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Hi Smith,<br>
<br>
this may be helpful:<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/papers/wd5073_reprint.pdf">https://www.phenix-online.org/papers/wd5073_reprint.pdf</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/22/15 02:36, Smith Liu wrote:<br>
</div>
<blockquote
cite="mid:52ccb885.1e33b.14eb51f77cc.Coremail.smith_liu123@163.com"
type="cite">
<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><br>
</div>
At 2015-07-22 12:26:09, "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
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
moz-do-not-send="true" class="moz-txt-link-rfc2396E"
href="mailto:pafonine@lbl.gov"><a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a></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>
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