[phenixbb] SA omit map
Pavel Afonine
PAfonine at lbl.gov
Fri Sep 11 08:16:32 PDT 2009
Hi Kendall,
could you please try the same command using the latest PHENIX from
nightly builds:
http://www.phenix-online.org/download/nightly_builds.cgi
?
I hope this will solve the problem, but please let me know if not.
Pavel.
On 9/11/09 7:41 AM, Kendall Nettles wrote:
> 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" <terwilliger at lanl.gov> 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 pegea at mednet.ucla.edu
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >>
>
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