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?

Hi JD,

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,
JD

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.

--Eric