PyMOL v2.0 Release Notes

Release Date: September 20th, 2017

Major Changes

  • Unified modern interface
    • PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms
  • Anaconda Python distribution
    • Better third-party plugin and custom scripting support
  • Open access incentive executables with new licensing mechanism

New Features

  • Native retina resolution / 4k display support
  • Dock/undock and rearrange certain panels (Builder, Feedback Browser, Volume Editor)
  • Support for trackpad gestures (pinch for zoom in/out, z-rotate)
  • Dedicated dialogs for opening MAE files, MTZ files, maps and trajectory files
  • New APBS Plugin panel
  • .pymolrc script editor with syntax highlighting
  • Properties editor
  • Improved Draw / RayTrace dialog
  • MPEG-4 and GIF movie export panel
  • Excel exporter plugin (Windows and Mac)
  • Open files by dragging from file browser to PyMOL window
  • wire and licorice representation aliases for combined lines/nonbonded and sticks/nb_spheres
  • New commands: “copy_to” and “uniquify”
  • Single-letter code labels (“label oneletter”)
  • Label Wizard menus for colors and transparency
  • Improved file types registration on Windows (Setting > Register File Extensions)

Settings changes

  • Changed default values for several settings:
    • opaque_background=off
    • cartoon_gap_cutoff=10
    • auto_show_classified=1 (=3 for > 500k atoms)
    • valence=on
    • stick_h_scale=0.4
    • smooth_surface_edges=on

Menu changes

  • “Open Recent” file menu
  • File > New Window opens new PyMOL window
  • Setting > Register File Extensions
  • Plugin > Legacy Plugins
  • New > Pseudoatom > Callout
  • A > Copy to object
  • A > State > Split

Bug fixes

  • Fixed slow performance of “extract” command
  • Better unicode/UTF-8 handling
  • Fixed inconsistent look of labels and connectors on Retina and non-Retina displays
  • Fixed label_relative_mode=2 raytracing
  • Improved Maestro and MOE format compatibility
  • Fixed internal GUI clipping on certain Windows systems with integrated Intel graphics

Updates

PyMOL v2.0.1 Hotfix Notes (Sep 26, 2017)

  • Linux fixes:
    • fix broken Intel HD graphics support
    • fix hardware stereo (PyMOL needs to be launched with -S)
    • disable automatic hardware stereo detection on Linux
  • Windows fixes:
    • add MSVC++ 12.0 runtime dependency
    • add missing mkl library dependency (required for numpy and mtz file loading)
  • enabled file drag to upper command line (inserts file name)
  • Object menu panel labeling: L > residues (oneletter)
  • Help > Email PyMOL Help: pre-populates email with platform details
  • pymol –help: shows location of license file
  • Scenes: fix visible objects inside hidden groups (1.7.6 regression)
  • Cosmetic changes:
    • File > Save > Export ... instead of Save
    • Hide “Edit > Start Dictation” on macOS

PyMOL v2.0.2 Hotfix Notes (Oct 2, 2017)

  • Fixed bugs:
    • ‘create’ command with suspend_undo=off could potentially crash PyMOL
    • File’ → ‘Export PNG’ not intuitive to save prior ray-traced image
    • alignment object was not always available as selection
    • QT_PLUGIN_PATH and PYTHONHOME could interfere with PyMOL startup
  • Windows bug fixes:
    • loading PWG files was broken on Windows
    • APBS and pdb2pqr failed if PyMOL was launched with PyMOLWin or pythonw -m pymol
  • Mac bug fixes:
    • PyMOL could occasionally display OpenGL errors or crash when running on external monitor

PyMOL v2.0.3 Hotfix Notes (Oct 5, 2017)

  • fixed movie export in batch mode (pymol -c)
  • PyMOL.app (macOS): fixed support for case-sensitive file systems
  • PyMOLWin (Windows): fixed support for UNC and and wide character file names
  • Linux bundle does not require /etc/machine-id (fix not sufficient for Ubuntu 14.04)

PyMOL v2.0.4 Hotfix Notes (Oct 13, 2017)

  • Windows: fixed support for “Send to PyMOL” from Maestro (requires 2017-4 and Windows 8+)
  • Windows: Added “Setting > Register with Maestro”
  • Linux bundle does not require /etc/machine-id (Ubuntu 14.04 compatible fix)
  • QT_PLUGIN_PATH and PYTHONHOME could interfere with PyMOL.app/Contents/MacOS/PyMOL
  • fix crash with several “Build” menu entries
  • fix crash with Python 3 while browsing “A” menu

PyMOL v2.0.4_1 Linux Bundle (Oct 20, 2017)

  • LD_LIBRARY_PATH independence

PyMOL v2.0.5 Hotfix Notes (Nov 8, 2017)

  • Windows: fixed support for “Send to PyMOL” from Maestro (Windows 7)
  • fix MPEG4 export with non-black background
  • fix flat cylinder caps with ortho=1
  • fix picking with transparency_mode=3
  • fix loading some elements wrong from SDF and XYZ
  • added MacPyMOL-like shortcuts:
    • Ctrl+S (Save Session)
    • Ctrl+O (Open...)
  • Python 3:

PyMOL v2.0.6 Hotfix Notes (Nov 17, 2017)

  • set working directory when loading script from GUI
  • fix loading some elements wrong from GRO (2.0.5 regression)
  • fix wrong license error message for server connection error
  • Bundle:
 
media/new2.txt
 
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