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 << eof
MODE UPDATE ALLATOMS/WATERS
FILES CCP4 XYZIN input_coordinates MAPREMOVE 3Fo-2Fc_map_file $\tt\backslash$



MAPFIND Fo-Fc_map_file_name 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] [KEEPZEROOCC MAINCHAIN/ALLATOMS]
END
eof

Note the new 'FILES' keyword. command line !!!

It might be more justified to use side_trace with command line input. It can be really used as a standalone program, not in connection with autobuilding or anything, just for a quick rebuild for all side chains or real space refinement, or for mutating a molecular replacement solution, or anything that you fancy at all. Here is an example script. Use your imagination to figure out what is what ... more in the next version.
side_trace mapin1 files/map_2mfoDfc_warpNtrace.map xyzin files/warpNtrace.brk xyzout Side_dock.brk /
seqin psp.pir << eof
MODE DOCK
RESI 1 999
RSFIT ALL
RESHUFLE YES
RSCYC 4
SYMM 5
CONFI 12 10
END
eof