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]> On Behalf Of Nikolas Sent: Friday, May 30, 2025 5:31 PM To: [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> ________________________________ 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 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/
