Science Blog of Dr. Yuan分享 This blog is mainly on Molecular molecular modelling and simulations


PyMOL 1.8.6 released

已有 2658 次阅读 2017-3-10 05:36 |系统分类:科研笔记

Source Code:

PyMol sponsors using SUSE Linux or openSUSE can download the CenOS version from: needed to be installed, and it can be obtained from here.

Tips for NVIDIA Optimus card:

The new version of PyMol might not work properly with Nvidia Optimus card. This problem can be solved with the following methods:

making soft link of libGL**.** pointing to the latest Nvidia library:









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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