Module to run phaser on a model
Phaser
(hklin, hklout, f, i, logfile, nmol, pdbin, pdbout, sgalternative, sigf, sigi, solvent, timeout, work_dir, hires, autohigh)[source]¶Bases: object
Class to run PHASER
Examples
>>> from simbad.mr.phaser_mr import Phaser
>>> phaser = Phaser('<hklin>', '<hklout>', '<f>', '<i>', '<logfile>', '<nmol>', '<pdbin>', '<pdbout>',
>>> '<sgalternative>', '<sigf>', '<sigi>', '<solvent>', '<timeout>', '<workdir>', '<autohigh>',
>>> '<hires>')
>>> phaser.run()
Files relating to the PHASER 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 |
f |
The F label from the input hkl |
i |
The I label from the input hkl |
logfile |
The logfile output |
pdbin |
The input pdb file |
pdbout |
The output pdb file |
sgalternative |
Whether to check for alternative space groups |
sigf |
The SIGF label from the input hkl |
sigi |
The SIGI label from the input hkl |
solvent |
The estimated solvent content of the crystal |
autohigh |
The high resolution limit in Angstroms for final high resolution refinement in MR_AUTO mode |
hires |
The high resolution limit of data used to find/refine this solution |
work_dir | (str) Path to the working directory were you want PHASER to run |
Methods
run () |
Function to run molecular replacement using PHASER |
autohigh
¶The high resolution limit in Angstroms for final high resolution refinement in MR_AUTO mode
f
¶The F label from the input hkl
hires
¶The high resolution limit of data used to find/refine this solution
hklin
¶The input hkl file
i
¶The I label from the input hkl
logfile
¶The logfile output
nmol
¶The number of molecules to look for
pdbin
¶The input pdb file
pdbout
¶The output pdb file
run
()[source]¶Function to run molecular replacement using PHASER
Returns: | file
file
|
---|
sgalternative
¶Whether to check for alternative space groups
sigf
¶The SIGF label from the input hkl
sigi
¶The SIGI label from the input hkl
solvent
¶The estimated solvent content of the crystal
timeout
¶The time in minutes before phaser is killed