<div dir="ltr">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 class="gmail_extra"><div class="gmail_quote">
<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>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><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>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>