Hi, I had a structure where a 15-residues loop is missing. So I want to create it but without moving the other atoms. I tried a lot of things (md_level= None, and so...) but I wasn't able to obtain a model where the non-loop atoms stayed in place. I think that there is still an optimization I can't stop. After that I could try to optimize my loop with the refine_loop.py from the advanced tutorial but first I need my model. Can someone help me please?
Mathieu Coincon PhD Student Universite de Montreal
On Wed, Oct 05, 2005 at 04:41:44PM -0400, mathieu coincon wrote: > Hi, > I had a structure where a 15-residues loop is missing. > So I want to create it but without moving the other atoms. > I tried a lot of things (md_level= None, and so...) but I wasn't able to > obtain a model where the non-loop atoms stayed in place. > I think that there is still an optimization I can't stop. > After that I could try to optimize my loop with the refine_loop.py from > the advanced tutorial but first I need my model. > Can someone help me please?
when you call automodel.make() use "exit=2" as the argument:
a = automodel( blah blah blah... a.make("exit=2")
This will exit after modeller does the 3D overlay according to the alignment and constructs the missing residues, and not do any MD. You will end up with the .ini file.
> > Mathieu Coincon > PhD Student > Universite de Montreal > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage
mathieu coincon wrote: > I had a structure where a 15-residues loop is missing. > So I want to create it but without moving the other atoms. > I tried a lot of things (md_level= None, and so...) but I wasn't able to > obtain a model where the non-loop atoms stayed in place. > I think that there is still an optimization I can't stop. > After that I could try to optimize my loop with the refine_loop.py from > the advanced tutorial but first I need my model.
The suggestion you received was nearly right - you should specify 'exit_stage=2' when you call automake.make(). See http://salilab.org/modeller/manual/node52.html
For example,
a = automodel(... a.make(exit_stage=2)
If you actually want to optimize the loop region, then simply select only the loop residues for optimization. See http://salilab.org/modeller/manual/node28.html for optimization using the standard potentials, and the second example at http://salilab.org/modeller/manual/node33.html for optimizing using Modeller's loop modeling potential.
Ben Webb, Modeller Caretaker
On Thu, Oct 06, 2005 at 12:37:22AM -0700, Modeller Caretaker wrote: > The suggestion you received was nearly right - you should specify > 'exit_stage=2' when you call automake.make(). See > http://salilab.org/modeller/manual/node52.html
Yeah sorry, I was doing it from memory...
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mathieu coincon -
Modeller Caretaker -
Peter C. Lai