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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