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

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)

Automatic stereochemistry labeling. Stereo labels can be imported from SDF and MAE files.

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

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

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

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)

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

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:
- add web.pymolhttpd legacy API (alias for pymol.pymolhttpd) (pymol-web-legacy)
- add PWG examples: share/pymol/modules/web/examples (pymol-web-examples)