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
--scriptcommand 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