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PyMOL Changelog

What's new in PyMOL 3.0.2

Apr 11, 2024
  • 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.

New in PyMOL 2.5.5-496 (Apr 12, 2023)

  • 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

New in PyMOL 2.5.2-294 (Aug 21, 2021)

  • Unified modern user interface:
  • PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms
  • Anaconda Python distribution:
  • Better third-party plugin and custom scripting support
  • Open access incentive executables:
  • Liberal evaluation policy

New in PyMOL 2.5.1-283 (Jul 1, 2021)

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

New in PyMOL 2.5.0-279 (May 10, 2021)

  • 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
  • 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

New in PyMOL 2.4.1-213 (Sep 23, 2020)

  • Looking Glass:
  • Add mouse interactions
  • Add “Display > Looking Glass” toggle to hide the LG window
  • Set line_smooth=off for better performance
  • On Windows, handle display scaling >100%
  • Support changing background color (bg_color)
  • mmCIF connect_mode=4: Ignore conflicting “_chem_comp_atom.alt_atom_id”
  • Fix isomesh selection=all
  • Fix isosurface ray_color_ramps regression (#115)
  • Fix isosurface isolevel regression

New in PyMOL 2.4.0 (May 20, 2020)

  • Exclusive Incentive PyMOL Features:
  • Support for Looking Glass Holographic Displays
  • New pi_interactions command finds Pi-Pi and Pi-Cation interactions (A > find > pi-interactions)
  • New WaterMap result presets (A > preset > WaterMap ...)
  • APBS Plugin: Support multi-state assemblies without splitting states
  • APBS Plugin: Support for `–with-ph=6.0 –ph-calc-method=propka`
  • MAE import: Consider `pdb_literal_names` setting
  • Desmond virtual site handling improved (pseudo-atoms hidden by default, won’t affect polar contacts)
  • Trajactory Handling:
  • Trajectories show states slider by default (even without a movie defined)
  • Load_traj: support netcdf format
  • Load_traj: support `selection` argument with all file formats
  • CCP4/MRC Map Support:
  • Distinguish .ccp4 and .mrc extensions (respect file format differences regarding origin)
  • Ignore N*START when loading MRC files with ORIGIN
  • .map extension: auto-detect the format
  • Uncategorized:
  • New distance mode 8 for distance to vdW ratio cutoff (for clashes)
  • MMTF export: Consider `pdb_retain_ids` setting
  • GLTF export (based on collada2gltf)
  • New “header” command in PWG language (e.g. “header add Access-Control-Allow-Origin *”)
  • New “internal_gui_name_color_mode” setting
  • MPEG4 Movie export: Apply `movie_fps` setting to exported file
  • Python API:
  • Improved error handling with exceptions. Error messages are now captured in the exception instead of printed directly to standard out. E.g. a plugin could catch selection errors and handle them gracefully.
  • New: cmd.rebond()
  • New: cmd.get_capabilities()
  • Cmd.fit() et al.: raise on errorFix: cmd.get_bonds() state off by one
  • Change: cmd.slice_new(): if the provided name is the same as a previously ex
  • Isting name of an object which is not a slice, the command will now result in an error.
  • Launch Options:
  • Restore “-V” launch argument for external GUI height
  • MacOS: “open” event opens new window
  • Graphics Drivers:
  • Do not blacklist “nouveau” driver
  • Bug Fixes
  • Eliminate selector word length limit
  • Objects inside hidden groups flash in scene movie
  • Handle “missing” CA atoms when building amino acids (fuse command)
  • MacOS: fix Zalman (byrow) stereo
  • Windows: workaround for crashing legacy plugins on window resizing (https://bugs.python.org/issue40075)
  • Fix secondary structure selection in builder wizard mode
  • Fix crash with pseudoatom state=0
  • Fix cmd.create(discrete=1) with multi-state input
  • Fix cmd.select_list() with state>0
  • Apply ignore_case more consistently

New in PyMOL 2.3.4 (Feb 26, 2020)

  • improve macOS 10.15 compatibility
  • fix a ray_volume regression

New in PyMOL 2.3.3 (Feb 26, 2020)

  • fix cmd.load_raw(format="mmtf") with Python 3
  • MMTF: avoid crash with optional groupType fields (MMTF v1.1dev feature)
  • fix plugin manager utf-8 metadata
  • Plugin installation: ignore "tests"
  • fix file dialogs for macOS 10.15 (don’t use native dialogs)
  • fix Zalman stereo on macOS
  • volume panel: handle pos < 0.0

