Lol
______________________________________________________
Rafael Marques da Silva
Mestrando em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +55 16 99766-0021
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> em nome de Bernhard Rupp
<hofkristall...@gmail.com>
Enviado: Friday, November 29, 2019 1:18:41 AM
Para: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Assunto: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
It has come to our attention that on this bulletin board insensitive and
hurtful comments have
been made towards animals with disability. Particularly concerning is the
display of white privilege
and racial bias towards a minority individual given that the turkey is also
referred to in German as 'Indian'.
In view of this non-inclusive and divisive display of unwokeness, the faculty
Bias Response Team
will contact you shortly and allow you to present your self-critique.
We want this board to remain a safe zone inclusive of all animals, complete or
not.
Stuffed, BR
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Jurgen Bosch
Sent: Thursday, November 28, 2019 13:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
Think of completeness with an analogy to turkey.
Say you happen to find a one-legged turkey (incomplete by conventional
standard) you could still stuff it and put it in the oven and enjoy 93% of the
turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)
Happy Thanksgiving everyone
Jürgen
P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & Kartoffelknödel
> On Nov 28, 2019, at 4:38 PM, Bernhard Rupp <hofkristall...@gmail.com> wrote:
>
> Sorry for being late on this thread -
>
> but the completeness myth is one of these conventional wisdoms I am
> seriously questioning and completeness as a global statistic is almost
> uninformative, short of telling you 'fewer than all recordable reflections up
> to the reported (likely isotropic) resolution limit given whatever (likely
> isotropic) cutoff was applied'. Sounds not very clear to me.
>
> Kay mentioned already that any information is better than no
> information, with the caveat that you cannot expect map quality (being
> an upper limit for model quality - not going into precision vs
> accuracy issue here) corresponding to the highest resolution reported, which
> is in reality frequently anisotropic (but not reported or reflected
> adequately in the PDB reports).
> We posted some remarks to this effect recently, pointing out that
> highly incomplete and anisotropic data can still yield limited but
> useful information as long as your claim remains correspondingly
> modest. Section 3.4 in
> http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
>
> Having said that, while random incompleteness is not problematic,
> systematic reciprocal space incompleteness leads to corresponding
> systematic real space effects on the map, the simplest being
> anisotropic data reflecting anisotropic reciprocal map resolution.
> This is different for example when wedges are missing or absence of serial
> extinctions makes space group determination more challenging (although we are
> almost in the age where 'record 360 deg of data and try every SG' works).
> James Holton has video examples for incompleteness effects and some images
> are also in my book.
> https://bl831.als.lbl.gov/~jamesh/movies/
>
> Cheers & Happy Thanksgiving, BR
>
> PS: A systemic rant regarding data quality representation can be found
> here
> https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
>
> ------------------------------------------------------
> Bernhard Rupp
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> ------------------------------------------------------
> All models are wrong
> but some are useful.
> ------------------------------------------------------
>
> -----Original Message-----
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Kay
> Diederichs
> Sent: Monday, November 25, 2019 08:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
>
> Dear Matthias,
>
> Of course, high completeness is better than low completeness.
> But as long as your low resolution is pretty much complete, there is no such
> thing as "too low completeness" at high resolution. Each reflection adds
> information to the map, and serves as a restraint in refinement.
>
> best,
> Kay
>
>
> On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke
> <oebbe...@staff.uni-marburg.de> wrote:
>
>> Dear ccp4 Bulletin Board,
>>
>> I collected a dataset at a synchrotron beamline and got the
>> statistics
>> (CORRECT.LP) after processing (using xds) shown in the attached
>> pdf-file.
>>
>> Do you think this dataset is usable, due to its low completeness? As
>> you can see in the attached file the completeness is just 50% in the
>> highest resolution shell, whereas the I over Sigma is above 2 and
>> also the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
>> Furthermore the overall statistic are good regarding R factor, CC 1/2
>> and I over Sigma. The only problem seems to be the completeness. If I
>> would set the cut-off at a lower resolution to get good completeness,
>> I would throw away nearly half of my reflections.
>>
>> I'm happy to here your opinion. In Addition to that: The space group
>> is orthorhombic and the dataset was collected over 120° using fine
>> slicing (0.1°).
>>
>>
>> Best regards,
>>
>> Matthias Oebbeke
>>
>>
>> --
>> Matthias Oebbeke, M.Sc.
>> Research Group of Professor Dr. G. Klebe Institute of Pharmaceutical
>> Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg,
>> Germany
>> Phone: +49-6421-28-21392
>> Mail: oebbe...@staff.uni-marburg.de
>> www.agklebe.de<http://www.agklebe.de>
>>
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