Hi Mark,
I need some help advice regarding anisotropic refinement, which I've never done before. My current Rfactors are R-work = 0.1587, R-free = 0.1726, resolution 1.26 Å.
two things I would do right away without thinking long: - add H atoms; - refine all macromolecular atoms with anisotropic ADPs (probably, except alternative conformations), and solvent with isotropic ADPs; Also, please make sure to use recent Phenix version. That may have impact in your case, since latest phenix.refine have improved handling of hydrogen atoms (*), and a new bulk-solvent and anisotropic scaling procedure (**). If you still want to define by hand which atoms to refine isotropically/anisotropically, then a parameter file like this should allow to do this: refinement { refine { adp { individual { isotropic = (chain A and resseq 1:100) or (chain X and resseq 300:900) or water anisotropic = (chain Z and resseq 123 and name CG1) or (element Au) } } } } Make sure you cover all atoms with isotropic = ... anisotropic = ... selections, because the default behavior is that if you change these parameters then phenix.refine assumes you know what you do. If you do not select all atoms with these selections, then B-factors of atoms that are not selected will not be refined. I don't like this and I will change this once I get a chance. For your specific example: refinement { refine { adp { individual { isotropic = not (chain A and (resseq 7:44 or resseq 61:149 or resseq 173:182 or resseq 202:254 or resseq 263:290)) anisotropic = chain A and (resseq 7:44 or resseq 61:149 or resseq 173:182 or resseq 202:254 or resseq 263:290) } } } } I've never tried but this might work too: refinement { refine { adp { individual { aniso_sel = chain A and (resseq 7:44 or resseq 61:149 or resseq 173:182 or resseq 202:254 or resseq 263:290) isotropic = not $aniso_sel anisotropic = $aniso_sel } } } } Phil experts may comment on this more. Let me know if you have any questions or need any help with this! Good luck, Pavel (*) "On contribution of hydrogen atoms to X-ray scattering" http://www.phenix-online.org/newsletter/ (**) http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf
I have TLS groups, and know I need to exclude these from individual anisotropic refinement.
Questions:
1) how to decide my atom selection for anisotropic refinement. I've identified segments with MC B below 20, but what to do for surface residues which have well ordered MC but B factors for side chains increase (e.g. along a well ordered Lys side chain) - should (can?) I
a) refine only MC anisotropically, b) refine whole residue anisotropically, c) refine isotropic
2) How to write a a parameter file for phenix.refine defining the atom selections.
The residues I'd like to use for anisotropic refinement are: A7-A44 A61-A149 A173-A182 A202-A254 A263-A290 all in chain A
I found following on phenix.refine online docs, but am not sure to to extend this for a more complex selection needed above, which Ideally I'd put into a file to be read in when I start refinement. Could yo show me how to do for A7-A44 and A61-A149, and I'll follow example for the rest.
adp.individual.anisotropic="resid 1:2 and not element H" adp.individual.isotropic="not (resid 1:2 and not element H)
Thanks for help.
Mark .