General Changes:
- optional icon to show and control menu selection mode (Append, Intersect, Replace, or Subtract)
- some Preferences reorganization, including new categories: Labels, Selection
- model silhouette attribute allows showing silhouettes for specific models (previously all or none)
- Ramachandran Plot probabilities can be assigned as a residue attribute
- new output movie format WMV2
- new input volume format VTK structured points, ASCII
- new export formats COLLADA, VTK
- more efficient save/restore of coordinates in session files (for MD trajectories or very large structures, ~5% smaller session files and 3X faster save/restore)
New Tools:
- Align Chain Sequences (Sequence) — generate a multiple sequence alignment (MSA) of structure chains using a Clustal Omega or MUSCLE web service hosted by the UCSF RBVI
Tool Changes:
- APBS (Surface/Binding Analysis) — by default, explicit solvent is omitted from the calculation
- Axes/Planes/Centroids (Structure Analysis) —
- axis, plane, and centroid objects are now surface models (improved behavior with transparency and shadows; can be recolored with Actions menu, color, scolor)
- axes can be calculated from centroids as well as atoms
- Build Structure (Structure Editing) —
- can build nucleic acid double helices
- join models (peptide bond option) allows specifying new φ angle
- button to delete selected atoms/bonds
- Color Key (Utilities) — tick mark length and width settings added
- Distances (Structure Analysis) — default distance monitor color, linewidth, and line style can be saved to preferences
- Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — option to display contact residues if not already shown
- Icosahedron Surface (Higher-Order Structure) — added line-width setting for mesh
- MD Movie (MD/Ensemble Analysis) —
- separate settings for including or omitting alkali metal ions, other metal ions, and monatomic anions from various calculations (RMSD, clustering, averaging)
- sessions support partly loaded trajectories
- Minimize Structure (Structure Editing) —
- default number of conjugate gradient steps decreased from 100 to 10
- improved logging
- Morph Conformations (Structure Comparison) — chain pairing uses chain IDs if the sets of IDs are identical
- Morph Map (Volume Data) — optionally interpolates colors if the maps have the same number of coloring thresholds
- Multalign Viewer (Sequence) —
- sequence names can be edited
- regular expression searching
- protein sequences with U (selenocysteine), O (pyrrolysine) can be aligned
- Clustal Omega or MUSCLE can be used via web service to realign the sequences
- active region contents can be opened in a new window
- Multiscale Models (Higher-Order Structure) — surfaces of different chains with the same sequence are colored alike
- Rotamers (Structure Editing) — added Dynameomics rotamer library
New Commands:
- adjust — change bond angle or bond length
- colorkey — command-line implementation of the Color Key tool, plus direct specification of color key placement
- leap — use a Leap Motion Controller with Chimera
- mda — BLAST-search and retrieve structures related to a query sequence, lay them out left→right in Chimera by N→C matches to the query
- struts — add pseudobonds to a molecule to strengthen it for 3D printing
Command Changes:
- angle — option to report angle between 1-2 and 3-4 vectors instead of 1-2-3-4 dihedral
- apbs —
- by default, explicit solvent is omitted from the calculation
- added options to use a local executable or an alternative Opal web service
- coulombic — atoms/charges to use can be specified independently of the surface to color; this allows coloring the surface of one molecule by the potential from another, for example, or coloring nonmolecular surfaces such as density isosurfaces
- define —
- axis, plane, and centroid objects are now surface models (improved behavior with transparency and shadows; can be recolored with Actions menu, color, scolor)
- axes can be calculated from centroids as well as atoms
- findclash — option to reveal (display) contact residues if not already shown
- matrixcopy — allows many-to-many transformation copying (previously just one-to-one or one-to-many)
- minimize — default number of conjugate gradient steps decreased from 100 to 10; improved logging
- morph — chain pairing uses chain IDs if the sets of IDs are identical
- pdb2pqr — added options to use a local executable or an alternative Opal web service
- ramachandran (undocumented in earlier versions) — can assign probabilities as a residue attribute
- reset —
- options such as holdSteady can be used with the default position
- moveModels can be used without holdSteady
- set — can enable/disable transparent background for subsequently saved images
- swapaa — added Dynameomics rotamer library
- vina — added options to use a local executable or an alternative Opal web service
- volume — added options to automatically set threshold (contour) level so that the surface encloses a target spatial volume
- vop —
- vop morph optionally interpolates colors if the maps have the same number of coloring thresholds
- vop maximum (new) takes pointwise maximum of input maps
- vop multiply (new) multiplies maps, for example to apply a mask
- vseries — added options to open and close volume series, jump playback to a specific frame, perform various types of processing such as alignment, normalization, cropping, and compression, and save to file in Chimera map format
Notable Bugfixes:
- Write Prmtop now works when using newer force fields
- Chimera menus and dialogs use system font size settings (tested mainly on Linux)
- Fixed bounding box calculation for transformed VRML nodes so that when exported VRML files are read back in, they rotate correctly
- Fixed problem with “missing structure” loop modeling that allowed an extra residue at the C-terminal end of the modeled part to move
- Fixed locking bug in suppport for "chimera --send"
Known Bugs:
- surfaces fail for some structures
- crash on Mac dual display systems. Details.