<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">hi,<br>i thought that also and checked everything with pdbtools.<br>but now i can get the error using one of your example pdb files<br>(1rxf_randomise.pdb ). so i dont think it is the pdb file.<br><br>thanks<br>jpd<br><br>--- On <b>Fri, 6/18/10, Nathaniel Echols <i><nechols@lbl.gov></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Nathaniel Echols <nechols@lbl.gov><br>Subject: Re: [phenixbb] simulated annealing<br>To: "PHENIX user mailing list" <phenixbb@phenix-online.org><br>Date: Friday, June 18, 2010, 6:13 PM<br><br><div id="yiv1021995921">On Fri, Jun 18, 2010 at 5:05 PM, jp d <span dir="ltr"><<a rel="nofollow" ymailto="mailto:yoyoq@yahoo.com" target="_blank" href="/mc/compose?to=yoyoq@yahoo.com">yoyoq@yahoo.com</a>></span> wrote:<br><div
class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top">hi,<br>using supplied phenix examples 1rxf.mtz and 1rxf_randomise.pdb <br>i can run the following command and it fails <br>
in phenix1.6.2 but not in phenix1.5-2<br><br>the error is: <br>RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1931 > 50</td></tr></tbody></table></blockquote><div><br></div><div>This is telling you that one of the bonds in the model is longer than the limit we've set - a simple sanity check that warns you there is something seriously wrong with the PDB file. This parameter appears to have been added since 1.5-2. It's possible that it's really a bug in the restraints generation, but usually these types of errors indicate corrupted coordinates. (For instance, in certain circumstances CNS sometimes outputs atoms at 999.99,999.99,999.99, which would probably trigger this error.)</div>
<div><br></div><div>You should still use 1.6.2. You can, if you'd like, add the parameter <span class="Apple-style-span" style="font-family: arial,sans-serif; font-size: 13px;">max_reasonable_bond_distance=None to force it to accept absurd bond lengths, but this is probably just going to mask a problem with either your PDB file or our code. We need to see the PDB file to tell for sure.</span></div>
<div><span class="Apple-style-span" style="font-family: arial,sans-serif; font-size: 13px;"><br></span></div><div><span class="Apple-style-span" style="font-family: arial,sans-serif; font-size: 13px;">-Nat</span></div>
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