[phenixbb] SA omit map

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Sep 10 20:52:14 PDT 2009

Hi Pascal,

I think that if you are only concerned about one ligand then there are
four overall options.  The first, going back before you added the ligand,
is likely to be the least biased, then the iterative-build omit, then the
SA-omit and kicked maps. The iterative-build omit map is probably the best
way to get rid of bias once it has been introduced, but it is also very
computationally intensive.

As you are only interested in the ligand, you probably do not need to do a
composite map, saving you a lot of time.

So the options are:

1. You can go back to the structure you had just prior to adding that
ligand, and simply refine that structure and look carefully at the maps.
As the structure has never seen the ligand, you have no worries about bias
at all in that map.  Of course that map may be from a much earlier stage,
so it may not be so clear either...leading to the other options of..

2. Take your current structure and run an SA-omit map or an
iterative-build omit map, omitting around a PDB file that you create that
contains only the ligand.

3. Or, pretty much equivalent to #2,  you can remove your ligand from the
structure and just do a run of SA or rebuild-in-place and calculate a map,

4. Or you can calculate a kicked map. For the kicked map, quoting Pavel

in your parameter file just add another map scope to the
electron_density_maps scope, like this:

  electron_density_maps {
    map {
      mtz_label_amplitudes = "2FOFCWT_kick"
      mtz_label_phases = "PH2FOFCWT_kick"
      likelihood_weighted = True
      obs_factor = 2
      calc_factor = 1
      kicked = True
      fill_missing_f_obs_with_weighted_f_model = False
    map {
      mtz_label_amplitudes = "FOFCWT_kick"
      mtz_label_phases = "PHFOFCWT_kick"
      likelihood_weighted = True
      obs_factor = 1
      calc_factor = 1
      kicked = True
      fill_missing_f_obs_with_weighted_f_model = False

This will create two additional kick maps in addition to the default maps.

All the best,
Tom T

 , >> Dear All,I have a theoretical/practical question about omit maps and
>> refinement.
>> I am completing the refinement (in Phenix) of a protein-ligand complex at
>> 1.3A resolution. I solved it by MR and automatic rebuilding of the protein
>> alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after
>> TLS and water-picking in Phenix. The model includes everything protein,
>> water, ligand and some ions.
>> However I have some slight doubts one region in my ligand.
>> What would be the best map, less biased, to look at this "very late" stage
>> of the refinement. Are  composite or systematic SA omit map useful options
>> at this stage ?
>> Thanks a lot in advance
>> Pascal F. Egea, PhD
>> Assistant Professor
>> UCLA, David Geffen School of Medicine
>> Department of Biological Chemistry
>> 314 Biomedical Sciences Research Building
>> office (310)-825-1013
>> lab (310)-825-8722
>> email pegea at mednet.ucla.edu
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list