CCL: new Chimera release

 Sent to CCL by: "Elaine  Meng" [meng]^[cgl.ucsf.edu]
 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
 * 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
 * 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,
 Elaine
 -----
 Elaine C. Meng, Ph.D.
 UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco