Hi Pavel, Indeed there was no charge on the Cd ions, and some of these Cd ions had improper annotations in columns 77-78. I must admit that I do not understand why these columns are used while the data (atom type) is provided before on the HETATM (or ATOM) record. Refining now (I hope). Fred. Pavel Afonine wrote:
Hi Fred,
Cd ions should create no problem for phenix.refine and you don't need to run any additional program... Make sure it is defined in your PDB file like this:
HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+
^^ Put the charge here
Charge is optional, but note: phenix.refine does not infer the charge from the atom name. It has to appear in the PDB charge columns 79-80 as shown above. To make sure it is recognized correctly, look in phenix.refine log file - in the above example you would see something like this:
Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0.
Pavel.