Selection of specific modes from Ensemble NMA
I'm trying to obtain fluctuations for specific modes (slow, intermediate and fast) from an enma object.
I used modes1 <- nma(pdbs, rm.gaps=FALSE, subspace=3, ncore=4) to obtain the first three non-trivial modes. I assume that the subspace mask does this. The obtained output includes: Details of Scheduled Calculation: ... 17 input structures ... storing 3 eigenvectors for each structure ... dimension of x$U.subspace: ( 453x3x17 )
Using plot(modes1, pdbs=pdbs, col=grps.rd, label=NULL) I obtained a plot that was identical to the one obtained from the complete set of modes (flag subspace=NULL).
I'd be grateful for any suggestions regarding the above. And I'd like to add the following question. Is there a way to obtain specific modes from an enma object and, if so, what is the syntax?
