[phenixbb] heavy atom sites in autobuild

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Dec 28 18:27:09 PST 2007

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


This will keep the ligand atoms if model (pdb) and ligand overlap

Good luck!
-Tom T

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