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

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

pdbs a list of class "pdbs" containing PDB file data, as obtained from read.fasta.pdb or pdbaln. numeric index pointing to the PDB in which the SSE should be provided. If ind=NULL, then the consensus SSE is returned. logical, if TRUE SSEs spanning gap containing columns are omitted from the output in the resulting sse object. logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence). logical, if TRUE function dssp will be called on the corresponding pdb object rather than to use pdbssse to obtain the SSE object. arguments passed to function dssp. ## 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. ## Value Returns a list object of class sse. ## References Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. ## Author Lars Skjaerven ## See also dssp, pdbaln, read.fasta.pdb. ## Examples if (FALSE) { attach(transducin) ## calculate RMSF rf <- rmsf(pdbsxyz)

## 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)
}