Cross-Correlation for Ensemble NMA (eNMA)

Calculate the cross-correlation matrices from an ensemble of NMA objects.

# S3 method for enma
dccm(x, ncore = NULL, na.rm=FALSE, ...)

Arguments

x	an object of class enma as obtained from function nma.pdbs.
ncore	number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
na.rm	logical, if FALSE the DCCM might containt NA values (applies only when the enma object is calculated with argument ‘rm.gaps=FALSE’).
...	additional arguments passed to dccm.nma.

Details

This is a wrapper function for calling dccm.nma on a collection of ‘nma’ objects as obtained from function nma.pdbs.

See examples for more details.

Value

Returns a list with the following components:

all.dccm

an array or list containing the correlation matrices for each ‘nma’ object. An array is returned when the ‘enma’ object is calculated with ‘rm.gaps=TRUE’, and a list is used when ‘rm.gaps=FALSE’.

avg.dccm

a numeric matrix containing the average correlation matrix. The average is only calculated when the ‘enma’ object is calculated with ‘rm.gaps=TRUE’.

References

Wynsberghe. A.W.V, Cui, Q. Structure 14, 1647--1653. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Author

Lars Skjaerven

See also

nma, dccm.nma, plot.dccm

Examples

# \donttest{
## Needs MUSCLE installed - testing excluded

if(check.utility("muscle")) {

## Fetch PDB files and split to chain A only PDB files
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
files <- get.pdb(ids, split = TRUE, path = tempdir())

## Sequence/Structure Alignement
pdbs <- pdbaln(files, outfile = tempfile())

## Normal mode analysis on aligned data
modes <- nma(pdbs)

## Calculate all 6 correlation matrices
cij <- dccm(modes)

## Plot correlations for first structure
plot.dccm(cij$all.dccm[,,1])

}
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1a70.pdb  exists. Skipping download
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1czp.pdb  exists. Skipping download
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1frd.pdb  exists. Skipping download
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1fxi.pdb  exists. Skipping download
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1iue.pdb  exists. Skipping download
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1pfd.pdb  exists. Skipping download
#> 
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#> Reading PDB files:
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1a70_A.pdb
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1czp_A.pdb
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1frd_A.pdb
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1fxi_A.pdb
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1iue_A.pdb
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1pfd_A.pdb
#> .   PDB has ALT records, taking A only, rm.alt=TRUE
#> .....
#> 
#> Extracting sequences
#> 
#> pdb/seq: 1   name: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1a70_A.pdb 
#> pdb/seq: 2   name: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1czp_A.pdb 
#>    PDB has ALT records, taking A only, rm.alt=TRUE
#> pdb/seq: 3   name: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1frd_A.pdb 
#> pdb/seq: 4   name: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1fxi_A.pdb 
#> pdb/seq: 5   name: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1iue_A.pdb 
#> pdb/seq: 6   name: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/split_chain/1pfd_A.pdb 
#> 
#> Details of Scheduled Calculation:
#>   ... 6 input structures 
#>   ... storing 282 eigenvectors for each structure 
#>   ... dimension of x$U.subspace: ( 288x282x6 )
#>   ... coordinate superposition prior to NM calculation 
#>   ... aligned eigenvectors (gap containing positions removed)  
#>   ... estimated memory usage of final 'eNMA' object: 3.7 Mb 
#> 
#> 
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# }