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PyMOL v3.0 Release Notes

Release Date: 2024-03-12

Revamped Top Toolbar

  • View-modifying buttons moved to Top Toolbar
  • Movie button shortcuts removed
  • Presets, Builder, and Scenes moved to Top Toolbar
  • and more…

Revamped Contents Panel UI

  • Contents toolbar now implemented in Python Qt (PyQt/PySide)
  • 3-buttons viewing map revamped
  • and more…

New Scenes Panel

  • Provides list of scenes with thumbnail previews
  • OpenGL/workspace buttons to recall scenes hidden in favor for Scenes Panel
  • Modifying actions easily possible with mouse
  • and more…

New Timeline/Movie Maker (Beta)

  • Movie-maker implemented in Python Qt
  • Movie programs are now implemented as clips rather than consecutive keyframes
  • Keyframes/Clips draggable by mouse
  • Multiple movies feasible with Compositions
  • and more…

New Presets Panel (Beta)

  • Visual presets editable in user-friendly UI implemented in Python Qt
  • Shareable presets via import/export
  • and more…

New 3D Workspace Gizmo

  • Ability to translate and rotate objects in the workspace
  • and more…

API Changes

PyMOL v3.0.1 Maintenance Release (2024-04-03)

  • Fix Gizmos rendering to thumbnails and exported movies via Timeline
  • Fix interpolation bars not updating when moving summary keyframes
  • Fix subtracks not deleted after requesting for track to be deleted
  • Fix errors from opening Morph Wizard in Panel menu
  • Fix errors from using the Render GUI to modify resolution
  • Fix label backgrounds not showing
  • Nested groups temporarily flattened until permanent resolution
  • Fix disappearance of some menus in the Contents panel
  • Fix conda commands not working in PyMOL command line

PyMOL v3.0.2 Maintenance Release (2024-04-10)

  • Fix duplication of State (Global) tracks in Timeline
  • Fix additional interpolation bar updates
  • Fix `morph` → `to object` submenu not listing objects
  • Fix `get_sasa_relative` command not working
  • Fix Timeline panel not opening when selecting New/Edit Composition
  • MTZ files now loaded properly on Windows
  • Fix grid_slot -2 rendering fullscreen
  • Fix sequence viewer not updating when object(s) are disabled.

PyMOL v3.0.3 Maintenance Release (2024-05-01)

  • Fixed issue where files could not be opened from MacOS finder.
  • `.sdfgz` now importable (`.sdf.gz` was already importable)
  • Fixed issue where non-ASCII characters in `.cms` files could not be read

PyMOL v3.0.4 Maintenance Release (2024-07-31)

  • Fixed issue where exporting PNG sequences only exported a single image.
  • Fixes Fullscreen mode which now hides toolbar and contents panel
  • Fixed wizard button toggling.
  • Fixed some crashing issues when attempting to display gizmos for non-molecular objects.
  • Fixed volume rendering displaying incorrectly.
  • Middle-click focus on contents panel added
  • Fixed crashes on surface_type 5, 6 (may still display incorrectly however)
  • Fixed various issues when using contents panel.
  • Fixed slow performance when using Timeline or contents panel with trajectories

PyMOL v3.0.5 Maintenance Release (2024-10-08)

  • Fixed crashes that occur with ligand cartoon preset and other procedures involving atoms with indeterminate coordinate values.
  • Fixed Gizmos not appearing in transparency mode 3
  • Fixed interpolation bars not updating when summary keyframes are moved in the Timeline
  • Fixed Timeline programs not loading their custom, overridden animation values
  • Fixed transparency and lighting for semi-transparent CGO spheres
  • Fixed Numpy 2.0 compatibility issues when loading hypothesis.xyz files.
  • Fixed crash when choosing “volume_color” when making movie (not currently available)
  • Fixed some crashes when cut, copying, pasting keyframes and programs to tracks.
  • Fixed off-by-one state storing in state-related programs
  • Fixed sped-up or slowed-down clips not colliding properly with other Timeline elements
  • Fixed transformed objects not being ray-traced sometimes
  • Fixed Scene keyframes inadvertently adding onto a state track for object targets.
media/new30.txt · Last modified: 2024/10/09 15:14 by johnson