simbad.mr.anomalous_util module¶

Class to run an anomalous phased fourier on MR results

class AnomSearch(mtz, output_dir, mr_program)[source]¶

Bases: object

An anomalous phased fourier running class

Attributes:	mtz : str The input MTZ file output_dir : str The path to the working directory model : class Class object containing the PDB code for the input model

Methods

cad()	Function to run CAD to combine the calculated structure factors and the anomalous signal
csymmatch()	Function to run csymmatch to correct for symmetry shifted coordinates
fft()	Function to run FFT to create phased anomalous fourier map
peakmax()	Function to run peakmax to return the peaks from FFT
run(model)	Function to run SFALL/CAD/FFT to create phased anomalous fourier map
search_results([min_dist])	Function to extract search results
sfall(model)	Function to run SFALL to calculated structure factors for the placed MR model

cad()[source]¶

Function to run CAD to combine the calculated structure factors and the anomalous signal

Parameters:

self.name : str unique identifier for the input model set by AnomSearch.run self.mtz : str mtz file input to :obj: AnomSearch self.work_dir : str working directory set by AnomSearch.run self._f : str f column label set by :obj: AnomSearch self._sigf : str sigf column label set by :obj: AnomSearch self._free : str free column label set by :obj: AnomSearch self._dano : str dano column label set by :obj: AnomSearch self._sigdano : str sigdano column label set by :obj: AnomSearch self._resolution : float mtz resolution set by :obj: AnomSearch

Returns:

file mtz file containing FCalc, PHICalc, DANO and SIGDANO columns

csymmatch()[source]¶

Function to run csymmatch to correct for symmetry shifted coordinates

Parameters:	self.name : str unique identifier for the input model set by AnomSearch.run self.work_dir : str working directory set by AnomSearch.run self.output_dir : str output directory input to :obj: AnomSearch
Returns:	file PDB file containing the symmetry corrected atom coordinates

fft()[source]¶

Function to run FFT to create phased anomalous fourier map

Parameters:	self.name : str unique identifier for the input model set by AnomSearch.run self.work_dir : str working directory set by AnomSearch.run
Returns:	file anomalous phased fourier map file file log file containing the results from the anomalous phased fourier

mr_program¶

The molecular replacement program to use

mtz¶

The input MTZ file

output_dir¶

The path to the working directory

peakmax()[source]¶

Function to run peakmax to return the peaks from FFT

Parameters:	self.name : str unique identifier for the input model set by AnomSearch.run self.work_dir : str working directory set by AnomSearch.run
Returns:	file PDB file containing peaks file HA file containing peaks file log file containing the peaks identified by the anomalous phased fourier

run(model)[source]¶

Function to run SFALL/CAD/FFT to create phased anomalous fourier map

search_results(min_dist=4.0)[source]¶

Function to extract search results

sfall(model)[source]¶

Function to run SFALL to calculated structure factors for the placed MR model

Parameters:	model : str path to placed model from MR self.name : str unique identifier for the input model set by AnomSearch.run self.mtz : str mtz file input to AnomSearch self.work_dir : str working directory set by AnomSearch.run self._f : str f column label set by :obj: AnomSearch self._sigf : str sigf column label set by :obj: AnomSearch self._free : str free column label set by :obj: AnomSearch
Returns:	file mtz file containing FCalc and PHICalc columns