Hi, Yes, I agree imperfections are the parts of the system. But given the field has spread so much, the acceptable level of imperfection might be different to different people.
This variation can be seen in the pdbs mentioned. For example in 5XHK, out of two molecules only catechol of one molecule seems to agree with ED. So your 20 bar 2, in this case becomes 5 bar 17. While in 6JKE, the inhibitor is refined in what is glycerol ED. So here it becomes 0 bar 22. I agree a dedicated moderated parallel forum for issues regarding pdbs, will certainly help in refining things better. Best, On Sun, Aug 22, 2021 at 3:56 AM Jon Cooper <[email protected]> wrote: > Maybe we need some sort of parallel moderated database where people can > comment on individual PDB entries, responsibly, of course. Maybe there is > one already, but at the moment this sort of discussion just seems to happen > on blogs and forums. > > With the huge amount of fragment screening going on, there is always going > to be the bottom decile of structures where the ligands are a bit sketchy > (it wasn't me ;-0), but papers where most or all of the structural results > are flimsy have always been a bit of a worry in the field. > > One thing is that with any experiment you never get perfect agreement > between the results and the theoretical model. When the agreement does > approach perfection, then you start to worry that the results themselves > are synthetic.... what am I trying to say (?)... say you've got good > density for an important ligand for all of the 20 atoms bar two, do you > refuse to publish and deposit, or can they be hidden behind the molecule in > that electron density figure and does pressure to publish win? I think the > latter (although it wasn't me again ;-0), so perhaps the system has to > allow for imperfections in a constructive way so that new interpretations > can be made where necessary. > > Sent from ProtonMail mobile > > > > > > > > > ------------------------------ > > 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/
