Milestone 1.4

New Features

• Compute charges: A command to calculate and assign atomic partial charges and Amber/GAFF atom types
• Dock prep: A tool to assist in the multistep preparation of structures for docking and other calculations: hydrogen and charge addition, removal of alternate atom locations, rotamer “repair” of incomplete side chains, etc. (#4794)
• Model loops: GUI for the loop-modeling command (done)

• Add volume data GUI interfaces (#4306):
  • Morph Map
  • Volume Filter - Gaussian, Median, Bin, Laplacian, Fourier, Scale, Flatten
  • Volume Series
  • Icosahedron Surface

• Surface clip cap GUI - subdivision, color, clip offset, disable

• Replace Opal with REST, ticket #5223

• Update sequence search for larger AlphaFold database.

• Improve bug reporter to cull out useless Windows and Linux crash reports, reduce bug triaging burden.

Done (from Change Log)

• AlphaFold for multimers

• Alternate residue numberings - biopolymer structures from the ​wwPDB can be switched between the residue numberings ​provided by the depositor (author, initial default), ​used internally by the PDB (canonical), or in the UniProt sequence (uniprot). This can be done by using setattr to change the res_numbering model attribute. Example: setattr #1 structure res_numbering uniprot

• Read ZDOCK output - ​ZDOCK quasi-PDB files can be opened with the format zdock option

• User interface toolkit update - switch to Qt 6, currently available separately as a "technology preview build" on the download page. After an appropriate amount of testing, will be incorporated into the regular daily build.

• ModBase target-template alignment and model scores - opening a comparative model from ModBase (mmCIF format) automatically shows the target-template sequence alignment in the Sequence Viewer, and model quality scores can be shown with log metadata

• Independent centers of rotation - added rotate independent mouse mode, automatically assigned by the tile command

• Align sequences with Clustal Omega or MUSCLE - sequence align command and Sequence Viewer context menu allow (re)aligning sequences with web services hosted by the RBVI

• Increment/decrement radii - size command allows changing settings relative to their current values by giving a +/-increment

• AlphaFold Database v2 - the AlphaFold tool and commands alphafold search and alphafold match search the new, larger AlphaFold Database (~800,000 sequences; ChimeraX 1.3 uses database v1 with ~360,000 sequences)

• Animated PNG - added movie output format apng

• AlphaFold Multimer - the AlphaFold tool and alphafold predict command can run multimer predictions on Google Colab (albeit with memory limits on total size)

• Local Modeller execution - The modeller comparative and modeller loops commands now support execution of a locally installed Modeller as an alternative to using the web service ("executableLocation" keyword).

• Edit model panel names/IDs - Model names and IDs can now be directly edited in the model panel by double clicking on the name or ID and entering a new value.

• Define axes - define axis command to calculate best-fit axes (shown as cylinders) that can be used in distance and angle measurements and used to specify vectors in other commands (for example, the axis of rotation for roll)

Infrastructure

Update Qt 5.15 to Qt 6 (#4119).

Native macOS build for ARM CPU (#4663).