NMA_with_arbitrary_defined_rigid_domains

[karolk]

Hi,

I want to perform the domain-based NMA, which would be performed for a structure with arbitrary defined 3 rigid domains.

The closest to this what I want to do is the rotation-translation block nma. Yet, the 'nmer' is always a single number.

Yet, instead of specifying a single number, which would define my block size, I want to define three rigid domains in my structure, so the nmer=sel.1, sel.2, sel.3., so the NMA will be performed with three rigid blocks.

Is there any way to do it in bio3d?

I checked documentation. I could not find anything.

thanks

[Lars Skjærven]

Hi Karolk, You're right- this is not implemented in bio3d. Not sure it's needed either, unless you have a very large structure. You should be able to run several thousands of residues with bio3d calpha ENM.

[karolk]

HI Lars,

My protein is quite specific. It has clearly defined hinge regions. Based on this what I read, I think that by defining rigid bodies of arbitrary size, I would be able to obtain modes, which would yield much better correlation with the experiment. Based on Yang 2007, Biophys. Journal. They call it domain-ENM method.

thanks

[Xinqiu Yao]

So far, nmer in aanma() has to be a single value. If you want to use user-defined blocks, you might need to "hack" the code, unfortunately...

Have you tried C-alpha based ENM? Was it still expensive to calculate?

[karolk]

Hi,

Can you point, which source file I should hack? Is it rtb.R in the R folder?

Yes, I tried ENM and it worked, but it is not about being computationally expensive. As I stated before, based on this what I read, it is likely that by performing domain-ENM, one can get much better results.

[Xinqiu Yao]

Yes, mostly functions in rtb.R but you might also need to look at the .nma.trim.hessian.rtb() in the nma_funs.R file. Normally, for all-atom ENM, we build the model based on all atoms but output modes for 'C-alpha' only, and thereby need to calculate effective Hessian using that function. If this is your case, check both files and modify if necessary.