You do not have to change dictionary. You can specify charges on atoms using element columns in the pdb file. For example:
ATOM 139 O HOH A 35 13.139 -4.487 5.983 1.00 31.43 AA1 O ATOM 140 CL CL A 35 13.139 -7.487 5.983 1.00 31.43 AA1 CL-1 Regards Garib On 1 Nov 2011, at 22:47, Ivan Shabalin wrote: > 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 Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
