[phenixbb] SA Fo-Fc omit map

Mengbin Chen mengbinc at sas.upenn.edu
Tue Dec 11 13:42:42 PST 2012

Dear Phenix Users,

I have been playing around with Phenix AutoBuild GUI to generate a fo-fc sa
omit map of the ligand in a protein structure, and I have the input files
as follows:

output.mtz (data type:experimental data)
ligand.pdb (data type: omit box atoms & ligands)
ligand.cif (data type: restraints of the ligand)
protein.pdb (data type: starting model)

omit map type: simulated annealing
omit region: omit around PDB fie

I have set the occupancies of all ligand atoms zero and deleted the ligand
coordinates in my starting model. After the run finished and I checked the
refined coordinates and map.mtz in COOT, I found that there was no electron
density around the ligand while the protein model was in electron density,
which was exactly opposite of what I wanted before. Furthermore, I have 3
Mg2+ ions in protein.pdb file, all of which moved away from where they were
after the refinement run, which was not wanted either.

Could anyone tell me how to do the sa omit map of ligand correctly?

Thanks in advance!

Mengbin Chen
Department of Chemistry
University of Pennsylvania
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