Robbie Joosten wrote:
Hi Martyn,I think the question is where the error was made - seeing the uploaded file would clear this up. But it seems unlikely to me that the depositor saw a huge R factor discrepancy at the end of refinement and just blithely uploaded it. So scenario 3 :- PDB : we cannot reproduce your R factor with our programs Depositor : that's your problem mate - it was fine when it left me...up to you to sort it... Which seems a sort of reasonable attitude to me.
Not quite, the depositor has to give, i.e. type, the space group (example depositions: https://www.ebi.ac.uk/pdbe-xdep/autodep/AutoDep?param=QovCsvhNv06Mpnr%2BvIkqqfuqeeBd8leFNAVymZgS%2Fe7mULyfrCaTMN8jsyaGZUTyUDQyN3gMF3o%3D). Don't ask me why, because it is clearly a source of error.
In my experience with RCSB autodep2, assuming the information was in the uploaded pdb file, this information is already pre-filled and the depositor just glances over to see it is correct. A missing or extra "(1)" might not be noticed. So perhaps it is a parsing error, perhaps related to the different ways the space group is represented on the CRYST1 card, and the different stringency of different programs in interpreting the CRYST1 card. But the validation report is included with the approval request letter, and major discrepancies are noted in the text of the validation letter in case the depositor is too busy to actually read the validation report. So if the depositor read more than the first line or two of the letter he should have known there was a problem. Then there is the 2-week default release policy: "No major issues were raised during data processing. A summary of some of the key annotations in your entry is shown below. Please verify that these are correct. If we do not hear from you within two weeks, we will consider this entry to have been approved by you. The entry will then be released according to the release/hold instructions you have provided." If this 2-week default release is the rule even when there are issues, the depositor may have put it aside to find the problem when time was available, and waited too long and let the default release kick in. eab
