General Changes:
- AmberTools updated to version 17
- EDS fetch uses PDBe instead of the Uppsala Electron Density Server
- EMDB fetch uses Chinese mirror site for .cn hosts
- PDB/mmCIF fetch uses www.rcsb.org instead of www.pdb.org
- updated Indiana SMILES info URL
- identify fetched EDS difference map as signed data (automatically display both positive and negative isosurfaces)
- try to handle Relion 2.0 MRC files that have uninitialized data for origin
- file browser initial location reset by most recent of: cd command, session file opened, or system command-line startup (non-Windows), in addition to open/save with file browser
- “click-to-center” mouse mode (default Ctrl-right button) uses surface vertex instead of entire surface
Tool Changes:
- Add Charge (Structure Analysis, Structure Editing) — precalculated charges from the Amber Parameter Database used for NAD and NDP
- Morph Conformations (Structure Comparison) — option to set core fraction used in hinge detection
Command Changes:
- addcharge — precalculated charges from the Amber Parameter Database used for NAD and NDP
- clip, thickness — automatically push the back plane slightly behind the front plane if their positions would have been reversed
- hbonds (findhbond) — lineType option to make H-bond pseudobonds dashed, dotted, etc. instead of the default solid lines
- morph — option to set core fraction used in hinge detection
- setattr — ~setattr changed to delete the attribute rather than to set it to no value; no value can be specified as none with the setattr command instead
Notable Bug Fixes:
- Mol2 output includes metal-coordination bonds
- Dock Prep consistent handling of alternate locations in adjacent residues
- fixed VRML output for labels with spaces (e.g., residue labels)
- fixed PIL initialization bug that occasionally prevented Chimera from starting
- Updated SSL libraries so that Chimera can successfully contact "https" URLs
Known Bugs:
- surfaces fail for some structures