overlap analysis only with positive or negative part of the movement

[karolk]

Dear All,

As you know, every mode gives a rise to two set of conformers, which correspond to "negative" and "positive" movements along the mode axis. Is it possible to perform overlap analysis only with positive or negative part of the movement?

I checked Bio3d documentation and I can't see a function, which would allow me to access neg./pos. parts of the movement. Is it possible to script it somehow in Bio3d?

If not, maybe you can recommend me a different software?

thank you

[Xinqiu Yao]

Can you explain in a bit more detail what exactly you want to do?

[karolk]

Hi,

Let us assume that the observed conformational changes proceed in both directions. I have been wondering whether overlap analysis or any other type of analysis, can distinguish between these directionalities? The problem is that the overlap between NMA and difference vector, is always the same. It is always 1, no matter the observed direction of a change, because negative and positive directions are equally probable in NMA. Right?

thank you

[Xinqiu Yao]

I am afraid bio3d does not support such comparisons and I don't know what software can do it. Note that eigenvectors are not unique and flipping an eigenvector is still an eigenvector of the covariance/Hessian matrix. Thereby, in my opion, it might be misleading to discuss directionality of PCA or NMA...

[karolk]

Hi,

I understand your point. Still, this directionality of a motion is experimentally observed and it might be important. That's way I want to somehow show it.

Nevertheless, thank you very much for your opinion.

You can close this ticket.