Milestone 1.11

Dark Mode - improve Linux dark mode

Scenes - initial version of ​Scenes tool and ​command to save and restore scenes (view + styles and colors of atoms, ribbons, volume data; more to be added later)

2D Labels and Arrows GUI - ​2D Labels and Arrows tool in menu under Tools... Depiction

Minimization GUI - ​Minimize Structure tool in menu under Tools... Structure Editing

General minimization - the ​minimize command energy-minimizes atomic structures, including nonstandard residues such as ligands, using ​OpenMM

Batch ligand-binding predictions - Predict binding of tens or hundreds of ligands to protein complexes using Boltz 2 in ChimeraX. Demonstration ​video.

Report chirality - the ​chirality command reports the chirality of stereocenters to the Log; see ​limitations...

Save MD plots - ​MD plots can be saved to an image file using the plot dialog's context menu

Boltz 2 structure prediction - structure prediction of proteins, nucleic acids, and small-molecule ligands, with affinity prediction (not available in the previous Boltz 1); details...

Trajectory H-bonds plotting - added plotting the number of hydrogen bonds per frame. Also added the ability to save plotted values (of any kind) to a comma/tab-separated value file, accessed from the plot dialog's context menu.

Trajectory RMSD plotting - added RMSD plotting for trajectories (in addition to the previous plotting of distances, angles, etc.)

New ViewDock interface - previous ViewDockX tool replaced with ​ViewDock tool with similarities to the Chimera version and the ChimeraX ​Blast Protein results, improvements ongoing

Enhanced command line search - Pressing the Alt/Option key while searching the command history with the up/down arrow keys (or control-P/N) will find the typed text anywhere in the command. The Shift key will continue to find the text only at the beginning of the command. Code enhancement courtesy of Roden Luo.

Thermal Ellipsoids GUI - ​Thermal Ellipsoids tool for showing atomic anisotropic B-factors as ellipsoids, axes, etc.