[phenixbb] on cif file

[Smith Lee]

 Dear All,
My protein containing the ADP-AlF3-Mg. In the protein  ADP-AlF3-Mg should be very close to each other so that they look like the ATP binding with the Mg. I have prepared the ADP.cif and the ALF3.cif, and have merged the 2 cif files with elbow.join_cif_files. However when I run phenix.real_space_refine with the merged cif file, there was a tendency that ADP, ALF3 and Mg separated from each other based on the map density, which seems did not comply with the prior knowledge on that ADP-AlF3-Mg should occupies the space of ATP-MG.
Will you please advice how to have ADP-AlF3-Mg occupies the space of ATP-MG rather than separated by the refine?
Best regards.
Smith
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