Hello,
It looks like you know how to do PCA via diagonalizing the covariance
matrix, so I will focus my responses on comments I have on the details of
what you're doing.
On Tue, Jan 25, 2011 at 2:31 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi all,
>
> I would like to make a PCA using ptraj module with ambertools - I am
> not quite sure how the syntax is though.
> for the backbone selection I use the following syntax
>
> .N,CA,C
>
> is there any easier way to select side chains?
>
No.
>
> for an analysis of the side chains will the following syntax make any
> sense?
>
> strip .N,CA,C
> matrix mwcovar name cc.matrix out cc.matrix
> analyze matrix cc.matrix out new.matrix
>
A couple comments here. First of all, I don't consider the remaining atoms
after N, CA, and C are removed as the *sidechain* atoms. I would not count
the carbonyl oxygen (O) or any of the alpha protons in my definition of the
side-chain. If I was just looking for sidechain components, I would use the
mask ".N,CA,HA,HA2,HA3,C,O" to select the backbone. Second, I see no reason
to "strip" the backbone here. Why not just provide a mask for the matrix
command? As Dwight pointed, out, you can select the sidechains by selecting
*not* the backbone:
matrix mwcovar name cc.matrix out cc.matrix "! .N,CA,HA,HA2,HA3,C,O"
analyze matrix cc.matrix out new.matrix
Others may interject if I am way off here.
Hope this helps,
Jason
> Thanks in advance,
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 25 2011 - 13:00:05 PST
