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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">
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style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<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"
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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>
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<br>
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