[chimera-dev] scripting rotation around a bond
pett at cgl.ucsf.edu
Wed Apr 29 12:16:06 PDT 2009
On Apr 29, 2009, at 3:34 AM, Jean Didier Pie Marechal wrote:
> Dear all,
> I'd like to generate from my script an ensemble of structures
> obtained by the rotation of a subgroup of the molecule around a
> given bond. Said in another way, I want to do something similar to
> the adjust torsion tools without getting to the interfase but
> defining myself the value of the angle I want to test.
> I can't figure out what is the module to load and how to use it and
> it seems there is no command line for this (rotation seems to accept
> only the atom specification for the bond as an argument). Could you
> give me a hand on this?
Basically, given a bond you want to rotate around, you create a
BondRot instance to do it:
br = chimera.BondRot(bond)
Then you can change it by a delta (in degrees) from it's _original_
(not current) position with the angle() method. You also have to
specify which side of the bond doesn't move:
br.angle = (10, br.biggerSide())
You can get back to the original position with br.reset() (or with a
delta of zero). Make sure to dispose of the BondRot with br.destroy()
when you're done with it.
You probably want to use a daily build here, otherwise the bond-
rotation GUI will pop up as you work with the BondRot. Which can be
kind of cool as the adjustment dial flies around like a movie clock in
a fast-forward sequence.
> By the way, I wanted to get the to the programmers's guide but I
> can't. You removed it from your server correct?
> All the best,
The Programmer's Guide is still there, it's just not a direct link off
the home page. Instead you have to click on the "Documentation" link
and it's in the list on the resulting page. We removed the auto-
generated reference section since it was very big and of little utility.
UCSF Computer Graphics Lab
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