[phenixbb] SA omit map

Pavel Afonine pafonine at lbl.gov
Wed Jul 6 08:45:12 PDT 2011

Hi Tjaar,

an easy and transparent way of doing what you want with just one command:

phenix.refin model.pdb data.mtz simulated_annealing=true 
modify_start_model.occupancies.set=0 modify_start_model.selection="chain 
A and resname LIG"

the residual map (Fourier map coefficients) in output MTZ file is the 
map you want (that you can open and see in Coot). The command 
phenix.mtz2map will convert this map into actual CCP4 or X-plor 
formatted map:


You can see the content of output MTZ file using phenix.mtz.dump command.

You should discard the output PDB file since will contain the ligand 
with zero occupancy.

> 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. 

This should be equivalent to what I described above, and if not then 
there is a problem that we need to fix.

> 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.

I don't know what this step does so can't comment.

Let me know if you have any questions or need help with this.


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