Hi Nahren, If you're used to VMD and got what you wanted, why would you want to use Pymol for doing the same? Not that Pymol's not worth knowing :) In Pymol, check the help for the 'align' command: 'help align'
Cheers, Tsjerk On Mon, Feb 2, 2009 at 11:51 AM, nahren manuel <meetnah...@yahoo.com> wrote: > 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 <tsje...@gmail.com> wrote: > > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] Porcupine Plots > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > 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 <mark.abra...@anu.edu.au> > 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 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 >> > > > > -- > 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 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 > -- 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 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
