[phenixbb] difficulties with the refinement of a Cadmium containing pdb file

Pavel Afonine pafonine at lbl.gov
Fri Apr 8 07:37:00 PDT 2011


Hi Fred,

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.

Pavel.


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).
>
> 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.



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