Hello Friday! Your question is answered here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 which is one of 13 occupancy refinement scenarios that is supported by phenix.refine. Happy to help with details, should there need be. Good luck! And happy Friday! Pavel On Fri, Feb 27, 2026 at 1:13 PM Friday < [email protected]> wrote: > Hi All, > > I have a questions for refinement of a partially hydrolysed GMPPNP > structure. From the Fo-Fc difference density, I can tell part of the > density for the gamma phosphate represents the original gamma phosphate of > GMPPNP, and part of the density represents PO4- ion which is the product > of GMPPNP hydrolysis. I tried to model both molecules (GMPPNP, and GNH+PO4 > -) and give 0.5 occupancy for both molecules. Obviously the refinement > did not work because 2 molecules are too close to each other. > > The questions is: how do I set up the phenix.refine so that the 2 > molecules can be refined together. > > > Thanks a lot! > > Friday > > ------------------------------ > > 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/
