<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi all,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>There is a new snapshot release (1.2251) available, with a potpourri of new features, listed below. The release is for all platforms, but on Mac we had a little difficulty getting things to work for OS X 10.3, so this release is 10.4 only, but the next production release will include 10.3 support.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P> ---<BR class="Apple-interchange-newline"> </DIV><DIV>1.2251 release (changes since 1.2199 release)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>GENERAL:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Session files are smaller, use less memory, and start faster.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>CIF/mmCIF files can be read (or fetched by ID from RCSB)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Electron density maps can be fetched by PDB ID from Electron Density Server</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Virus Particle Explorer (VIPER) files can be fetched by ID</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>VIPER input automatically starts Multiscale Models and constructs viral capsid</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thinner default ribbons</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Files opened by scripts (either Python or Chimera commands) are now</DIV><DIV> searched for relative to the script location, not Chimera's startup location.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Can switch to sequential stereo mid-session without having used --stereo</DIV><DIV> at startup (except on certain Windows systems)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>New stereo mode: anaglyph (offset red/cyan-tinged views, like 3D movies)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>NEW TOOLS:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Add Charge (Structure Editing) - assigns partial charges to atoms; </DIV><DIV> Amber (Cornell et al. 1995) charges used for standard residues,</DIV><DIV> Amber's Antechamber module (now included with Chimera) used to </DIV><DIV> calculate charges for nonstandard residues</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Build Structure (Structure Editing) - under construction but basic functions work;</DIV><DIV> not much documentation</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>ReadStdin (Utilities) - allows communication with Chimera through standard input/output</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>TOOL CHANGES:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>AddH (Structure Editing)</DIV><DIV> - new options including how to treat histidines</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Adjust Torsions (Structure Editing) </DIV><DIV> - interface reorganized to show atoms defining a torsion in order 1-2-3-4</DIV><DIV> - options added to control decimal places and show degree symbol in angle labels</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Dock Prep (moved to Structure Editing)</DIV><DIV> - option added to delete alternate locations of atoms</DIV><DIV> - hydrogen addition and charge addition details split off into separate tools</DIV><DIV> called from Dock Prep (AddH and Add Charge, respectively)</DIV><DIV> - terminal carboxylates/amines completed as appropriate</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Effects (Viewing Controls)</DIV><DIV> - background transparency option added </DIV><DIV> (previously only available as --bgopacity startup option)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Minrms Plot (Structure Comparison)</DIV><DIV> - Show Alignment option added</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>MPOSE extension removed (Structure Comparison)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Multalign Viewer (Structure Comparison)</DIV><DIV> - .ali extension interpreted as PIR format</DIV><DIV> - .pfam extension no longer indicates Stockholm format, instead indicates Pfam format</DIV><DIV> ("Plain Pfam format" at the Sanger Institute Pfam site)</DIV><DIV> - changed default residue letter/region colors for improved readability</DIV><DIV> - improved editing response time</DIV><DIV> - editing no longer pushes residues that are not in the active region</DIV><DIV> - added control over whether a region depiction spans gaps</DIV><DIV> - option to associate a structure chain with the best-matching sequence in the alignment</DIV><DIV> (when criteria for automatic association are not met)</DIV><DIV> - new Edit menu allowing sequence reordering and deletion, gap column addition and deletion</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>COMMAND CHANGES:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>ribbonjr removed</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>NEW COMMANDS:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>addcharge - assign partial charges to atoms</DIV><DIV> (command-line implementation of new Add Charge tool)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>intersurf - generate and display interface surfaces</DIV><DIV> (command-line implementation of Intersurf)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>setattr - set a new or existing attribute to a specified value</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>surftransparency - adjust molecular surface transparency</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>COMMAND CHANGES:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>longbond - now takes an atom or model specification to restrict the calculation</DIV><DIV> to certain models</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>TUTORIALS:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>figures added to Getting Started tutorials</DIV><DIV><BR class="khtml-block-placeholder"></DIV></BODY></HTML>