Elves have only done a partial set-up of ARP/wARP for you. To get ARP/wARP running, you may need to download a copy from the website: netscape http://www.embl-hamburg.de/ARP/ Once you have ARP/wARP installed, assuming it's in /programs/xtal/arp_warp_5.1/bin/Linux, you need to type this: setenv warpbin /programs/xtal/arp_warp_5.1/bin/Linux set path = ( $warpbin $path ) arp_warp_setup.sh and then answer the questions you see there. Alternately, Elves have written a shortcut around arp_warp_setup.sh called "setup_warp.com" in this directory. All you have to do is provide this script with a phased mtz file: setup_warp.com best_phased.mtz or setup_warp.com ../mtz/all.mtz model.pdb (i.e. model.pdb is a molecular replacement solution) ...and a basic warp.par file will be produced you should then be able to run: arp_warp.sh mode warpNtrace side or any of the other ARP/wARP programs Elves will have included your protein sequence in seq.pir, which is needed for automated side-chain tracing in ARP/wARP 5.1 Elves will, eventually, place what they believe to be the "best" phasing solution to your data in ./best_phased.mtz, but you can use whatever mtz you want in arp_warp_setup.sh or setup_warp.com