From owner-chemistry@ccl.net Mon Dec 13 15:11:00 2010
From: "David Mannock dmannock _ ualberta.ca" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: software for selective alignment of different elements of the small molecules
Message-Id: <-43375-101213141404-25587-JbmysGzLgSMkXNqIi9yUSQ:-:server.ccl.net>
X-Original-From: David Mannock <dmannock-x-ualberta.ca>
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Date: Mon, 13 Dec 2010 12:13:54 -0700
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Sent to CCL by: David Mannock [dmannock{=}ualberta.ca]
Andrey, I have recently done this with a set of sterol side-chain 
conformers and used DSvisualizer 2.X or DS viewerpro 6.0 using a 
semi-automatic method for conformations generated by Verachem's Vconf. 
Go to align structures and add tethers to the key parts of the molecule 
in the region that you want to overlay. I have overlaid many molecules 
very accurately using this method. There is not much need for tweaking 
the results if the points are correctly chosen. OS is MS WinXP in my 
case. Dave

  On 11/12/2010 1:30 PM, Andrew Voronkov drugdesign*yandex.ru wrote:
> Sent to CCL by: Andrew Voronkov [drugdesign-x-yandex.ru]
>
> Dear CCL users,
> I'd like to find the software for alignment of the selected  small molecule elements. For example I have a series of conformations and I am getting alignment with one shared element, while I'd like to try to use another. Let's say I have parts A, B, C, D and E and I want to get parts D and E alignmed so that I can see the differences in parts A and B orientation. Can you please recommend software packages which can help me to do selective alignment?
>
> It would be nice to use something free or with evaluation version.
>
>
>
> Sincerely yours,
> Andrey>
>
>
>