simbad.mr.phaser_mr module¶

Module to run phaser on a model

class Phaser(hklin, 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>', '<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:

Returns:	file Output pdb file file Output log file

file

Output pdb file

file

Output log 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