Dear Refmac users, Im a bit confused how Refmac treats ions. In the monomers library I can find Cl.cif:
CL . 'chlorine ' non-polymer 1 1 . # data_comp_CL # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge CL CL CL CL 0.000 It does not have charge and atom.atom_id is CL, but not Cl-1 (I believe, it is important for the scattering factor). I tried to change these fields but refmac crushed. Searching through CCP4BB I found that Ions from nonions are distinguished by just addition charge on the element column in the PDB file. So, for Cl I have to type Cl-1 in the last field of PDB-file line. I tried and it worked, at least REFMAC uses different coefficients for atomic scattering factor for the ion and B-factors are changed a bit. But I never seen in PDB files that somebody specifies Cl-1 or Mg+2. And when you bring new ligand with Coot id does not specify the charge. I have two questions: 1) Cl and Cl- have very different atomic radii and the scattering factor coefficients are quite different. But, does it really make significant difference for refining? 2) Is it possible to specify atom type in the library, so that the scattering factor coefficients will be taken into account by Refmac? Or changing PDB-file manually is the only way? Thank you very much for any comments!! With best regards, Ivan Shabalin, Ph.D. Research Associate, University of Virginia 4-224 Jordan Hall, 1340 Jefferson Park Ave. Charlottesville, VA 22908
