mode molrep: using Molecular Replacement solutions

The mode molrep is the one to run if you already have a reasonable model from Molecular Replacement. This script will use the model for providing geometrical restraints to the refinement. If your model isn't so brilliant, but you have data to at least 2.3 Å resolution, it may be not a bad idea to run mode warpNtrace, see above.
Anyway, to start it just run arp_warp.sh mode molrep. You will see that you will be asked for two files: One should contain the model (molrep.brk) and the other some PROTIN commands (protin.custom) for setting up proper restraints (see below in the paragraph for solvent building).
Tricks and Tips

• If your refinement gets stuck for whatever reasons, try the shake.sh script (see below).
• Some rigid body refinement of your molecular replacement solution for example with REFMAC seems to us a brilliant idea.