Hi Nikolas, I think that in crystallography it is becoming more common that reviewers ask for the structure factors and coordiates before reviewing a manuscript, I always do. And also more common that journals ask for these during submission, IUCr journals (https://journals.iucr.org/) and other journals do this, hopefully to be followed by all.
Mark van Raaij Dpto de Estructura de Macromoleculas, lab B5B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 31 May 2025, at 19:44, Nikolas <[email protected]> wrote: > > 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 > <[email protected] > <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >>> > <mailto:[email protected]>> on behalf of Robbie >>> > Joosten <[email protected] <mailto:[email protected]>> >>> > Sent: Saturday, May 31, 2025 11:03:47 AM >>> > To: [email protected] <mailto:[email protected]> >>> > <[email protected] <mailto:[email protected]>> >>> > 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 <[email protected] >>> > > <mailto:[email protected]>> On Behalf Of >>> > Nikolas >>> > > Sent: Friday, May 30, 2025 23:31 >>> > > To: [email protected] <mailto:[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://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 > ######################################################################## 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/
