Milestone 1.6

Deadlines

• Branch and release candidate on web site: Wednesday March 22, 2023
• Production release: May 1, 2023
• Make Chimera release around same time to handle Opal shutdown.

Plans

1. Initial ChimeraX library on PyPi or Conda #1470 (CZI).
2. Investigate and possibly switch to Python 3 limited C API (R01) (waiting for Cython 3.0)
3. Possible update from Python 3.9 to 3.11 (R01) (delay to 1.7 daily builds to give third party developers more time)
4. Chimera to ChimeraX volume session conversion #6505 (CZI).
5. Fetch Cancer Imaging Archive database files #8390 (NIAID).
6. User interface to Phenix "emplace local" cryoEM structure fitting (Phenix R24).
7. Linux flatpak distribution to support more Linux distributions #8187 (R01).

Completed

New GUI tools

• ESMFold GUIs - ESMFold and ESMFold Error Plot for getting and evaluating ESMFold-predicted protein structures (tool equivalents of the esmfold command) #7970 (R01/NIAID)
• Dock Prep GUI - tool equivalent of dockprep command #4794 (R01/NIAID)
• Add Charges GUI - tool equivalent of addcharge command (R01/NIAID)
• Bare-bones Render by Attribute tool - only does coloring based on attribute values, not setting atomic radii, changing tube thickness, or selecting (unlike Chimera version of the tool). The tool will be enhanced in future releases. #5952 (NIAID)

New commands

• Nucleic acid virtual mutation - with the swapna command #5887 (R01)
• Blast Protein sequence input - Blast Protein tool and command allow specifying the query sequence by UniProt ID/name, or as plain text pasted into the dialog or command line #5055 (R01)
• ESMFold protein structure prediction - added esmfold command to predict protein structures from sequence or to fetch pre-computed structures from the ​ESM Metagenomic Atlas #7970 (R01/NIAID)

New options

• Blast from Sequence Viewer - start the Blast Protein tool from the ​Sequence Viewer context menu #5055 (R01)
• Coulombic ESP map - coulombic command option to create a volume model from the computed electrostatic potential (ESP) #3596 (NIAID)
• Surface smoothing - smoothing options added to surface and segmentation surfaces commands (the latter also in the 1.5 release branch) #7870 (NIAID)
• Invert substituent geometry from Build Structure's Invert tab or via "build invert" command

New file formats

• CIF format reader - initial support for reading (uncomplicated) small-molecule CIF files, as well as fetching from the ​Crystallography Open Database and ​Predicted Crystallography Open Database (NIAID) #4479 (NIAID)
• Read SwissDock format #4232 (R01)