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