<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.&nbsp;Then&nbsp;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" &lt;pafonine@lbl.gov&gt; 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"£İfor the
          refinement. If I want to measure the H-bond&nbsp;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">&lt;pafonine@lbl.gov&gt;</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>&nbsp;</o:p></p>
              <p class="MsoNormal"><span>Hi all,<o:p></o:p></span></p>
              <p class="MsoNormal"><span><o:p>&nbsp;</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>&nbsp;</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>&nbsp;</o:p></span></p>
              <p class="MsoNormal"><span>Regards<o:p></o:p></span></p>
              <p class="MsoNormal"><span><o:p>&nbsp;</o:p></span></p>
              <p class="MsoNormal"><span>Joel</span><br>
              </p>
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