rmsip(...)"rmsip"(enma, ncore=NULL, subset=10, ...)"rmsip"(modes.a, modes.b, subset=10, row.name="a", col.name="b", ...)
"enma"
obtained from function
nma.pdbs
. ncore>1
requires package ‘parallel’ installed. "pca"
or "nma"
as
obtained from functions pca.xyz
or nma
. "pca"
or "nma"
as
obtained from functions pca.xyz
or nma
. Calculate the RMSIP between two mode subspaces.
RMSIP is a measure for the similarity between two set of modes obtained from principal component or normal modes analysis.
rmsip
object with the following components:
For function rmsip.enma
a numeric matrix containing all
pairwise RMSIP values of the modes stored in the enma
object.
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Amadei, A. et al. (1999) Proteins 36, 19--424.
# Load data for HIV example trj <- read.dcd(system.file("examples/hivp.dcd", package="bio3d"))NATOM = 198 NFRAME= 117 ISTART= 0 last = 117 nstep = 117 nfile = 117 NSAVE = 1 NDEGF = 0 version 24 Reading (x100) |======================================================================| 100%pdb <- read.pdb(system.file("examples/hivp.pdb", package="bio3d")) # Do PCA on simulation data xyz.md <- fit.xyz(pdb$xyz, trj, fixed.inds=1:ncol(trj)) pc.sim <- pca.xyz(xyz.md) # NMA modes <- nma(pdb)Warning message: Possible multi-chain structure or missing in-structure residue(s) present Fluctuations at neighboring positions may be affected.Building Hessian... Done in 0.079 seconds. Diagonalizing Hessian... Done in 0.464 seconds.# Calculate the RMSIP between the MD-PCs and the NMA-MODEs r <- rmsip(modes, pc.sim, subset=10, row.name="NMA", col.name="PCA") # Plot pairwise overlap values plot(r, xlab="NMA", ylab="PCA")
pca
, nma
,
overlap
.
Other similarity measures:
sip
, covsoverlap
,
bhattacharyya
.