swamp.wrappers.wrefmac module

class wRefmac(workdir, pdbin, mtzin, make_hydr='N', weight_matrix='0.01', ncyc='100', ridg_dist_sigm='0.02', logger=None, phased_mtz=None, silent_start=False)[source]

Bases: swamp.wrappers.wrapper.Wrapper

Refmac5 wrapper

Parameters:
  • workdir (str) – working directory where refmac will be executed
  • pdbin (str) – pdb filename with the placed search model
  • mtzin (str) – target’s mtz filename
  • make_hydr (str) – mset MAKE_HYDR (default: ‘N’)
  • weight_matrix (str) – set WEIGHT MATRIX stdin value for jelly body refinement (default: ‘0.01’)
  • ridg_dist_sigm (str) – set RIDG DIST SIGM stdin value for jelly body refinement (default: ‘0.02’)
  • ncyc (str) – number of refinement cycles (default: ‘100’)
  • phased_mtz (str) – target’s mtz filename containing phases (default: None)
  • 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:
  • rfree (str) – calculated Rfree after refinement
  • rfactor (str) – calculated Rfactor after refinement
  • rfactor_delta (tuple) – a tuple with the intial and final Rfactor
  • rfree_delta (tuple) – a tuple with the intial and final Rfree
  • bondlenght_delta (tuple) – a tuple with the intial and final Bond length
  • bondangle_delta (tuple) – a tuple with the intial and final Bond angle
  • chirvol_delta (tuple) – a tuple with the intial and final Chirvol
  • ovarall_CC (str) – overall correlation coefficient between phases at phased_mtz and the refined search model
  • local_CC (str) – local correlation coefficient between phases at phased_mtz and the refined search model
Example: 
>>> from swamp.wrappers import wRefmac
>>> my_refmac = wRefmac('<workdir>', '<pdbin>', '<mtzin>')
>>> my_refmac.run()
>>> my_refmac.make_logfile()
cmd

Command to be executed on the shell

get_scores(logfile=None)[source]

Parse the logfile and extract scores after refinement using a RefmacParser instance

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

Keywords tos be passed to refmac5 through the stdin

summary_results

String representation of a summary of the obtained figures of merit

wrapper_name

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