[phenixbb] data fill in in phenix refine?
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.
> 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.
>> 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 Schulze-Gahmen, Ph.D.
>>> Project Scientist
>>> UC Berkeley, QB3
>>> 360 Stanley Hall #3220
>>> Berkeley, CA 94720-3220
>>> (510) 643 9491
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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