[phenixbb] SA omit map

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Sep 11 07:13:18 PDT 2009


Hi Frank and Pascal,
I would agree with Frank's point. In general I have been hard-pressed to
see significant bias in finished recent structures in the PDB at any
resolution.  In our paper on iterative-build omit maps I got some help
from Gerard Kleywegt to find the structure that we used as an example with
significant model bias.
All the best,
Tom T

. >> Óf course, at 1.3A resolution, chances are pretty slim that your
>> structure is riddled with bias -- so you probably will just have to suck
>> it up that part of your ligand is disordered.
>>
>> (By all means, try these suggestions - but bias things start rearing
>> their head above 2-ish, and it's when you're heading towards 3 that you
>> *seriously* need these tools.)
>> phx
>>
>>
>>
>>
>> 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 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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>>
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