New in PyMOL 2.3.2 (Feb 26, 2020)

  • fix stick_transparency ray tracing
  • fix crash clicking lower command line
  • fix isomesh draw
  • MAE export: fix blank (space) chain identifier export
  • macOS: no XQuartz dependency for Plugin Manager

New in PyMOL 2.3.1 (Feb 26, 2020)

  • Windows: fix SSL certificate location for HTTPS
  • Handle Python 2 pymolpluginsrc syntax error
  • MAE import: distinguish undefined (<>) and string with value “<>”
  • MAE export: write undefined properties as <>
  • MAE export properties: b-factor, partial charge, ANISOU

New in PyMOL 2.3.0 (Feb 26, 2020)

  • Features:
  • Atom-level cartoon transparency
  • Fast MMTF export
  • Sequence viewer: display gaps (seq_view_gap_mode)
  • Load alignment files as alignment objects
  • Save alignment files for Nucleic Acids (clustal aln format)
  • Read origin from MRC 2000 maps
  • Reimplemented pdb_use_ter_records
  • Features (Incentive PyMOL only)
  • Builder panel: Nucleotides
  • APBS plugin: support RNA out-of-the box (use residue names RA, RC, RG, RU)
  • MAE user label support
  • MAE import dialog: Expose “Multiple entries” option
  • Properties are loaded by default now (new settings defaults):
  • load_object_props_default=”*”
  • load_atom_props_default=”*”
  • API:
  • New cmd.set_raw_alignment() function
  • fetch command now async=0 by default
  • Runtime (conda packages)
  • Bundles with Python 3.7
  • Bug Fixes:
  • Picking with use_shaders=off and lines/nonbonded
  • Display SPC waters in presets
  • Don’t ignore insertion codes when reading CMS files
  • Ambient occlusion random patchiness
  • dynamic_measures updated when doing alignments
  • fix “rebuild” memory leak
  • MPEG4 export pixelated (anaconda::ffmpeg vs. conda-forge::ffmpeg)
  • legacy plugins: fix crash with modal dialogs (macOS and Windows)

New in PyMOL 2.2.3 (Nov 15, 2018)

  • Driver hotfix (improved): precomputed_lighting for Intel driver 24.20.100.*
  • Ignore BOM (unicode byte order mark) in license files
  • Fix pip wrapper

New in PyMOL 2.2.2 (Oct 15, 2018)

  • Driver hotfix: precomputed_lighting for Intel HD Graphics 620
  • Detect display HiDPI change (e.g. when unplugging mirrored display)
  • MacOS: Gatekeeper friendly license location fallback: “/Library/Application Support/Schrodinger/licenses”

New in PyMOL 2.2.0 (Jul 24, 2018)

  • Features:
  • MAE export with basic styling (color, representation, labels)
  • MAE export with group hierarchy
  • Nucleic acid mutagenesis wizard
  • Features (Incentive PyMOL only):
  • MAE export with properties
  • Stereochemistry (”stereo”) labeling with RDKit or $SCHRODINGER backend (external dependencies)
  • GUI:
  • Grouping in object menu: A > group > ...
  • Secondary structure update from sequence viewer: right-click > ss > ...
  • Atom right-click > object > disable others
  • API:
  • cmd.get_fastastr() per chain
  • cmd.get_fastastr() for nucleic acids
  • Runtime (conda packages):
  • Anaconda 5.0.0 build environment
  • Python 2.7 and 3.6 for all platforms (Windows, Linux, macOS - 64bit)
  • Open-Source PyMOL Updates:
  • Moved code repository to github
  • Ported graphics shaders and related code from Incentive PyMOL:
  • improved labels: multiline support, background color, connectors (various label_* settings)
  • support for background images (bg_image_filename)
  • Order-independent transparency (transparency_mode 3)
  • fixes stick_ball setting
  • fixes “lines” crash with certain low-end graphics drivers
  • Bug Fixes:
  • selection with double wildcard (A*B*C) https://sourceforge.net/p/pymol/bugs/209/
  • APBS plugin: 4-digit coordinate handling (e.g. x >= 1000.0)
  • SDF export: don’t write zero-order bonds
  • anaglyph stereo in batch mode https://sourceforge.net/p/pymol/mailman/message/36301454/
  • distance measurements between states with all_states=on

