Re (in reply to Tsjerk): [gmx-users] Porcupine Plots

[Tsjerk Wassenaar]

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 <meetnahren at 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 <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
>
> 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.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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-- 
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