VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Mon Nov 19 2012 - 20:37:26 CST

While it wasn't originally my question, I'm curious. Do you have any theory on why STRIDE might have failed in this case? Also, why, if it fails to calculate secondary structure does it just not appear as opposed to being rendered as random coil?
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of John Stone [johns_at_ks.uiuc.edu]
Sent: Monday, November 19, 2012 6:18 PM
To: Larry Guy
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: VMD can't display new PDB secondary structure properly ( pyMol, jMol can). .

Hi,
  VMD uses STRIDE to compute secondary structure, as it works both
for static structures and can also be used for trajectories.
One change I've been thinking of making would be to have VMD
use the PDB-assigned secondary structure in cases where it's available.
That would give the same behavior you observe in PyMol, for example.
You can override the secondary structure assignments made by STRIDE
using atom selections if you are willing to do some scripting:
 http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 19, 2012 at 05:00:29PM -0500, Larry Guy wrote:
> 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! 

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