[phenixbb] SA omit map

[Folmer Fredslund]

Dear Pavel,



onsdag den 6. juli 2011 skrev Pavel Afonine <pafonine at lbl.gov>:
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>     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" <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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>         > phenixbb at phenix-online.org
>         > http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
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-- 
Folmer Fredslund
Maj Allé 86
2730 Herlev
Mobil: (+45) 61 468 009
Mail: folmerf at gmail.com