In case you are a user of (free via MacPorts) PyMOL and haven’t heard the news, the upgrade to the latest Mac OS X release—Yosemite (10.10)—breaks the installation process. Which really sucks because you ideally need to reinstall the ports collection after upgrading (or fresh installing) to Yosemite. Thankfully, the port maintainer finally posted a temporary fix to get things working in the interim until the port can be properly updated. However, it may not be the most intuitive fix for everyone to employ.

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As I’ve mentioned previously, some of the command line tricks for batch processing PDB coordinates for electrostatics models throw some errors back at you, although they don’t implicitly prevent you from using APBS. They just make the surface models look a bit ugly, as you’ll have conflicting charges confined in an unnatural environment, yielding bizarre electrostatics representations (I’ll have to generate an image sometime).

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So, in a slight change of events, instead of the typical personal blog posts I’ve been doing lately, I feel a need to make a more technical one. Either for others’ benefit or for my own, in the event I happen to lose said notes on how to do this stuff. In any case, these are the summation of online searches, trial & error, and a bit of ingenuity in other random spots, all directed towards the generation, editing, and mapping of surface electrostatics maps on structural models of crystallized proteins. I’ll drop in cited links when I can, pending whether or not I can track some of them down again!

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