PyMOL v2.3 Release Notes

Release Date: Feb 11, 2019

• 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

• 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=”*”

• New cmd.set_raw_alignment() function
• fetch command now async=0 by default

• Bundles with Python 3.7

• 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)

• 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

• 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

• 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

• improve macOS 10.15 compatibility
• fix a ray_volume regression

• fix notarization of the macOS bundle for macOS 10.15
• fix a crash with “pseudoatom; h_add”
• fix loading of PSE with corrupted CGO
• fix loading of PSE with UTF-8 labels (Python 3 version)

• Windows: workaround for https://bugs.python.org/issue40075
• Upgrade FlexLM library