Dear Dr. Tsjerk, thanks for your reply. I got the clue from your reply and i did the same via VMD. But can you please be little more speicific about Pymol. I am not quite used to that software.
regards, nahren --- On Mon, 2/2/09, Tsjerk Wassenaar <[email protected]> wrote: From: Tsjerk Wassenaar <[email protected]> Subject: Re: [gmx-users] Porcupine Plots To: "Discussion list for GROMACS users" <[email protected]> Date: Monday, February 2, 2009, 2:06 PM Hi Nahren, Gromacs does not include a tool for generation of porcupine plots. But if you're offered a means to do it through a webservice, all you really need is to take the extreme projections (two frames: g_anaeig -extr) and submit them. In a sense, you'll get the same thing if you load the extreme projections into pymol and use 'align extrA,extrB,object=displacement'. Then hiding one of the structures basically gives you a porcupine plot. Hope it helps, Tsjerk On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham <[email protected]> wrote: > nahren manuel wrote: >> >> Dear Gromacs Users, >> I have done PCA of my MD , I want to visually represent the motions in >> terms of porcupine plots. I came across Dynamite (web server) for this >> purpose. But it only considers 500 frames of the xtc file. >> Is there any other way how i could generate porcupine plots based on tools >> of GROMACS ? > > I've never heard of such plots - perhaps you should look for pointers > wherever you came across them in the first place? > > Users on this list might help with some nuts and bolts, but first you need > to make sure we can have access to useful information - like URLs and > algorithm descriptions. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
