Forwarded to modeller_usage from the listowner.
------ Forwarded Message
From: Liisa laakkonen <>
Reply-To:
Date: Wed, 26 Feb 2003 12:30:50 +0200
To:
Subject: heteroatoms & loop_select
Dear Modeller-Man,
A question about loops.
I cannot get the atom selection for loops to work. I
SET DO_LOOPS = 1
and then select_loops as in example 3. Whatever numbers I put
in for the loops (from the beginning of the chain, or from the middle),
the whole protein is "initialized" to a neat straight polypeptide chain.
Any suggestions?
I also include a question from two weeks ago, for the case
it was lost during your move.
----------------------------
I have a heteroatom problem. The system is as follows:
the template (actually 3 but 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 studied:
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 inthe alignemnt, OR
about the missing backbone atoms in the BLK, whichever I edit.
The only way I can see possibly working is to edit stronly 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
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