[phenixbb] Refining Anomalous Groups

Nathaniel Echols nechols at lbl.gov
Mon Nov 19 18:29:24 PST 2012

On Mon, Nov 19, 2012 at 6:11 PM, Brennan Bonnet <
Brennan.Bonnet at lightsource.ca> wrote:

> I am trying to use phenix.refine to refine partially occupied xenon sites
> using the Anomalous Groups selection under "Refinement settings".  My list
> of anomalous scatters initially consisted of 22 peaks as located by HySS.
>  Some of these were removed as they originated from S atoms from Met and
> Cys residues and a few others were removed after previous refinement steps
> due to having zero occupancy.  My remaining sites consist of my xenons
> (hopefully) and other metals such as Mg or Zn which are mixed in and look
> like partially occupied xenon sites.  My problem is that when I try to
> define the 11 remaining sites for the "refine anomalous groups" selection
> the software complains:
> Invalid combination: F-obs not anomalous, but refinement of 11
> f_double_prime values requested (11 scatterers): Please provide anomalous
> reflection data or fix all f_double_prime values (see
> refinement.refine.anomalous_scatterer.group input blocks)
> I can't figure out exactly what I need to change to make it work and can't
> find a guide anywhere.  Do I need to provide additional data or is the
> syntax for the sites incorrect maybe?

No, the error message means exactly what it says: you need to supply
anomalous data as input.  This almost always means that the selected data
labels should have "+" and "-" in them, and there will usually be 4 labels
(e.g. "F(+),SIGF(+),F(-),SIGF(-)").  Data named "F,SIGF", on the other
hand, is almost always merged/non-anomalous (although I think CNS files may
break this assumption).

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20121119/a49ba4a3/attachment.htm>

More information about the phenixbb mailing list