[phenixbb] data fill in in phenix refine?

Pavel Afonine pafonine at lbl.gov
Thu Oct 26 08:29:06 PDT 2017

This only influences maps. Filled in reflections are not used in refinement.

On 10/26/17 08:26, Edward A. Berry wrote:
> Just to clarify, is it the case that this "fill-in" issue only affects 
> the maps? The warning that Ursula quoted, which I find overly 
> alarmist, would seem to imply the use of filled-in reflections by the 
> refinement program, which (I think) is nonsense.
> eab
> On 10/26/2017 09:43 AM, Pavel Afonine wrote:
>> 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.
>> Pavel
>> 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
>>> _______________________________________________
>>> phenixbb mailing list
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