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 Ralf