[phenixbb] phenix.pdbtools and anomalous?

Pavel Afonine PAfonine at lbl.gov
Sun Jan 10 13:32:18 PST 2010

Hi Kay,

yes, it is missing in phenix.pdbtools. I will add it next week.

I guess you can do it in phenix.refine by specifying f_prime and 
f_double_prime in:

refinement.refine.anomalous_scatterers {
      group {
        selection = None
        f_prime = 0
        f_double_prime = 0
        refine = f_prime f_double_prime

The command would be :

phenix.refine model.pdb data.mtz main.number_of_mac=0 
strategy=group_anomalous main.bulk_sol=false export_final_f_model=mtz 
main.outliers_rejection=false params

where "params" file contains the above defined anomalous scatterer 

Note, the Fcalc will correspond to whatever dataset you have in data.mtz.

Please let me know if you have any questions.


On 1/10/10 1:09 PM, Kay Diederichs wrote:
> Hi,
> I like the way I can obtain Fcalc with phenix.pdbtools --f-model.
> However I need to have the anomalous signal as well, for certain atoms,
> and a given wavelength. This does not seem to be possible with
> phenix.pdbtools. Is there a way to do this with phenix.refine ?
> thanks,
> Kay
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