CCL: Chimera 1.5 release

["Elaine Meng" <meng .. cgl.ucsf.edu>]

 Sent to CCL by: "Elaine  Meng" [meng(!)cgl.ucsf.edu]
 Hello everybody,
 A new production release of UCSF Chimera (version 1.5) is available:
 http://www.cgl.ucsf.edu/chimera/download.html
 Download is free for noncommercial use.
 Platforms: Windows, Mac, Linux
 64-bit versions are now available for all three platforms.  These
 are useful for large data sets (large density maps, trajectories,
 etc.) and recommended for machines with 4Gbytes or more of memory.
 New features in Chimera 1.5 include Ramachandran plots, a graphical
 interface to the Modeller program for homology modeling, metal ion
 coordination analysis, Segger tools for electron microscopy and
 tomography (Segment Map, Fit to Segments), and calculation of
 theoretical SAXS profiles.
 More details are given below, as well as in the release notes:
 http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.5.html
 Graphics, Depiction:
 * several new lighting modes including ambient-only
 http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/p53/p53ambient.html
 * smoother default sticks
 * improved transparent ribbons
 * ring and nucleotide display options in menu
 * improved 3D label offsets, more options for residue labels
 * 2D Labels tool allows drawing arrows in any orientation
 * Render by Attribute (shows B-factor, hydrophobicity, etc.)
    includes built-in color palettes
 * shape command can create ellipsoids and other new shapes
 Structure Analysis and Modeling:
 * Ramachandran plot function in Model Panel
 http://www.cgl.ucsf.edu/chimera/1.5/docs/ContributedSoftware/ramachandran/ramachandran.html
 * Metal Geometry tool for coordination analysis
 http://www.cgl.ucsf.edu/chimera/1.5/docs/ContributedSoftware/metalgeom/metalgeom.html
 * centroid calculation, display, use in measurements
 * Thermal Ellipsoids
   - more display options
   - reads anisotropic B-factors from CIF/mmCIF
   - saved in sessions
 * H-bond, clash/contact calculations can be restricted to
   two independently specified sets of atoms
 * trajectory clustering in MD Movie
 * Build Structure improvements, including Join Models section
 * interface to Modeller homology modeling program & web service
 http://www.cgl.ucsf.edu/chimera/1.5/docs/ContributedSoftware/multalignviewer/modeller.html
 * Segment Map and Fit to Segments (Segger EM tools)
 http://www.cgl.ucsf.edu/chimera/1.5/docs/ContributedSoftware/segger/segment.html
 * calculation of theoretical SAXS profiles
 http://www.cgl.ucsf.edu/chimera/1.5/docs/ContributedSoftware/saxs/saxs.html
 User Interface and I/O:
 * user-defined action aliases appear in Aliases menu
 * Color Actions dialog more convenient than repeated use of menu
 * PQR files read, including charge and radii assignments
 Sequence-related:
 * phylogenetic trees saved in sessions
 * sequence alignment headers can include symbols
 * HSSP files read
 * Match->Align reports structural similarity as SDM, Q-score
 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