Yes, the validation is created to help prevent this. But the PDB is not the police, in the end it is up to the authors to take care of the validation warnings (or not). The PDB cannot refuse a deposition. You could argue that they should, and I would tend to agree that they could be a bit stricter. At the same time, where would one draw the line? Somewhere between clear error (i.e. a main chain in the wrong place) and a trivial difference of opiinion (little blob of density that could be a partially occupied water), but exactly where?
Mark J van Raaij Dpto de Estructura de Macromoleculas, lab B5 Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 2 Jun 2025, at 15:05, Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com> > 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 <CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Nikolas > Sent: Friday, May 30, 2025 5:31 PM > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > 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 > > > 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. Any unauthorized use > or disclosure of the contents of this message is not permitted and may be > unlawful. > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
