PyMOL v1.8.2 Release Notes

Release Date: Apr-20-2016

New Settings

  • cartoon_gap_cutoff: draw dashed cartoon over gaps of size < cartoon_gap_cutoff
  • auto_show_classified: When loading a file, show cartoon for polymer, sticks for organic, and spheres for inorganic molecules (Setting > Auto Show... > ... by Classification)
  • ignore_case_chain setting (ignore_case=1 default restored in 1.8.0.5)
  • collada_background_box (off by default, previous versions unconditionally created a large box to mimic the scene background color)

File Import/Export

  • support atom name/resn/segi with more than 4 letters (e.g. from CIF files)
  • MOL2
    • loading
      • improve resn reconstruction from subst_name
      • improve formal_charge guessing
    • export
      • write SUBSTRUCTURE record for chain support
  • MAE loading: sort atoms
  • amber topology loading: set all bond orders to 1 instead of 0

Misc

  • new “Distances between rings” measurement mode in Measurements Wizard
  • new “byring” selection operator
  • new distance mode=4: distance between centroids
  • cartoon representation
    • cartoon dash: New loop-like cartoon type which skips every second segment
    • auto-detect CA-only models for cartoon and ribbon (no cartoon_trace_atoms needed)
  • enable ignore_case and ignore_case_chain for “rms” and “update”
  • grid_mode=3: prid per object-state

Scripting

  • iterate/alter
    • list(s) → list of atom-level setting indices (or atom-state-level settings with iterate_state)
    • improve exception handling and error reporting
    • disable automatic text_type assignment with atom_type_format=”“ (empty string)

Bug Fixes

PyMOL v1.8.2.0-r1 Hotfix Notes (May 2, 2016)

  • fix “A > generate > vacuum electrostatics”
  • MacPyMOL: fix “Get View” button

PyMOL v1.8.2.1 Hotfix Notes (May 27, 2016)

  • fix mutagenesis wizard “No Mutation” (update and rms commands)
  • new setting “pick32bit” allows forcing of 16bit picking
  • fixed pse_binary_dump + pse_export_version<1.77 combination

PyMOL v1.8.2.2 Hotfix Notes (Jun 17, 2016)

  • fix crash with ray tracing very large images
  • fix crash with “align” and atoms without coordinates
  • fix automatic stereochemistry labeling

PyMOL v1.8.2.3 Hotfix Notes (Jul 20, 2016)

  • fix picking bug: wrong picking after re-enabling previously picked objects
  • fix restoring “filter” wizard from PyMOL 1.6 session files
  • fix “scene auto, clear” (Scene > Delete)

PyMOL v1.8.2.4 Hotfix Notes (pending)

  • fix quadbuffer stereo non-black background issue
 
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