calcBvalue: Calculate B-value

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

Description

Calculate the B-value for an atom.

Usage

calcBvalue(rmsfValue)

Arguments

rmsfValue

rmsf value calculated by bio3d::rmsf()

Details

The B-value (aka B-factor) is calcualted from the rmsf from a collection of atoms. The rmsf is calculated using bio3d::rmsf().

B-value = rmsf^2 * 8 * pi^2

The calculated B-values are returned within the BoundWaterEnvironment() results and used to define the size of conserved waters for the depiction of MDS conserved waters.

Value

B-value (aka B-factor) in Angstroms^2^

Author(s)

Emilio Xavier Esposito [e-mail]

References

Eaton E Lattman & Patrick J Loll. Protein Crystallography: A Concise Guide. Baltimore, Maryland, USA: The Johns Hopkins University Press, 2008. QP551.L345 2008. ISBN: 978-0-8018-8808-3 website

See Also

Other "Bound Water Environment": BoundWaterEnvironment.interact, BoundWaterEnvironment.quality, BoundWaterEnvironment, Mobility, NormalizedBvalue, calcNearbyHydrationFraction, calcNumHydrogenBonds

Examples

  calcBvalue(rmsfValue=0.25)
  # [1] 4.935
  calcBvalue(rmsfValue=0.50)
  # [1] 19.74
  calcBvalue(rmsfValue=0.75)
  # [1] 44.41
  calcBvalue(rmsfValue=1.0)
  # [1] 78.96
  calcBvalue(rmsfValue=1.25)
  # [1] 123.4

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