RayMol 1.9.0

RayMol 1.9.0

A feature release: Design mode brings on-device protein sequence design to
RayMol, scenes now remember where you put things, and RayMol gets a startup
script of its own.

Design mode

• Redesign sequences on your Mac — offline. A new Design mode (⌃D),
  peer to Move and Measure, runs ProteinMPNN entirely on-device. Nothing is
  uploaded and no server is involved; the model ships inside the app.
• Per-residue confidence coloring. Color a structure by how well the model
  thinks each position fits the residue that's actually there (Native-fit) or
  by how sure it is of its own pick (Certainty), with a legend and inline
  help.
• Propensity inspector. Hover or pin any residue to see its full
  20-amino-acid propensity distribution, with element-colored side-chain sticks
  previewed on hover — nothing is modified.
• Point mutations with live rescore and repack. Mutate a position and
  RayMol immediately re-scores the sequence and repacks the side chain in
  place. Auto-repack is a toggle, and every edit lands in a working copy you
  can keep or discard.
• Region redesign. Pick a selection and redesign that whole region with the
  rest of the structure held fixed — with one-level revert, and a pill row for
  restricting which amino acids the model may use.

Design mode is macOS-only for now.

Scenes

• Scenes remember object placement. A scene now stores each object's
  Move-mode position and orientation alongside the camera, so recalling it
  restores the arrangement you built — not just the viewpoint. Movies built
  from scenes interpolate that object motion between keyframes.

Startup

• ~/.raymolrc startup script. RayMol now runs ~/.raymolrc (or
  ~/.raymolrc.py) at launch, after the theme defaults so your script can
  override them. Bare cmd.… calls work as they do in the command-line PyMOL.
  If you have a ~/.pymolrc and no ~/.raymolrc, RayMol offers — once — to
  import it; declining is remembered.

Fixes

• Escape exits Move, Design, and Measure mode. Entering a mode by keyboard
  (⌃M / ⌃D) no longer means hunting for a mouse target to leave it. Esc
  dismisses an open sheet or popover first, then leaves the active mode, then
  falls through to clearing the selection.
• Entering Design mode no longer strands the move gizmo. Switching modes
  now runs each mode's real teardown, so the on-screen gizmo can't be left
  behind in the scene.
• A multi-file open loads every file. open a.pdb b.pdb c.pdb, Finder's
  "Open With" on a multi-selection, and dropping several files on the Dock icon
  now load all of them as separate structures instead of just the first.
• Also included for anyone coming from 1.8.0: the 1.8.1 fix for the object
  panel freezing and spamming the log in sessions with many objects or
  selections.

Built on the open-source PyMOL engine. Updates install automatically via the in-app updater (Check for Updates… in the app menu).