[chimera-dev] scripting rotation around a bond

Jean Didier Pie Marechal JeanDidier.Marechal at uab.cat
Wed May 6 01:13:01 PDT 2009

Hi Eric,

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
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
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 
> 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu

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