fluorescent_scan: Find optimal wavelength for anomalous phasing

Description Usage Arguments Value Examples

View source: R/reciprocal_space.R

Description

This function mimics the behaviour of the fluorescent scan operated at synchrotron beamlines to find out the optimal wavelength which maximises the anomalous signal used to phase a structure.

Usage

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fluorescent_scan(chem_el, lambda_range = NULL)

Arguments

chem_el

1- or 2-letters character string. The chemical symbol of interest.

lambda_range

Real vector of length 2. The two values are the extremes of the wavelength window inside which to carry out the search. Default is for the search to be carried out across the full available range.

Value

A named list with two elements: 1) idx is the integer indicating the row in the anomalous_data dataframe related to the specific chemical element, corresponding to the optimal wavelength; 2) the optimal wavelength in angstroms.

Examples

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# Optimal wavelength for iron
lFe <- fluorescent_scan("Fe")
print(lFe$lambda)
idx <- lFe$idx

# Load anomalous dataframe for Fe
adFe <- load_anomalous_data("Fe")
print(adFe[idx,])  # Same wavelength as before!

# Optimal wavelength with window restriction
lFe <- fluorescent_scan("Fe",lambda_range=c(6,8))
print(lFe$lambda)

jfoadi/crone documentation built on May 17, 2017, 7:19 p.m.