özge kül wrote:
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Alif M Latif
Sent: 02 May 2008 09:42
To: gmx-users@gromacs.org
Subject: [gmx-users] Plotting B-factor
Dear GROMACS users and developers,
I want to plot B-factor of a protein structure against residue. How can I do
that?. Using option -oq in g_rmsf only produce bfac.pdb which is in .pdb file
and assigned at each atom. Is there another way I can get the plot B-factor vs
residue?. Any link to example or tutorial will be very helpful.
Comments and Suggestions are greatly appreciated. Thank you.
Take the g_rmsf -res output, square it and multiply it by (IIRC) 800
pi^2/3 (you can do all this in xmgrace). Check the factor.
Muhammad Alif Mohammad Latif
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA
--- On *Wed, 2/4/09, David van der Spoel /<sp...@xray.bmc.uu.se>/* wrote:
From: David van der Spoel <sp...@xray.bmc.uu.se>
Subject: Re: [gmx-users] analyzing beta factor
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Wednesday, February 4, 2009, 2:16 AM
özge kül wrote:
> Hi users,
>
> I want to plot beta factor versus residue number plot at the analyzing
part.I read manual and search in the web but I could not find a reasonable
result for this plot.I wonder if anybody know about it.
>
What is the beta factor?
> Thank you,
> Özge
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please
search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
