[phenixbb] SA omit map

[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?

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.

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" <pafonine at lbl.gov 
> <mailto: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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>
>
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