Hi,
On Fri, Jul 16, 2021 at 3:43 PM Jenny 148 <jenny.rs140.gmail.com> wrote:
> 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
It's not clear what you mean here - which file had 11 columns? Can you
post the exact input you are using, and point out the file that you
unsure about that has 11 columns?
> 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
Yes. You are projecting the coordinates of CA atoms of residues 1-831
on the eigenvectors read in from evectors.dat (presumably generated
from the same coordinate selection), only for eigenvectors (modes) 1
and 2.
Hope this helps,
-Dan
> principal component of my trajectory?
>
> --
> Jenny R.S
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 20 2021 - 11:30:02 PDT
