CCL: UCSF Chimera new release

 Sent to CCL by: "Elaine  Meng" [meng .. cgl.ucsf.edu]
 Hello everybody,
 A new production release of UCSF Chimera (version 1.9) is available:
 http://www.rbvi.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).
 New features include multiple sequence alignment using Clustal Omega
 or MUSCLE web services, building double-helical nucleic acids,
 "colorkey" command, "struts" command to reinforce structures
 for
 3D printing, "vseries" volume series playback and processing options,
 more efficient save/restore of coordinates in sessions, Dynameomics
 amino acid rotamer library, WMV2 movie output, COLLADA export.
 More details are given below; see release notes for the full list:
 http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html
 Display, Interface:
 * icon for menu selection mode: Append, Intersect, Replace, Subtract
 * distance monitor line style and color can be saved as preferences
 * silhouette outlines can be controlled per-model
 * Axes/Planes/Centroids objects can be recolored with Actions menu
 * "colorkey" command implementation of Color Key tool
 Structure Analysis and Modeling:
 * new Align Chain Sequences tool for multiple sequence alignment of
  structure chains using a Clustal Omega or MUSCLE web service
  (these can also be called to realign the sequences in an existing
  Multalign Viewer window)
 * "mda" command to Blast-search and retrieve structures similar to
  a query sequence, lay them out left->right by N->C along the query
 * APBS interface omits explicit solvent by default
 * "coulombic" command allows specifying atoms/charges to use for ESP
  calculation independent of the surface to color
 * Build Structure tool allows generating nucleic acid double helices,
  specifying phi angle when joining peptides
 * "adjust" command to change bond angle or length
 * MD Movie session support for partly loaded trajectories
 * Morph Conformations pairs chains by ID if the sets of IDs are same
 * "ramachandran" command can assign probabilities as attributes
 * Rotamers/swapaa include Dynameomics rotamer library (Daggett group)
 Volume Data (density maps, ESP maps):
 * "vop" volume operations to take pointwise maximum or multiply maps
 * "vseries" command options to open and close volume time series,
  jump playback to a specific frame, perform various processing such
  as alignment, normalization, cropping, compressing, save to file
 * new volume input format VTK structured points (ASCII)
 General, I/O:
 * some Preferences reorganization, new categories: Labels, Selection
 * more efficient save/restore of coordinates in sessions
 * new output movie format WMV2
 * new export formats COLLADA, VTK
 * "struts" command to add strengthening bonds for 3D printing
 * "leap" command for using Chimera with a Leap Motion Controller
 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