Re: [modeller_usage] Modeling a larger protein with multiple templates
To: nornik <>
Subject: Re: [modeller_usage] Modeling a larger protein with multiple templates
From: Modeller Caretaker <>
Date: Tue, 09 Feb 2010 11:40:20 -0800
Cc: "" <>
On 02/09/2010 08:57 AM, nornik wrote:
When I used salign with several templates I noticed that the *fit_fit*
files have new coordinates.
Sure, because it sounds like you asked SALIGN to perform a structural
alignment.
I assumed that MODELLER tried to place them
in the same coordinate system according to the sequence alignment
produced by salign to get "better" starting positions before energy
minimization.
No - the comparative modeling procedure does not use SALIGN (or any
other structural alignment) by default.
I have compared the different *fit* "clusters" and, to me, it seems like
the first fit sort of places the main (top) template in some sort of
origo and the following fits (*fit_fit*, *fit_fit_fit*) align the other
templates with the main one according to the sequence alignment produced
by salign.
Yes, this will be the behavior if you set the SALIGN option fit_on_first
to True.
Due to these observations I assumed that you had to transpose the
template pdb files so that they were sort of placed "correctly" with
respect to eachother.
No, that only affects the generation of the initial structure.
"If no additional information is available about the relative
orientation of the two domains the resulting model will probably have an
incorrect relative orientation of the two domains when the overlap
between A and B is non-existing or short. To obtain satisfactory
relative orientation of modeled domains in such cases, orient the two
template structures appropriately before the modeling."
Yes, this will give a better initial model. But if there is no overlap,
there will be no restraints between the domains, so they will move around.
But with sufficient overlaps you think I can just use the original
template pdb files and disregard the fit steps performed by salign?