Macs in Chemistry

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Using PYMOL and PLUGINS

I was browsing through the contents of Chemistry Central and I noticed a new plugin for PyMOL called PocketPicker which helps with the identification and evaluation of surface binding pockets in proteins. Many people will be aware of the Python based molecule viewer PyMOL. The current PyMOL Open-Source Source Code is free, and builds on Linux and Mac OS X / X11, it supports plugins, but end-users will need to build the code themselves. The current MacPyMOL builds are free for students & teachers, but a paid subscription is required for use in research (academic or commercial). These builds have the ability to run under both Aqua and X11, BUT plugins are only supported in the latter case.

The standard download affords an executable called MacPyMOL.app this uses Aqua to provide the interface and has a very Maclike look and feel.

pymol

However in this form PyMOL does not support plugins and there are an increasing selection of useful plugins. However it is possible to use the plugins, the trick is to rename the executable from MacPyMOL.app to PyMOLX11Hybrid.app. Right click (or control click) on MacPyMOL and choose Get Info in the Panel change the Name & Extension to PyMOLX11Hybrid.app.

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That will force MacPyMOL to run under X11 using the Tcl/Tk GUI which is compatible with plugins. As seen in the menu bar if you now restart the application.

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Several plugins are included, To add new plugins they need to be added to /Applications/PyMOLX11Hybrid.app/pymol/modules/pmgtk/startup/ To access this folder control-click on the PyMOLX11Hybrid application and select "Show Package Contents" from the dropdown menu and navigate to the desired folder. For example the LIQUID fuzzy pharmacophore model plugin is available here to install expand the archive and copy all file into /Applications/PyMOLX11Hybrid.app/pymol/modules/pmgtk/startup/ Whilst many of the plugins work fine, you may need to amend some file paths, in this case in LIQUID_Plugin.py Change

PATH_PyMOL='~/pymol/'

to

PATH_PyMOL='/Applications/PyMOLX11Hybrid.app/pymol/'

When you restart PyMOL you will find the new Liquid Pharmacophore option in the plugins menu and you can use it to identify and display pharmacophoric features.

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