Branch and release candidates: Discuss October 24, 2023.

Completed

New graphical user intefaces

• Map Filter tool - Map Filter graphical interface to several kinds of map filtering and transformation (Gaussian, Laplacian, etc.)
• Bond angle GUI - the Adjust Angles section of Build Structure can be used to modify bond angles and other angles defined by three atoms
• Bond rotation GUI - the Adjust Torsions section of Build Structure can be used to modify torsion angles; one way to add a torsion to this interface is by control-double-clicking a bond and choosing "Adjust Torsion" from the resulting pop-up menu
• File→Fetch By ID menu item has been added to conveniently fetch atomic structures, density maps, and protein sequences from online sources.
• Medical imaging. Slice view and 2d and 3d segmentation tool (Zach). #9677, #8997, #9720

New file fetching, opening and saving capabilities

• Fetch EMDB map + fit structures - if the EMDB map metadata refers to fit models, the corresponding atomic structures can be fetched in the same open command with fits true or by specifying the fetch source as "emdb_fits"
• Combine sessions - opening a session with the open command option combine true (e.g.,"open session-file.cxs combine true") merges the incoming session with the current session instead of closing it first. Model IDs in the incoming session may be changed to avoid duplicate ID numbers. Please report any bugs you encounter with this feature, since some tools may need further enhancements to work correctly when combining sessions.
• ViewDockX starts automatically - by default, opening a file recognized as ligand docking results shows the ViewDockX tool
• mmCIF reader - memory leak fixed
• Fetch by IUPAC name - IUPAC name translation to SMILES using a ​web service provided by the Centre for Molecular Informatics (University of Cambridge) followed by the existing SMILES fetch process; available in the open command and Build Structure tool
• Save Blast results to TSV file - button added to save all Blast Protein results as a tab-separated values file

Improved mouse, trackpad, keyboard shortcut interactions

• Z-translation with mouse - additionally pressing the Ctrl key when using a translation mouse mode (translate selected models, move picked model, etc.) switches to Z-translation
• Centering mouse mode - mousemode function added to center the view on the clicked item
• Invert selection in selected models - option to invert the selection but only within the selected models added to the Select menu and available as right/left arrow shortcut (Shift-right/left arrow to invert in all models)
• Easy selection inversion - the left/right arrow keys will invert the selection (same as Selection→Invert menu item)
• Voice interface initial study to produce commands for VR (Zach) #9737

New commands and command options

• Rotate view to Z-align centroids of two sets of atoms - view zalign option can take two sets of atoms separated by inFrontOf keyword to align their geometric centers front to back (previously required exactly 2 atoms)
• Adjust default settings for new maps - volume defaultvalues command allows setting user defaults for subsequently opened maps
• Better separation of trackpad multitouch zoom and rotate - pinch-zoom and twist can no longer occur simultaneously; the gesture will be interpreted as one or the other rather than both
• Copy settings from one atomic structure to another - mcopy command implemented
• Save GLTF options - new options for saving GLTF: whether to cull surface backfaces, omit per-vertex colors when an entire object is a single color, and omit normal vectors (show triangles as facets instead of smooth-shaded)
• Save info to file - saveFile option added to the info command file (e.g., one can save a list of the selected atoms to a file)

Infrastructure improvements

• Python 3.11 updating from from Python 3.9 used in ChimeraX 1.6.
• Task manager for long running calculations. Allow canceling. (Zach) #7094
• OpenXR virtual reality protocol supported in addition to SteamVR for display and meetings (Tom) #9640