mode solvent n: Solvent Building

When you have a complete protein model, all you have to do is to copy it to the files/ directory, under the name final_model_0.brk. Then you run arp_warp.sh mode solvent 0. This will run for as many cycles as are indicated for restrained refinement in the warp.par file. Then the script will create a file called final_model_0_waters.brk. You can go to the graphics, look at this file and modify if necessary. If you want more water-finding cycles, copy this last file to a file called final_model_1.brk and continue as previously described.
You also need a file called protin.custom placed in your work directory, which should look like:

CHNNAM ID A CHNTYP 1
CHNNAM ID W CHNTYP 2
CHNTYP 1 NTER 1 MET 3 CTER 52 ALA 2
CHNTYP 2 WAT
Refer to the CCP4 protin.doc for how to define chains, etc.
Tricks and Tips

• The current scripts do not allow to customise REFMAC very extensively. If you need to do that, then you hate automated scripts, so please read the relevant section.