Hi all, A new Chimera production release (version 1.1951) is now available for download. I've summarized the major additions since the last snapshot (1.1917) below. A list of all the changes since the last production release (1.1872) is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.1951.html Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu Changes since 1.1917: General changes --------------- Newly opened models are shown larger (as well as models after a 'window' or 'focus' command) Selections can be written out as parsable text files (Actions->Write... or from the Selection Inspector) New residue attributes: kdHydrophobicity (Kyte-Doolittle hydropathy, amino acids only) mavPercentConserved (% conserved in a sequence alignment open in Multalign Viewer) above for use with Render/Select by attribute tools Double-picking a bond brings up a menu with Rotate Bond and Select Bonded (the latter is new and selects the atoms); double-picking a pseudobond bring up a menu with just Select Bonded; "select bonded" also now in Pseudobond Panel As much as possible, can handle PDB files with 100000+ atoms (e.g. AMBER output). Some PDB records (e.g. CONECT records) have no room for 6-digit atom serial numbers, so only can be used for the first 99,999 atoms. A new tutorial describing preparing images for publication Select by Attribute Value... in Selection menu and Model Panel New Tools --------- Lighting (Viewing Parameters): change and save lighting parameters Color Secondary Structure (Graphics): color peptides/proteins by secondary structure Render Attributes (Graphics): color or otherwise change atom, residue, or model displays based on attribute values; was in 1.1917 release but several changes have been made and documentation added Demo (its own category; entries are individual demos): create/replay demos in Chimera; example demo included (Cyclooxygenase) Tool Changes ------------ Adjust Torsions now allows a bond to be rotated with mouse motions in the graphics window Movie has File->Save PDB for writing out either the current frame or all frames that have been viewed Multalign Viewer: ClustalX-style residue letter coloring added and made the default; can save alignment depiction as an EPS file; can hide Consensus and/or Conservation lines RibbonStyleEditor now has two panels in which scalings and cross-sections can be defined and named; named cross-section are analogous to the built-in cross-sections (flat, edged, round) and can be accessed from the Actions menu or with ribrepr; nucleic acids are now treated separately in the scalings panel New "Graphics" category; Per-Model Clipping, PipesAndPlanks, ResProp, and Ribbon Style Editor moved into it SimpleSession saves lighting, ribbon scaling and cross-section(s), B-factor and occupancy values Web Data asks for confirmation before accepting certain files; associated option in Preferences Command Changes --------------- alias: $1, $2, $3, ... may be used to indicate the first, second, third... arguments of the alias conic: works on Windows, and the -s flag now works on Linux (besides Mac, SGI) write: has "trajectory" keyword to write all frames that have been viewed (loaded) [analogous option added to Model Panel's "write PDB" dialog] ribbackbone: now applies to nucleic acids also