame count, executing at multiframe intervals
* "roll" and "turn" command options for precession motion

Structure Analysis and Modeling:
* AmberTools updated to v12, default charges etc. now Amber ff12SB
* "click-to-center" mouse mode (default Ctrl-right button)
* "show distances to nearby residues" added to atom context menu
* interface to Modeller for building missing segments 
* interface to APBS Poisson-Boltzmann electrostatics calculations
* interface to PDB2PQR charge and radius assignment
* interface to AutoDock Vina single-ligand docking
* ViewDock support for AutoDock/Vina .pdbqt, GOLD .mol2 files
* MD Movie can calculate average structures, plot RMSD vs. frame,
  read GROMACS .xtc format; occupancy calculation can treat atoms 
  as VDW spheres (as opposed to points only)
* Build Structure bond length slider, bond angle control
* Multalign Viewer can use a subset of the existing sequences
  (rather than all) to guide alignment of a new sequence; the
  Region Browser lists individual-sequence regions separately 
  (now that a sequence can have many UniProt annotations)

Density Maps:
* Volume Viewer orthogonal planes feature
* Volume Tracer default mode includes placing markers on planes
* "fitmap" option to fit multiple models independently
* "vop cover" can extend a map using its symmetries 

Enjoy! On behalf of the Chimera team,


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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