swamp.wrappers.shelxe module

class Shelxe(workdir, pdbin, mtzin, solvent='0.45', autotracing_ncyc='20', density_modif_ncyc='10', use_f=True, prune_residues=True, apply_ncs=True, init_time='4', nreflections=40000, alphahelix=True, logger=None, resolution=2.0, silent_start=False)[source]

Bases: swamp.wrappers.wrapper.Wrapper

Wrapper around shelxe

Parameters:
  • workdir (str) – working directory
  • mtzin (str) – target structure mtz file name
  • pdbin (str) – pdb file name with the refined search model
  • solvent (str) – estimated solvent content for the crystal (default 0.45)
  • autotracing_ncyc (str) – number of autotracing cycles to run
  • density_modif_ncyc (str) – number of density modification cycles to run
  • bool use_f (bool) – if True use F labels in the mtz file
  • prune_residues (bool) – if True set -o option (default True)
  • apply_ncs (bool) – sets parameter -n (default True)
  • init_time (str) – parameter to set -t (default True)
  • nreflections (int) – number of reflections in the mtz file (default 40000)
  • alphahelix (bool) – if True sets the -t parameter (default True)
  • resolution (float) – resolution of the data in the mtz file (default 2.0)
  • silent_start (bool) – if True, the logger will not display the start banner (default False)
  • logger (SwampLogger) – logging interface for the wrapper (default None)
Variables:
  • error (bool) – if True an error has occurred along the process
  • cc_eobs_ecalc (str) – the correlation coeff. between Eobs and Ecalc
  • cc (str) – correlation coeff. obtained with the best tracing cycle
  • acl (str) – average chain length obtained with the best tracing cycle
  • average_cc_delta (str) – the average delta of correlation coeff. between tracing cycles
  • solution (str) – ‘YES’ if correlation coeff > 25 otherwise ‘NO’
Examples: 
>>> from swamp.wrappers import Shelxe
>>> my_shelxe = Shelxe('<workdir>', '<mtzin>', '<pdbin>')
>>> my_shelxe.run()
>>> my_shelxe.make_logfile()
cmd

Command to be executed on the shell

get_scores(logfile=None)[source]

Extract the figures of merit from the logfile and the pdb output file using ShelxeParser

Parameters:logfile (None) – Not in use (default None)
input_hkl

The input .hkl file name for shelxe

input_pda

The input .pda file name for shelxe

keywords

Keywords to be used with shelxe

pdbout

Override pdbout so that it corresponds with the real output .pdb file name created by shelxe

summary_results

String representation of a summary of the figures of merit obtained

wrapper_name

The name of this ~swamp.wrapper.wrapper.Wrapper child class (shelxe)