<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Thanks for your quick reply! However now I get the following error message,</span><div style="font-family:arial,sans-serif;font-size:13px"><br></div>
<div style="font-family:arial,sans-serif;font-size:13px">"Fatal problems interpreting model file: NUmber of atoms with unkown nonbonded energy type symbols: 3 Please edit the model file to resolve the problems nd/org supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Alternatively, to continue despite this problem use: stop_for_unknown=False"</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">the log file says,</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><div class="im"><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><div> apply_cif_link:</div><div> data_link: NAG-ASN</div><div> mod_id_1: DEL-O1</div><div> mod_id_2: DEL-HD22</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> apply_cif_link:</div><div> data_link: BETA1-4</div><div> mod_id_1: DEL-HO4</div><div> mod_id_2: DEL-O1</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> apply_cif_link:</div><div> data_link: NAG-ASN</div><div> mod_id_1: DEL-O1</div><div> mod_id_2: DEL-HD22</div><div> residue_selection_1: chain B and resname NAG and resid 401</div>
<div> residue_selection_2: chain B and resname ASN and resid 74</div><div> apply_cif_link:</div><div> data_link: BETA1-4</div><div> mod_id_1: DEL-HO4</div><div> mod_id_2: DEL-O1</div><div> residue_selection_1: chain B and resname NAG and resid 401</div>
<div> residue_selection_2: chain B and resname NAG and resid 402</div><div class="im"><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><div> Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}</div>
<div> Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}</div><div class="im"> Classifications: {'undetermined': 2, 'peptide': 317}</div><div> Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1}</div>
<div class="im"><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><div class="im"><div> Conformer: "B"</div><div> Number of residues, atoms: 319, 4675</div></div><div> Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}</div>
<div> Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}</div><div class="im"> Classifications: {'undetermined': 2, 'peptide': 317}</div><div> Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1}</div>
<div class="im"><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><div> bond proxies already assigned to first conformer: 4309</div><div> Chain: "B"</div><div>[...]</div><div> Chain: "C"</div><div>[...]</div><div> Residues with excluded nonbonded symmetry interactions: 26</div>
<div> residue:</div><div>[...]</div><div> Number of atoms with unknown nonbonded energy type symbols: 3</div><div> "ATOM 5046 HO4 NAG A 401 .*.A H "</div><div> "ATOM 6215 HD22 ASN B 74 .*.B H "</div>
<div> "ATOM 10057 HO4 NAG B 401 .*.B H "</div><div> Time building chain proxies: 4.05, per 1000 atoms: 0.36</div></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do the trick - as I explicitly want to refine hydrogens I reckon they are added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link instead of using the BETA1-4?</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Thanks again!</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
B</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-12 10:54 GMT+02:00 Benjamin Stauch <span dir="ltr"><<a href="mailto:bs448c@gmail.com" target="_blank">bs448c@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thanks for your quick reply! However now I get the following error message,<div><br></div><div>"Fatal problems interpreting model file: NUmber of atoms with unkown nonbonded energy type symbols: 3 Please edit the model file to resolve the problems nd/org supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Alternatively, to continue despite this problem use: stop_for_unknown=False"</div>
<div><br></div><div>the log file says,</div><div><br></div><div><br></div><div><br></div><div><div class=""><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><div> apply_cif_link:</div><div> data_link: NAG-ASN</div><div> mod_id_1: DEL-O1</div><div> mod_id_2: DEL-HD22</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> apply_cif_link:</div><div> data_link: BETA1-4</div><div> mod_id_1: DEL-HO4</div><div> mod_id_2: DEL-O1</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> apply_cif_link:</div><div> data_link: NAG-ASN</div><div> mod_id_1: DEL-O1</div><div> mod_id_2: DEL-HD22</div><div> residue_selection_1: chain B and resname NAG and resid 401</div>
<div> residue_selection_2: chain B and resname ASN and resid 74</div><div> apply_cif_link:</div><div> data_link: BETA1-4</div><div> mod_id_1: DEL-HO4</div><div> mod_id_2: DEL-O1</div><div> residue_selection_1: chain B and resname NAG and resid 401</div>
<div> residue_selection_2: chain B and resname NAG and resid 402</div><div class=""><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><div> Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}</div><div> Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}</div>
<div class="">
<div> Classifications: {'undetermined': 2, 'peptide': 317}</div></div><div> Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1}</div>
<div class=""><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><div class=""><div> Conformer: "B"</div><div>
Number of residues, atoms: 319, 4675</div>
</div><div> Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}</div><div> Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}</div><div class=""><div> Classifications: {'undetermined': 2, 'peptide': 317}</div>
</div><div> Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1}</div><div class=""><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><div> bond proxies already assigned to first conformer: 4309</div>
<div> Chain: "B"</div><div>[...]</div><div> Chain: "C"</div><div>[...]</div><div> Residues with excluded nonbonded symmetry interactions: 26</div><div> residue:</div><div>[...]</div><div> Number of atoms with unknown nonbonded energy type symbols: 3</div>
<div> "ATOM 5046 HO4 NAG A 401 .*.A H "</div><div> "ATOM 6215 HD22 ASN B 74 .*.B H "</div><div> "ATOM 10057 HO4 NAG B 401 .*.B H "</div><div> Time building chain proxies: 4.05, per 1000 atoms: 0.36</div>
</div><div><br></div><div><br></div><div>Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do the trick - as I explicitly want to refine hydrogens I reckon they are added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link instead of using the BETA1-4?</div>
<div><br></div><div>Thanks again!</div><div><br></div><div>B</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-12 2:12 GMT+02:00 Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span>:<div>
<div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <span dir="ltr"><<a href="mailto:bs448c@gmail.com" target="_blank">bs448c@gmail.com</a>></span> wrote:<br>
</div><div class="gmail_extra"><div class="gmail_quote"><div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><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></blockquote><div><br></div></div><div>Okay, I think this may be part of the problem - you are missing the outer "scope" for these parameter blocks, so they are not processed correctly. If you change "apply_cif_link" to "refinement.pdb_interpretation.apply_cif_link" in both places it may fix the problem.</div>
<div>
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><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></blockquote><div><br></div></div><div>Sorry, this is actually my bug (those atoms should not be included in covalently linked sugars), and I think I still have an email complaining about this in my inbox from late 2012. I need to overhaul that bit of code anyway so I will see if Nigel and I can come up with something smarter.</div>
<div><br></div><div>-Nat</div></div></div></div>
</blockquote></div></div></div><br></div>
</blockquote></div><br></div>