Some questions on RMSF analysis

[Former user]

I'm dealing with an ensemble of 17 structures that purportedly adopt the same fold. Their pairwise sequence identity is as low as 10%. The only common feature they share is three equispaced disulfide bonds. My objective is to determine whether they share a common signature profile. I've conducted nma, pca and rmsf analysis of the ensemble.

My question is whether it is possible to decompose the ensemble rmsf to the rmsf of individual structures.

I've calculated and ensemble RMSF as follows:

rf <- rmsf(xyz[, gaps.pos$f.inds])

My question is whether there's a way to calculate the rmsf of individual structures.

Many thanks in advance for any suggestions

[Xinqiu Yao]

Hi,

RMSF meas Root Mean Square Fluctuation, which is a concept about dynamics. Hence, in principle, you will always need an ensemble of conformations/structures to calculate RMSF.

However, for a single structure, there does have a way to calculate "RMSF": You calculate dynamics using normal model analysis (the nma() function) first and then obtain RMSF out of it.

Take a look of the bio3d tutorials here: http://thegrantlab.org/bio3d/tutorials, especially, ensemble NMA (part I and II).

Hope it helps.

[Xinqiu Yao]

Not a bug.