General Changes:
- “connected fragment” inserted into selection cascade between residue and chain
- SMILES-to-3D uses the translator at cactus.nci.nih.gov if the smi23d service does not produce a result
- session notes and thumbnail can be saved via File... Save Session As... and later viewed by clicking the session filename in the Restore Session dialog (previously session notes could only be seen/edited in Notepad)
- items can be deleted from the recent data list in Rapid Access
- duplicate consecutive commands can be removed from the command history
- new volume input format, Amira mesh (scalar)
- new 3D object input format, AutoPack results
- support added for Rich Molecular Format, including an interface for exploring the contents
- support added for Gromacs 4.6 trajectories
- quit-Chimera confirmation default “conditional” instead of “always” (General preferences)
- Mac multi-touch trackpad support (General preferences)
- more efficient use of memory by multi-copy multiscale surfaces
- REST interface (see New Tools)
New Tools:
- RESTServer (Utilities) — allow communication with Chimera through REST interface
Tool Changes:
- 2D Labels (Utilities) — existing arrows can be repositioned
- Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — intramolecular interactions can be excluded, where a molecule is defined as a covalently bonded set of atoms
- FindHBond (Structure Analysis, Surface/Binding Analysis) — intramolecular and/or intraresidue H-bonds can be excluded
New Commands:
- apbs — command-line implementation of APBS interface
- pdb2pqr — command-line implementation of PDB2PQR interface
- rna — build rough but potentially large-scale models of RNA and DNA
- vina — command-line implementation of AutoDock Vina interface
- vseries — display an ordered sequence of volume data sets (command implementation of Volume Series)
Command Changes:
- 2dlabels — existing arrows can be repositioned (achange start/end options)
- colordef — option to list all user-defined color names
- findclash — intramolecular interactions can be excluded, where a molecule is defined as a covalently bonded set of atoms
- findhbond — intramolecular and/or intraresidue H-bonds can be excluded
- getcrd — can report transformed coordinates
- mask —
- modelId option to specify model number of output map
- extend option to specify padding in grid units
- measure —
- fieldLines to show electric field lines for potential maps
- mapStats to calculate map mean, standard deviation from mean, and RMS deviation from zero (command implementation of Volume Mean, SD, RMS)
- mapSum to sum map values above a specified threshold
- ~namesel to “forget” a previously named selection
- reset — options allow partially restoring a position (can keep the viewpoint fixed on one model and move only a subset of the others)
- sop —
- split to split disconnected parts of a surface into independently selectable pieces
- split — can split a model based on ligands, bonded sets of atoms, etc. (formerly just chains)
- surface — probe radius, vertex density, and whether to calculate multiple components can be specified directly in the command
- vop —
- threshold to reassign values that are below a specified minimum and/or above a specified maximum
- localCorrelation — subtractMean option to subtract the local mean before calculating each correlation value
Notable Bugfixes:
- Animation mouse drag uses left mouse button instead of middle
- Animation supports custom surface colorings
- Animation works with volume isosurfaces
- Autodock Vina prep scripts check for receptor and ligand hydrogens, add them if missing (previously no hydrogens were added if the user chose not to add hydrogens with Chimera)
- ViewDock correctly reads mol2 files again
- Fixed export for bond cylinders that were parallel to the Y-axis
Known Bugs:
- surfaces fail for some structures
- Nvidia Quadro graphics on Windows 7 cause ten-second freezes when picking atoms (Ctrl-mouseclick) of large models (20000 atoms). This is caused by the graphics driver "adaptive" power management setting. Using Nvidia Control Panel, Manage 3-D Settings, Global Settings tab to change Power Management to "Prefer maximum performance" solves this problem. Bug report #11315.