REFMAC (CCP4: Supported Program)

User's manual for the program refmac_5.0.*


Example of using the user supplied ligand description. ions.cif contains description of ligands supplied by user. This file may contain all users ligands. Ligands present in this file may or may not be in the list of the stadard ligands. If one of the ligands (in this case it is MO6) is present in the standard ligand list then program will use users definition. Users ligands file may contain different ligands and links. If program finds link or ligand present in the coordinate file not described by user and not present in the standard ligand list then refmac will create description for this ligand and write to file specified by LIB_OUT <out.lib>, default new.lib. All ligands from LIB_IN also will be copied to the output ligand file

#!/bin/csh -fv

refmac5  xyzin   beta29.pdb   hklin beta_nat3_phase_ano.mtz \
  xyzout beta_r.pdb  hklout $SCRATCH/junk \
  lib_in ions.cif \
  << eop

#   Input mtz labels.
labin FP=Fnat3 SIGFP=SIGFnat3 FREE=FreeR_flag  
#  Output mtz labels


# this keyword should be activated to see if there are any links in the
# coordinate file not defined in the coordinate file
#make link y

#  This keyword forces refmac to stop after checking coordinates and 
#  making restraints if MAKE HYDR N has been specified. It is better to
#  have formatted restraint file.
#make format f
#make exit y

# Refinement parameters
ncycle 1
# Weight x-ray and geometry according this weighting scheme
weight matrix 0.5
#First and last cycles will give full statistics. Intermediate cycles
#will give only minimum overall statistics