Re (in reply to Tsjerk): [gmx-users] Porcupine Plots
meetnahren at yahoo.com
Mon Feb 2 11:51:12 CET 2009
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.
--- On Mon, 2/2/09, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Porcupine Plots
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, February 2, 2009, 2:06 PM
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,
On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
> nahren manuel wrote:
>> Dear Gromacs Users,
>> I have done PCA of my MD , I want to visually represent the motions
>> 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
>> 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.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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