Thank you for the suggestions I will try again by setting the occupancy of the entire ligand to the single average occupancy and re-do the refinement with Buster, Phenix refine and Remac5 with full positional and B-factor refinement and check the B-factor of the neighbouring residues. The ligand is a 30 atom containing molecule binding at a shallow solvent-exposed site.
On Thu, 3 Mar 2022 at 20:38, Wim Burmeister <wim.burmeis...@ibs.fr> wrote: > 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 ther 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 > > > -- > *Wim Burmeister* > Professor > Institut de Biologie Structurale (IBS) CIBB > 71 avenue des Martyrs > <https://www.google.com/maps/search/71+avenue+des+Martyrs?entry=gmail&source=g> > / CS 20192 > 38044 Grenoble Cedex 9, FRANCE > E-mail: wim.burmeis...@ibs.fr > Mobile: +33 (0) 7 50 49 19 91 > website > <http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/> > > > > ------------------------------ > > 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/
