[phenixbb] difficulties with the refinement of a Cadmium containing pdb file
pafonine at lbl.gov
Fri Apr 8 07:37:00 PDT 2011
columns 77-78 define chemical element type. Atom label is not enough to
unambiguously define it. For example, CA can be C-alpha or Calcium. Of
course residue name can help further, but if you have a ligand then
things get more complicated.
On 4/8/11 12:19 AM, Vellieux Frederic wrote:
> 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).
> 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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