CCL: new release of UCSF Chimera

 Sent to CCL by: "Elaine  Meng" [meng_-_cgl.ucsf.edu]
 Hello everybody,
 A new production release of UCSF Chimera (version 1.7) 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).
 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:
 http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.7.html
 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:
 * 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,
 Elaine
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 Elaine C. Meng, Ph.D.
 UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco