VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Fri May 28 2010 - 10:47:05 CDT

A common mistake I make is that
vmd's "residue" and "resid"
are different and I always have to look this one up.

One is a zero based index of the residues and the other actually represents
the residue numbers as found in the pdb file that's loaded. consult the
documentation or try it yourself.

Example: if you load a file from the RCSB that has two identical chains, e.g.
A and B form a homodimer in the structure, and if the residues are numbered to
match biological numbering for a protein. Then there will be TWO residues that
have the same residue number they will belong to different chains and have
different residue index values.

If you don't start w/ a PDB but say an amber parm/top or some other format,
say your desmond files, then you'll have to see for yourself what resid and
residue represent.

If you load a pdb, then an amber parm/top onto the pdd then I'm not sure what
happens.

Tom

On Friday 28 May 2010 08:24:45 am Axel Kohlmeyer wrote:
> On Fri, 2010-05-28 at 08:29 -0400, Sally Fisher wrote:
> > Hi all,
>
> dear sally,
>
> > This is a follow-up on a question I asked earlier. VMD does not seem
> > to be assigning the residue numbers properly for my desmond files upon
> > import, causing the sequence to be displayed completely out of order
> > in Multiseq and Sequence Viewer. Should I be concerned about my
> > structure files? Is there anyway to correct this issue?
>
> at the moment, it is not even clear that there is
> an issue. you'll first have to provide some examples
> and explanations that document the difference between
> what you see and what you expect.
>
> in my experience, a lot of the confusion about residue
> numbering goes back to people not understanding correctly
> what VMD shows them where. every once in a while a legitimate
> problem shows up and then this can be fixed, if there is
> a way to reproduce it.
>
> sequence numbers are typically ignored in simulations
> (unless you use them for special purposes).
>
> cheers,
> axel.
>
> > Thanks,
> > Sally Fisher
> > Department of Chemistry
> > University of Richmond, VA 23173
>

*******************************
   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392
http://dna.ccs.tulane.edu
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