VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 13 2008 - 13:07:04 CDT

Hi,
  Just FYI, I've worked through this patch and am rewriting it to make
it more bulletproof for large inorganic structures and for a wider
range of input parameters. The original implementation could crash VMD
if one selected a large enough cutoff distance when a dense silicon
structure was loaded. I hope to have a test version that's more
robust in the next day or so. I'll send a note when I've got a test
build posted.

Cheers,
  John

On Wed, Jul 16, 2008 at 11:20:22PM +0100, FX wrote:
> 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/ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078