The selection field in the GUI is also a general atom selection string. I.e. in your case you need to enter name CD In other cases you may want to enter things like chain A and resname LIG and name CD See the section on atom selections in the phenix.refine documentation. Ralf

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 or chain X and resname LIG and name CD For more examples of atom selection syntax see phenix.refine manual section "Atom selection examples": http://www.phenix-online.org/documentation/refinement.htm 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. Pavel. 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

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