VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 21 2005 - 16:40:07 CDT

Hi guys,
  I get the same behavior, so clearly VMD doesn't like something
about that part of the structure. I haven't had an opportunity to
fully trace through the code, but what you suggest or something along
those lines may indeed be the source of the problem.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 20, 2005 at 03:34:14PM -0600, Chang, Christopher wrote:
> Wei,
>
> It's telling that the problems are with the backbone-dependent representations. It looks like it's related to the presence of an disulfide bond between the two Cys 229 residues. Perhaps VMD is treating the entirety of chain B as part of the CysA229 side chain, at least on some level? Anyway, if I decrease the x coordinate of the chain A Cys229 sulfur atom by 1 (thereby moving it out of the distance for which VMD finds a bond), then chain B displays normally.
> Perhaps the developers can shed further insight...
>
> Chris
>
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu
> > [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> > Of Wei Chen
> > Sent: Wednesday, April 20, 2005 1:21 PM
> > To: vmd-l_at_ks.uiuc.edu
> > Subject: vmd-l: representation_problem
> >
> >
> > Hi,
> >
> > I met a problem with VMD. When I loaded 1E4K.pdb in VMD and
> > chose Cartoon or
> > Tube representation, chain B could not be shown. Only when I
> > deleted Cys229 of
> > chain A, chain B could be shown in Tube. I checked this in
> > detail. And I found
> > this probably is due to a large turn from Pro230 of chain A
> > to Cys229 of chain
> > A.
> >
> > Does anybody have this situation?
> >
> > Wei Chen
> >
> > --
> >
> >
> > 

-- 
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