VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 04 2010 - 17:03:59 CDT

Hi,
  You can pick 5 and 6 membered rings like this:
(ringsize 5 from all) or (ringsize 6 from all)

You can also do things with a range of ring sizes, e.g.:
  maxringsize 6 from all

You can also query the Hill-Reilly ring pucker with "$sel get pucker",
which should only return non-zero values for 5- and 6-membered rings,
as I recall.

We don't have an atom selection query for Cremer-Pople parameters
in the atom selection language at present, but in principle it wouldn't
difficult to add. If people would find this useful, I can put it on the
TODO list, long though it already is.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 04, 2010 at 10:46:30AM +0200, Nicolas Sapay wrote:
> Hello,
>
> I need to follow the conformation of a couple of rings (with 5 or 6
> atoms) over a trajectory. The ring conformation can be visualize with
> the paper chain representation but I need to put the data in some text
> file for complementary analysis. Is there a way to get the ring
> conformation and/or the Cremer-Pople spherical coordinates directly from
> the paper chain representation? If not, is there at least an easy way to
> select 5 or 6 membered rings?
>
> Regards,
> Nicolas 

-- 
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