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

[Eric Pettersen]

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

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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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