[phenixbb] SA omit map

Tjaard Pijning t.pijning at rug.nl
Wed Jul 6 06:30:05 PDT 2011


I would like to generate an SA-omit Fo-Fc map for a ligand bound to protein.
Using the GUI I selected the AutoBuild-Create Omit Map module and set the 
following :
- data.mtz
- protein.pdb (no ligand, no solvent) = start model
- ligand.pdb (just ligand) = omit map atoms
- omit map type = simulated annealing
- omit region = omit around pdb
The resulting map (/OMIT/resolve_composite_map.mtz) shows density for both 
the protein and the ligand. When I feed this into the CCP4 module FFT to 
generate an nF1-mF2 map (with n=1 and m=1) I still get density for both the 
protein and ligand. However I need only the ligand Fo-Fc density.
What is the right way to do this ?


Ing. Tjaard Pijning
Research Assistant
Protein Crystallography Group
Nijenborgh 7
9747 AG Groningen
The Netherlands
(31)(0)50 363 43 85 

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