General:
- switched from using the Numeric Python extension to NumPy — this may break third-party extensions
- POV-Ray now included for direct production of shadowed images (see File... Save Image):
- new POV-Ray Options section of Preferences
- ribbon style supersmooth added for use with raytracing
- standard and 2D labels included
- as with all raytracers, images with transparency take significantly longer to render
- Save Image dialog changed to use pixels as the default units and to include the supersampling and print resolution settings (formerly in the Image Setup preferences)
- Presets menu added for convenient access to display settings for interactive and publication usage scenarios
- new built-in ribbon scaling, licorice (does not vary with secondary structure); minor changes in Chimera default scaling
- VRML import now supports PROTOs (ie., should work for molden, and older Honig lab GRASS, output)
- new input format MDL MOL/SDF
- new Fetch by ID types: EDS (fo-fc) electron density difference map, PQS predicted biological unit
- opening electrostatic potential data (APBS, Delphi, Grasp, UHBD) now starts Electrostatic Surface Coloring instead of Volume Viewer
- compressed files (*.Z) can be recognized and opened for many input types if gzip is on the user's execution path
- multiple models saved to a single PDB file are delimited by MODEL/ENDMDL records instead of END records
- Select... Chain menu now includes rollovers for chain IDs that appear in more than one model, allowing selection of a chain within a specific model or (as before) all models
- Select... Structure menu now includes nucleic acid and protein
- Actions... Atoms/Bonds now has three options for displaying backbone only: chain trace, full, and minimal
- Actions... Focus adjusts the view as before, but then sets the center of rotation to track the center of view (rather than setting a fixed center based on the specified atoms)
- changes in preferences:
- a preferences file can be specified at startup with --preferences
- the preferences file location is reported but can no longer be changed from within the Preferences dialog
- the preferences file can be designated read-only
- settings in each tab of the Viewing tool can be explicitly saved to and restored from the preferences file
- Collaboratory and Image Setup sections removed
- VRex row stereo mode removed
- camera mode and stereo parameters are saved in sessions
- improved session merging (opening a session in the presence of pre-existing models)
- mouse mode for pop-up Chimera menu implemented (see the Mouse preferences)
- on Windows, rolling the mouse scroll wheel is another way to scale
- added 64-bit Linux AMD64/EMT64 production release
- added Mac OS X Aqua snapshot release (for users who need stereo, full-window antialiasing, and/or background transparency)
- added orthographic support to export formats
- export labels to X3D and POV-Ray files
New Tools:
- Fit Map in Map (Volume Data) — locally optimize the overlap of two density maps
Tool Changes:
- Add Charge (Structure Editing) — updated to recognize v3.0 PDB naming conventions
- AddH (Structure Editing) —
- updated to give the hydrogens v3.0 PDB names if input is v3.0
- includes peptide terminus recognition with OXT addition as needed
- Camera (Viewing Controls) —
- DTI side-by-side mode added for stereo viewing with technology from Dimension Technologies Inc.
- allows control over additional parameters affecting stereo and the amount of perspective
- Collaboratory removed (use version 1.2309 for this tool)
- DelPhiController (Surface/Binding Analysis, Volume Data) —
- can Browse to the DelPhi executable location
- improved handling of pathnames and retention of parameter settings within a Chimera session
- DelPhiViewer portion removed; use Electrostatic Surface Coloring and/or Volume Viewer instead
- Dock Prep (Structure Editing) —
- peptide terminus recognition moved out of this tool and into AddH
- option to delete ions added
- EnsembleTile (Structure Comparison, MD/Ensemble Analysis) — Border scale parameter added to control spacing
- Fit Model in Map (Volume Data) — more detailed information sent to the Reply Log
- MatchMaker (Structure Comparison) — nucleic acid residues lacking C4' atoms are paired using P atoms instead
- MD Movie (MD/Ensemble Analysis) —
- GROMACS support added
- for PDB inputs only, coordinates supplied for a frame may now include just the atoms that moved relative to the previous frame
- added option to ignore hydrogens when calculating RMSD values
- specifying end frame as "pipe" allows reading piped trajectories
- movie recording default image format PPM, frames can be supersampled or raytraced, movie can be encoded as a "round trip"
- Measure Volume and Area (Surface/Binding Analysis, Volume Data) — can update measurements automatically as a surface changes (excluding molecular surfaces)
- Morph Conformations (Structure Comparison) — improved to handle structures with different numbering, different numbers of residues, and even different sequences
- Movie Recorder (Utilities) —
- default image format changed to PPM (faster to save than PNG)
- image frames can be supersampled or raytraced
- movie can be encoded as a "round trip" (A→B and then in reverse, B→A)
- Multalign Viewer (Structure Comparison) —
- Find Subsequence, Find PROSITE Pattern, and Alignment Annotations moved from Tools menu to Edit menu
- a tree (Newick format) can be read and displayed alongside the corresponding sequence alignment
- sequences from structures open in Chimera can be added to an alignment
- Nucleotides (Depiction) — updated to recognize v3.0 PDB naming conventions
- Render by Attribute (Depiction, Structure Analysis) — attribute values can be saved to a file (File... Save Attributes)
- Shininess Control (Viewing Controls) — made a subpart of the Lighting tool
- Side View (Viewing Controls) —
- double-clicking the eye position brings up a menu for changing the camera mode (mono and stereo options)
- top view interface added for interactive adjustment of stereo parameters and perspective
- Surface Color (Volume Data) — allows coloring by volume data gradient norm
- ViewDock (Surface/Binding Analysis) —
- starts up with the first ligand displayed (rather than all)
- descriptors such as DOCK scores are now assigned as attributes (can be used for coloring, selection, etc.)
- which columns to display can be specified in a text file
New Commands:
- bondzone — make zoning tools use points along bonds
- namesel — name and save the current selection
- ribscale — set ribbon scaling (named set of secondary-structure-specific dimensions)
- windowsize — set graphics window dimensions
Command Changes:
- in specifications by attribute, a color can be indicated with a comma-separated list of component values (red, green, blue, and optionally alpha, in that order) as well as by name
- ~color — requires target specifiers (r for ribbon, etc.) to be comma-separated (this was already the case for color)
- copy — raytracing keywords added
- focus — adjusts the view as before, but then sets the center of rotation to track the center of view (rather than setting a fixed center based on the specified atoms)
- match — allows use of <4 atom pairs (although transformations are not unique for 1-2 pairs)
- movie — default image format PPM, frames can be supersampled or raytraced, movie can be encoded as a "round trip"
- open — noprefs keyword added to bypass the New Molecules preferences when a structure is opened (prevents inconsistent behavior of scripts potentially caused by the different preferences settings of different users)
- rmsd — allows use of <4 atom pairs
- savepos — includes positions of any per-model clipping planes
Documentation Changes:
(other than updates/additions reflecting the changes above)
- DelPhiController documentation expanded significantly to explain parameters and link to DelPhi documentation at Honig site
- Introduction to PDB Format updated and converted from PDF to HTML
Major Bugs Fixed:
- molecule coordinates can be saved relative to a volume display (or other non-molecule model)
- cross-eye stereo mode fixed
- corrected stereo image saving with the "same as screen" option when the graphics window is in cross-eye or wall-eye mode
- corrected label position/scale in saved images smaller than the current display (standard and 2D labels)
- accept Sweet2 generated PDB files
- export transparency correctly to POV-Ray files
- don't export undisplayed models
chimera --sendnow always returns even if a new chimera is started