From: John Stone (
Date: Fri Nov 22 2013 - 14:43:21 CST

  The changes seem logical to me in my reading through your patch.
I will commit this to CVS so that you and I and Jan can continue
testing and validating it, and it will show up in the next test
builds I produce. So long as we don't find any problems we'll use
this version of the code.


On Fri, Nov 22, 2013 at 02:13:43PM +0100, FX wrote:
> 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 it?s good that I could test it, because the patch was not enough. There?s 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 it?s 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 it?s possible to set maxnatoms = 200.
> Cheers,
> FX

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