<div dir="ltr">Miao<div><br></div><div>The glycans should be automatically linked and listed in the log file. You can do a quick check there.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Aug 8, 2018 at 2:28 AM Miao Gui <<a href="mailto:gmhust2007@163.com">gmhust2007@163.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Pavel,</div><div><br></div><div>Thank you very much for your reply.</div><div>Actually, the models as well as the glycans look quite good after PHENIX real-space refinement. I just want to make sure that this is the right way since it's my first time to refine a glycan.</div><div><br></div><div>Hope to see you in Tsinghua!</div><div><br></div><div>Best wishes,</div><div><br></div><div>Miao </div><br><br><br><br><div style="zoom:1"></div><div id="m_-3665370923614767209divNeteaseMailCard"></div><br>At 2018-08-08 00:46:37, "Pavel Afonine" <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> wrote:<br> <blockquote id="m_-3665370923614767209isReplyContent" style="PADDING-LEFT:1ex;MARGIN:0px 0px 0px 0.8ex;BORDER-LEFT:#ccc 1px solid">
Hi,<br>
<br>
yes, as long as the map shows the glycans clearly enough so that you
can model them, then there is no problem refining your model using
phenix.real_space_refine. Normally, there is no need to add anything
special. <br>
Now I'm puzzled.. do you have a reason to believe that something
isn't working correctly?<br>
<br>
By the way, we will be at Tsinghua University first week of
September running Phenix workshop. We can discuss things while
there!<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="m_-3665370923614767209moz-cite-prefix">On 8/7/18 08:16, Miao Gui wrote:<br>
</div>
<blockquote type="cite">
<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>Dear phenix developers,</div>
<div><br>
</div>
<div>I'm a PHENIX user. PHENIX helped me a lot when refining
structural models against cryo-EM maps.</div>
<div><br>
</div>
<div>Recently, I built a structural model of a glycoprotein and
added the glycans using COOT against a 3.4 A cryo-EM map. Then
I want to refine the model using PHENIX.real_space_refine. I
always add the second structure restrains when refining the
models against cryo-EM maps. Do I need to add other restrains
for the glycans? Is it appropriate to refine the glycoprotein
using the real_space_refine?</div>
<div>Thank you.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Dr. Miao Gui</div>
<div>Tsinghua University, Beijing</div>
</div>
<br>
<br>
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