Subject: Re: [modeller_usage] problems modeling a multimer
From: Modeller Caretaker <>
Date: Tue, 15 May 2007 13:30:27 -0700
Cc:
Douglas Kojetin wrote:
I would like create a hexameric model using a target sequence and a
hexameric PDB template. I am trying to create an alignment using
input files that have the \ character to separate the chains. Example:
Do you actually mean the / character here? '/' designates a chain break,
but '\' has no special meaning in Modeller alignments.
Using modeller9v1 (linux RPM), I started the above calculation
(python align2d.py), but it has not finished after 20 hours
I suggest you try setting the max_gap_length argument to align2d to
something smaller than the default - say 20. By default it will
backtrack through your alignment matrix to try and find the very best
alignment, and for long sequences this can be extremely time consuming,
so it is best to limit the gap length.
according to 'top'). Although I used log.verbose(), there is very
little output in the associated log (see below).
Yes - you won't see any output from align2d until it has finished.
You may also want to try aligning each chain individually. There is no
clear way to align chain breaks, so most of Modeller's alignment
routines will either remove them entirely or simply ignore them. In many
cases you want the chain breaks in your templates to be "aligned" with
the chain breaks in the model, and one way to do that is to make
separate alignments for each chain, and then recombine them later.