VMD-L Mailing List

From: FX (fxcoudert_at_gmail.com)
Date: Wed Jul 16 2008 - 17:20:22 CDT

Hi all,

I've used VMD quite a bit by now, including for hybrid organic-
inorganic systems. For those, it is quite useful to draw the metal
centres as polyhedra, with the neighbours of the metal centre as
corners of the polyhedra. So far, I use scripts to achieve that, but
it's not very intuitive to handle, so I've written a patch to add
this representation "natively" in VMD. I write to the list because I
don't know exactly how patch should be submitted for VMD, and I'd be
happy to have some feedback on the patch itself (it's my first VMD
patch and the first time I write C++, which I am learning for the
occasion).

The polyhedra representation works in the following way: for each
atom of the selection, it looks for all atoms (possibly not in the
selection) of the molecule within a given distance ; when more than 3
atoms are inside the cutoff radius, a polyhedron is drawn with these
atoms as corners. In simple words, the representation draws polyhedra
from atoms surrounding the selected atoms. I have attached a
screenshot of what the result looks like in the case of MOF-5, where
each inorganic unit has 4 Zn atoms (hence 4 tetrahedra) joined by a
common oxygen.

I hope this can make it into the codebase. If there is any legal
aspect to consider (e.g., transfer of copyright), please advise me of
the course to follow.

Thanks,
FX

PS: I'm sending this message a second time, as the first one didn't
appear to make it through (but no error or bounce received... that's
weird). The attachment are not attached this time, but can be found
here:

-- patch: http://www.homepages.ucl.ac.uk/~uccafco/tmp/patch-vmd-
polyhedra.diff
-- screenshot: http://www.homepages.ucl.ac.uk/~uccafco/tmp/MOF-5.png 

-- 
François-Xavier Coudert
http://www.homepages.ucl.ac.uk/~uccafco/