Hi Raj, Yes, autobuild can make an omit map excluding the region defined by your loop, and it can use that map in rebuilding the loop. The command you list below will do that.

I have a loop that was improperly built when I ran autobuild. the density according to the Fobs-Fcalc maps is not that great.

Someone told me that autobuild can use omit maps to build / rebuild the loops so you dont have to do it by hand.

Looking at the manual, I found the command, but am a little confused.

The model used is the entire model correct?

That is correct.

the target.pdb is the chain or region that was not correctly built.

Yes, that's right.

For iterative building...how many cycles should I go for?

A few cycles should do everything that will happen...say 2-4 cycles.

phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb \ composite_omit_type=iterative_build_omit

Note that this command was designed to make the omit map, omitting the target.pdb-defined region...however it will indeed rebuild your model in this region. It will set occupancies to 0.0 for atoms in the omit region and not include them in refinement as well. If you want you can take the resolve_composite_map.mtz from this omit procedure and use it as an input_map_file in a separate run of autobuild, with 1 cycle of rebuilding, to refine the model. Or you can just run phenix.refine on the model and data, after setting the occupancies back to 1.0. All the best, Tom T