PyMOL v2.4 Release Notes

Release Date: 2020-05-20

Exclusive Incentive PyMOL Features

  • 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 error
  • Fix: cmd.get_bonds() state off by one
  • Change: cmd.slice_new(): if the provided name is the same as a previously existing 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

PyMOL v2.4.1 Maintenance Release (pending)

    • 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%
  • mmCIF connect_mode=4: Ignore conflicting “_chem_comp_atom.alt_atom_id”
  • Fix isomesh selection=all
 
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