General Changes:
- AmberTools updated to version 14 (new force field, etc.)
- Fetch by ID now includes PDB biounit, CATH domain
- “ligand” definition expanded to include residues that are bonded to a chain but not in the chain's main sequence (e.g., retinal in rhodopsin, glycosylations)
- protein SSE (helix, strand, or other) inserted into ↑↓ selection cascade between residue and connected set of atoms
- keyboard shortcuts rn, rp, ri to shift selection to next residue in chain, previous residue in chain, and to include intervening residues, respectively
- New Molecules preferences —
- option to show/hide atoms added
- reorganization, graying-out to clarify which settings are overridden by smart initial display
- Reply Log shows more information about accessed web services (software version, etc.)
- structure-derived amino acid substitution matrices SDM, HSDM added (more choices for MatchMaker and Multalign Viewer alignment scoring and AL2CO sum-of-pairs conservation calculations)
- added green-magenta (trioscopic) stereo mode
- new input format: COLLADA (.dae)
New Tools:
- RR Distance Maps (Structure Comparison) — create a protein contact map color-coded by distance (and/or standard deviation, if comparing multiple structures)
Tool Changes:
- Add Charge (Structure Editing) — force field options changed, new default: Amber ff14SB (same charges as ff12SB, but different sidechain dihedral restraints, thus mainly affects any subsequent minimization)
- Axes/Planes/Centroids (Structure Analysis) — can center and align chosen axis or chosen plane's normal vector along X,Y, or Z
- Modeller comparative modeling interface (called from Multalign Viewer) —
- new options: thorough optimization, specify distance restraints file
- Multalign Viewer (Sequence) —
- RMSD header renamed “RMSD: ca”, additional headers “RMSD: backbone” and “RMSD: full” available
- can map feature annotations from the NCBI Conserved Domain Database (CDD) onto a sequence
- regions can be included/excluded from the Region Browser listing based on data source (UniProt, CDD, Chimera built-in)
- shortcut to associate all members of a structural ensemble with the same sequence (supplants tedious one-by-one approach)
- searching by full or partial sequence name added to Edit menu
Command Changes:
- addcharge — force field options changed, new default: Amber ff14SB (same charges as ff12SB, but different sidechain dihedral restraints, thus mainly affects any subsequent minimization)
- mda (MultiDomain Assembler) —
- assigns attributes for custom-coloring BLAST hits (potential templates) by BLAST score, %ID, etc.
- shows the BLAST sequence alignment and the Modeller dialog
- provides additional options for limiting hits
- open —
- PDB biological assembly fetch, prefix biounitID:
- CATH domain fetch, prefix cath:
- rainbow — can assign a unique color to each helix and/or strand in a protein chain
- set —
- set echo (new) echoes command-file lines in the Reply Log and status line as they are executed, along with line numbers
- sop —
- sop smooth (new) smooths surfaces by moving each vertex toward the average position of its neighbors
- volume —
- dumpHeader option to write MRC or CCP4 file header contents to the Reply Log
- toggle to show volume models that are hidden, hide those that are shown
- vop —
- vop gaussian can use different half-widths along X,Y,Z
- vop mininum (new) takes the mininum values pointwise from two or more input maps
- vop ridges (new) skeletonizes a map by emphasizing ridges or filamentous structures in the density
- vop scale normalization options:
- rms - scale to give the specified root-mean-square
- sd - shift to zero mean, then scale to give the specified root-mean-square
- vseries —
- vseries measure (new) tracks volume series surface area, enclosed volume, centroid position
Notable Bugfixes:
- surfaces read from STL files are saved in sessions
Known Bugs:
- surfaces fail for some structures