<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-size:12.7273px">Hi </span>Firdous<span style="font-size:12.7273px">,</span></div><div><span style="font-size:12.7273px"><br></span></div><div><span style="font-size:12.7273px">Can you please update to 1.19.2 version of Phenix here:</span></div><div><span style="font-size:12.7273px"><br></span></div><div><span style="font-size:12.7273px"><a href="https://www.phenix-online.org/download/" target="_blank">https://www.phenix-online.org/download/</a></span><br></div><div><span style="font-size:12.7273px"><br></span></div><div><span style="font-size:12.7273px">and confirm that the problem still exists? If so, can you please share the files or point me to publicly available databases?</span></div><div><span style="font-size:12.7273px"><br></span></div><div><span style="font-size:12.7273px">Best regards,</span></div><div><span style="font-size:12.7273px">Oleg Sobolev.</span></div></div></div>
<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 26, 2021 at 12:51 AM Firdous Tarique <<a href="mailto:kahkashantarique@gmail.com">kahkashantarique@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi</div><div><br></div><div>I am getting the following error during real space refinement of the model and map. Can anybody suggest what it is actually about. It is something about geometry_restraints but I am not able to figure it out<br></div><div>where.</div><div><br></div><div>Can we do something in refinement settings Or change any threshold value to avoid these problems? <br></div><div><br></div><div>Input is 80S.pdb ribosome and its corresponding em map.<br></div><div><br></div><div> File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1486, in energies_sites<br> flags=flags, sites_cart=sites_cart, site_labels=site_labels)<br><br> File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1388, in pair_proxies<br> check_bonded_distance_cutoff(sites_frac=sites_frac)<br><br> File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1269, in check_bonded_distance_cutoff<br> raise RuntimeError(msg)</div><div><br></div><div>Best regards</div><div><br></div><div>Firdous<br></div></div>
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