Hi Lu, Cadmium(II) seems to be in the standard monomer library in both Coot and CCP4. Thus you do not need to make it by yourself. I guess your problem was due to that you have put a "Cd" instead of "CD" when adding it in Coot. Refmac is case sensitive when identifying the compounds or atoms. All ions need to be in upper case to match their .cif files.
Please check the "share\coot\lib\data\monomers\c" and "ccp4-6.2.0\lib\data\monomers\c" folder. You should have a "CD.cif" there. This file is the monomer definition for Cd(II) ions. Please take a look in the file, especially this part: 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 _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z CD CD CD CD 2.000 0.000 0.000 0.000 The 2.000 in the last line corresponds to the "_chem_comp_atom.partial_charge" entry. The 2.000 indicates that this is for a Cd(II) ion. If your Cadmium is Cd(II) then you are OK. No more worries. If you think your Cadmium is Cd(III), then you need to change the partial_charge value to 3.000, and change all the "CD"s in this file to "CD3", then save it as another file, "CD3.cif" (make sure "CD3" is a unique name in the whole library), and use it for your refinement. Also in this case you need to put "CD3"s in your PDB file instead of "CD". This is a simple case so you can edit by hand. Please take a look in the "FE.cif" and "FE2.cif" in the "f" folder to see how such cases should be handled. Also please note that the FE1.cif and FE3.cif are not for iron at all. This is an example showing that we should always have a look in the cif files to make sure the descriptions are correct for our ligand. If not we need to find the right one or make our own. Zhijie From: Lu Yu Sent: Monday, November 28, 2011 3:16 PM To: [email protected] Subject: [ccp4bb] how to add Cadmium ion to structure and do the refinement Hi ALL, This is the first structure I am working with. As the title said, I was stuck in the middle of model building using coot, and I found a big positive peak for Cadmium ion. The coot program doesn't *know* the cadmium ion when I add a Cd atom there (under the "place atom at pointer" menu--> "Other" ), and the refinement program doesn't *know* how to refine this (failed when I refine the whole structure, and it may need appropriate values as restraints, but I don't know how to add these values ). So I am wondering any one can give me any suggestion about, how to add cadmium ion in the position and do the refinement. Thanks in advance, Lu
