Announcements:
This is the last release for 32-bit operating systems.
General Changes:
- model-display checkboxes can be shown below the command line, and the model-active checkboxes can be hidden (see Preferences, Command Line)
- new input format: IMAGIC density map
- mouse focus (so that Chimera accepts typed input) can be restored by clicking into the Side View as well as the main window
- command-line “atomspec” expanded to handle surface piece names (such as from Multiscale Models)
- new flat ribbon publication preset
- “wall-eye stereo pair” option added to Save Image dialog
- revamped Getting Started tutorials, new Ribbon Styles image tutorial
- molecule descriptions (shown in the status line on mouseover) now read from mmCIF, not just PDB
- PubChem fetch changed to get structures from PubChem3D (NCBI) instead of Pub3D (Indiana University)
- command history navigation skips completely identical lines, and additionally pressing Shift (along with Ctrl-p, Ctrl-n, ↑, or ↓) goes to the previous/next occurrence of the same command (same initial string) instead of the immediately adjacent command
- atom specification tolerates spaces after commas
- implemented standard keyboard shortcuts Ctrl-o,s,S,q (on Mac, Command instead of Ctrl) for File menu entries Open, Save Session, Save Session As, and Quit, respectively
New Tools:
- pre-existing Color Actions dialog now also listed as a tool under Depiction
- Molecular Dynamics Simulation (MD/Ensemble Analysis) — interface to setup tools and MMTK molecular dynamics; thanks to Victor Muñoz Robles and Jean-Didier Maréchal (Universitat Autònoma de Barcelona)
Tool Changes:
- Add Ions (Structure Editing, Amber) — many more ion types available
- Axes/Planes/Centroids (Structure Analysis) — option to define axes normal to previously defined planes
- MatchMaker (Structure Comparison) — if the fit is iterated, now reports RMSD over all pairs as well as the pruned set of pairs
- MD Movie (MD/Ensemble Analysis) — residue interaction network (RIN) calculation and display; currently requires starting Chimera from Cytoscape via the structureViz app
- Model Panel (General Controls) — select-chains dialog includes chain descriptions from the PDB, if available
- RR Distance Maps (Structure Comparison) —
- can show distance differences for pairs of structures (means and standard deviations were previously available)
- can export data to files as tab- or comma-separated values
- Segment Map (Volume Data) — updated version of Segger
New Commands:
- pipes — command-line implementation of PipesAndPlanks
Command Changes:
- clip — allows placing front/back clipping planes a specified distance from the center of rotation
- coordset — option to load coordinates for all frames (default true)
- define — can define an axis normal to a plane
- shape — can make a triangle
- matchmaker — if the fit is iterated, now reports RMSD over all pairs as well as the pruned set of pairs
- mclip — a per-model clipping plane can be positioned onto a plane object previously defined with Axes/Planes/Centroids or the command define
- molmap —
- default output model number now unique instead of the same as the input atoms
- onGrid option to generate map on the grid of another
- move — move cofr to translate models to the current center of rotation
- set —
- showCofR to show “+” crosshairs at the center of rotation
- eyeSeparation for stereo
- screenDistance for stereo
- screenWidth for stereo
- sop —
- colorCopy to copy colors from one surface piece to other pieces, or from N to N pieces
- invertShown to show hidden blobs and hide shown blobs (can show previously hidden “dust” for masking purposes)
- turn, rock, roll — can use an axis previously defined with Axes/Planes/Centroids (or define) as the axis of rotation
- vina —
- prep option to run prep only, not docking
- wait option to prevent premature exit from Chimera nogui
- volume —
- rmsLevel for specifying threshold (contour level) in root-mean-square deviations from zero
- sdLevel for specifying threshold in standard deviations from the mean
- vop —
- vop boxes cube length can be specified in grid units with the isize option; this facilitates getting cubes of exactly the same size
- map sharpening implemented as invert option to vop gaussian
- vop new to create empty (zero-valued) map
Notable Bug Fixes:
- MultiDomain Assembler (mda command)
- works with sequence file input
- residue attributes mda_blastscore, mda_percentid, mda_alignment saved in sessions
- reset command works with position names containing spaces, providing the names are enclosed in quotation marks
- molecule descriptions (shown in the status line on mouseover) saved in sessions
- PDB2PQR link to web service updated to 2.0.0 (1.9.0 no longer available)
- Adding charges to non-standard residues would sometimes fail, complaining about not finding libquadmath
- fewer triangles in STL output for atom/bond representations
Known Bugs:
- surfaces fail for some structures
Notable Bug Fixes:
- backport Tk bug fix for Mac OS X dual display crash
- speed up opening of large non-molecule structures with no bonds
- suppress excessive warnings when opening PDB files
- make sure output goes to right place when opening mmCIF files
- NCBI URLs have to use https now
- rainbow helix recognizes abutting helices as distinct
- fix Join Models tab in Build Structure so the setting of the phi angle never moves the "non-moving" side
- fix ion parameter in APBS
- handle plots with closed models more gracefully in RRDistMaps
Enhancements:
- User's Guide includes attribute assignment file for Moon-Fleming hydrophobicity scale
- put Chimera version in X3D output
- struts command takes into account the currently displayed pseudobonds (H-bonds, distance monitors) and ignores bonds that are hidden
- surface command warnLarge false option to bypass having to confirm a large calculation