Molecular Replacement subpackage¶

Class to run MR on SIMBAD results

class MrSubmit(mtz, mr_program, refine_program, refine_type, refine_cycles, output_dir, tmp_dir, timeout, sgalternative=None)[source]¶

Bases: object

Class to run MR on a defined set of models

Examples

>>> from simbad.mr import MrSubmit
>>> MR = MrSubmit('<mtz>', '<mr_program>', '<refine_program>', '<refine_type>', '<output_dir>', '<sgalternative>')
>>> MR.submit_jobs('<results>', '<nproc>', '<submit_cluster>', '<submit_qtype>', '<submit_queue>',
...                '<submit_array>', '<submit_max_array>', '<process_all>', '<monitor>')

If a solution is found and process_all is not set, the queued jobs will be terminated.

Attributes

mtz	The input MTZ file
mr_program	The molecular replacement program to use
refine_program	The refinement program to use
refine_type	The refinement type to use
refine_cycles	The number of refinement cycles to use
output_dir	The path to the output directory
sgalternative	Whether to check for alternative space groups

results

(obj) Results from :obj: ‘_LatticeParameterScore’ or :obj: ‘_AmoreRotationScore’

Methods

fft(hklin, mapout, map_type)	Function to run fft to generate difference maps for uglymol
get_mtz_info(mtz)	Get various information from the input MTZ
submit_jobs(results[, nproc, process_all, …])	Submit jobs to run in serial or on a cluster
summarize(csv_file)	Summarize the search results

cell_parameters¶

The cell parameters of the input MTZ file

f¶

The F column label of the input MTZ file

static fft(hklin, mapout, map_type)[source]¶

Function to run fft to generate difference maps for uglymol

Parameters:	hklin : str Path to input HKL file mapout : str Path to output MAP file map_type : str Define type of run, either mfo-dfc or 2mfo-dfc
Returns:	list cmd str stdin
Raises:	ValueError Unknown map type

free¶

The FREE column label of the input MTZ file

get_mtz_info(mtz)[source]¶

Get various information from the input MTZ

Parameters:	mtz : str Path to the input MTZ
Returns:	self._cell_parameters : list The parameters that descibe the unit cell self._resolution : float The resolution of the data self._space_group : str The space group of the data self._f : str The column label for F self._sigf : str The column label for SIGF self._free : str The column label for FREE self._solvent : float The predicted solvent content of the protein

i¶

The I column label of the input MTZ file

mr_program¶

The molecular replacement program to use

mr_python_module¶

The MR python module

mtz¶

The input MTZ file

output_dir¶

The path to the output directory

refine_cycles¶

The number of refinement cycles to use

refine_program¶

The refinement program to use

refine_python_module¶

The Refinement python module

refine_type¶

The refinement type to use

resolution¶

The resolution of the input MTZ file

search_results¶

The results from the amore rotation search

sgalternative¶

Whether to check for alternative space groups

sigf¶

The SIGF column label of the input MTZ file

sigi¶

The SIGI column label of the input MTZ file

space_group¶

The space group of the input MTZ file

submit_jobs(results, nproc=1, process_all=False, submit_qtype=None, submit_queue=False, monitor=None)[source]¶

Submit jobs to run in serial or on a cluster

Parameters:	results : class Results from :obj: ‘_LatticeParameterScore’ or :obj: ‘_AmoreRotationScore’ nproc : int, optional Number of processors to use [default: 1] process_all : bool, optional Terminate MR after a success [default: True] submit_qtype : str The cluster submission queue type - currently support SGE and LSF submit_queue : str The queue to submit to on the cluster monitor : str
Returns:	file Output pdb from mr file Output hkl from mr - if using phaser file Output log file from mr program file Output pdb from refinement file Output hkl from refinement file Output log file from refinement program

summarize(csv_file)[source]¶

Summarize the search results

Parameters:	csv_file : str The path for a backup CSV file
Raises:	No results found

timeout¶

The time in minutes before phaser is killed

mr_succeeded_csvfile(f)[source]¶

Check a Molecular Replacement job for it’s success

Parameters:	f : str The path to f
Returns:	bool Success status of the MR run

mr_succeeded_log(log)[source]¶

Check a Molecular Replacement job for it’s success

Parameters:	log : str The path to a log file
Returns:	bool Success status of the MR run