Density Modification (#2,#3)

After running arp_warp_setup.sh all you need to do is run warp.sh. If you have experimental phases, we recommend to first run this script to get better phases and follow with automated model building.

At the end, you can find in the files/ directory a file called FoFOM.map calculated with the averaged phases, or just a file called next_for_use_1 (which is the same as model_1_rc3.brk) if you did not request averaging . Both can be used for running warpNtrace.sh, as explained in the next session, 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.

• This script basically utilises four other scripts: warp_build.sh calculates initial experimental maps and does the building of the free atoms, refiner.sh is the heart of the system and does all the actual refinement, shake.sh does extensive bad atoms rejection and the randomisation of coordinates, and finally, warp_average.sh does the actual averaging, if requested.