I would also be suspicious of the space group/unit cell if you have 10 mols in the A.U. especially if the R-free is unusually high but still reasonable.
Best, Omid From: CCP4 bulletin board <[email protected]> On Behalf Of Rafael Marques Sent: January 7, 2026 8:05 AM To: [email protected] Subject: Re: [ccp4bb] Unusually low B-factors for 'waters' [△EXTERNAL] Very interesting topic, Sorry for highjacking a bit the discussion, but I always pay attention to the model b-factor instead the individual ones. In this specific case, what b-factors should be expected for the water molecules? Best wishes ______________________________________________________ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +44 07861 273773 "A sorte acompanha uma mente bem treinada" ________________________________________________ ________________________________ De: CCP4 bulletin board <[email protected]<mailto:[email protected]>> em nome de Clemens Vonrhein <[email protected]<mailto:[email protected]>> Enviado: quarta-feira, 7 de janeiro de 2026 11:21 Para: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Assunto: Re: [ccp4bb] Unusually low B-factors for 'waters' As an addition to that good idea: you could run BUSTER (via "aB_autorefine" command-line) starting from an empty model to get automatic water addition, TLS, occ-refinement, hydrogen handling etc as a 2nd/3rd opinion. If you need help getting started with BUSTER, contact us off-list ;-) Cheers Clemens On Tue, Jan 06, 2026 at 12:47:45PM -0800, Pavel Afonine wrote: > get a second opinion. Phenix, Refmac, or Shelxl are your options. If you > refined your model with one of them, try another. If you choose > phenix.refine, let it find/build/refine waters automatically. This way, you > can rule out a bug in the software you used to obtain this result or > modeling error. Of course, if this happens with Phenix, feel free to send > me the files off-list, and I will have a close look! > > Good luck! > Pavel > > > On Tue, Jan 6, 2026 at 6:48 AM Kyle Gregory < > [email protected]<mailto:[email protected]>> > wrote: > > > Dear all, > > > > I have a 2.6 angstrom structure, which has 10 molecules in the ASU. I have > > modelled approx 200 water molecules. They fit spherical density nicely and > > make suitable contacts with the protein. The only problem is nearly every > > single water molecule has a lower B-factor than the protein atoms they > > coordinate. E.g protein atoms could be 30/40 while water is 16 angstrom^2. > > > > Does anyone have a suggestion as to why, and whether there are some things > > I should be trouble shooting? > > > > Kind regards, > > Kyle > > > > ------------------------------ > > > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions > are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., 9 Journey Campus, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com<http://www.globalphasing.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 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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 ######################################################################## 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/
