Hi Nikolas, I don’t know much about crystallography beyond the big picture from school. But with cryoEM structures, the class of big problems you described in your first email can be detected from the validation report only, especially from the pictures of map and model overlayed, and from the per-residue Q-scores mapped to the sequence and model. The atom inclusion plot at the recommended contour level is also a quick way to detect if large parts of the model are out of density (but less visual). Of course, direct inspection of the map and model is best, especially for catching more subtle problems.
I agree with Julia that PDB entries should be released at the time a preprint is made public. This is the official stance of the wwPDB since the 15th of October 2024 anyway: they consider that a preprint constitutes publication and therefore triggers the release of an entry marked "on hold until publication" (HPUB). See: https://www.wwpdb.org/news/news?year=2024#670d48435697788818ca8c34 Cheers, Guillaume On 1 Jun 2025, at 11:42, Julia Griese <julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se>> wrote: Dear Nikolas, To answer your follow-up question, I believe it would indeed be a good idea to give reviewers access to the model and map. This is already a fairly standard procedure for manuscripts containing cryo-EM structures, so why not for crystal structures? Maybe because the crystallography community is “older” and more set in their ways, maybe because the validation report is more useful/more likely to catch problems in the case of crystallographic data because validation of cryo-EM data is still lagging behind (although we do have useful metrics by now)? I don’t know. What I would like to add is that the more I am asked to review manuscripts the more I realise that it is not at all standard practice for journals to require submission of the PDB validation report. I always request it in that case, but that doesn’t necessarily result in me actually seeing it before the manuscript is published. Also, too many authors still hold back on releasing their PDB entries when they’ve deposited a preprint (by not authorising the entry). I don’t see why you wouldn’t when the preprint is out there. Best, Julia Sent from Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Nikolas <nikolas.ca...@gmail.com<mailto:nikolas.ca...@gmail.com>> Sent: Saturday, May 31, 2025 7:44:59 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] How to address deposited structures poorly modeled? Hi, Thank you all for the incredibly instructive responses. Being this my first time happening upon such a "situation" and I'm very glad it brought to a fruitful conversation as well as a set of instructions on how to address such things. Indeed mistakes can be made and sometimes models cannot be improved beyond a specific point for several reasons, just as sometimes things are rushed -unfortunately- due to deadlines. Personally, I didn't think of it as malevolence but more of it as a genuine oversight or mistake. I sincerely thought that was a pity, considering the rest of the structure. But maybe that's just me intertwining the joy of determining a structure with the pride of making it the best I could with the means given (while also seeking second opinions and help, if necessary). I will try to re-refine, PDB-REDO and then, if any improvements are observed, reach out to the depositors. I will then try to give another prompt, since we are on topic: what would be the best way to spot such mistakes early on, after the structures have left the authors, aside from the Curators? Should we provide reviewers with the mtz and the model instead of just the validation report? Should they ask for it, while reviewing a manuscript? Once again, thank you all; you've been wonderful. My opinion about the depositors of such models is not suitable for this public forum. I've probably laughed too hard at this. Cheers, Nikolas Il giorno sab 31 mag 2025 alle ore 07:40 Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> ha scritto: Don’t be too judgmental- Phil Evans once said - well, I have spent 95% of my refinement time tweeking the 5% of the water molecules which no one will ever ever look at! Gross errors - bad; deliberate errors indefensible , but I don’t think I have ever deposited a structure which couldn’t be “improved”. On Sat, 31 May 2025 at 12:20, Robbie Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>> wrote: Hi Matthew, > are you willing to elaborate on the motives for “molecular crippleware”? They seem to stem from the idea that you have a competitive advantage by not fully disclosing your structure model. This is by now, fortunately, a very old-fashioned way of thinking. But people have fought long and hard to get fellow crystallographers to deposit their models and their experimental data. Believe it or not, in the past there were several programs that could turn a stereo image into 3D coordinates to deal with people not depositing their coordinates. > Now that the extraordinary predictive potential of the PDB data has been > proven I would say that it's not justifiable to deposit anything where the > model is only complete to the extent that the primary research aims are met, > who knows what future patterns might be degraded? This is what I teach, but having the time and resources to really optimise a structure model before deposition is also a bit of a luxury in some settings. > I would hope that if I was ever responsible for something like this it would > be > due to a mix-up with versions etc... but either way I would want to know! If it is a clear mix-up I always try to get in touch with the depositors and I hope that this discussion will encourage other to do the same. Cheers, Robbie > > Best > > Matthew. > > Sent from Outlook for iOS <https://aka.ms/o0ukef> > ________________________________ > > From: CCP4 bulletin board > <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Robbie > Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>> > Sent: Saturday, May 31, 2025 11:03:47 AM > To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> > Subject: Re: [ccp4bb] How to address deposited structures poorly modeled? > > 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 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 > > <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of > Nikolas > > Sent: Friday, May 30, 2025 23:31 > > 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC > > .exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4- > STeHd1x > > qiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ- > l0xMfnCZKvB5o24 > > BIUg$[jiscmail[.]ac[.]uk] > > > ############################################################### > ######### > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA- > JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4- > STeHd1xqiTlYckYQhazL-JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ- > l0xMfnCZKvB5o24BIUg$[jiscmail[.]ac[.]uk] > > This message was issued to members of > https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!PDiH4E > Nfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL- > JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ- > l0xMfnCZKvB4gf54SaA$[jiscmail[.]ac[.]uk], a mailing list hosted by > https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!PDiH4ENfjr2_Jw! > DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL- > JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ- > l0xMfnCZKvB4tB7WRHg$[jiscmail[.]ac[.]uk], terms & conditions are available > at > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/_ > _;!!PDiH4ENfjr2_Jw!DIetizJCm94LYkFe6Jy4-STeHd1xqiTlYckYQhazL- > JqrMkZQz1W00Onif_FtXKpKof041v7RfEwi3adRQ- > l0xMfnCZKvB6BG0ZtyQ$[jiscmail[.]ac[.]uk] ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ 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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. 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