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Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in ccp4 suite and generated the .cif file of this monomer. However, I could not make it bind with other nucleotides in the nucleic acid chain. I have tried to write LINK lines into PDB file, and also edited .edits file for phenix.refine. In both conditions, phenix.refine works except that it wouldn't add covalent bonds between the residues as I expected. I have used .edits file for covalent binding between residues before, and it worked well. So there must be something wrong with my input files. But I couldn't fighure out where the problem is. Thanks a lot and best regards! Xiaoming