vanddraabe (version 1.1.1)

AlignOverlap: Alignment Overlap Check

Description

Determine if two protein structures are aligned using C-alpha atoms.

Usage

AlignOverlap(aligned.dir = "blast_fitlsq_1.0ang", out.dir = "blast",
  ref.PDBid = "1hai", overlap = 0.7, removal = 0.1, CA.dist = 1.25,
  filename = "ProteinSystem")

Arguments

aligned.dir

Directory with aligned structures

out.dir

Directory prefix for the correctly and incorrectly aligned structures. The out.dir variable is also used to construct the Excel workbook with the summary of the alignment evaluation

ref.PDBid

Reference structure PDB ID, four character ID, used to compare all other aligned structures

overlap

The ratio of overlapping C-alpha atoms; default 0.70

removal

The ratio of overlapping C-alpha atoms to remove a chain from a collection of chains passing the overlap requirement; default: 0.10

CA.dist

The minimum distance between C-alpha atoms for the two C-alpha atoms to be considered aligned; default: 1.25

filename

The filename of the Excel workbook containing all the results from the analysis.

Value

This function returns:

• Overlapping sturctures: PDB structures satisfying the overlap requirements are written to the out.dir_alignedGood directory

• Non-Overlapping sturctures: PDB structures not satisfying the overlap requirement are written to out.dir_alignedPoor

• AlignOverlap.summary: data.frame of the information written to the Excel workbook

• call: The user provided parameters for the function

Details

Using the C-alpha atoms of two aligned proteins, the amount of atomic overlap is determined and the overlapped chains are written to individual PDB files in the NAME_alignedGood directory. The PDB files have the PDBID_aligned_pruned.pdb naming convention where the PDBID is the RCSB four-character identification code. Structures not meeting the user defined overlap ratio are written to the NAME_alignedPoor directory. The structures are written using the bio3d::write.pdb() function of the bio3d package.

See Also

Other "Alignment Overlap": CalcAlignOverlap

Examples

# NOT RUN {
 
# }
# NOT RUN {
  ## example from the Thrombin vignette
  AlignOverlap(aligned.dir = "",
               out.dir = "OVERLAP",
               ref.PDBid = "1hai",
               overlap = 0.70, removal = 0.10,
               CA.dist = 1.25,
               filename = "Thrombin")
 
# }
# NOT RUN {
# }