VMD-L Mailing List

From: Larry Guy (gglarry0_at_gmail.com)
Date: Mon Nov 19 2012 - 18:52:52 CST

It turns out that removing the n-terminal amino acid from the offending
chain fixes the problem. I tried removing other residues and it didn't
help. The mystery remains as to why VMD won't display the entire original
pdb while other programs will. If anybody wants to investigate I can
provide the pdb. Or if you want to start with the original pdb it's 4G7O
and the offending residue is C 64.

Thanks

On Mon, Nov 19, 2012 at 6:30 PM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

> 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!
>