Module to run phaser rotation search on a model
Phaser
(hklin, f, i, logfile, nmol, pdbin, sigf, sigi, solvent, timeout, work_dir, hires, eid)[source]¶Bases: object
Class to run PHASER
hklin
¶str – Path to the input hkl file
f
¶str – The column label for F
i
¶str – The column label for I
pdbin
¶str – Path to the input pdb file
pdbout
¶str – Path to the output pdb file
sigf
¶str – The column label for SIGF
sigi
¶str – The column label for SIGI
solvent
¶int float – The estimated solvent content of the crystal
work_dir
¶str – Path to the working directory were you want PHASER to run
hires
¶str – The high resolution limit of data used to find/refine this solution
Examples
>>> from simbad.rotsearch.phaser_rotation_search import Phaser
>>> phaser = Phaser('<hklin>', '<f>', '<i>', '<logfile>', '<nmol>', '<pdbin>', '<pdbout>', '<sgalternative>',
>>> '<sigf>', '<sigi>', '<solvent>', '<timeout>', '<workdir>', '<autohigh>', '<hires>', '<eid>')
>>> 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.
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
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