Re: [AMBER] How to visualize PCA

From: Daniel Roe <>
Date: Mon, 18 Aug 2014 21:11:24 -0600


You can create pseudo-trajectories along each eigenvector by using the
'modes trajout' analysis in cpptraj. For example, you could use the

parm mytop.parm7
readdata myevecs.dat
modes name myevecs.dat trajout trajoutfmt netcdf trajoutmask <mask> \
    pcmin <min> pcmax <max> trajmode 1

which will generate a pseudo trajectory along the first eigenvector
(trajmode 1) in myevecs.dat in netcdf format. The <mask> should
correspond to the original mask you used to create the covariance
matrix, and pcmin and pcmax are values you can obtain from e.g.
histogramming the projection values from the first eigenvector. Note
you will need a topology that corresponds to <mask> to view the
trajectory, which can be easily generated by:

parm mytop.parm7
parmstrip !(<mask>)
parmwrite out modes.parm7

Hope this helps,


On Mon, Aug 18, 2014 at 7:08 PM, Tamara Meirelles
<> wrote:
> Hi all,
> Could somebody point out what software can be used to visualize the results
> of a principal component analysis? I have produced the eigenvector and
> projection files (using ptraj) but I have no idea how to analyze them :)
> Thanks in advance
> Tamara
> --
> *P *Please consider the environment before printing my email.
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 18 2014 - 20:30:03 PDT
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