Hi Ethan, DM with a mask of the ligand in chain A then applying the NCS matrices and looking at the resulting density perhaps ? Theoretically it should improve, this is of course assuming that your ligand does not adopt different conformations in the three chains. In Refmac you can also add a NCS restraint per residue - I assume a ligand is considered a residue but I have not tried this.
Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu On Jan 30, 2015, at 7:38 PM, Ethan A Merritt <merr...@u.washington.edu<mailto:merr...@u.washington.edu>> wrote: Is there some way to apply NCS restraints to the binding pose of a ligand during refmac refinement? That is, suppose I have 3 copies of the binding site and the density in each copy is OK but not great. I would be more confident of a refined pose that jointly satisfied the electron density at all 3 sites than a refinement that resulting in slightly different poses at each site. If not, is there an equivalent to the shelxl SAME directive? I.e. is there a way to tell it "I don't know what the true distance is from ligand atom X to protein atom Y, but I want to restrain it to be the same in all 3 copies"? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
