From owner-chemistry@ccl.net Tue Dec 14 19:33:00 2010 From: "Elaine Meng meng[A]cgl.ucsf.edu" To: CCL Subject: CCL: Chimera 1.5 release Message-Id: <-43387-101214191142-19707-j4/kCW3ZZPy7I9aAJqu87w=server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 14 Dec 2010 19:11:39 -0500 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