Re: [AMBER] PCA analysis and porcupine plots

From: <>
Date: Fri, 20 Sep 2013 11:52:07 +0530



Porcupine plots can be generated by pymol also.

On 2013-09-20 11:28, Soma Ghosh wrote:

> Dear AMBER Users,
> I am trying to study domain motions in my protein using PCA analysis of the
> ptraj module. I have successfully performed PCA and have got the projection
> files.
> The next problem is to visualize the motions and generate porcupine plots. For
> this, I installed ied-2.02 as a plugin in VMD 1.8.6. The plugin seems to work
> fine with gromacs examples but fails to work with AMBER format files. I checked
> online and it says that ied can only use formats generated using ptraj8. Is this
> true?? Also i am not able to draw the arrows using this plugin , which seems to
> be a bug with vmd 1.8.6.
> I can use PCASuite, however my CRD files are in the .gz format and PCASuite is
> not able to read the gunzipped files. Also, I have a set of 20 CRD files and I
> want PCASuite to read all the CRD files one after another, how can this be
> done???? Is there a way of scripting PCASuite, wherein one can use trajin
> command and PCAsuite in combination ??
> Finally, can some one take me through the process of generating poocupine plots
> from the PCA analysis done using ptraj of AMBER 9. Also, is there a way of
> quantifying domain motions. Is it ok if i calculate the angles between two set
> of residues from the centre of the domains ???
> Thanks,
> Soma

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Received on Thu Sep 19 2013 - 23:30:03 PDT
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