New in PyMOL 2.0.7 (Jan 20, 2018)

  • Major Changes:
  • Unified modern interface
  • PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms
  • Anaconda Python distribution
  • Better third-party plugin and custom scripting support
  • Open access incentive executables with new licensing mechanism
  • New Features:
  • Native retina resolution / 4k display support
  • Dock/undock and rearrange certain panels (Builder, Feedback Browser, Volume Editor)
  • Support for trackpad gestures (pinch for zoom in/out, z-rotate)
  • Dedicated dialogs for opening MAE files, MTZ files, maps and trajectory files
  • New APBS Plugin panel
  • .pymolrc script editor with syntax highlighting
  • Properties editor
  • Improved Draw / RayTrace dialog
  • MPEG-4 and GIF movie export panel
  • Excel exporter plugin (Windows and Mac)
  • Open files by dragging from file browser to PyMOL window
  • wire and licorice representation aliases for combined lines/nonbonded and sticks/nb_spheres
  • New commands: “copy_to” and “uniquify”
  • Single-letter code labels (“label oneletter”)
  • Label Wizard menus for colors and transparency
  • Improved file types registration on Windows (Setting > Register File Extensions)
  • Settings changes:
  • Changed default values for several settings:
  • opaque_background=off
  • cartoon_gap_cutoff=10
  • auto_show_classified=1 (=3 for > 500k atoms)
  • valence=on
  • stick_h_scale=0.4
  • smooth_surface_edges=on
  • Menu changes:
  • “Open Recent” file menu
  • File > New Window opens new PyMOL window
  • Setting > Register File Extensions
  • Plugin > Legacy Plugins
  • New > Pseudoatom > Callout
  • A > Copy to object
  • A > State > Split
  • Bug fixes:
  • Fixed slow performance of “extract” command
  • Better unicode/UTF-8 handling
  • Fixed inconsistent look of labels and connectors on Retina and non-Retina displays
  • Fixed label_relative_mode=2 raytracing
  • Improved Maestro and MOE format compatibility
  • Fixed internal GUI clipping on certain Windows systems with integrated Intel graphics

New in PyMOL 2.0.6 (Nov 17, 2017)

  • set working directory when loading script from GUI
  • fix loading some elements wrong from GRO (2.0.5 regression)
  • fix wrong license error message for server connection error
  • Bundle:
  • add web.pymolhttpd legacy API (alias for pymol.pymolhttpd) (pymol-web-legacy)
  • add PWG examples: share/pymol/modules/web/examples (pymol-web-examples)

New in PyMOL 2.0.5 (Nov 9, 2017)

  • Windows: fixed support for “Send to PyMOL” from Maestro (Windows 7)
  • fix MPEG4 export with non-black background
  • fix flat cylinder caps with ortho=1
  • fix picking with transparency_mode=3
  • fix loading some elements wrong from SDF and XYZ
  • added MacPyMOL-like shortcuts:
  • Ctrl+S (Save Session)
  • Ctrl+O (Open...)
  • Python 3:
  • experimental support for pse_export_version
  • fix COLLADA export

New in PyMOL 2.0.4 (Oct 14, 2017)

  • Windows: fixed support for “Send to PyMOL” from Maestro (requires 2017-4)
  • Windows: Added “Setting > Register with Maestro”
  • QT_PLUGIN_PATH and PYTHONHOME could interfere with PyMOL.app/Contents/MacOS/PyMOL
  • Fix crash with several “Build” menu entries
  • Fix crash with Python 3 while browsing “A” menu

New in PyMOL 2.0.3 (Oct 11, 2017)

  • Windows fixes:
  • add MSVC++ 12.0 runtime dependency
  • add missing mkl library dependency (required for numpy and mtz file loading)
  • enabled file drag to upper command line (inserts file name)
  • Object menu panel labeling: L > residues (oneletter)
  • Help > Email PyMOL Help: pre-populates email with platform details
  • pymol –help: shows location of license file
  • Scenes: fix visible objects inside hidden groups (1.7.6 regression)
  • Cosmetic changes:
  • File > Save > Export ... instead of Save

New in PyMOL 1.4.1 (Aug 12, 2011)

  • fixed shader bug