Hi Bryan,

i'm confused about treatment of heavy atom sites in autobuild. couple questions :

1. since heavy atom sites can be treated as single atoms, should phenix.autobuild simply refine the positions within a protein model? i.e. heavy atom sites should not need to be treated as ligands, with a .cif -- right?

"should" is unfortunately not the same as "does"... AutoBuild needs to strip off all HETATMs (waters, single atoms, ligands etc) before rebuilding, because resolve model-building doesn't know anything about any of these. Then the AutoBuild wizard puts these atoms back in the file for refinement.

2. if i want autobuild to build around the heavy atom site, can i just use input_pdb_file=heavy.pdb? input_lig_file_list= is not working.

I'm guessing you mean "not build on top of the heavy atom site". In this case you can use input_lig_file_list=heavy.pdb and also specify keep_pdb_atoms=False This will keep the ligand atoms if model (pdb) and ligand overlap Good luck! -Tom T