VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 13 2008 - 18:14:03 CDT

Hi,
  I've implemented a revised version of the polyhedral representation
that made the code portable, and reduces the chances of crashing VMD
in various cases. It still needs more work to greatly reduce the
amount of memory consumed for the graphics geometry it generates for
large structures, but it should be fine for people to try out now.
I've posted test builds of the latest version which includes the
new polyhedral representation on the VMD alpha directory in biofs,
described here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Give it a spin and let me know how it goes. I'll continue working
on the graphics part of the code to reduce memory consumption for
large structures, but it should be quite usable on small things already.
  
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