[chimera-dev] Chimera-dev Digest, Vol 46, Issue 7

[Jean-Didier Maréchal]

Hi Eric,

both information have been of great interest for me. 
I actually read Walt mail when it came to the list, though, I forgot
about it afterward...

Thanks
JD

On Tue, 2007-11-27 at 12:00 -0800, chimera-dev-request at cgl.ucsf.edu
wrote:
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> Today's Topics:
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>    1. Re: Different models (Thomas Goddard)
>    2. Re: Molecular Editing: metal ion chelation (Eric Pettersen)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 26 Nov 2007 14:27:08 -0800
> From: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] Different models
> To: Marco Mernberger <mernberger at Mathematik.Uni-Marburg.de>
> Cc: chimera-dev at cgl.ucsf.edu
> Message-ID: <474B483C.3050804 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi Marco,
> 
>    The Chimera volume path tracer tool has some similarity to your 
> proposed Chimera tool.  It allows you to place markers on volume data 
> and connect them up.  The markers could represent molecules, domains, 
> ... and are implemented as a Chimera molecule, so all the coloring, 
> selecting, hiding/displaying capabilities of molecules are available to 
> the user.
> 
>    The volume path tool is implemented all in Python in directory
> 
> 	chimera/share/VolumePath
> 
> Look specifically at the markerset.py file which defines classes 
> Marker_Set, Marker, and Link that are wrappers for Chimera Molecule, 
> Atom and Bond.
> 
> 	Tom
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 26 Nov 2007 15:59:09 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] Molecular Editing: metal ion chelation
> To: Jean-Didier Mar?chal <jeandidier.marechal at uab.es>
> Cc: chimera-dev at cgl.ucsf.edu
> Message-ID: <629CBC57-7D4F-4612-A50E-DD80312697D9 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 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 Mar?chal 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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