Hi Phenix,

apologies for the beginner question, and I do realise that there are some related threads already but nothing so far has helped me to solve this problem.

I want to refine a model that has two NAGs linked to an Asn - the sugars are already part of my initial coordinate file, but upon refinement the link between the NAGs gets lost. I have defined a cif_link file as follows that I load (using the GUI),

apply_cif_link {

data_link = "NAG-ASN"

residue_selection_1 = "chain A and resname NAG and resid 401"

residue_selection_2 = "chain A and resname ASN and resid 74"

}

apply_cif_link {

data_link = "BETA1-4"

residue_selection_1 = "chain A and resname NAG and resid 401"

residue_selection_2 = "chain A and resname NAG and resid 402"

}

when checking the .geo file phenix.refine outputs, I do not see any restraints between Asn and NAG, nor NAG and NAG.

There might be some clues in the refine.log file:

Build ligand and use monomer library to name atoms : NAG

Using monomer library entry NAG as template

which I guess looks good, and then something like this which could be where things are going wrong:

Monomer Library directory:

"c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib"

Total number of atoms: 11298

Number of models: 1

Model: ""

Number of chains: 4

Chain: "A"

Number of atoms: 5075

Number of conformers: 2

Conformer: "A"

Number of residues, atoms: 319, 4675

Unusual residues: {'NAG': 2}

Classifications: {'undetermined': 2, 'peptide': 317}

Modifications used: {'NH3': 1}

Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}

Not linked:

pdbres="ALA A 317 " segid="A "

pdbres="NAG A 401 " segid="A "

Not linked:

pdbres="NAG A 401 " segid="A "

pdbres="NAG A 402 " segid="A "

Unresolved non-hydrogen bonds: 2

Unresolved non-hydrogen angles: 4

Unresolved non-hydrogen chiralities: 2

Refinement doesn't crash or produce errors as far as I can see, however when checking the MolProbity output after refinement, it complains of missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant)

Furthermore there's still a HO4 attached to the O4 of NAG ... while the BETA1-4 should care to delete it .. however the mon_lib reads

BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose

glycosidic_bond_beta1-4

which doesn't seem entirely relevant for my case?

Any help would be appreciated

Thanks!

Ben