Examples

A typical set of ARP/wARP commands for applications #1, 2, 5 and 6 (unrestrained or restrained refinement for MR, MIR, ab initio solutions or building of solvent structure) could look something like this:

arp_warp XYZIN input_coordinates MAPIN1 3Fo-2Fc_map_file $\tt\backslash$
MAPIN2 Fo-Fc_map_file XYZOUT output_coordinates << eof
MODE update allatoms/waters
[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] [keep zeroocc]
END
eof

Keywords FIND and REMOVE are half optional, by that we mean that at least one of them must be given. Both MAPIN1 ( 3F_o-2F_c / 2mF_o-DF_c, $\alpha_c$) and MAPIN2 (Fo-Fc / mFo-DFc, ac) maps must be provided.

Another typical set of ARP/wARP commands, this time for application #2 (filling the MIR(AS) map with a set of pseudo protein atoms for further unrestrained refinement or multiple refinements):

arp_warp MAPIN2 Fo-Fc_map_file XYZOUT1/2/3 output_coordinates << eof
MODE mirbuild
CELL cell parameters
SYMM spacegroup
RESOLUTION resmin resmax
MIRBUILD atoms number models number
END
eof

Input MAPIN2 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 application #3 (obtaining different independent models for multiple refinement):

arp_warp XYZIN input_file XYZOUT output_file << eof
MODE shakemodel light/allatoms
[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, again for application #3 (averaging of multiple refinements of different independent models):

arp_warp HKLIN mul_ref_Fs HKLOUT nice_output << eof
MODE reflaver
RESOLUTION resmin resmax
LABIN input labels for FP  SIGFP  [FREE]  FCx  PHICx
LABOUT output labels for FC_AVER  PH_AVER  FOM_AVER
END
eof