Hi,
See comments below:
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?
>
> 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
>
> matrix mwcovar name cc.matrix out cc.matrix !.CA,C,N
analyze matrix cc.matrix out new.matrix
so that will do everybody except for atoms that correspond to CA, C and N
what you have above works as well.
> Thanks in advance,
>
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--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jan 25 2011 - 12:30:03 PST
