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
file.
# 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
