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 correctly).

Den 06/07/2011 17.46 skrev "Pavel Afonine" <[email protected]>:
> 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.
>
> _______________________________________________
> phenixbb mailing list
> [email protected]
> http://phenix-online.org/mailman/listinfo/phenixbb