Depiction

• Select by attribute GUI - Render/Select by Attribute set to its Select tab can be opened from the Select menu

• Show attribute values with atomic radii - command size byattribute, Radii section in Render by Attribute

• Worms - create specialized cartoons in which "worm" fatness shows values of an attribute (bfactor, seq_conservation, ...) with Render by Attribute or commands worm or cartoon byattribute

• Label models - label command models option

• Model Panel capabilities for rapidly flipping through models - context menu allows adding Next/Previous/Skip controls

Analysis

• Join models generalized to any covalent bond - build join bond allows joining models in the general case (bonds other than peptide); this feature is also available in the Build Structure GUI

• Combine models without changing chain IDs - combine command option retainIds true

• Command to create pseudobonds - pbond command

• View multiple alternate locations at the same time - altlocs show command

• Surface-surface contact area - measure contactarea command to report the area of one surface within a cutoff distance of another surface

• Read PAE files from Alphafold3 - Alphafold Error Plot updated to handle PAE (predicted aligned error) output from Alphafold3

• Batch AlphaFold predictions - New ​commands to set up batch alphafold predictions to predict protein-protein interactions.

• Prototyped UMAP clustering of structure conformations, command diffplot

New file formats

• PDB-REDO fetch - fetch atomic structures from the ​PDB-REDO database using Fetch by ID or the open command

• Fetch/read PDB NMR-STAR format - NMR-STAR restraints can be shown as pseudobonds on associated structures (details...)

• View docking results from MOE - ViewDockX recognizes molecular docking results in Mol2 format from ​MOE

• Save tables as comma- or tab-separated values - various sortable-table dialogs now have a context menu option to Save CSV or TSV File... (e.g. Rotamers, Check Waters, Axes/Planes/Centroids table of objects)

Volume data

• Segmentations tool applies to any volume data - the Segmentations tool for manual plane-by-plane segmentation can be used on any type of volume data (previously only medical images)

• Updates to interactive segmentation - several fixes and usability improvements to the Segmentations tool, including new Medical Image Toolbar icons to easily assign/deassign associated mouse and VR hand-controller modes; implementation of some functions as a segmentations command

• Prototyped local orthoplane volume rendering enhancements for EM tomography, orthopick mouse mode in 1.9 daily build.