Re: [modeller_usage] Modeling a larger protein with multiple templates
Hello again I might have misunderstood something then.
When I used salign with several templates I noticed that the *fit_fit* files have new coordinates. 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.
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.
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.
The first FAQ entry (as you probably know :) ) says:
"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."
But with sufficient overlaps you think I can just use the original template pdb files and disregard the fit steps performed by salign?
Thank you very much Niklas
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?
Yes, that should be fine.
Ben Webb, Modeller Caretaker
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nornik