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]> 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]> on behalf of Robbie > > Joosten <[email protected]> > > Sent: Saturday, May 31, 2025 11:03:47 AM > > To: [email protected] <[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]> 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://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, a > mailing list hosted by 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 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/
