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

[Eric Pettersen]

It's good to hear about interest in these kinds of things -- it helps  
us prioritize what features get worked on.

--Eric

On Nov 28, 2007, at 2:18 AM, Jean-Didier Maréchal wrote:

> 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:
>>
>>    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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