VMD-L Mailing List

From: Scazzocchio, Claudio (c.scazzocchio_at_imperial.ac.uk)
Date: Fri Jul 22 2016 - 02:22:27 CDT

Thanks a a lot indeed stamps does not recognise some residues. The problem is that up to know

I never had any problem with ligands of any protein. I think that in this case the problem is, after discussing with Prof. Cesar Millan

(whom I think for this and previous clarifications) that Met 1 in one of the structures is modified to MSE.

Claudio

Prof. Claudio Scazzocchio
Dept. of Microbiology,
Imperial College London
South Kensington Campus
Flowers Building
Armstrong Road
London SW7 2AZ.
UK
Tel int-44(0)20 7594 7409
c.scazzocchio_at_imperial.ac.uk
________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: 22 July 2016 00:02:26
To: Scazzocchio, Claudio
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Problerm with STAMP

I assume that this error is indicating that multiseq and/or STAMP
do not recognize some of the residues in your structure. The question
marks in particular would seem to indicate that to me. I know that STAMP
was designed for proteins. It's not clear to me what it does in the
case of unrecognized residue codes. You could try using one of the
other VMD alignment tools if you can make a selection of common structure,
and they should be more forgiving of this issue since they don't care about
the residue types involved and perform the alignments using only the
atomic coordinates of the selected atoms.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jul 17, 2016 at 04:46:54PM +0000, Scazzocchio, Claudio wrote:
> I am a relatively unsophisticated user of VMD. I encounter the following
> problem. While using the STAMP alignment, trying to structurally align a
> downloaded structure and with one modelled in I-Tasser, I get the
> following message:
>
> The selection in sequence 5c3o was not completely composed of protein
> residues and can not be aligned by STAMP.
> while executing
> "error "The selection in sequence [::SeqData::getName $sequenceID] was not
> completely composed of $sequenceType residues and can not be aligned by
> STAM..."
>
> One of the sequences showed a whole load of question marks in the
> C-terminus, which I removed. It did not help
>
> I had never had that problem before, even when the structure contains
> ligands.
>
> I could superimpose easily both structures in Magic Fit in
> Swiss-PD-viewer.
>
> Any ideas?,
>
> Thanks
>
> Claudio
>
> Prof. Claudio Scazzocchio
> Dept. of Microbiology,
> Imperial College London
> South Kensington Campus
> Flowers Building
> Armstrong Road
> London SW7 2AZ.
> UK
> Tel int-44(0)20 7594 7409
> c.scazzocchio_at_imperial.ac.uk 

--
NIH Center 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
John E. Stone<http://www.ks.uiuc.edu/~johns/>
www.ks.uiuc.edu
John E. Stone. Senior Research Programmer, Theoretical and Computational Biophysics Group and NIH Center for Macromolecular Modeling and Bioinformatics
http://www.ks.uiuc.edu/Research/vmd/