Re: [phenixbb] SA omit map

6 Jul 2011


      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
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
-- 
Folmer Fredslund
Maj Allé 86
2730 Herlev
Mobil: (+45) 61 468 009
Mail: [email protected]