[phenixbb] data fill in in phenix refine?

Pavel Afonine pafonine at lbl.gov
Thu Oct 26 06:43:47 PDT 2017

Hi All,

I addressed some of these questions off-list, and now I realize I've 
never replied to the list. In summary:

- phenix.refine always outputs two sets of 2mFo-DFc, using original Fo 
and complete set with missing reflections filled in. In case of using 
data massaging tools, such as STARANISO or UCLA anisotropy correction 
servers, it's best to inspect both maps, because in some cases "filled 
map" may be more model biased than the other one. Note, Coot load filled 
map by default, so you will need to load the other one manually.

- If using massaged data, please make sure to deposit both, massaged and 
original reflection data.

- If using massaged data, it may be desirable to do the final refinement 
run using all data.


On 10/13/17 11:47, Ursula Schulze-Gahmen wrote:
> I have data from a crystal with anisotropic diffraction. After scaling 
> and merging using the webserver staraniso, I would like to refine 
> using phenix refine. Could you tell me if phenixrefine will try to 
> fill in the missing reflections that were removed in the staraniso 
> procedure? If so, is there a a way to prevent this fill in? Following 
> is the warning message for the Staraniso server:
> We are grateful to Andrew Leslie (MRC-LMB) for identifying a 
> potentially undesirable 'feature' of CCP4/REFMAC (and possibly other 
> refinement software), namely the 'fill-in' of unobserved data with 
> /DF/calc which makes it effectively /incompatible/ with the MTZ file 
> output by STARANISO.  Our advice is therefore to use *BUSTER 
> <http://www.globalphasing.com/buster>* for refinement using the 
> downloaded MTZ file, unless the user can find a way to disable that 
> feature in the alternative software.
> In general, any treatment of STARANISO's output data that adds missing 
> reflections out to the resolution limit may result in a very high 
> proportion of unobserved data compared with data that have had a 
> cut-off applied according to an isotropic criterion.  Where missing 
> reflections have been added in this way the user should take care to 
> verify that any applications used to process the data subsequently can 
> handle it correctly.
> Ursula
> -- 
> Ursula Schulze-Gahmen, Ph.D.
> Project Scientist
> UC Berkeley, QB3
> 360 Stanley Hall #3220
> Berkeley, CA 94720-3220
> (510) 643 9491
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