vanddraabe (version 1.1.1)

getRCSBdata: Clean RCSB Dataset

Description

Clean the protein dataset based on quality values.

Usage

getRCSBdata(prefix = "./alignTesting", resolution = 3, rFree = 0.26,
  rObserved = 0.2, filename = "ProteinSystem")

Arguments

prefix

Directory of aligned structures; string.

resolution

Structures with a resolution value greater than this value are removed from analysis; default: 3.0

rFree

Structures with a rFree values greater than this value are removed from analysis; default: 0.26

rObserved

Structures with a rObserved values greater than this value are removed from analysis; default: 0.20

filename

The filename prefix for the returned results. Default is "ProteinSystem"

Value

This function returns:

• PDB.info: RCSB provided information for all protein structures

• PDB.info.passed: RCSB provided information for all protein structures passing the user defined parameters

• PDB.info.rejected: RCSB provided information for all protein structures failing the user defined parameters

• call: parameters provided by the user

• Excel workbook: containing the PDB.info, PDB.info.passed, and PDB.info.rejected data as individual tabs

Details

The provided protein models determined by X-ray crystallography and downloaded from the RCSB include structure quality measures. The resolution, rObservation, and rFree are the three commonly used and referenced evaluation measures.

The B-value normalization exclusion value is user defined within the main ConservedWaters() function but has a default value of 1.0.

Examples

# NOT RUN {
  
# }
# NOT RUN {
  proteins.info <- getRCSBdata(prefix="./thrombin_fitlsq_1.0ang/",
                               resolution=3.0, rFree=NULL, rObserved= 0.20,
                               filename="ProteinSystem")
  
# }
# NOT RUN {
# }