Dear all,

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:

Sorry: Fatal problems interpreting model file:
Number of atoms with unknown nonbonded energy type symbols: 19
    Please edit the model file to resolve the problems and/or supply a
    CIF file with matching restraint definitions, along with
    apply_cif_modification and apply_cif_link parameter definitions

if necessary.

Any suggestions how to do this would be greatly appreciated.
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.

Best wishes!
Lu

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Lu Zuokun, Ph.D. Candidate

College of Life Science, Nankai University