Hello everybody, A new production release of UCSF Chimera (version 1.10) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7. New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.10.html I/O, Display: * new web fetch options: PDB biounit, CATH domain * improved New Molecules preferences (initial structure display) * protein SSE (secondary structure element) inserted into up/down-arrow selection cascade * shortcuts rn, rp, ri to shift the selection to the next, previous, and intervening residues in a chain * "rainbow" command can assign a unique color to each SSE * green-magenta (trioscopic) stereo mode * new input format: COLLADA (.dae) Structure Analysis and Modeling: * new RR Distance Maps tool: protein contact maps color-coded by distance (and/or std dev, if comparing structures) * update to AmberTools 14 (new force field options) * Multalign Viewer sequence alignment window: - can plot backbone and all-atom RMSDs, not just CA-RMSDs - show feature annotations from NCBI Conserved Domain Database - search by full or partial sequence name * structure-derived amino acid substitution matrices SDM, HSDM (more choices for sequence alignment and conservation calcs) * Modeller options: thorough optimization, distance restraints * "mda" command (MultiDomain Assembler): - shows BLAST alignment in Multalign Viewer - provides more options for template selection - calls Modeller dialog Volume Data (density maps, electrostatic potential): * "vop" command new options: take pointwise minimum of two or more maps, skeletonize, normalize density maps * "vseries measure" to track isosurface area, enclosed volume, and centroid position across time series 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