vanddraabe (version 1.1.1)

CreatePyMOLscript: Create PyMOL Script File

Description

Create PyMOL script file to visualize conserved waters

Usage

CreatePyMOLscript(conservedWaters.data, passed.waters = TRUE,
  PDBid.ref = "1hai", LigResname.ref = NULL, hbond = 3.75,
  lig.carbon.color = "cyan", filename = "thrombin10")

Arguments

conservedWaters.data

The h2o.clusters.summary data.frame from the ConservedWaters() function containing the nBvalue.mu information. This data.frame is found within the h2o.cluster.passed and h2o.cluster.all

passed.waters

Logical indicator to plot results for waters passing Mobility() and NormalizedBvalue() OR using all waters within the PDB files.

PDBid.ref

name for reference structure in PyMOL; e.g., "1hai"

LigResname.ref

PDB residue code for reference ligand; e.g., "0g6"

hbond

The minimum distance between hydrogen bond acceptor and donor; default: 3.75

lig.carbon.color

One of the ten pre-defined carbon-color options using PyMOL's util.cbaX command. The X represents the user defined color of carbon atoms. X can be g: green; c: cyan; m: magenta; y: yellow; s: salmon; w: grey; b: slate; o: orange; p: purple; and k: pink; default: cyan

filename

Prefix for the PyMOL script files. It is probably best to use the initial portion of the conserved waters PDB filename; e.g., "thrombin10"

Details

The ability to visualize the conserved waters is important and their surroundings is when exploring conserved water results.

Conserved waters within 6 Angstroms of the PyMOL identified ligands are displayed. The conserved waters are colored based on their percent conservation range using the same color scheme as the Percent Conservation plot. Waters conserved less than 50% are colored light grey, 50-69% are red, 70-79% are dark red, 80-89% are light blue, 90-99% are medium blue, and 100% are dark blue. The conserved waters are labeled using their ranking based on percent conseration.

This function creates two PyMOL script files; one with a black background and another with a white background. The color of the pocket residues is changed based on the background. The pocket residues are colored light-grey for the black background and dark-grey for the white background. The ligand is assigned the user-defined color for both representations. Pocket residues -- and associated molecular surface -- are defined as those within 5 Angstroms of the conserved waters. The depicted cartoon representation is for residues within 15 Angstroms of the ligand(s).

The potential hydrogen bonds are depicted between:

• conserved waters and ligand: orange dashed line

• conserved waters and protein: green dashed line

• conserved waters: blue dashed line

Examples

# NOT RUN {
  
# }
# NOT RUN {
  current.time <- Sys.time()
  CreatePyMOLfile(PDBid.ref = "Thrombin_initial10_alignedGood/1hai_aligned_pruned.pdb",
                  PDBid.ref = "1hai",
                  LigResname.ref = "0g6",
                  conserved.waters = "Thrombin_initial10_ConservedWaters_PASSED_mar292017_1535.pdb",
                  hbond = 3.75,
                  lig.carbon.color = "cyan",
                  filename = "thrombin10_ConservedWaters_PASSED")
  
# }
# NOT RUN {
# }