[phenixbb] refinement of N-glycosylation

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Feb 24 13:25:06 PST 2010

> I?m quite new to crystallography and I?m refining a structure with
> ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to
> do it, but I?m making a small mistake somewhere and can?t figure out what
> I?m doing wrong. Must be just one paranthesis or so, I guess.
> In command line just for testing I put:
> phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb
> cif_link.params BMA.cif strategy=individual_sites+individual_adp
> main.number_of_macro_cycles=2 --overwrite

Did you get an error message?
If not, look in the .eff file for your "apply_cif" definitions.
If they don't appear there something went wrong.
The file name doesn't matter at all, not even the extension,
but it is important that the syntax is correct. To run the syntax
check only:

  iotbx.phil cif_link.params


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