Re: [phenixbb] SA omit map

11 Sep 2009

      I got an error in my refinement when I added the map scope below to my refinement parameters file:

Traceback (most recent call last):
  File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 86, in run
    map_manger = refine_object.open_map_files()
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 949, in open_map_files
    return map_manager(refine_object=self)
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1151, in __init__
    self.map_type_labels.append(self.map_to_str(emap))
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1177, in map_to_str
    if(abs(emap.obs_factor-int(emap.obs_factor))>1.e-4):
TypeError: int() argument must be a string or a number, not 'NoneType'

Any suggestions? I'm still learning the syntax, so I wonder if I missed something? My parameters are listed below.

Best Regards,
Kendall Nettles

refinement.main {
    ordered_solvent=true
}
refinement.refine {
    strategy = *individual_sites \
                rigid_body \
                *individual_adp \
                group_adp \
                tls \
                   *occupancies \
                   group_anomalous    \
                none
   adp {
      individual {
        isotropic = All
        anisotropic = None
      }}}

refinement.ncs {
find_automatically = False
excessive_distance_limit=3
restraint_group {
    reference = chain A and (resid 306:329 or resid 332:461 or resid 465:526 or resid 533:546 )
    selection = chain B and (resid 306:329 or resid 332:461 or resid 465:526 or resid 533:546 )

}

restraint_group {
    reference = chain C and (resid 306:329 or resid 332:461 or resid 471:526 or resid 533:546 )
    selection = chain D and (resid 306:329 or resid 332:461 or resid 471:526 or resid 533:546 )
    }
}

refinement{
 electron_density_maps {
    map_format = *xplor
    map_coefficients_format = *mtz phs
    suppress = None
    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
    }

         }}

On 9/10/09 11:52 PM, "Thomas C. Terwilliger"  wrote:

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
Afonine:

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 [email protected]
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