Ernst,
Depositing images is very easy these days with services like SbGrid,
proteindiffraction.org (also known as IRRMC), and Zenodo.
For example, for depositing images to proteindiffraction.org (which is
run by Wladek Minor) you just need to create an account, tar your
images, upload them to the server, and specify the PDB code. All the
metadata will be extracted and curated by the server. And you dont even
need to tell the DOI of the dataset to the PDB - RCSB will automatically
communicate to proteindiffraction.org and link the PDB entry to the
DOI. In this scenario, the deposition to the PDB goes first, and the
deposition of images goes second.
Thanks,
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 8/1/19 03:48, 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 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 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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