[phenixbb] phenix real space refine & free R reflections
Tristan Croll
tic20 at cam.ac.uk
Fri May 5 08:26:29 PDT 2017
This is essentially what I do by default when making real-space maps to
work with. The relevant portion(s) of my maps.params file for
phenix.maps would typically look like:
map {
map_type = 2mFo-DFc
format = xplor *ccp4
file_name = None
fill_missing_f_obs = True
grid_resolution_factor = 1/4.
region = *selection cell
atom_selection = None
atom_selection_buffer = 10
sharpening = False
sharpening_b_factor = None
exclude_free_r_reflections = True
isotropize = True
}
Cheers,
Tristan
On 2017-05-05 15:54, Edward A. Berry wrote:
> On 05/05/2017 05:01 AM, Hillen, Hauke wrote:
>> Dear Phenix bb,
>>
>> I have a rather conceptual question regarding the treatment of free R
>> flags in phenix.refine and phenix.real_space_refine. I am refining an
>> xray structure using phenix.refine (but not using the real space
>> refinement implemented there) and at some point decided to play a bit
>> with the standalone program phenix.real_space_refine. In particular, I
>> was interested in testing real space refinement against different maps
>> (experimental map vs. model-phased). Being used to the excellent
>> handling of free R flags in Phenix, I assumed giving
>> phenix.real_space_refine the output MTZ of a previous phenix.refine
>> run as a map would be safe to do. But I then saw the phenix.refine FAQ
>> states the following:
>>
>> "Are R-free flagged reflections included in the maps used for
>> real-space refinement?
>> No, this is almost guaranteed to bias R-free; these reflections are
>> removed internally prior to map calculation. However, the output maps
>> will include these reflections unless you explicitly request
>> otherwise.”
>>
>> While it makes sense to me that including the free reflections in the
>> maps used for real space refinement will bias R-free, I wonder why the
>> default behavior of phenix.refine is to output maps which include
>> these reflections. I assume most users will use these output maps (for
>> example via the OPEN IN COOT button in the GUI) to iteratively improve
>> their model by local real space refinement in Coot. Conceptually, how
>> is real space refinement performed by phenix.refine (where the free R
>> reflections are not used to calculate the map to refine against)
>> different from manual local real space refinement in Coot? Will the
>> latter not also bias R-free when the default output maps from
>> phenix.refine are used?
>>
>
> I would argue just the opposite- free reflections should be included
> in the maps used for RS refinement. Excluding free reflections is the
> same as setting them to zero amplitude, so you are still biasing these
> reflections, just biasing them toward a drastically wrong value (zero)
> instead of biasing them toward fobs.
>
> If the evidence for bias is that R-free gets "better" when you include
> the free reflections, isn't it more because you avoid biasing them
> toward zero than because you do bias them toward the Fobs? In the case
> of density modification, which has the same problem, Ivan Rayment*
> showed the importance of using the "fill-in" method for missing
> reflections in making maps. That would seem to be the correct way of
> implementing R-free for density modification or real-space refinement:
> you don't give away your Fobs, but at the same time you don't keep
> forcing the free reflections toward zero.
> *Acta Crystallogr B. 1983 Aug;39(4):505-516.
> Acta Cryst. (1983). A39, 102-116
>
> eab
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