Dear Marcin, Thank you for these examples! It is reassuring to see that multiple crystallographic models do not break validation for example. I assume only the validation of the first model and first reflection file is shown. I can imagine that it is still a substantial change and may require an extended description to make such depositions fully functional. I will ask the PDB, but this made me optimistic. It would be easy to implement Tim's method if it works for deposition.
Best wishes, Gergely -----Original Message----- From: Marcin Wojdyr <woj...@gmail.com> Sent: den 1 juni 2021 21:23 To: Gergely Katona <gergely.kat...@gu.se> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Meaning of a pdb entry Dear Gergely, For authoritative advice you'd need to ask the PDB. Below is my take. > I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif > format for storing multiple crystallographic models. It's possible, there are a few examples such as 2VTU. They represent "ensemble refinement" of a crystal structure. So it's one refinement of one dataset, but with multiple models. > I assume it is already possible to store multiple structure factor files (for > refinement, for phasing, different crystals etc) under the same entry. yes > In my mind, it would be a small step to associate different data sets > distinguished by crystal ID or data block with a particular model number, but > maybe it is not that simple. > It'd be a substantial change, but indeed, the changes in the file format would not be that big. As you wrote, model IDs would need to be associated with crystal IDs. And probably other associations would be needed, such as unit cell with crystal. > I do not want to create multiple pdb entries just to provide evidence for the > robustness/reproducibility of crystals and crystallographic models. I would > rather use different pdb entries for different sampling intentions: for > example entry 1 contains all the control crystals, entry 2 contains all the > crystals subjected to treatment A, etc. I think it's similar to PanDDA depositions, but I don't know what's the current best practice. Initially, one Deposition Group would have hundreds of PDB entries (each with a single dataset). But later on I've seen entries with a single model and hundreds of datasets. I haven't looked into it closely, so perhaps someone else can advise. Concatenating multiple mmCIF files (with coordinates) would produce a syntactically valid file, but I don't think that such file would get through the deposition process. Marcin ######################################################################## 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/
