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Hi Kendall,<br>
<br>
could you please try the same command using the latest PHENIX from
nightly builds:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/nightly_builds.cgi">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
?<br>
<br>
I hope this will solve the problem, but please let me know if not.<br>
<br>
Pavel.<br>
<br>
<br>
On 9/11/09 7:41 AM, Kendall Nettles wrote:
<blockquote cite="mid:C6CFD9E3.160F6%25knettles@scripps.edu" type="cite">
<title>Re: [phenixbb] SA omit map</title>
<font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;">I
got an error in my refinement when I added the map scope below to my
refinement parameters file:<br>
<br>
Traceback (most recent call last):<br>
File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py",
line 9, in <module><br>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])<br>
File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py",
line 86, in run<br>
map_manger = refine_object.open_map_files()<br>
File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py",
line 949, in open_map_files<br>
return map_manager(refine_object=self)<br>
File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py",
line 1151, in __init__<br>
self.map_type_labels.append(self.map_to_str(emap))<br>
File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py",
line 1177, in map_to_str<br>
if(abs(emap.obs_factor-int(emap.obs_factor))>1.e-4):<br>
TypeError: int() argument must be a string or a number, not 'NoneType'<br>
<br>
<br>
Any suggestions? I’m still learning the syntax, so I wonder if I missed
something? My parameters are listed below. <br>
<br>
Best Regards,<br>
Kendall Nettles <br>
<br>
<br>
</span><font size="2"><span style="font-size: 10px;">refinement.main {<br>
ordered_solvent=true<br>
}<br>
refinement.refine {<br>
strategy = *individual_sites \<br>
rigid_body \<br>
*individual_adp \<br>
group_adp \<br>
tls \<br>
*occupancies \<br>
group_anomalous \<br>
none<br>
adp {<br>
individual {<br>
isotropic = All<br>
anisotropic = None<br>
}}}<br>
<br>
refinement.ncs {<br>
find_automatically = False<br>
excessive_distance_limit=3<br>
restraint_group {<br>
reference = chain A and (resid 306:329 or resid 332:461 or resid
465:526 or resid 533:546 ) <br>
selection = chain B and (resid 306:329 or resid 332:461 or resid
465:526 or resid 533:546 )<br>
<br>
}<br>
<br>
restraint_group {<br>
reference = chain C and (resid 306:329 or resid 332:461 or resid
471:526 or resid 533:546 ) <br>
selection = chain D and (resid 306:329 or resid 332:461 or resid
471:526 or resid 533:546 )<br>
}<br>
}<br>
<br>
refinement{ <br>
electron_density_maps {<br>
map_format = *xplor<br>
map_coefficients_format = *mtz phs<br>
suppress = None<br>
map {<br>
mtz_label_amplitudes = "2FOFCWT_kick"<br>
mtz_label_phases = "PH2FOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 2<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = False<br>
}<br>
map {<br>
mtz_label_amplitudes = "FOFCWT_kick"<br>
mtz_label_phases = "PHFOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 1<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = False<br>
}<br>
<br>
}}<br>
</span></font><span style="font-size: 12px;"><br>
<br>
<br>
On 9/10/09 11:52 PM, "Thomas C. Terwilliger"
<a class="moz-txt-link-rfc2396E" href="mailto:terwilliger@lanl.gov"><terwilliger@lanl.gov></a> wrote:<br>
<br>
</span></font>
<blockquote><font face="Verdana, Helvetica, Arial"><span
style="font-size: 12px;">Hi Pascal,<br>
<br>
I think that if you are only concerned about one ligand then there are<br>
four overall options. The first, going back before you added the
ligand,<br>
is likely to be the least biased, then the iterative-build omit, then
the<br>
SA-omit and kicked maps. The iterative-build omit map is probably the
best<br>
way to get rid of bias once it has been introduced, but it is also very<br>
computationally intensive.<br>
<br>
As you are only interested in the ligand, you probably do not need to
do a<br>
composite map, saving you a lot of time.<br>
<br>
So the options are:<br>
<br>
1. You can go back to the structure you had just prior to adding that<br>
ligand, and simply refine that structure and look carefully at the maps.<br>
As the structure has never seen the ligand, you have no worries about
bias<br>
at all in that map. Of course that map may be from a much earlier
stage,<br>
so it may not be so clear either...leading to the other options of..<br>
<br>
2. Take your current structure and run an SA-omit map or an<br>
iterative-build omit map, omitting around a PDB file that you create
that<br>
contains only the ligand.<br>
<br>
3. Or, pretty much equivalent to #2, you can remove your ligand from
the<br>
structure and just do a run of SA or rebuild-in-place and calculate a
map,<br>
<br>
4. Or you can calculate a kicked map. For the kicked map, quoting Pavel<br>
Afonine:<br>
<br>
in your parameter file just add another map scope to the<br>
electron_density_maps scope, like this:<br>
<br>
electron_density_maps {<br>
map {<br>
mtz_label_amplitudes = "2FOFCWT_kick"<br>
mtz_label_phases = "PH2FOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 2<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = False<br>
}<br>
map {<br>
mtz_label_amplitudes = "FOFCWT_kick"<br>
mtz_label_phases = "PHFOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 1<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = False<br>
}<br>
}<br>
<br>
This will create two additional kick maps in addition to the default
maps.<br>
<br>
All the best,<br>
Tom T<br>
<br>
<br>
, >> Dear All,I have a theoretical/practical question about omit
maps and<br>
>> refinement.<br>
>> I am completing the refinement (in Phenix) of a protein-ligand
complex at<br>
>> 1.3A resolution. I solved it by MR and automatic rebuilding of
the protein<br>
>> alone first then built in the ligand. Rfree and Rfac are
19.4%/18.2% after<br>
>> TLS and water-picking in Phenix. The model includes everything
protein,<br>
>> water, ligand and some ions.<br>
>> However I have some slight doubts one region in my ligand.<br>
>> What would be the best map, less biased, to look at this "very
late" stage<br>
>> of the refinement. Are composite or systematic SA omit map
useful options<br>
>> at this stage ?<br>
>><br>
>> Thanks a lot in advance<br>
>><br>
>><br>
>> Pascal F. Egea, PhD<br>
>> Assistant Professor<br>
>> UCLA, David Geffen School of Medicine<br>
>> Department of Biological Chemistry<br>
>> 314 Biomedical Sciences Research Building<br>
>> office (310)-825-1013<br>
>> lab (310)-825-8722<br>
>> email <a class="moz-txt-link-abbreviated" href="mailto:pegea@mednet.ucla.edu">pegea@mednet.ucla.edu</a><br>
>> _______________________________________________<br>
>> phenixbb mailing list<br>
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>><br>
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