mode warp: phase extension, modification and averaging

All you need to do is run arp_warp.sh mode warp. If you have experimental phases, we recommend to run this script to get better phases and follow with automated model building. If you did not ask for averaging, only free atom model building and refinement will be executed. If you asked for multiple models, then the averaging script, warp.sh will be launched automatically and will do the job ... take care in this case of all the things that are described about rhosts and remote processes.
At the end, you can find in the files/ directory a file called warp_free.brk in the case of refinement of a single model. If you asked for multiple models and averaging a file called FoFOM.map calculated with the averaged phases will be there, so will a file called allaver.mtz, guess what it's content is ... Any of these can be used for mode warpNtrace, as explained above, or for manual building in the graphics.
Tricks and Tips

• In case of a crash of a time consuming job, or whatever, you can restart from an intermediate point. warp.sh accepts four different command line arguments: 1, 2, 3 tell it to go and start from the first, second and third refinement cycle respectively. Note, however, that in all cases it will use the models from files/ directory named, next_for_use_1, next_for_use_2, etc. The number at the end of the file name shows for which of the parallel refinement runs this file will be used. If you do not run parallel refinement only _1 will be present. The fourth argument is average and this will just go and average the latest next_for_use_n models.