Thank you for the explanation can you suggest what technique can be used in
place of PCA?
Best regards
Aashish
On Wed, Sep 11, 2019 at 6:51 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> Aashish,
>
> What did trajectory visualization show? Did you see some part of your
> protein moving more than others?
>
> These kinds of results could be real. Protein motions can be anharmonic,
> which certainly seems to be the case for your protein. This is indicated by
> the projection on first PCA vector showing additional peak(s) with small
> populations. Please remember PCA is a quasi-harmonic approximation of the
> motions (fitting a second order/harmonic curve). If there are multiple
> peaks along a projection, it implies that there are multiple wells along
> the same eigenvector, in such cases PCA may not be the best technique to
> obtain accurate results.
>
> Pratul
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 9/11/2019 6:22 AM, Aashish Bhatt wrote:
>
> Dear Sir/Ma'am
>
> I am interested in PCA calculation for the my wild type protein. I had gone
> through the tutorial (
> http://www.amber.utah.edu/AMBER-workshop/London-2015/
> pca/ <http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/>) and
> prepared this cpptraj script.
>
> My problem is that in 2D PC1 and PC2 image they have coming -250 to 70. I
> am suspect that the projection on X axis is very negative.
> Could you give me some comment why it showing negative or something i am
> doing is wrong.
>
>
>
> Best Regards
>
> Aashish
>
>
>
>
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Received on Wed Sep 11 2019 - 22:30:02 PDT
