<div dir="ltr">Thanks Oleg. <div><br></div><div>This was fixed by increasing the default excessive_bond_distance_limit. My restraint file looks like :</div><div><div>refinement.geometry_restraints.edits {</div><div> excessive_bond_distance_limit = 15</div>
<div> C8_C1=chain C and resid 8 and name C1'</div><div> D10_C1=chain D and resid 10 and name C1'</div><div> bond {</div><div> action = *add</div><div> atom_selection_1 = $C8_C1</div><div> atom_selection_2 = $D10_C1</div>
<div> distance_ideal = 9.1</div><div> sigma = 0.02</div><div> slack = 0.5</div><div> }</div></div><div>}</div><div><br></div><div>And now it works!</div><div><br></div><div>Thank you Oleg!</div><div><br></div><div>
Bradley</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jul 17, 2014 at 8:05 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Bradley<div><br></div><div>Send me your example off-line so I can test it and maybe modify.</div><div><br>
</div><div>Nigel</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="">On Thu, Jul 17, 2014 at 12:52 PM, Bradley Hintze <span dir="ltr"><<a href="mailto:bradley.hintze@duke.edu" target="_blank">bradley.hintze@duke.edu</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hey PHENIX,<div><br></div><div>I am wondering if I can define a distant restraint longer that 3A in a custom restraint file? The conventional way of doing this is to provide :</div>
<div><br></div><div><div>refinement.geometry_restraints.edits {</div>
<div> C8_C1=chain C and resid 8 and name C1'</div><div> D10_C1=chain D and resid 10 and name C1'</div><div> bond {</div><div> action = *add</div><div> atom_selection_1 = $C8_C1</div><div> atom_selection_2 = $D10_C1</div>
<div> distance_ideal = 9.1</div><div> sigma = 0.02</div><div> slack = 0.5</div><div> }</div><div><br></div><div> Obviously this is a distant and not bond restraint. 9.1 exceeds the allowed length of 3 for a bond. Is there a different type of restraint that allows longer distances?</div>
<div><br></div><div>Thanks!</div><span><font color="#888888">-- <br><div>Bradley J. Hintze</div><div>Duke University</div><div>PhD Candidate</div><div>Department of Biochemistry</div>
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<br></div></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>Phone : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Bradley J. Hintze</div><div>Duke University</div><div>PhD Candidate</div><div>Department of Biochemistry</div>
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