[chimera-dev] a request again...adjust torsion for pseudo bonds

Eric Pettersen pett at cgl.ucsf.edu
Tue May 26 14:15:15 PDT 2009

Hi JD,
	I don't really understand your usage scenario.  It seems to me that  
rotating around the chelation bond will either be like rotating around  
a hydrogen/heavy-atom bond (produces no relative motion) or around a  
ring bond (tears the structure apart).  Nonetheless I think you can  
accomplish what you want one of two ways:

1) temporarily form a "real" bond with the metal and then destroy it  
afterward (bond/~bond commands)

2) use the roll command to rotate around the metal/chelating-atom axis  
(use an "axis" argument which is an atom spec selecting the metal and  
chelating atom; a "center" argument which is one of the two atoms; and  
a "models" argument which is the model(s) containing the metal and  
chelating residue).  These arguments to the roll command are only  
available in the daily build.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On May 22, 2009, at 7:49 AM, Jean Didier Pie Marechal wrote:

> Dear all,
> sorry to bother you again.
> I want to perform a conformational search rotating residues around  
> their chelation bond with a metal. With the adjust torsion tool, I  
> can't rotate around  pseudo bond, and I actually need to transform  
> the different pseudo bonds in bonds.
> Could you authorize pseudo bonds to be rotated around? (in the  
> contrary I'll continue with transforming pseudo bonds in bonds, but  
> I thought that remaining with pseudo bonds is better especially when  
> you do "add hydrogens" or other stuffs afterwards )
> All the best,
> JD
> Dr. Jean-Didier Maréchal
> Lecturer
> Computational Biotechnological Chemistry @ Transmet
> Unitat de Química Física
> Departament de Química
> Universitat Autònoma de Barcelona
> Edifici C.n.
> 08193 Cerdanyola (Barcelona)
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