UCSF Chimera Version 1 Build 2304 Release Notes

Changes since the previous production release (1.2199):

General:

• smaller session files, faster session save/restore
• CIF/mmCIF files can be read (local or fetched by ID from the PDB)
• electron density maps can be fetched by PDB ID from the Electron Density Server
• Virus Particle Explorer (VIPER) files can be fetched by ID
• VIPER input automatically starts Multiscale Models, constructs viral capsid
• Save File dialog adjusted to clarify how to save untransformed coordinates
• smaller default ribbon height/width (ribbon scaling)
• can color by heteroatom (same as by element except carbons not affected)
• in the command line, :30-40 (for example) now specifies those residues in any/all chains, whereas :20-30. specifies those residues in blank-ID chains
• locations of files opened by command files and python scripts now specified relative to the location of the command file/script, or with absolute pathnames
• rules defining solvent and ions adjusted slightly, so that small coordination complexes, such as cobalt hexammine, are classified as ions
• VRML export works for all scene data, not just surfaces
• can switch to sequential stereo mid-session without having used --stereo at startup (except on certain Windows systems)
• stereo images can be saved
• red-cyan (anaglyph) stereo option added
• faster methodology used for displaying labels
• improved silhouette edge rendering
• on the Mac, starting Chimera starts X11 automatically, and after Chimera has been started, clicking the Chimera icon in the dock will bring the Chimera window to the front

New Tools:

• Add Charge (Structure Editing) —
  • assigns partial charges to atoms
  • Amber (Cornell et al. 1995) charges used for standard residues, Amber's Antechamber module (now included with Chimera) used to calculate charges for nonstandard residues
• Build Structure (Structure Editing) — perform simple structure-building operations (in early development, may change significantly)
• Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — identify clashes and/or contacts (see also command findclash)
• Minimize Structure (Structure Editing) — energy-minimize structures (in early development, likely to change)
• Model Loops (Structure Editing) — interface to Modeller (obtained separately) for generating alternative conformations of peptide segments already present in a structure (in early development, likely to change)
• Morph Conformations (Structure Comparison) — create a trajectory that morphs between two or more conformations of a structure
• ReadStdin (Utilities) — allows communication with Chimera through standard input/output

Tool Changes:

• AddH (Structure Editing) — new options including how to treat histidines
• Adjust Torsions (Structure Editing) —
  • interface reorganized to show atoms defining a torsion in order 1-2-3-4
  • options added to control decimal places and show degree symbol in angle labels
• Dock Prep (moved to Structure Editing) —
  • option added to delete alternate locations of atoms
  • hydrogen addition and charge addition details split off into separate tools called from Dock Prep (AddH and Add Charge, respectively)
• Effects (Viewing Controls) — background transparency option added (previously only available as --bgopacity startup option)
• Icosahedron Surface (Higher-Order Structure) — more Orientation options
• Measure Volume and Area (Surface/Binding Analysis, Volume Data) —
  • now measures surface area (formerly just volume and was named Measure Volume)
  • made faster by moving calculations from Python to C++
• Minrms Plot (Structure Comparison) — Show Alignment option added
• Model Panel (General Controls) — shows model colors with mini color wells
• Movie Recorder (Utilities) —
  • new output format, AVI MSMPEG-4v2;
  • constant bit rate encoding is now available and is the default (the old default was variable bit rate, which some players did not handle well, resulting in uneven playback)
  • see also the command movie
• MPOSE extension removed (Structure Comparison)
• Multalign Viewer (Structure Comparison) —
  • *.ali interpreted as PIR format
  • *.pfam no longer indicates Stockholm format, instead indicates Pfam format (Plain Pfam format at the Sanger Institute Pfam site)
  • darker yellow used in Clustal X coloring
  • changed default colors of regions showing secondary structure
  • improved editing response time
  • editing no longer pushes residues that are not in the active region
  • added control over whether a region includes gaps
  • option to associate a structure chain with the best-matching sequence in the alignment (when criteria for automatic association are not met)
  • new Edit menu allowing sequence reordering, addition (with alignment to existing sequences), and deletion, gap column addition and deletion
  • can expand a selection to include all other residues associated with the same column(s) of the alignment
• Volume Path Tracer (Volume Data) — interface reorganized significantly
• Volume Viewer (Volume Data) — added Square mesh option

New Commands:

• addcharge — assign partial charges to atoms (command-line implementation of new tool Add Charge)
• findclash — identify clashes and/or contacts (command-line implementation of new tool Find Clashes/Contacts)
• intersurf — generate and display interface surfaces (command-line implementation of Intersurf)
• minimize — energy-minimize structures (command-line implementation of new tool Minimize Structure)
• setattr — set a new or existing attribute to a specified value
• start — start a given tool
• surftransparency — adjust molecular surface transparency

Command Changes:

• close — new keyword session to close alignments and 2D labels in addition to all the models with model numbers
• hbonds — new keyword log to write info to the Reply Log
• longbond — now used to hide/show missing segments pseudobonds rather than to break bonds (also, behavior reversed: now ~longbond hides, longbond shows)
• movie —
  • new AVI MSMPEG-4v2 format
  • defaults to constant bit rate encoding
  • new encode keywords bitrate, buffersize
• reset — can interpolate between positions over a specified number of frames
• ribbonjr removed
• vdwdefine — syntax simplified (no longer necessary to supply atom/res names) and ~vdwdefine added to restore default VDW radii

Tutorials:

• new Alignments tutorial, covers MatchMaker and Match->Align
• figures added to Getting Started, Sequences and Structures, and ViewDock tutorials
• part 1 of Attributes tutorial changed significantly, now includes assignment of partial charges

Major Bugs Fixed:

• dashed lines are no longer compressed in saved images
• when objects are clipped by the hither clip plane, insides are lit
• a bug where the graphics would stop being redrawn is fixed
• graphics doesn't drift if then same command script is rerun
• some PDB files with incomplete ribbon information weren't drawn
• translucent ribbons work again
• POV-ray output fixed
• fixed unreadable initial label problem on Macs

Known Bugs:

• surfaces fail for some structures
• bond rotations in large molecules are slow
• cross-eye stereo parallax is wrong