Hmmm - TLS may not be applied to the waters . The interaction between 10 fold ncs snd TLS snd water positions could have strange outcomes! Like Kyle I wonder e what happens if you deactivate both those options?
On Tue, 6 Jan 2026 at 18:14, Kay Diederichs < [email protected]> wrote: > Dear Kyle, > > interesting finding - worth looking into! > > According to Wlodawer et al (2024) ( > https://journals.iucr.org/m/issues/2024/06/00/be5300/index.html) ,"An > analysis of the contents of the PDB indicated that the expected ratio of > the number of water molecules to the number of amino-acid residues exceeds > 1.5 in atomic resolution structures, decreasing to 0.25 at around 2.5 Å > resolution." > So I'd expect your structure to have around 800 residues, is that about > right? > > A lot may depend on the details of data processing ... which program; is > there anisotropy? How did you determine/perform the high-resolution cutoff? > Could you go to higher resolution? Do you have other datasets from the same > project - do they show the same behaviour? > > I can imagine refinement/water-adding workflows where some atoms have > surprising B-values e.g. TLS refinement mistakenly leading to anisotropic > B-values, or waters being deleted and re-added with a default B-value of > 16. Could you give details? > As a simple test, just remove any lines from your PDB file except the > ATOM, HETATM, DISU and the CRYST1 and END records. Then refine with a > standard Refmac protocol and check the B-values afterwards. > > HTH, > Kay > > ######################################################################## > > 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/ > ######################################################################## 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/
