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
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Peter C. Lai
Cesium Hyperfine Enterprises
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