Dear Ernst,
There are several ways to deposit raw data, such as IRRMC, SBGrid and
Zenodo. The data are findable through a doi. During the depostion in the
PDB the doi linking to the raw data can be provided. See e.g.
http://www.ebi.ac.uk/pdbe/entry/pdb/5cy2 where is link to the raw data
in SBgrid is provided.
Best wishes,
Loes
On 08/01/19 09:48, Schonbrunn, Ernst wrote:
I totally agree with the deposition of raw data along with the
coordinate set(s). It is the only way to independently validate a
model that has been generated by somewhat subjective procedures of
data reduction and scaling, structure solution and refinement.
More importantly, algorithms and procedures steadily evolve, thanks to
you folks. Raw data of important structures re-processed using
future (or present) algorithms may result in much clearer pictures of
structure-function relationships than those of original interpretations.
What would be the best way to deposit raw data? How much would this
add to the storage and maintenance capabilities of RCSB? Likely
requires additional funding. If grant opportunities exist one could
make a strong case.
Ernst
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Kay
Diederichs
*Sent:* Thursday, August 1, 2019 1:54 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge
not relevant
First of all, you are of course correct, Rmerge (as Rmeas, Rpim,
CC1/2, I/sigma ...) is not detector-dependent.
Second, when looking at the "experiment" section of the PDB
deposition, I note that some Rmerge values are even given there! The
statistics there are dubious, e.g. seemingly the I/sigma in the high
resolution shell is 2.2 meaning that they could have used higher
resolution data.
Third, look at the sliders on the entry page: the validity of this PDB
entry is suspicious - quite bad Rfree and geometry.
One more case for the deposition of raw data. In my eyes, the RCSB
policy should be that raw data must be deposited when accepting such a
bad entry.
HTH,
Kay
On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane <wesl...@gmail.com
<mailto:wesl...@gmail.com>> wrote:
>I was looking at the following structure in the PDB:
http://www.rcsb.org/structure/6HR5
<http://www.rcsb.org/structure/6HR5> I noticed that the R/Rfree stats
were pretty high for 2.9A resolution so I followed up by looking for
the "Table 1" statistics in the journal article. Link to article:
https://www.nature.com/articles/s41589-019-0311-9
<https://www.nature.com/articles/s41589-019-0311-9> Table is located
in the supplemental materials "Table 9".
>
>From the processing statistics it's clear that the diffraction from
that crystal wasn't great but I don't want to get hung up on the
processing or the validity of the structure. What struck me what this
little explanation the authors included to explain the outlier
statistics in the table:
>
>"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge
data are not relevant."
>
>We all know that Rmerge isn't a great metric for data quality but
I've never heard that it's detector-dependent. This doesn't make sense
to me. If it's actually true can someone explain, please?
>
>Thanks!
>
>Wes
>
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__________________________________________
Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands
E-mail : l.m.j.kroon-batenb...@uu.nl
phone : +31-30-2532865
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