Examples

A typical set of ARP/wARP commands for most applications (unrestrained or restrained refinement for MR, MIR, ab initio solutions or building of solvent structure) looks something like this:

arp_warp << eof
MODE update allatoms/waters
FILES CCP4 XYZIN input_coordinates MAPREMOVE 3Fo-2Fc_map_file $\tt\backslash$
MAPFIND Fo-Fc_map_file XYZOUT output_coordinates
[CELL cell parameters]
[REFINE waters/allatoms]
SYMM spacegroup
RESOLUTION resmin resmax
FIND atoms number chain string cutsigma number/auto
REMOVE atoms number cutsigma number [merge number] $\tt\backslash$ [keepzeroocc mainchain/allatoms ]
END
eof
Keywords FIND and REMOVE are half optional, by that we mean that at least one of them must be given. Both MAPREMOVE ( 3F_o-2F_c / 2mF_o-DF_c, $\alpha_c$) and MAPFIND (Fo-Fc / mFo-DFc, ac) maps must be provided.
Another typical set of ARP/wARP commands, this time for filling the MIR(AS) map with a set of pseudo protein atoms for further unrestrained refinement or multiple refinements):

arp_warp << eof
MODE mirbuild
FILES CCP4 MAPFIND Fo-Fc_map_file XYZOUT1/2/3 output_coordinates
CELL cell parameters
SYMM spacegroup
RESOLUTION resmin resmax
MIRBUILD atoms number models number
END
eof

Input MAPFIND is the available starting map. Several models for multiple refinements are output to XYZOUT1/XYZOUT2/XYZOUT3.
Yet another typical set of ARP/wARP commands, now for obtaining different independent models for multiple refinement:

arp_warp << eof
MODE shakemodel light/allatoms
FILES CCP4 XYZIN input_file XYZOUT output_file
[CELL cell parameters]
SYMM spacegroup
SHAKEMODEL [ bexcl n1 ] [ breset n1 n2 ] [ randomise x ] [ shift x y z ]
END
eof

And another typical set of ARP/wARP commands, now for averaging of multiple refinements of different independent models):

arp_warp << eof
MODE reflaver
FILES CCP4 HKLIN mul_ref_Fs HKLOUT nice_output
RESOLUTION resmin resmax
LABIN input labels for FP  SIGFP  [FREE]  FCx  PHICx
END
eof