<div dir="ltr">Hi Phenix,<div><br></div><div>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. </div><div><br></div><div>
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),</div>
<div><br></div><div><div> apply_cif_link {</div><div> data_link = "NAG-ASN"</div><div> residue_selection_1 = "chain A and resname NAG and resid 401"</div><div> residue_selection_2 = "chain A and resname ASN and resid 74"</div>
<div> }</div><div> apply_cif_link {</div><div> data_link = "BETA1-4"</div><div> residue_selection_1 = "chain A and resname NAG and resid 401"</div><div> residue_selection_2 = "chain A and resname NAG and resid 402"</div>
<div> }</div></div><div><br></div><div>when checking the .geo file phenix.refine outputs, I do not see any restraints between Asn and NAG, nor NAG and NAG. </div><div><br></div><div>There might be some clues in the refine.log file:</div>
<div><br></div><div><div> Build ligand and use monomer library to name atoms : NAG</div><div> Using monomer library entry NAG as template</div></div><div><br></div><div>which I guess looks good, and then something like this which could be where things are going wrong:</div>
<div><br></div><div><div> Monomer Library directory:</div><div> "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib"</div><div> Total number of atoms: 11298</div><div> Number of models: 1</div>
<div> Model: ""</div><div> Number of chains: 4</div><div> Chain: "A"</div><div> Number of atoms: 5075</div><div> Number of conformers: 2</div><div> Conformer: "A"</div><div>
Number of residues, atoms: 319, 4675</div><div> Unusual residues: {'NAG': 2}</div><div> Classifications: {'undetermined': 2, 'peptide': 317}</div><div> Modifications used: {'NH3': 1}</div>
<div> Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}</div><div> Not linked:</div><div> pdbres="ALA A 317 " segid="A "</div><div> pdbres="NAG A 401 " segid="A "</div>
<div> Not linked:</div><div> pdbres="NAG A 401 " segid="A "</div><div> pdbres="NAG A 402 " segid="A "</div><div> Unresolved non-hydrogen bonds: 2</div>
<div> Unresolved non-hydrogen angles: 4</div><div> Unresolved non-hydrogen chiralities: 2</div></div><div><br></div><div> </div><div>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)</div>
<div><br></div><div>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</div><div><br></div><div><div>BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose</div>
<div> glycosidic_bond_beta1-4</div></div><div><br></div><div>which doesn't seem entirely relevant for my case?</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>Any help would be appreciated</div>
<div><br></div><div>Thanks!</div><div><br></div><div>Ben</div></div>