simbad.mr.refmac_refine module¶

Module to run REFMAC on a model

class Refmac(hklin, hklout, logfile, pdbin, pdbout, work_dir)[source]¶

Bases: object

Class to run refmac

Examples

>>> from simbad.mr.refmac_refine import Refmac
>>> refmac = Refmac('<hklin>', '<hklout>', '<logfile>', '<pdbin>', '<pdbout>', '<work_dir>')
>>> refmac.run('<ncyc>')

Files relating to the REFMAC run will be contained within the work_dir however the location of the output hkl, pdb and logfile can be specified.

Attributes

hklin	The input hkl file
hklout	The output hkl file
pdbin	The input pdb file
pdbout	The output pdb file
logfile	The logfile output
work_dir	The path to the working directory

key	(str) REFMAC key words
ncyc	(int float) The number of cycles of refinement to perform [default : 30]

Methods

refmac(hklin, hklout, pdbin, pdbout, …)	Function to run refinement using REFMAC
run(type[, ncyc])	Function to run refinement using REFMAC

hklin¶

The input hkl file

hklout¶

The output hkl file

logfile¶

The logfile output

pdbin¶

The input pdb file

pdbout¶

The output pdb file

static refmac(hklin, hklout, pdbin, pdbout, logfile, key)[source]¶

Function to run refinement using REFMAC

Parameters:	hklin : str Path to the input hkl file hklout : str Path to the output hkl file pdbin : str Path to the input pdb file pdbout : str Path to the output pdb file logfile : str Path to the output logfile key : str REFMAC key words
Returns:	file Output hkl file file Output pdb file file Output log file

run(type, ncyc=30)[source]¶

Function to run refinement using REFMAC

Parameters:	type : str The type of refinement to run ncyc : int float The number of cycles of refinement to perform [default : 30]
Returns:	file Output hkl file file Output pdb file file Output log file

work_dir¶

The path to the working directory