From: FX (fxcoudert_at_gmail.com)
Date: Fri Nov 22 2013 - 07:13:43 CST

Hi John,

> I'm out of town at SC2013 until tomorrow night, but once I return I can
> take a look at this and do tests. If the patch does well in testing,
> then I could definitely apply it and make new test builds with it.

I have finally managed to build VMD on my new laptop: Mac OS 10.9 has two different C++ libraries, and apparently my previous build had somewhat mixed up the two (c++ option -stdlib option, for the posterity).

And itís good that I could test it, because the patch was not enough. Thereís more to be done: while partial random sampling of the atoms of the structure is a good idea, it turns out you cannot use it for scoring, at least now the way itís currently used (in trans_overlap()). An updated patch, which passes my own tests, can be found attached.

Also, given the increase in CPU power, I would recommend increasing the threshold for full symmetry calculation (maxnatoms, defined at line 244 of MeasureSymmetry.C). A full symmetry calculation on a structure with 200 atoms on my laptop takes less than one second, so maybe itís possible to set maxnatoms = 200.

Cheers,
FX