Dear Ernst, depositing raw data would add about 100 Bytes of storage per structure to the RCSB, about the length of a DOI. This is because there are existing repositories for data storage: data.sbgrid.org (only data related to an already published manuscript), zenodo.org, and a few more.
They may not have the capacity for serial crystallography data sets, but for the typical data set, they should be sufficient. In neither case to depositors have to pay. Best regards, Tim On Thursday, August 1, 2019 9:48:40 AM CEST 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/a > >rticles/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 > > > >######################################################################## > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://www.j > >iscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://www.ji > scmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> > Please consider the environment before printing this email. > > This transmission may be confidential or protected from disclosure and is > only for review and use by the intended recipient. Access by anyone else is > unauthorized. Any unauthorized reader is hereby notified that any review, > use, dissemination, disclosure or copying of this information, or any act > or omission taken in reliance on it, is prohibited and may be unlawful. If > you received this transmission in error, please notify the sender > immediately. Thank you. > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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