VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 19 2012 - 21:02:20 CST

Hi,
  I think Brian's explanation is indeed the cause of this particular failure,
or at least that's the cause on my Windows laptop (which is the only
machine I can test on while I'm traveling). I'm not sure why STRIDE
thinks there are so many H-bonds, but I'll probably have to wait on that
until I get back home and have a better test environment for deteremining
what STRIDE is doing and why.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 19, 2012 at 08:03:29PM -0600, Martin, Erik W wrote:
> I actually enjoy a good mystery, and downloaded this structure, wrote the C chain to its own pdb and loaded it alone to see if it would solve the problem... it did not (hence my not posting anything). There are also no odd indicies or names that would obviously cause a stride error. I'm stumped, and am really curious to see if anyone comes up with an explanation.
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Bennion, Brian [Bennion1_at_llnl.gov]
> Sent: Monday, November 19, 2012 5:30 PM
> To: Larry Guy; vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: VMD can't display new PDB secondary structure properly ( pyMol, jMol can). .
>
> Could it be that stride gives and error if the selection is too big? There is a limit of 10000 hbonds. Not sure how the other viewers calculate the cartoons.
>
> brian
>
>
> ________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Larry Guy [gglarry0_at_gmail.com]
> Sent: Monday, November 19, 2012 2:00 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: VMD can't display new PDB secondary structure properly (pyMol, jMol can)
>
> Hi all,
>
> I hope that somebody here can help me solve a mystery regarding a newly released pdb 4G7O. Chain C of this protein can't be visualized using the ribbons or cartoon representations. Some smaller sections of chain C that I have removed and put in to a new pdb files show up fine in new cartoon representation. pyMol, jMol and other visualization software packages handle this structure with no problems, displaying all of chain C.
>
> What could be happening in VMD that would cause this kind of problem in the cartoon representation of chain C?
>
>
> Thanks in advance for your help!
>
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
> 

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