how to use filter.dccm on multiple MD simulations

[Former user]

Hi,

I have several MD simulations. I'd like to generate consensus DCCM for those simulations as described, say, in your G protein paper from 2016. It's probably a trivial task, but my knowledge in R or bio3d is too weak to handle it. My question is: how do I merge several cij's from DCCMs from several individual simulations as an input into filter.dccm? Right now, the provided examples use NMA where multiple cij's are merged automatically (cij <- dccm(modes)).

Best regards,

Visvaldas

[Xinqiu Yao]

filter.dccm() takes a 3-D array containing multiple cij matrices directly as the input. You can make such an array by, e.g., cijs <- array(c(cij1, cij2, ...), dim=c(nres, nres, ntrajs)), where cij1, cij2, etc. are the cij matrix from each simulation, nres is the number of residues (i.e., the dimension of a cij matrix), and ntrajs the number of simulations. Alternatively, you can use the abind package and type abind::abind(cij1, cij2, ..., along=3).

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Hope it helps.

[visvaldask]

Thank you, it works.

Visvaldas