nma.pdbs with rm.gaps=TRUE

[Lars Skjærven]

Currently the resulting 'enma' object has matrices with dimensions dim(pdbs$ali[, gaps$f.inds]). Would it make more sense to output full dimensions?

e.g. for fluctuations:

modes <- nma(pdbs, rm.gaps=T)
gaps = gap.inspect(pdbs$ali)
f2 <- matrix(NA, nrow=nrow(pdbs$ali), ncol=ncol(pdbs$ali))
f2[, gaps$f.inds] <- modes$fluctuations
plot.fluct(f2)

[Lars Skjærven]

or alternatively provide this feature in plot.enma when pdbs is provided?

[Barry Grant]

I think returning the same dims as the input is sensible.

This would look after the output from plot.enma() (i.e. the full dims with gaps would be there by default). I guess plot.enma() could have an option to drop gaps but keep all the residue numbering etc.?

[Xinqiu Yao]

Isn't it controlled by rm.gaps=TRUE/FALSE? Yes returning the full dimension by default and have option to drop gaps in plot() functions would be more sensible.

[Lars Skjærven]

Ok- I will change nma.pdbs() to output same dimensions as input pdbs object. Then add an argument rm.gaps to function plot.enma() to drop gaps. Thanks for input