VMD-L Mailing List

From: Nathan C. Rockwell (ncrockwell_at_ucdavis.edu)
Date: Fri May 25 2007 - 11:20:57 CDT

On 5/24/07 7:15 PM, "Stern, Julie" <jvstern_at_bnl.gov> wrote:

> Hello,
> I've built a non-standard residue and I'm having troubling viewing it with
> vmd. It won't show
> up as connected to the standard residues at all. The tube representation
> doesn't show anything.

That will vary depending on the representation; things like Ribbons invoke a
call to STRIDE to assign the secondary structure, and STRIDE won't know what
to do with your creation.

> The sequence viewer doesn't show that the residue is there. In fact, I can
> only view it by asking
> for it by residue number the CPK view, but its also not connected to the
> neighboring residue.

I think that also hits the STRIDE issue (note that the sequence viewer also
shows secondary structure assignments). If you ask only for that residue
number, it will not show up connected to other residues that are part of a
different representation. If you select (by residue number, or by resname,
or by some combination) your new residue AND the things to which it's
supposed to be attached, in a single representation, then the attachment
will be there to see, IF your new residue is close enough that VMD thinks
there should be a bond there based on its distance search. Not otherwise.

> So, I'm wondering if I didn't make the standard residue correctly, OR does
> anyone know how
> vmd typically handles these?
>

Too soon to tell. Things that would help answer that:
1. load it by itself and see how the bond lengths, angles, etc. are showing
up in VMD.

2. Do some searches on the VMD mailing list for similar issues. IIRC, the
question of the VMD distance search comes up fairly frequently.

3. If there is still no connection with everything in a single
representation, measure the distances between the atoms you think need to be
bonded. You might need to shift them a bit to get the distances closer.

> Thanks.
>
> --Julie
>

hope that gets you started in figuring it out,
nr