Hmmm - of course you are free to contact the authors and explain what you have found. There are many sub-optimal structures deposited and the pdb tries to validate them ; more strictly now than in the past .
In this case I would refer to the pdb-redo site and check if that has corrected some errors . Then if necessary, and if you want to use the structure in some way, re-refine it yourself. That is the beauty of the PDB deposition - we can all access and use the data for our ends. Thank you - PDB ancestors! Eleanor On Fri, 30 May 2025 at 22:30, Nikolas <[email protected]> wrote: > *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 > ######################################################################## 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/
