[modeller_usage] modelling discarding part of a template
To:
Subject: [modeller_usage] modelling discarding part of a template
From: Anna Marabotti <>
Date: Wed, 05 May 2010 12:57:00 +0200
Hi,
sorry for a probable
trivial question, but I couldn't find a solution browsing the mailing
list by myself.
I want to model a
protein using two different templates, in particular they differ in the
position of a loop. My protein is very similar to template 1, but should have
that loop in the same conformation found in template 2. So I'd like to "say" to
modeller: please model my protein using template 1 as much as possible, but use
only template 2 to model that loop. Please take in mind that both templates
cover the entire sequence and show the loop (in different
conformations).
I tried to do this
by replacing the residues that I would like to be discarded (in
correspondence of the loop) in template 1 with gaps in the alignment. So
for example:
target: AAAAAAAAAAAAAAAAA
template
1: BBBB-------BBBBBB
template
2: ZZZZZZZZZZZZZZZZZ
(the part with gaps
in template 1 is present in PDB file)
But Modeller
returned me an error saying:
Sequence difference
between alignment and PDB:
Alignment:
BBBBBBBBBB
Sequence:
BBBBBBBBBBBBBBBBB
I understand that
Modeller "interpret" my alignment as a gap would present in the structure, and
since this is not the case, it returns me an error. The question is: how to
correctly send information to Modeller in order to "force" it to follow only a
template to model a portion of the sequence, even if the other template is
present? It seems to me that there was a way to do it
without modifying the PDB file of the first template in order to
cancel this loop. Am I correct? Is there a solution?
Thank you very much
for kind assistance and best regards