[AMBER] pc1 vs pc2 principal component analysis

From: Jenny 148 <jenny.rs140.gmail.com>
Date: Sat, 17 Jul 2021 01:12:29 +0530

Dear all,

 I am working with a protein system. I have constructed the
diagonalized coordinate covariance matrix for eigenmodes in a file
evectors.dat with the command line being beg 1 end 20 (though I had only 11
columns, the reason of which I am not sure. After that using the following
lines, I projected the trajectory under consideration to the evectors.dat
# Read in modes
readdata evectors.dat name Modes
# Now create separate PC projections for each trajectory
projection A1 modes Modes out pca12-ca beg 1 end 2 :1-831.CA

After which I get a file pca12-ca, which looked somewhat like this:
#Frame Mode1 Mode2
       1 36.824 5.205
       2 35.917 5.359
       3 34.797 6.404
       4 34.637 8.611
       5 35.224 9.040
      ...........(Blanking out the rest)

My query is whether the pca12-ca file which I got, the actual PC1 vs PC2
file? I mean, would plotting the 2nd and 3rd column in the above file as X
and Y axis, allow me to get a scatter plot between the First and second
principal component of my trajectory?

Jenny R.S
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Received on Fri Jul 16 2021 - 13:00:03 PDT
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