From: M. Madhu (madhu7_at_hotmail.com)
Date: Sun Mar 12 2006 - 09:44:59 CST
Hi Nicolas,
Thank you very much for sharing your script for estimating the area per
lipid and explaining how you have done it. Eventhough I am not familiar
with python script, I am sure that your script will be very helpful. I will
try
to use it soon. Once again, thank you for your kindness.
Madhu
>From: Nicolas Sapay <n.sapay_at_ibcp.fr>
>To: "M. Madhu" <madhu7_at_hotmail.com>
>CC: namd-l_at_ks.uiuc.edu
>Subject: Re: namd-l: area per lipid for a protein embedded membrane system
>Date: 11 Mar 2006 11:42:32 +0100
>
>Hi,
>Well in this case I may have something that can help you. It is a python
>script that I have written some months ago. Unfortunaly, It works with
>the MDtools python library (no longer developped), is awfully coded and
>incredibly slow :-). Basically, the script projects each lipid on a grid
>and count the bins filled by the projection. This tends probably to
>over-estimate the area per lipid; a Voronoï tessellation would probably
>be a better method.
>
>Nico
>
>enjoy
>
>Le ven 10/03/2006 à 19:25, M. Madhu a écrit :
> Hi Nicolas,
>
> What I meant is "transmembrane protein in a membrane sytem". Thank
>you.
>
> Madhu
>
> >From: nsapay_at_ibcp.fr
> >To: "M. Madhu" <madhu7_at_hotmail.com>
> >CC: namd-l_at_ks.uiuc.edu
> >Subject: Re: namd-l: area per lipid for a protein embedded membrane
>system
> >Date: Fri, 10 Mar 2006 19:08:54 +0100
> >
> >Hello Madhu,
> >What do you mean by embedded? You mean the protein is transmembrane
>or just
> >inserted in the membrane interface as the Prostaglandin H2 synthase?
> >
> >Nicolas
> >
> >Selon "M. Madhu" <madhu7_at_hotmail.com>:
> >
> > >
> > > Hi All,
> > >
> > > Could someone share a script file for calculating area per lipid
> > > for a membrane protein embedded in a bilayer system? Or, any
> > > suggestions to measure it? Thank you.
> > >
> > > Madhu
> > >
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> >
> >
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>--
>[ Dr Nicolas Sapay ]
>Institut de Biologie et Chimie des Proteines
>CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
>Phone: +33 (0)4 72 72 26 46 - Fax: +33 (0)4 72 72 26 04
>Address: 7 passage du Vercors, 69367-F Lyon cedex 07, France
><< area.tar.gz >>
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