[chimera-dev] scripting rotation around a bond
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Wed May 6 01:13:01 PDT 2009
thanks a lot that is what I wanted. One question though: How do you inverse the part of the molecule you want to rotate? (The reverse in the GUI).
Dr. Jean-Didier Maréchal
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
08193 Cerdanyola (Barcelona)
e-mail: JeanDidier.Marechal at uab.es
----- Missatge original -----
De: Eric Pettersen <pett at cgl.ucsf.edu>
Data: Dimecres, Abril 29, 2009 9:16 pm
Assumpte: Re: [chimera-dev] scripting rotation around a bond
> 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
> > 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
> > it seems there is no command line for this (rotation seems to
> > only the atom specification for the bond as an argument). Could
> > 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
> (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
> delta of zero). Make sure to dispose of the BondRot with
> 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
> kind of cool as the adjustment dial flies around like a movie clock
> 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
> the home page. Instead you have to click on the "Documentation"
> 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
> Eric Pettersen
> UCSF Computer Graphics Lab
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