UCSF Chimera Version 1 Build 1951 Release Notes

Changes since the previous production release (1.1872):

• Improved lighting control — see Viewing Parameters tool category: Effects, Lighting, and Shininess Control
• Initial scale of models is typically larger (also used by window and focus commands)
• Selections can be written as parsable text files with Actions... Write... dialog
• Additional residue attributes:
  • kdHydrophobicity — Kyte-Doolittle hydropathy, amino acids only
  • mavPercentConserved — % conserved in a sequence alignment open in Multalign Viewer
• Double-picking (a double-click pick) a bond pops up a menu with Rotate Bond and Select Bonded choices (the latter is new); double-picking a pseudobond only gives the Select Bonded choice. Select Bonded selects the atoms the bond connects.
• Extended PDB format to allow for 999999 atoms (10X larger) with ATOM 1, ATOM 2, ..., ATOM 9 records. Corresponding changes to CONECT records were not made.
• Ribbons track subdivision quality to improve appearance
• Nucleic acid ribbons hide the backbone atoms (by default; can be controlled with the command ribbackbone)
• On Apple OS X, chimera registers to open PDB and chimerax files (more file types can be added with new Browser Configuration tool)
• Documentation for all new features
• New tutorial:
  • Images for Publication — detailed examples of making quality images for publication
• New tools:
  • Browser Configuration (Utilities)
    • Configure web browsers to send files to Chimera
    • Configuring the browser also configures the desktop on Apple OS X and Microsoft Windows
  • Color Secondary Structure (Graphics)
    • Color peptides/proteins by secondary structure
  • Demo (its own category; entries are individual demos)
    • Create/replay demos in Chimera
    • Cyclooxygenase demo included as an example
  • Export Surfaces as VRML (Utilities)
    • Save surfaces made by Multiscale Models and Volume Viewer as VRML files
  • Lighting (Viewing Parameters)
    • Change and save key and fill light parameters
  • Render Attributes (Graphics)
    • Color or otherwise change atom, residue, and model displays based on attribute values
  • Shininess Control (Viewing Parameters)
    • Adjust shininess, brightness, and the color used for shiny highlights
• Tool changes:
  • Adjust Torsions — allow a bond to be rotated with the mouse in the graphics window
  • Collaboratory — work with firewalls and NATs by allowing rendezvous port number and IP address to given explicitly in Preferences Collaboratory category
  • Effects — allow "local viewer" to be set for more accurate (and slower) specular highlight direction calculation
  • FindHBond
    • Allow line width to be set
    • Labeling option removed
  • Match->Align can create sequence alignments for multiple aligned structures (not just pairs)
  • Movie
    • Read GROMOS files (in addition to those from AMBER)
    • Allow definition of scripts to be run at each step
    • Allow looping to be turned off
    • File... Save PDB writes the current frame or all frames that have been viewed
    • Trajectory files can be bigger than 2 GBytes
  • Multalign Viewer
    • Allow structure residue selection by arbitrary % identity conservation in alignment
    • New interface shows alignment annotations and allows them to be changed
    • Clustal X coloring added and made default
    • Can save EPS (File... Save EPS)
    • Can hide Consensus and Conservation lines
  • Multiscale Models — add ViPER matrix support
  • PBReader — allow line width to be set
  • Per-Model Clipping, PipesAndPlanks, ResProp, and Ribbon Style Editor moved to new Graphics category
  • SimpleSession
    • Saves label font/size, secondary structure assignments, lighting, ribbon scaling and style(s), B-factor and occupancy values
    • Session file compiled when opened
  • PseudoBond Panel — "select bonded" function added
  • Ribbon Style Editor
    • Now has two panels, in which scalings and cross-section styles can be defined and named
    • Named cross-section styles are analogous to the built-in styles and can be accessed from the Actions menu and with ribrepr
    • Nucleic acids treated separately in scalings panel
  • Volume Viewer options added to subdivide and smooth isosurfaces
  • Web Data section added to Preferences
    • Controls whether Chimera can be used as a helper application
    • Controls whether/how often to ask for confirmation before accepting certain files
• New commands:
  • bondcolor — color bonds independent of flanking atoms
  • bonddisplay — how bond display depends on flanking atom display
  • bondrepr — change bond representation
  • hbonds — command implementation of the FindHBond tool
  • rlabel — control whether residue name/number is included in the first atom label per residue
  • ribbackbone — control whether ribbon and backbone atoms can be shown simultaneously (applies to nucleic acids as well as amino acids)
• Command changes:
  • Commands are erased upon execution
  • Recent commands and the full Command History are available from a pulldown menu
  • alias — $1, $2, $3 ... may be used to indicate the first, second, third ... arguments of the alias
  • copy
    • Include supersampling
    • Provide additional formats (PS, EPS)
    • Save background translucency when --bgopacity startup argument is given
  • conic — works on Windows, -s flag works on Linux (in addition to Mac, SGI)
  • write — trajectory keyword to write all frames that have been viewed (analogous option added to "write PDB" dialog opened from Model Panel)

Major bugs fixed

• Preferences Reset/Restore functions were swapped
• Lines (wireframe mode) no longer disappear in high resolution saved images
• Adding an extension directory won't crash chimera
• Selection outlines were occasionally in the wrong place in saved images
• On Linux, detect inconsistent graphics driver configuration

Known bugs:

MultAlign Viewer's "Select by Conservation..." menu item generates an error if it is chosen before the attribute render/select dialog has been opened. The error is inconvenient but not fatal; you can still navigate the dialog to the mavPercentConserved attribute and so forth. The workaround is to bring up the attribute render/select dialog before choosing the menu item (either by Select→By Attribute Value or by Tools→Graphics→Render Attributes).

Cross-eye stereo parallax is wrong.

Bond rotations in large molecules are slow.