Global refinement parameters - use statistical model for missing atoms
Hi All, Does it make sense that when the box for "use statistical model for missing atoms" is picked under the GUI's "Global refinement parameters options" that one might obtain "better" Free-R values? I seem to be seeing that for a 2.3 A refinement of a crystal with a monomer of 550 residues in the asymmetric unit and 68% solvent content. When I uncheck the box I get about a 3% increase in Free-R. Is there more information about what this option is actually doing and when it might be useful to employ? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
Hi Joe, I added this option with a high expert level: use_statistical_model_for_missing_atoms = False .type = bool .expert_level=2 so it's not too visible at the moment... I'm still working on it. This will be a way to explicitly account for missing atoms in severely incomplete models. I will write a quick notice on phenixbb once it is available for general use. Pavel.
Hi All,
Does it make sense that when the box for "use statistical model for missing atoms" is picked under the GUI's "Global refinement parameters options" that one might obtain "better" Free-R values? I seem to be seeing that for a 2.3 A refinement of a crystal with a monomer of 550 residues in the asymmetric unit and 68% solvent content. When I uncheck the box I get about a 3% increase in Free-R. Is there more information about what this option is actually doing and when it might be useful to employ?
Joe
participants (2)
-
Joseph Noel -
Pavel Afonine