UCSF Chimera Version 1 Build 2470 Release Notes

Changes since the previous production release (1.2422):

General:

• can fetch modeled structures from ModBase using the prefix modbase: and a SwissProt, TrEMBL, GenPept or PIR accession code (with the command open)
• show only added under Actions... Atoms/Bonds
• New Surfaces category added to Preferences &mdash set parameters for newly created molecular surfaces
• can read IMOD segmentation files (binary)
• file browser File type menu now arranged in columns when the list is long
• further decrease in session file sizes (up to 10%) and restore times
• fullscreen graphics mode available on Windows
• added --script command line option for tool builders that embed chimera
• reduced size of exported X3D, VRML, and POV-Ray files
• make unicode filenames work on Windows

New Tools:

• Crystal Contacts (Higher-Order Structure) — identify clashes between PDB symmetry copies
• Flatten Icosahedron (Higher-Order Structure) — rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
• Fourier Transform (Volume Data) — generate 3D Fourier transform of volume data
• Gaussian Filter (Volume Data) — perform Gaussian smoothing of volume data
• Morph Map (Volume Data) — morph between two related sets of volume data
• Movement Mouse Mode (Movement) — move just part of a structure with the mouse
• Pick Surface Pieces (Volume Data) — color and measure disconnected parts of a contour surface
• Rotamers (Structure Editing) —
  • display amino acid sidechain rotamer sets
  • evaluate rotamer clashes, H-bonds, agreement with a density map
  • incorporate a chosen rotamer into a structure
• Split Volume by Color Zone (Volume Data) — split volume data into separate sets based on zones previously defined in the Color Zone tool
• Transform Molecule Coordinates (Movement) — transform a structure by specified Euler angles and shifts
• Volume Mean, SD, RMS (Volume Data) — calculate volume data statistics
• Volume Series (Volume Data) — display a sequence of volume data sets

Tool Changes:

• Accelerator List (General Controls) — several volume-related accelerators added
• Effects (Viewing Controls) — can set silhouette edge linewidth
• Intersurf (Surface/Binding Analysis) — can select interface atoms
• MatchMaker (Structure Comparison) — residues used in the final fit iteration are boxed in the sequence alignment
• Model Loops (Structure Editing) — updated to work with MODELLER Release 9 (courtesy of Ben Webb)
• Multalign Viewer (Structure Comparison) —
  • can show sequence numbering to the left and/or right of each row
  • Tree menu added for loading Newick trees and extracting subalignments corresponding to chosen nodes
  • Preferences (Regions section) can control initial appearance of regions created by structure association
• Multiscale Models (Higher-Order Structure) — when a multiscale model is created, the display of the original structure is kept the same; only additional copies are shown as low-res surfaces
• Volume Viewer (Volume Data) —
  • added input formats TIFF image stack, HDF map
  • improved handling of large data sets, 3X higher size limit for contour surface calculations
  • file-reading progress reported in status messages, reading can be cancelled
  • many interface changes: can show multiple data histograms at once, "eye" icon shows/hides, Tools menu lists volume-related tools
  • different colors used for successively opened data sets
  • by default, isosurfaces now cap faces of the volume data box where high values would be exposed
  • controls added for single-plane and few-plane display
  • can resample data to generate grids not aligned with the original axes
  • changes in transparent solid rendering
  • solid display now correct for non-orthogonal crystal data

New Commands:

• crystalcontacts — identify clashes between PDB symmetry copies (command-line implementation of Crystal Contacts)
• hkcage — create a hexagon/pentagon mesh that covers an icosahedron
• mask — segment volume data using bounding surfaces
• meshmol — create a "molecule" from surface mesh for stick display
• msc — color multiscale surfaces to match atoms
• preset — apply a predefined combination of display settings (command-line implementation of the Presets menu)
• split — make the chains of a structure separate submodels
• sym — generate copies of a structure at symmetric positions that update automatically
• volume — command-line implementation of many Volume Viewer features

Command Changes:

• align — can align centroids of two sets of atoms (formerly just aligned two atoms)
• hbonds — can cache donor and acceptor information (useful when repeatedly calculating hydrogen bonds for different conformations of the same structure)
• intersurf — can select interface atoms
• surface — syntax slightly simplified (identical in most cases)
• swapaa — completely replaced with Rotamers functionality: although the syntax is backwards-compatible, output conformations are from rotamer libraries and can be chosen based on clashes, H-bonds, agreement with density, or library probability values
• write — can save Mol2 files (formerly just PDB)

Bug Fixes:

• POV-Ray images created from Chimera now include depth-cueing
• Display Amira-generated VRML files
• Display Ribbons-generated VRML files (the *_inline.wrl files)

Known Bugs:

• surfaces fail for some structures