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 > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://www.jiscmail.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.jiscmail.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
