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). 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" :

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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Dear Pavel, onsdag den 6. juli 2011 skrev Pavel Afonine :

Hi Folmer,

I'm not sure I understand this. Isn't it a matter of displaying density: compute all but show on graphics only what you want?

Yes. But if people come from e.g. CNS they might not be used to thinking that way? (maps as mtz vs "calculated maps" representing specific parts of the Unit cell).

If you still want to compute density around selected atoms only then you can do it using phenix.maps: http://phenix-online.org/documentation/phenix_maps.htm

see "atom_selection" keyword in map {...} scope of parameters. Of course you can do it in the GUI too.

Yes, thats the way to do it. I just thought this was actually what Tjaard was asking, or at least this will help him. Best regards, Folmer

Pavel.

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). 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" : > 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

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