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PyMOL v2.5 Release Notes

Release Date: 2021-05-10

Exclusive Incentive PyMOL Features

  • Multi-level undo/redo for all PyMOL actions
  • MAE import: more ribbon styles and label improvements
  • MAE import dialog: discrete states support
  • Builder: Nucleotides from the PDB can now be extended
  • APBS plugin: PDB2PQR 3 compatibility
  • STL export: average normals when exporting
  • `sphere_mode` s 10/11 scaled
  • Builder: “Remove Residue” button added
  • Load collada as CGO

File Import/Export

  • DX binary map import support (*dxbin)
  • PDB/MMTF export: symmetry information now added
  • Improved FASTA import
  • Support for map.gz and mrc.gz extensions

Builder & Panels

  • Builder: Improved fuse command (disallows hypervalent bonds, substitute monovalent atoms instead of attaching to them)
  • Panel: Customizable Keyboard Shortcut Menu
  • Panel: Properties inspector now supports unsetting settings with “Delete” key

Graphics & Visualization

  • Ray interior colors now match primitives with `set ray_interior_color, atomic` 120
  • Isomesh transparency support
  • `sphere_mode` 5 removed (9 as replacement)
  • Curved cartoon cylindrical helices `cartoon_cylindrical_helices=1` (previous =2) . #131
  • Isosurface generation via marching cubes with setting `isosurface_algorithm, (0, 1)` (0 requires VTKm)

PBC Handling

  • Periodic boundary conditions supported in rebond, smooth, and intra_fit


  • Python 2 support removed
  • pbc argument added to rebond, smooth, and intra_fit
  • png(None) returns bytes
  • scene_order() allows list for `names`
  • pbc_wrap() and pbc_unwrap added
  • matrix_reset() supports `state=0` for all states
  • editing_ring() added
  • unset now restores the default value for global settings
  • load_traj now uses state=1 by default
  • get_area command and dots representation: Exclude “flag ignore” atoms

PyMOL v2.5.1 Maintenance Release (2021-07-01)

  • Fix align and related commands output regression
  • Fix crash when moving labels on MacOS
  • Fix quiet argument for png

PyMOL v2.5.2 Maintenance Release (2021-08-20)

  • Fix gromacs file reading
  • Fix movie slider not appearing upon reinitialize
  • Fix debug asserts being fired on Macs

PyMOL v2.5.3 Maintenance Release (2022-07-08)

  • Fix workspace disappearing on specific display resolutions
  • Fix pair_fit crash while undo is active
  • Fix movie commands referencing out-of-bound frames
  • Fix repeating builder undo warning message
  • Fix command name sometimes not appearing in undo menu
  • Fix guide selector bug (submitted by Thomas Holder)
  • Fetch path blacklisted (submitted by Thomas Holder)
  • Fix small-value-included CGOs sometimes not appearing
  • Fix builder crash occurring when sometimes attempting to add residue internally

PyMOL v2.5.4 Maintenance Release (2022-08-17)

  • Fix grid_mode not working in batch mode
  • Fix stalling when creating a program
  • Fix quiet argument for cif file loads

PyMOL v2.5.5 Maintenance Release (2023-03-27)

  • Fix set_name throwing error on success
  • Fix crash when loading discrete object
  • Fix TypeError for Lighting Plugin (later Python versions)
  • Fix Build Residues not working from menu

PyMOL v2.5.6 Maintenance Release (2023-07-06)

  • Fix quiet argument not working on `load_coordset`
  • Fix quiet argument not working in `scene`
  • Fix crash in `find_molfile_plugin` (submitted by Thomas Holder)
  • Fix GIL for `object_ttt` and related functions (submitted by Thomas Holder)

PyMOL v2.5.7 Maintenance Release (2023-10-20)

  • Update RCSB URLs
  • Fix multiple undo not restoring `delete all`

PyMOL v2.5.8 Maintenance Release (2024-01-18)

  • rebond with pbc=1 now rebonds all states in a trajectory by distance.
  • Fix occasional get_sasa_relative crashes
  • Fix failing of get_atom_coords with obj/sele names (submitted by Thomas Holder)
  • Fix GIL issue for get_unused_name (Python 3.12 crashes) (submitted by Thomas Holder)
  • Fix Volume editor Python3.10+ (submitted by Thomas Holder)
  • Fix broken mouse_selection_mode=3 (submitted by Thomas Holder)
  • Bundles now includes patched version of curl/libcurl
  • Fil occasional GIL issue for wizard annotation
  • Mae2PyMOL: Duplicate state titles removed

Upcoming Known Issues to be Fixed

  • Electrostatic demo periodically crashing on Windows
  • 3Dconnexion connection no longer working
  • Ability to disable undo in pymolrc
  • conda commands not working in PyMOL
media/new25.txt · Last modified: 2024/01/18 17:45 by johnson