[chimera-dev] Molecular Editing: metal ion chelation

[Eric Pettersen]

Hi JD,
	Unfortunately, Chimera isn't really being as smart here as you are  
giving it credit for.  Many PDB files specify coordination bonds in  
CONECT records.  Chimera identifies those bonds and converts them to  
pseudobonds (otherwise its atom-typing code, which depends on correct  
covalent bonding, would get the bonded atoms wrong).  So PDB files  
that do not identify the coordination bonds with CONECT records (e.g.  
1lwx) will not have any coordination bonds in Chimera.
	I'm wondering if what you are hoping to do is along the lines of  
this previous mail to chimera-users:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001529.html

--Eric

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

On Nov 23, 2007, at 9:30 AM, Jean-Didier Maréchal wrote:

> Hi Eric,
>
> Thanks for that. I have been able to get a bit further.
>
> To follow with my problem, I have one question more though.  
> Basically, I
> would like to know how chimera "Recognizes" metal chelation and
> coordination bounds.
>
> What I see is that when you open a pdb with a metal ion, the program
> places correctly "semi bounds" corresponding to coordination
> interactions. Unfortunately, I work with a series of protein  
> structures
> where metals do not adopt a typical geometries (ex: 1lwx). First, I
> would like to be able to improve the number of acceptable metal
> geometries, but my questions are: how does chimera recognize the right
> geometry of the metal ions? Is it implemented in a python module?  
> It is
> a C++ code?
>
> All the best,
> JD
>
>
>



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