For the record, occupancy refinement scenario you're looking for is described here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 Cheers, Pavel On Thu, Mar 3, 2022 at 7:09 AM Jon Cooper < [email protected]> wrote: > Hello, the ligand needs to be treated as one occupancy group since > refining individual occupancies would be a case of refining too many > parameters, unless it was a very fragmentary compound!! It is one keyword > in refmac, but I can't remember for phenix, sorry! Ta jc > > > Sent from ProtonMail mobile > > > > -------- Original Message -------- > On 3 Mar 2022, 14:15, Akanksha Tomar < [email protected]> wrote: > > > Hi everyone, > > I am trying to refine the occupancy of a bound ligand. After fixing the > protein model and water I fitted the ligand into it. Currently, I am using > Phenix Refine with occupancy refinement for individual atoms switched on. > After the refinement, the overall occupancy of the ligand is 0.7 and the > RSCC value is 0.86. The resolution of the structure is 2.1 Å. > > Now the problem is that the program has assigned different occupancies to > different atoms of the ligand. For some cases, it has assigned 0 > occupancies to atoms for which there is a clear positive peak. > > Why it has been done so and is it acceptable? > > Any help would be greatly appreciated. > > Thank you. > > -- > Best Regards, > Akanksha Tomar > Pre-Doctoral Fellow, > C\o Dr. Arockiasamy Arulandu, > Membrane Protein Biology Group, > International Center for Genetic Engineering and Biotechnology, > New Delhi, India > > ------------------------------ > > 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 > > ######################################################################## 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/
