Hello, at 2.1 A resolution, atomic temperature factors and occupancy are strongly correlated. So you have to be very careful with the results. So the best is just to set the inhibitor to the average occupancy and then to include it into a full positional and B-factor refinement. You can check whether the result is coherent by comparing the B-factors of the ligand and of the atoms, which are in contact with it. If this is not the case, you may want to adjust the occupancy manually. As there are also solvent atoms at the ligand positions, when it is not bound, there is another source of inaccuracy and theoretically you would have to model the site with the solvent and an occupancy 1-q and the ligand with an occupancy q as alternate structures. But nobody does that and it is not really required. Best Wim
De: "Akanksha Tomar" <akankshat...@gmail.com> À: "CCP4BB" <CCP4BB@JISCMAIL.AC.UK> Envoyé: Jeudi 3 Mars 2022 15:15:07 Objet: [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 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] -- Wim Burmeister Professor Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs / CS 20192 38044 Grenoble Cedex 9, FRANCE E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] Mobile: +33 (0) 7 50 49 19 91 [ http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/ | website ] ######################################################################## 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/
