[Chimera-users] scan and minimization of dihedral angle

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 26 10:02:03 PDT 2014


Hi Milo,
here are a couple of previous posts on saving information from the Reply Log:
> 
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html>

Elaine


On Aug 26, 2014, at 9:47 AM, Milo Westler <milo at nmrfam.wisc.edu> wrote:

> Eric,
>   I've got most things running that I want for my potential energy scan however  there are a couple of things I still have to do manually. I am looking for commands or a python script to:
> 
> 1). clear the "reply log" and then save the results from the "reply log" to a file
> 2). create a torsion angle and write that value to a file (Tools-> Structure Analysis -> Angles/Torsions -> select ->create->save)
> 
> My current script goes as:
> 
> from chimera import runCommand as rc
> rc("minimize nogui true")
> rc("rotation 1 @C4 at C5")
> rc("rotation 1 30")
> rc("~rotation 1")
> rc("select @C3 at C4@C5 at C6")
> rc("minimize nogui true freeze selected")
> rc("~select")
> 
> rc("rotation 1 @C4 at C5")
> rc("rotation 1 30")
> rc("~rotation 1")
> rc("select @C3 at C4@C5 at C6")
> rc("minimize nogui true freeze selected")
> rc("~select")
> 
> rc("rotation 1 @C4 at C5")
> rc("rotation 1 30")
> rc("~rotation 1")
> rc("select @C3 at C4@C5 at C6")
> rc("minimize nogui true freeze selected")
> rc("~select")
> .
> .
> .
> And so on through a full rotation.
> 
> Thanks,
> 




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