I Hate Automated Scripts

If you insist on using command files rather than our wonderful automated scripts - no problem. See the chapter on ARP/wARP keywords for a detailed description. If you have a working command file from a previous release just change the ARP part to look like this:

arp_warp XYZIN input_coordinates MAPIN1 3Fo-2Fc_map_file $\tt\backslash$
MAPIN2 Fo-Fc_map_file_name 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