FW: modeller problem (fwd) - modeller_usage

26 Feb 2003


      --
Andrej Sali, Professor
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and 
    California Institute for Quantitative Biomedical Research
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-----Original Message-----
From: Bozidar Yerkovich [mailto:bozidar@salilab.org] 
Sent: Wednesday, February 26, 2003 4:29 PM
To: Andrej Sali
Subject: modeller problem (fwd)
---------- Forwarded message ----------
Date: Tue, 18 Feb 2003 10:40:55 +0200
From: Liisa laakkonen llaakkon@pcu.helsinki.fi
Reply-To: liisa.laakkonen@helsinki.fi
To: bozidar@salilab.org
Subject: modeller problem
Hello,
and good luck in the new place,
I have a heteroatom problem. The system is as follows:
the template (actually 3 but I try first one)
the sequence
the alignement
        includes one chain of the template only
        and the middle part only
        e.g.
        structureX:templ:25:A:400:A:undefined:undefined:1.00:1.0
The prosthetic groups are defined as a separate chain, X,
and they are observed in the unknown structure, too.
I've included:
        set hetatm_io = on
        -----/..,  in the alignement
        BLK residue for fixed unknown structure
        (+ have ch27 topology files for it)
DON'T KNOW how to mark two chains in the alignment
Is it possible?
Clearly, the program would like to get the number of residues right, and and
complains about the dots in the alignemnt, OR about the missing backbone
atoms in the BLK, whichever I edit. The only way I can see possibly working
is to edit styronly the pdb files, cut away the C-termini, mark heteroatoms
to belong to the subunit A, and change their numbering. I would not like to
do this, because I might need the tails later, and eliminating true residue
numbers nearly always causes trouble.
Any help would be most welcome.
Sincerely,
        Liisa Laakkonen
        University of Helsinki