Hi Harry, My advice would be to use one of those new-fangled predicted models. You can find a model in the AlphaFold database at the EBI (https://alphafold.ebi.ac.uk/entry/P01132). If you look at it, there are parts (likely corresponding to the constructs that were crystallised) that look confidently predicted, connected by poorly-predicted loops. If you take the PDB file and the PAE matrix, you can run process_predicted_model either from Phenix or CCP4, which will give you individual files for the confident parts of the full prediction that are likely to have the correct relative orientations. (If you want to use the models for molecular replacement, you’ll find that the least-confident parts are downweighted by being assigned high B-factors, which is much better than having the best parts of the models, with pLDDT near 100, downweighted the most by interpreting pLDDT as a B-factor.) I would bet that these models will be more accurate than typical NMR models.
Best wishes, Randy > On 3 May 2023, at 11:45, Harry Powell > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi folks > > I was wondering. > > If there is a UniProt entry (for example, P01132, but there are plenty of > others) for which I want the “best” (whatever that might mean) representative > _experimental_ structure (i.e. not one of these new-fangled predicted models > that some folk say have removed the need for actually doing experiments), but > there are only NMR models - how do I choose? > > I don’t mean “which model from the ensemble do I choose” - that’s a different > question. > > For P01132, for example, I could choose (from the PDB) 1A3P, 1EGF, 1EPG, > 1EPH, 1EPI, 1EPJ, 1GK5 or 3EGF. Note that some of these are from the same > paper, so may be in different conditions (e.g. pH). All except the first > (1A3P) cover the same bit of sequence. > > Specifically, what should I look for in the downloadable files (mmCIF, for > example) from the PDB? > > Thoughts? > > Harry > ######################################################################## > > 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 http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.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/
