before making the PBD id public I would give the authors some time to respond (as others and Nikolas himself have suggested). Then it is more likely to be solved in a friendly, efficient and thorough way. While it’s possible to resolve problems with the current structure factors and model, having the authors themselves look into it first is better, they might realise some other problem, such as the wrong structure factors having been uploaded for example.
Mark J van Raaij Dpto de Estructura de Macromoleculas, lab B5 Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 1 Jun 2025, at 18:24, srikannathasan velupillai > <0000b52eb5457384-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Nick, > Thanks for raising the issue. You mentioned that you're relatively new to the > field—if so, that's absolutely fine, and we all appreciate your engagement. > If you've worked on this structure yourself and believe there may be issues, > have you considered depositing your version for comparison? Even if there’s > already a PDB entry, reviewing different interpretations can still be > valuable. > > You mentioned that the existing model may be incorrectly built. Would you be > able to share a few more details—such as the PDB ID (if available), electron > density maps, or screenshots of the specific problem areas? > > Several people have already offered advice, but having a bit more context > would really help the community provide more constructive feedback. Sharing > this via the CCP4 forum or directly here could allow others with relevant > experience to assist further. > > Looking forward to hearing more about your observations. > > > > Thank you > > kannan > > > > On Sat, 31 May 2025 at 09:09, Guillaume Gaullier > <guillaume.gaull...@kemi.uu.se <mailto:guillaume.gaull...@kemi.uu.se>> wrote: >> Hi Nikolas, >> >> Contacting the original authors/depositors of this entry is indeed a good >> thing to do. Try putting yourself in their shoes: if you were to receive an >> email essentially saying that your model is very poor, how would you like it >> phrased? Then phrase your request as nicely as you can to get these people >> on your side (i.e. willing to revise their model). >> >> If they don’t follow up, or worse get angry at you, well at least you tried. >> And then you are free to propose your own revised model: this is what >> publicly available data is for. >> >> In this situation, I would get in touch first and maybe offer to help revise >> the model (if this is something I am willing to spend time on) depending on >> how the initial contact goes. If this went nowhere and I still needed a >> correct model, I would revise it myself for my own use. >> I don’t know what the PDB’s policy is in cases where one wants to >> independently deposit a revised model for an existing entry they did not >> deposit themselves. But if the original authors/depositors are willing to >> cooperate, then it’s relatively easy: all PDB entries are versioned, so >> depositing a revised atomic model is only a matter of issuing a new version >> (the accession code will remain the same). It is even possible to amend the >> depositor list, so the original authors can give you credit this way if you >> did more work than only pointing out a poor model. >> >> Different people will receive this kind of request differently, and you >> don’t know until you try. >> >> Alternatively, if you don’t want to initiate such a discussion and only want >> a revised model quickly, check if it has been re-refined by PDB-REDO: >> https://pdb-redo.eu <https://pdb-redo.eu/> >> It won’t do miracles for very large errors though, and in such cases manual >> rebuilding may be best. But could be useful to check. >> >> I hope this helps! >> Cheers, >> >> Guillaume >> >> >>> On 30 May 2025, at 23:30, Nikolas <nikolas.ca...@gmail.com >>> <mailto:nikolas.ca...@gmail.com>> 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 >>> >>> >>> >>> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner >>> igen avsändaren och vet att innehållet är säkert. >>> CAUTION: Do not click on links or open attachments unless you recognise the >>> sender and know the content is safe. >>> >>> >> >> >> >> >> >> >> >> >> >> När du har kontakt med oss på Uppsala universitet med e-post så innebär det >> att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det >> kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ >> >> E-mailing Uppsala University means that we will process your personal data. >> For more information on how this is performed, please read here: >> http://www.uu.se/en/about-uu/data-protection-policy >> >> 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/
