Release Date: September 20th, 2017

• 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.

• 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

• “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

• 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

• LD_LIBRARY_PATH independence

• 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:
  • experimental support for pse_export_version
  • fix COLLADA export

• 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)

• prevent crashes due to Python exceptions in Qt threads
• fix “File > Save Session” recent menu update with non-ascii file names
• fix memory leaks with saving session files
• fix loading of PDBQT atom types