[phenixbb] heavy atom sites in autobuild
Thomas C. Terwilliger
terwilliger at lanl.gov
Fri Dec 28 18:27:09 PST 2007
> 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 --
"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
This will keep the ligand atoms if model (pdb) and ligand overlap
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