Hi Lu,

The protein was covalently linked by my ligand and I used JLigand to generate the link record and the .cif file. This file can be used in Refmac successfully. But the .cif file cannot be recognized by phenix.model_vs_data nor phenix.refine. The program runs with the following message:

Phenix has tools to deal with ligands, including tools to create CIF files, and other means to represent the restraints. The outcome of these tools should be compatible with other Phenix programs.
If you use external tools to do this (such as Jligand) then the resulting CIF may or may not work with Phenix tools, this is not unexpected.

Any suggestions how to do this would be greatly appreciated.

Use ReadySet or eLBOW to generate ligand-related files. If those still don't work for you then please get back to us with more details and someone here will investigate.

Another question is, how can I generate a restraints file for COOT to do real space refinement? The .cif file is imported in COOT, but when I do real space refinement, the link bond still takes apart.

See above. Also, you can do real-space refinement using phenix.real_space_refine, from command line or GUI.

All the best,
Pavel