[phenixbb] difficulties with the refinement of a Cadmium containing pdb file
Frederic.Vellieux at ibs.fr
Fri Apr 8 00:19:44 PDT 2011
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).
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.
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