overlap. bio3d 2.3-0

Usage

overlap(modes, dv, nmodes=20)

Arguments

modes: an object of class "pca" or "nma" as obtained from function pca.xyz or nma. Alternatively a 3NxM matrix of eigenvectors can be provided.
dv: a displacement vector of length 3N.
nmodes: the number of modes in which the calculation should be based.

Description

Calculate the squared overlap between sets of vectors.

Details

Squared overlap (or dot product) is used to measure the similiarity between a displacement vector (e.g. a difference vector between two conformational states) and mode vectors obtained from principal component or normal modes analysis.

By definition the cumulative sum of the overlap values equals to one.

Structure modes$U (or alternatively, the 3NxM matrix of eigenvectors) should be of same length (3N) as dv.

Value

overlap: a numeric vector of the squared dot products (overlap values) between the (normalized) vector (dv) and each mode in mode.
overlap.cum: a numeric vector of the cumulative squared overlap values.

References

Skjaerven, L. et al. (2011) Proteins 79, 232--243. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

attach(kinesin)
     
# Ignore gap containing positions
##gaps.res <- gap.inspect(pdbs$ali)
gaps.pos <- gap.inspect(pdbs$xyz)
     
#-- Do PCA
pc.xray <- pca.xyz(pdbs$xyz[, gaps.pos$f.inds])
    
# Define a difference vector between two structural states
diff.inds <- c(grep("d1v8ka", pdbs$id), 
               grep("d1goja", pdbs$id))

dv <- difference.vector( pdbs$xyz[diff.inds,], gaps.pos$f.inds )

# Calculate the squared overlap between the PCs and the difference vector  
o <- overlap(pc.xray, dv)
o <- overlap(pc.xray$U, dv)

# Plot results
plot(o$overlap, type='h', ylim=c(0,1))
points(o$overlap)

lines(o$overlap.cum, type='b', col='red')




detach(kinesin)

## Calculate overlap from NMA
pdb.a <- read.pdb("1cmk")

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE

pdb.b <- read.pdb("3dnd")

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE


## Fetch CA coordinates
sele.a <- atom.select(pdb.a, chain='E', resno=c(15:350), elety='CA')
sele.b <- atom.select(pdb.b, chain='A', resno=c(1:350), elety='CA')

xyz <- rbind(pdb.a$xyz[sele.a$xyz],
             pdb.b$xyz[sele.b$xyz])

## Superimpose
xyz[2,] <- fit.xyz(xyz[1,], xyz[2,], 1:ncol(xyz))

## The difference between the two conformations
dv <- difference.vector( xyz )

## Calculate normal modes
modes <- nma(pdb.a, inds=sele.a)

 Building Hessian...		Done in 0.187 seconds.
 Diagonalizing Hessian...	Done in 2.028 seconds.


# Calculate the squared overlap between the normal modes 
# and the difference vector  
o <- overlap(modes, dv)

Author

Lars Skjaerven

Overlap analysis