media:new25
PyMOL v2.5 Release Notes
Exclusive Incentive PyMOL Features
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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)
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Panel: Properties inspector now supports unsetting settings with “Delete” key
Graphics & Visualization
`sphere_mode` 5 removed (9 as replacement)
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Isosurface generation via marching cubes with setting `isosurface_algorithm, (0, 1)` (0 requires VTKm)
PBC Handling
API CHANGES
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)
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)
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