[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
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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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