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

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@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)

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Message: 1 Date: Mon, 26 Nov 2007 14:27:08 -0800 From: Thomas Goddard Subject: Re: [chimera-dev] Different models To: Marco Mernberger Cc: chimera-dev@cgl.ucsf.edu Message-ID: <474B483C.3050804@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

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Message: 2 Date: Mon, 26 Nov 2007 15:59:09 -0800 From: Eric Pettersen Subject: Re: [chimera-dev] Molecular Editing: metal ion chelation To: Jean-Didier Mar?chal Cc: chimera-dev@cgl.ucsf.edu Message-ID: <629CBC57-7D4F-4612-A50E-DD80312697D9@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