bio3d (version 2.3-4)

pdbs2sse: SSE annotation for a PDBs Object

Description

Returns secondary structure element (SSE) annotation ("sse" object) for a structure in the provided "pdbs" object.

Usage

pdbs2sse(pdbs, ind = NULL, rm.gaps = TRUE, resno = TRUE, pdb = FALSE, …)

Arguments

pdbs

a list of class "pdbs" containing PDB file data, as obtained from read.fasta.pdb or pdbaln.

ind

numeric index pointing to the PDB in which the SSE should be provided. If ind=NULL, then the consensus SSE is returned.

rm.gaps

logical, if TRUE SSEs spanning gap containing columns are omitted from the output in the resulting sse object.

resno

logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence).

pdb

logical, if TRUE function dssp will be called on the corresponding pdb object rather than to use pdbs$sse to obtain the SSE object.

…

arguments passed to function dssp.

Value

Returns a list object of class sse.

Details

This function provides a "sse" list object containing secondary structure elements (SSE) annotation data for a particular structure in the provided "pdbs" object. Residue numbers are provided relative to the alignment in the "pdbs" object.

When ind=NULL the function will attemt to return the consensus SSE annotation, i.e. where there are SSEs across all structures. This will only work SSE data is found in the "pdbs" object.

See examples for more details.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

dssp, pdbaln, read.fasta.pdb.

Examples

# NOT RUN {
attach(transducin)

## calculate RMSF
rf <- rmsf(pdbs$xyz)

## Fetch SSE annotation, output in terms of alignment index
sse <- pdbs2sse(pdbs, ind=1, rm.gaps=FALSE, resno=FALSE)

## Add SSE annotation to plot
plotb3(rf, sse=sse)


## Calculate RMSF only for non-gap columns
gaps.pos <- gap.inspect(pdbs$xyz)
rf <- rmsf(pdbs$xyz[, gaps.pos$f.inds])

## With gap columns removed, output in terms of residue number
sse <- pdbs2sse(pdbs, ind=1, rm.gaps=TRUE, resno=TRUE)
gaps.res <- gap.inspect(pdbs$ali)
plotb3(rf, sse=sse, resno=pdbs$resno[1, gaps.res$f.inds])

detach(transducin)
# }