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[Fwd: "MODELLER SUPPORT": Re: Adding missing coordinates]
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Hi Dan,

OK, I did not know the exact situation. You need to trick it manually.

If a whole segment is missing, that is a problem, indeed. You need to add at
least some ad hoc coordinates, e.g. manually to the pdb file. It does not
matter if they does not make any sense (in the loop region)  because that
segment will be completely randomized when loop modeling will be done on it,
subsequently after model building. I assume that was your plan.

But you are right, modeller does require some kind of coordinate entries, for
each residue, at least a backbone trace for the given region as input.


Andras

Dan Thomas Major wrote:
> 
> Dear Prof. Fiser,
> thank you very much for your answer.
> I tried previously to read in the template which is a dimer missing 10 amino
> acid residues in loop regions (I only read monomer A). I had trouble reading
> in the template, since there was a a different number of residues in the
> template pdb file and its alignment file with the target protein that I want
> to model.
> Regards,
> Dan
> 
> ----- Original Message -----
> From: Andras Fiser <andras AT tuba.rockefeller.edu>
> To: Dan Thomas Major <majord AT mail.biu.ac.il>
> Cc: <modeller_usage@listsrv.ucsf.edu>
> Sent: éåí çîéùé 06 ãöîáø 2001 18:44
> Subject: "MODELLER SUPPORT": Re: Adding missing coordinates
> 
> > Dan,
> >
> > You do not need to add them for the template (there is no point to do
> that).
> > They will be built automatically in the model.
> >
> > E.g. if you have a backbone trace only in your template, MODELLER will
> > construct a full atom model  in the target.
> >
> > Andras
> >
> > Dan Thomas Major wrote:
> > >
> > > I want to add missing coordinates to a pdb template file before using it
> for
> > > modelling, but I'm not succeeding!
> > > I would greatly appreciate some help.
> > > Dan
> > >
> > > --
> > > Dan Thomas Major (at Dr. B. Fischer's lab)
> > > Bar-Ilan University
> > > Ramat-Gan, Israel
> > >
> > >
> >
> > --
> >     ,
> > Andras Fiser, PhD            # phone: (212) 327 7216
> > The Rockefeller University   # fax:   (212) 327 7540
> > Box 270, 1230 York Avenue    # e-mail:fisera AT rockefeller.edu
> > New York, NY 10021-6399, USA # http://salilab.org/~andras
> >

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:fisera AT rockefeller.edu
New York, NY 10021-6399, USA # http://salilab.org/~andras

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