Using Molecular Replacement Solutions (#1)

The script arp_molrep.sh 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 2.0 Å resolution, it might not be a bad idea to run warpNtrace.sh, which will auto-build a new model and will keep on auto-building, thus providing a significantly higher radius of convergence.

Anyway, to start it just run arp_molrep.sh. 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 copying your latest file to a file called next_for_use_1.brk and run shake.sh 1. This will reject a load of badly placed atoms and might well make life much easier. If too many atoms get rejected shake.sh 2 should be preferred.

• Some rigid body refinement of your molecular replacement solution for example with REFMAC seems to us a brilliant idea.