<html><head></head><body bgcolor="#FFFFFF"><div>Dear Smith,</div><div>These two articles will offer you the possibility to do what you wish for non-covalent atom pairs:-</div><a href="http://dx.doi.org/10.1107/S1600576715006287">http://dx.doi.org/10.1107/S1600576715006287</a><div><a href="http://dx.doi.org/10.1107/S2052252513031485">http://dx.doi.org/10.1107/S2052252513031485</a> <br><div>Best wishes,</div><div>John <br><br><div>Emeritus Prof John R Helliwell DSc_Physics </div><div>FInstP FRSC FSocBiol Fellow of the ACA</div><div>Emeritus Member of the British Biochemical Society</div><div>School of Chemistry, University of Manchester, M13 9PL, UK.</div><div><br></div></div><div><br>On 22 Jul 2015, at 10:36, "Smith Liu" <<a href="mailto:smith_liu123@163.com">smith_liu123@163.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Pavel,</div><div><br></div><div>Thanks for your interpretation. But for most of the crystal structure, they were got from 2-4 A crystal rather than from around 1 A crystal. Then how can we analyse the non-covalent bonds based on the 3-D crystal structure? As I know, there were crystal papers which analyse non-covalent bonds or protein-protein interaction based on the 3-D crystal structure.</div><div><br></div><div>Best regards.</div><div><br></div><div>Smith</div><div><br></div><div><br><br><br><br></div><div style="position: relative; -ms-zoom: 1;"></div><div id="divNeteaseMailCard"></div><div><br></div>At 2015-07-22 12:26:09, "Pavel Afonine" <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br> <blockquote id="isReplyContent" style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;">
Hi Smith,<br>
<br>
2-3 A is not atomic resolution, so you cannot meaningfully measure
distances between individual atoms in your model at this resolution,
I think (I guess it is safer to say that you can measure these
distances, technically, but their meaning is not going to be
straightforward to interpret).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/21/15 20:10, Smith Liu wrote:<br>
</div>
<blockquote cite="mid:a9d8662.16840.14eb3bdc98e.Coremail.smith_liu123@163.com" type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;">
<div>Dear Pavel,</div>
<div><br>
</div>
<div>Related to Joel's question, suppose the resolution is about
2-3 A, and I have added H (should be modelled "H"）for the
refinement. If I want to measure the H-bond length between the
NE2 and H of OH of Tyr, I need to measure the distance between
NE2 and the "modelled H" of OH of Tyr. Is this "modelled H"
position reliable for the length measurement of the H-bond?</div>
<div><br>
</div>
<div>Best regards.</div>
<div><br>
</div>
<div>Smith<br>
<br>
<br>
<br>
<br>
</div>
<div><br>
</div>
At 2015-07-22 10:04:39, "Pavel Afonine" <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a>
wrote:<br>
<blockquote id="isReplyContent" style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;"> Hi
Joel,<br>
<br>
as was suggested main.nqh_flips=False should disable this. <br>
<br>
However I'm puzzled about this. NQH flips functionality is
designed to flip these residues such that the clashes are
minimized and plausible H-bonding is achieved. So I wonder why
it is not working in your case?<br>
<br>
Would it be possible to send me input files (off list) so that
I can reproduce this and investigate. Also please indicate HIS
in question.<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/21/15 02:07, Joel Tyndall
wrote:<br>
</div>
<blockquote cite="mid:0DDD35E86921D947AFE9571F16DA7D6B2F707995@ITS-EXM-P05.registry.otago.ac.nz" type="cite">
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span>Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span><o:p> </o:p></span></p>
<p class="MsoNormal"><span>We are trying to optimise a
histidine interaction where NE2 would ideally make a
hydrogen bond with an adjacent tyrosine hydroxyl. The
starting point contains the hydrogen bond. However
upon refinement the ring flips (chi2 x 180 degrees) to
place the CE1 adjacent to the tyrosine hydroxyl. <o:p></o:p></span></p>
<p class="MsoNormal"><span><o:p> </o:p></span></p>
<p class="MsoNormal"><span>Is it possible to stop this as
I see no reason why phenix.refine would want to do
this<o:p></o:p></span></p>
<p class="MsoNormal"><span><o:p> </o:p></span></p>
<p class="MsoNormal"><span>Regards<o:p></o:p></span></p>
<p class="MsoNormal"><span><o:p> </o:p></span></p>
<p class="MsoNormal"><span>Joel</span><br>
</p>
</div>
</blockquote>
<br>
</blockquote>
</div>
<br>
<br>
<span title="neteasefooter"><span id="netease_mail_footer"></span></span>
</blockquote>
<br>
</blockquote></div><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>phenixbb mailing list</span><br><span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></span><br><span><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br><span>Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></span></div></blockquote></div></body></html>