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]> 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, a mailing > list hosted by 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 *-------------------------------------------------------------- ######################################################################## 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/
