Re: [modeller_usage] modeller 9.2: spaghetti effect with multipletemplates
To: Modeller Caretaker <>
Subject: Re: [modeller_usage] modeller 9.2: spaghetti effect with multipletemplates
From: Raik Gruenberg <>
Date: Wed, 11 Jul 2007 11:29:29 +0200
Cc: , Pedro Beltrao <>,
Dear Ben,
thanks for your prompt reply!
Modeller Caretaker wrote:
Raik Gruenberg wrote:
So to what extend differs the multiple-template treatment of Modeller
9 from previous versions? Do I need to use different parameters for
multi-template modeling in the new version? Or is the general default
modeling protocol different now?
The multiple-template treatment did not change at all between Modeller 8
and Modeller 9, so I'm surprised that you're seeing such different models.
I can't deduce anything more from your output PDB files. If you can make
a zip file of your inputs (see
http://salilab.org/modeller/manual/node10.html) then I can take a look
to see whether you're running into a bug.
I double-checked things this morning and I am indeed getting very different
results from the two modeller versions running on the same machine, using the
same alignment, structures etc. I am going to send you the complete input and
the different results in a separate e-mail.
The large number of templates isn't perhaps the main issue. I just repeated the
test with only the three best templates (42 - 86% ID). And again modeller 8
fares well but modeller 9 produces knots and wrong topologies in many of the 10
output models. Of course this is still using the same automatic input alignment
which may be less than perfect (T-Coffee consensus of a structure alignment of
*all* 10 templates combined with 2 more alignments from a global sequence search).
One obvious thing to check is the generated .rsr file for both 8 and 9.
If you're getting different models, then either the multiple-template
treatment (or some other part of the restraints generation) is making a
different set of restraints, or you have the same restraints in both
cases but they are being optimized differently.
The first page or so of this file is identical between the two versions but then
things seem to diverge. Please have a look yourself.
So here is our (old-style) input file:
Is this being generated by the Biskit framework? If so, why does it
generate deprecated TOP files when Python scripts give you more
flexibility?
:-) Well, we implemented the homology modeling module of Biskit already back in
2004 starting with Modeller 6 (!) if I remember right. We just never really
advertised it. I would say, it testifies to your good software development that
the same wrapper is still working 3 versions later. But you have a point there.
We should switch the default template to the current standard also to allow
better customization.
Besides, and this really leads off-topic now, we also are not actually mixing
"your python" with "our python". Seeing how you are transforming Modeller into a
full-fledged python library, that would probably give interesting possibilities,
though perhaps at the cost of simplicity, modularity, "installability", ...
Anyway, that would make a different discussion.