[phenixbb] advice for refinement with anomalous information

Pavel Afonine pafonine at lbl.gov
Thu Aug 26 21:51:51 PDT 2010

  Hi John,

what you have found in FAQ is for the command line version of phenix.refine.

In the GUI you most likely see something like

Anomalous scatterer group (1)

Atom selection :

So you need to type atom selection string in "Atom selection : " prompt. 
It should select your CD atoms. Something like this

element Cd


chain X and resname LIG and name CD

For more examples of atom selection syntax see phenix.refine manual 
section "Atom selection examples":

Let me know if you have any questions or problems. Also, you can send me 
a PDB file and I will reply back with the directions on how you should 
select your Cd atoms.


On 8/26/10 9:41 PM, John Rose wrote:
> Hi,
> I am refining my first structure (Cd-SAD) with the Phenix (GUI) and 
> would like to refine anomalous f' and f".  When i check the box, a 
> menu appears and I have no idea of how to define the Cd atoms.
> I looked at the help and FAQ and found this:
> refinement.refine.anomalous_scatterers {
>    group {
>      selection = name BR
>      f_prime = 0
>      f_double_prime = 0
>      refine = *f_prime *f_double_prime
> So I thought the name should be input as CD in the gui but when I 
> submitted the refinement I got an error.
> Any help here would be appreciated?
> Thanks,
> John Rose
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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