Dear Akanksha Tomar, By default, phenix.refine will assign a single occupancy for the ligand as long as all atoms have the _same_ occupancy (0<q<1) in the initial model. So you probably have at least one atom with a deviating occupancy.
Btw, what do you mean with "overall occupancy" -- an average q? Best regards Oliver ================================================== PD Dr. Oliver H. Weiergräber Institut für Biologische Informationsprozesse IBI-7: Strukturbiochemie Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================== ________________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Akanksha Tomar [[email protected]] Sent: 03 March 2022 15:15 To: [email protected] Subject: [ccp4bb] Ligand occupancy refinement 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ ######################################################################## 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/
