<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Dr. Tsjerk,<br><br>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.<br><br>regards,<br>nahren<br><br><br>--- On <b>Mon, 2/2/09, Tsjerk Wassenaar <i><tsjerkw@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">From: Tsjerk Wassenaar <tsjerkw@gmail.com><br>Subject: Re: [gmx-users] Porcupine Plots<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Monday, February 2, 2009, 2:06 PM<br><br><pre>Hi Nahren,<br><br>Gromacs does not include a tool for generation of porcupine plots. But<br>if you're offered a means to do it through a webservice, all you<br>really need is to take the extreme projections (two frames:
g_anaeig<br>-extr) and submit them. In a sense, you'll get the same thing if you<br>load the extreme projections into pymol and use 'align<br>extrA,extrB,object=displacement'. Then hiding one of the structures<br>basically gives you a porcupine plot.<br><br>Hope it helps,<br><br>Tsjerk<br><br>On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham <Mark.Abraham@anu.edu.au><br>wrote:<br>> nahren manuel wrote:<br>>><br>>> Dear Gromacs Users,<br>>> I have done PCA of my MD , I want to visually represent the motions<br>in<br>>> terms of porcupine plots. I came across Dynamite (web server) for this<br>>> purpose. But it only considers 500 frames of the xtc file.<br>>> Is there any other way how i could generate porcupine plots based on<br>tools<br>>> of GROMACS ?<br>><br>> I've never heard of such plots - perhaps you should look for pointers<br>> wherever you came across them in the first
place?<br>><br>> Users on this list might help with some nuts and bolts, but first you need<br>> to make sure we can have access to useful information - like URLs and<br>> algorithm descriptions.<br>><br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www<br>interface<br>> or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>><br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F:
+31-30-2537623<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></pre></blockquote></td></tr></table><br>