[gmx-users] Porcupine Plots

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 2 09:36:55 CET 2009

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,


On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham <Mark.Abraham at 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
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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

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