I agree. We must remember, people are human, they have lives and can and most likely make mistakes.
Many metrics are also open to interpretation, even the PDB shows a quality and percentile rank (relative to all and close resolutions), but it doesn’t tell anyone if its "bad" or "good" that is a human judgement call. The PDB is not there to decide what is good and what is bad, just a depository that allows discussions like this to occur. -- Kelvin Lau https://people.epfl.ch/kelvin.lau <https://people.epfl.ch/kelvin.lau> Scientist - Protein production and structure core facility – PTPSP Co-President – EPFL Scientific Staff Association – ELSA EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: [email protected] <mailto:[email protected]> Phone: +41 21 69 30267 <tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494 <tel:+41%2021%2069%C2%A030267> On 02.06.2025, 17:14, "CCP4 bulletin board on behalf of Phil Jeffrey" <[email protected] <mailto:[email protected]> on behalf of [email protected] <mailto:[email protected]>> wrote: I really don't think that 22% R-free AT 2.0 Å constitutes "gross disagreement" barring deliberate data manipulation, although it doesn't eliminate the possibility of significant errors in lower quantities. The review-quality validation report should report bad fits to density (although somewhat exaggerated at time) but I don't think it has an assay of difference density peaks (say >5 sigma) that were not fit. Perhaps a coot-like list of unmodelled blobs would be a worthy addition. I doubt the validation protocol would find, e.g., mis-assignment unless it happened at a large scale, and the areas that it's more likely to occur (partly disordered) aren't going to show a strong signal. Hard to replace the human brain when trying to interpret ambiguous regions. Phil Princeton On 6/2/25 9:05 AM, Oganesyan, Vaheh wrote: > Hello, > > All suggestions on what and how to handle this case are good. However, > aren’t we missing a major point? > > How could a model that exhibits gross disagreement with data be allowed > in PDB? Isn’t validation protocol created to prevent cases like this? > > Vaheh > > *From:*CCP4 bulletin board <[email protected] > <mailto:[email protected]>> *On Behalf Of *Nikolas > *Sent:* Friday, May 30, 2025 5:31 PM > *To:* [email protected] <mailto:[email protected]> > *Subject:* [ccp4bb] How to address deposited structures poorly modeled? > > *enters the BB and kneels in reverence* > > Dear BB, > > Recently, delving among papers and structures for a current project, I > came across a deposited structure of interest that is terribly modeled. > In the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the quality > indicators are not terrible but upon opening it and checking the maps > there are some severe mistakes in the modeling. > > For instance, a full chain that is in the negative Fo-Fc while positive > density is present, some density that is quite clear for SO4 molecules > (buffer) modeled as water and density for water molecules neglected. > Some parts seem like “coot:runwater” has been used and not checked. The > catalytic site is well defined. > > Now, I’ve started my journey in crystallography not too long ago and > I’ve got many years, structures to solve and things to learn, and I know > that sometimes the dataset “is what it is” but these seems quite big > mistakes. Especially because I’ve worked with such proteins before and I > know the systems. > > My question thus is: would it be right to contact the author of this > structure and point to these issues? What’s the best way to address such > things, possibly without coming off as obnoxious? > > Thank you for your wisdom. > > Cheers, > > Nikolas > > *bows and leaves the BB* > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> > > ------------------------------------------------------------------------ > > *Confidentiality Notice: *This message is private and may contain > confidential and proprietary information. If you have received this > message in error, please notify us and remove it from your system and > note that you must not copy, distribute or take any action in reliance > on it. 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