VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 12 2008 - 00:22:46 CDT

Hi,
  I'll need to make some fresh builds with the cyclic rendering
code as my last ones are somewhat stale presently.
I'm finishing a paper so I won't have time to do new builds of the
cyclic rendering code until next week. In the mean time, if
you want to see what they look like, you'll want to check out
Amarda Shehu's page at Rice, she was the first person to use the
cyclic renderings in VMD and has a nice paper with images created
using a number of VMD's sophisticated features along with the
test version of the cyclic structure rendering capability:
  http://www.cs.rice.edu/~shehua/
  http://www.proteinscience.org/cgi/content/full/17/3/482

Cheers,
  John

On Wed, Jun 11, 2008 at 11:30:05AM -0700, Rabab Toubar wrote:
> Hi Prof. Stone,
>
> Thanks a lot for your reply. Sure would like to try it out and see how the results look like. So when do you expect this to be included in the released version?
>
> Thanks
> Rabab
>
> --- On Wed, 6/11/08, John Stone <johns_at_ks.uiuc.edu> wrote:
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: psf generation of circular proteins
> To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> Cc: vmd-l_at_ks.uiuc.edu
> Date: Wednesday, June 11, 2008, 11:18 AM
>
> Hi Rabab,
> The released production versions of VMD aren't able to render
> cyclic structures quite correctly. I have an experimental build
> of VMD that handles cyclic structures that you can try out if you
> like, but I'm still working on perfecting this code and integrating
> it into the main source tree. It's not quite done yet. Let me know
> if you want to try it out.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Jun 08, 2008 at 07:36:00AM -0700, Rabab Toubar wrote:
> > Dear Sirs,
> >  
> > I generated the psf file of a circular protein manually using VMD. On
> visualization, I noticed that the protein is no longer circular (open at one
> end), and some of the bonds are not connected. Is there a way to do this right,
> especially when I noticed that from the archives it is tricky using VMD with
> circular proteins.
> >  
> > Thanks
> > Rabab
> >
> >
> >
> --
> 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
>
>
> 

-- 
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