Dear Mohamed, The situation you describe applies also to multiple crystal structures studied as a function not only of time but also of temperatures and pressures. I enquired if the numberings of discussed waters and so on could be retained across the related crystal structures in the PDB. The reply was that the single model for a single diffraction dataset prevented retaining the same numbering across these crystal structures. I found a simple alternative solution, as referee or author, albeit not ideal for the reader, of a numbering of key waters table in the associated publication with table columns labelled time, pressure or temperature. I have had mixed success retaining this explanatory table in the main text however versus being forced to put it into the Supplementary. Hope this helps, Best wishes, John
Emeritus Professor John R Helliwell DSc > On 1 Nov 2021, at 15:44, Mohamed Ibrahim <m.essam.ibra...@gmail.com> wrote: > > > Hi All, > > I have a very similar question; why can't we retain the same water numbering > as the deposited files. For articles that discuss waters, it is a > considerable challenge. For example, for serial crystallography structures, > it becomes confusing and harder for the readers to follow the water > numbering. Since the authors use the same numbering system for the similar > waters in the different structures of the same protein at different time > points during the enzyme activity, however, after depositing, the waters are > renumbered in each model differently. > > Cheers, > Mohamed > >> On Mon, Nov 1, 2021 at 4:01 PM Oganesyan, Vaheh >> <vaheh.oganes...@astrazeneca.com> wrote: >> Hi All, >> >> >> >> This question is mostly for RCSB and PDBe: why are you renaming chains in >> the deposited PDB files? Why does it matter what letter is assigned to the >> chain? For 1,2 or 3 chain structures it is manageable, but for more chains >> and/or many complexes per asu this becomes quite a challenge. And if chains >> are similar in shape it is a real pain. Reading associated manuscripts and >> looking at those structures is an additive that feels unnecessary. >> >> >> >> Thank you in advance for explaining the logic behind. >> >> >> >> Vaheh Oganesyan, Ph.D. >> >> <image001.png> >> >> R&D | Biologics Engineering >> >> One Medimmune Way, Gaithersburg, MD 20878 >> >> T: 301-398-5851 >> >> vaheh.oganes...@astrazeneca.com >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > > -- > ---------------------------------- > Dr. Mohamed Ibrahim > Postdoctoral Researcher > Humboldt University > Berlin, Germany > Tel: +49 30 209347931 > > 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/
