Hi Nikolas, There are many reasons for PDB entries to be worse then they could be. The most obvious is just that when the models were made the tools were not as easy to use as now and the depositors were less experienced then they are now. This is natural and, as Guillaume mentioned, to some extent PDB-REDO can help here. Sometimes a lot, sometimes surprisingly little and on rare occasions even making things worse (tell me if you find such a case). There now is a related effort from Foldot where the community is encouraged to treat a specific PDB entry as a model versus map puzzle. If the models from that are clearly better than the PDB model (e.g. for the chain you mention) then it will drip through to PDB-REDO.
Another reason for models appearing worse then expected is simple mix-ups. I have seen cases where just an older version of the model, rather than the final version, was deposited by accident. Also in series of structures there are sometimes mix-ups where the wrong set of reflections were uploaded making the map look terrible in relation to the model. These cases you can sometimes tell from the cell dimensions and resolution of the reflection data. I found a case of that last year, contacted the depositors and they updated their PDB entry with te help of te PDB annotators. A friendly email can work miracles is you have a good estimate of what is going on. I'm sure there are many cases where people were just rushed into depositing an unfinished model. We all know the pressures in our line of work. It is not pretty, but understandable. Sometimes the models can be fixed by automated means, sometimes it requires a bit more work. The depositors may be quite well-willing to update their model if you take some of the burden of fixing it out of their hands. Then there are cases where there is genuine incompetence. That is, the depositor really didn’t know they were doing things wrong or their supervisor didn't supervise well (or at all). Sometimes reaching out to the depositor can help (I have seen successful cases of that), but you may run into significant resistance. Nobody likes to be told, however nicely, that they were wrong. Here it also really matter whether the model is just suboptimal or it really leads to wrong conclusions or, even worse, has lead to the wrong conclusions. You risk putting yourself in a situation where you have to tell someone that this part of their paper is wrong because the model is wrong. You can reach out to the authors b hind the scenes, but it is also legitimate to just in your scientific work on the topic mention the issue a set the record straight without making it personal. You can also use such examples for teaching to make sure the new generation is more competent. All in all these are cases not just examples of individual failure but also of a failure of us as a community. In the long run, leading by example by making sure your students are well trained and supervised is key. CCP4 organises a lot of courses in crystallography where we help people improve their skill and knowledge in the matter. I am of course completely biased, but I highly recommend such courses. Indifference is another reason for poor models in the PDB. The part of the model in which the depositors were interested is perfectly fine but the rest clearly lacks attention. Without knowing any of the details, the model you mention may fall in this category. You may be able to get in touch with the depositors to update the model, but don't hold your breath. If it is an older model (pre 2008) just appreciate that they were bothered to deposit the model and data at all. If the model answered the scientific question for which the model was made correctly, then it is a sound model. It's just not that useful for other applications. Devil's advocate: who are we to decide that other researchers shut invest resources into improving a model beyond what is needed for their primary research? The final category is malevolence. Yes, there are cases in the PDB where people purposely deposited worse models than what they describe in the paper. I call that molecular crippleware. Most of the cases predate 2008 although there was one case after that about which I complained to the PDB. Unfortunately there was very little they could do. There were also documented cases of outright fraud, but these models actually appeared (in some aspects at least) quite alright. My opinion about the depositors of such models is not suitable for this public forum. Anyway, good of you to reach out to the bulletin board and keep fighting the good fight. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <[email protected]> On Behalf Of Nikolas > Sent: Friday, May 30, 2025 23:31 > 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 ######################################################################## 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/
