Hi Daniel,
thank you for these articles. yes i could not demonstrate my thought well but your guess is exactly the same that what i want.
> Date: Tue, 16 Feb 2016 08:26:47 -0700
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] want to ask you about PCA plotting
>
> Hi,
>
> On Tue, Feb 16, 2016 at 2:58 AM, Ayesha Kanwal
> <ayesha_comsian.hotmail.com> wrote:
> > Hi All,
> > i want to calculate PCA of protein and want to present in graphical way.
> > is there any script that can i use for plotting and calculation of PCA?
>
> Your question is a bit vague. I'm guessing that you mean you want to
> plot projections of your coordinates along principal components. For
> some recent papers that incorporate of these kinds of calculations (as
> well as example cpptraj scripts) see these articles and their
> supporting info:
>
> http://pubs.acs.org/doi/abs/10.1021/jp4125099
> http://pubs.acs.org/doi/abs/10.1021/ct400862k
>
> Note that these examples are just the tip of the iceberg - there are
> many, many other examples of people analyzing and plotting various
> quantities from principal component analysis in the literature.
>
> Hope this helps,
>
> -Dan
>
> >
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Tue Feb 16 2016 - 13:00:03 PST
