[phenixbb] SA omit map

Folmer Fredslund folmerf at gmail.com
Wed Jul 6 08:56:28 PDT 2011

Dear Pavel,
This would still yield "normal" density in the entire unit cell. It seems to
me that Tjaard wants a map covering only the ligand (if I understand

Using my phone, so I can't comment on what phenix programs would be good.

Venlig hilsen
Folmer Fredslund
(and sorry for top posting)
Den 06/07/2011 17.46 skrev "Pavel Afonine" <pafonine at lbl.gov>:
> 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:
> http://phenix-online.org/documentation/mtz2map.htm
> 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.
> Pavel.
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