Please take a look here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015827
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 9/12/2019 1:15 AM, Aashish Bhatt wrote:
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><mailto: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/><
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 Thu Sep 12 2019 - 06:00:03 PDT
