MobNormBvalEvalPlots: Mobility and Normalized B-values Evaluation Plots

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Mean bound water environment summary per percent conservation

Usage

MobNormBvalEvalPlots(data, passed.waters = TRUE,
  title = "Mobility and Normalized B-value Evaluation")

Arguments

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.
title	The title for the plot

Details

Constructs a series of scatterplots illustrating the relationship between mobility and normalized B-values and (i) percent water conservation, (ii) mean distance between waters in a cluster, and (iii) mean distance between waters in a cluster and the cluster's centroid. The dots are colored based on water cluster "percent conservation":

• light grey dots: less than 50% conservation

• dark red dots: 50% to 69% conservations

• red dots: 70% to 79% conservation

• light blue dots: 80% to 89% conservation

• blue dots: 90% to 99% conservation

• dark blue dots: 100% conservation (all structures contribute to the water cluster).

The mean distance plots will have a column of dots at a distance of 0.0 if there are clusters composed of a single water molecule. Thus, these clusters have a zero distance between and to other waters in their cluster because there are no other waters in their cluster.

This plot was inspired by Figure 2 of Ogata and Wodak (2002).

Author(s)

Emilio Xavier Esposito [e-mail]

References

Koji Ogata and Shoshana J Wodak. Conserved water molecules in MHC class-I molecules and their putative structural and functional roles. Protein Engineering, 2002, 15 (8), pp 697-705. DOI: 10.1093/protein/15.8.697 PMID: 12364585

See Also

Other plots: BoundWaterEnvPlots, BoundWaterEnvSummaryPlot, BvalueBarplot.summ, BvalueBarplot, ClusterSummaryPlots, MobilityBarplot.summ, MobilityBarplot, OccupancyBarplot.summ, OccupancyBarplot, nBvalueBarplot, normBvalueBarplot.summ

Examples

  ## Not run: 
  bwe.summary.plot <- MobNormBvalEvalPlots(data=thrombin10.conservedWaters,
                                           passed.waters=TRUE,
                                           title="Mobility and Normalized B-value Evaluation")
  
## End(Not run)

vanddraabe documentation built on June 8, 2019, 1:03 a.m.