Module to run REFMAC on a model
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
refmac
(hklin, hklout, pdbin, pdbout, logfile, key)[source]¶Function to run refinement using REFMAC
Parameters: | hklin : str
hklout : str
pdbin : str
pdbout : str
logfile : str
key : str
|
---|---|
Returns: | file
file
file
|
run
(type, ncyc=30)[source]¶Function to run refinement using REFMAC
Parameters: | type : str
ncyc : int float
|
---|---|
Returns: | file
file
file
|
work_dir
¶The path to the working directory