PyMOL v1.8.6 Release Notes

Release Date: March 9, 2017

Incentive PyMOL Only

  • chromadepth improvements:
    • ray-tracing support
    • chromadepth=2: post-lighting and luminance scaled
    • correct linear depth in non-orthoscopic projection
  • surface_smooth_edges: Smooth edges on partial surfaces

Incentive Features moved to Open-Source

  • Protein-Protein interface preset (A > preset > protein interface)

File types

  • fast MMTF load support
  • unrecognized extension raises error instead of handling as PDB
  • added: vdb (VIPERdb), cor (CHARMM), ...


  • CTRL-L ligand zoom (main windows needs to have focus)
  • fetch command
    • new fetch_type_default setting
    • fetch ..., type=mmtf
    • three letter codes → type=cc (e.g. fetch ALA)
  • avoid selection keyword name conflicts: Append underscore to conflicting names
  • added width and height arguments to mpng and movie.produce



  • new fetch_type_default setting
  • new default: ray_transparency_oblique_power=4.0
  • new editor_auto_measure setting: transient measurements in editing mode when more than one atom is picked


  • “update” command: support “current state” (-1)
  • alter elem → update protons and vdw
  • “pluggable” dictionaries of load and save functions (subject to change)

Bug Fixes

  • fix selection indicators rendering problem (affects some Intel HD Graphics chips)
  • connect_mode=4: N-H1 and N-H3 bonds
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