[phenixbb] SA omit map

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Fri Sep 11 02:31:18 PDT 2009


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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