<div dir="ltr"><div>Hi Pavel,</div><div>I sent you a separate email with all the files. Thank you very much for your help!</div><div>Best,</div><div>Yangqi<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at 8:31 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi Yangqi,<br>
<br>
it depends what you call "worse" and also keep in mind that
clashscore is not the only metric of success. Some metrics get get
worse and some better, and changes in some may be just fine and some
may indicate problems.<br>
It's hard to comment meaningfully based upon rather scarce amount of
information you provide. <br>
I can have a look if you share (off list!) map, models (input and
output) and the log file from refinement.<br>
<br>
Pavel<br>
<br>
<div>On 1/21/20 17:19, Yangqi Gu wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Thank you Tom and Oleg. I tried refinement as you
suggested. I did local refinement after I did the rigid body.
However, the first couple of cycles, the clashscore and
everything (statistics) seems improved, but then getting worse
after more cycles. I did both 5 and 10 cycles, the final outputs
are all worse than what I started with, which means only after
rigid body fitting. Is this normal?
<div>Best,</div>
<div>Yangqi</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at 5:32
PM Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi Yangqi,
<div><br>
</div>
<div>Yes, phenix.simple_ncs_from_pdb is the tool to search
for NCS in models. Documentation:</div>
<div><a href="https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html" target="_blank">https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html</a><br>
</div>
<div><br>
</div>
<div>Also, it is available in GUI: "Select atoms" ->
"NCS" -> "Find NCS" but with less options available.
For matrices you'll have to run command-line.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at
1:17 PM BuddySphinx <<a href="mailto:yangqi.gu@yale.edu" target="_blank">yangqi.gu@yale.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div>
<p class="MsoNormal">Also, another question. Could I
find ncs from my pdb model? I tried with map, but it
failed to find the correct symmetry. Can I use
phenix.simple.ncs to generate the ncs operator file?</p>
<p class="MsoNormal">Best,</p>
<p class="MsoNormal">Yangqi</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a>
for Windows 10</p>
<p class="MsoNormal"> </p>
<div style="border-color:rgb(225,225,225) currentcolor currentcolor;border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in">
<p class="MsoNormal" style="border:medium none;padding:0in"><b>From:
</b><a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Tom
Terwilliger</a><br>
<b>Sent: </b>Tuesday, January 21, 2020 9:18 AM<br>
<b>To: </b><a href="mailto:yangqi.gu@yale.edu" target="_blank">Yangqi Gu</a>;
<a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Thomas
Charles Terwilliger</a><br>
<b>Cc: </b><a href="mailto:phenixbb@phenix-online.org" target="_blank">PHENIX
user mailing list</a><br>
<b>Subject: </b>Re: [phenixbb] How critical is
ncs operator for real space refinement</p>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">Hi Yangqi,</p>
</div>
<div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">You don't actually need the
NCS relationships in order to refine with NCS
restraints because the default is to use
torsion-angle restraints which only use local
relationships, not overall NCS matrices.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">So you can go ahead and use
your rigid-body-refined starting model with
torsion-angle restraints in
phenix.real_space_refine. That will not
impose perfect helical restraints, but I am
guessing that your map already has
near-perfect helical symmetry so that should
not matter very much.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Also you might first run
with just one monomer which will be much
quicker and give you almost the same answer.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Let us know if that does
not do it!</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">All the best,</p>
</div>
<div>
<p class="MsoNormal">Tom T</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Mon, Jan 20, 2020 at
9:33 PM Yangqi Gu <<a href="mailto:yangqi.gu@yale.edu" target="_blank">yangqi.gu@yale.edu</a>>
wrote:</p>
</div>
<blockquote style="border-color:currentcolor currentcolor currentcolor rgb(204,204,204);border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">Dear PHENIX developers,</p>
<div>
<p class="MsoNormal">I have a question about
NCS operator. Since I have a cryo-EM map
and I want to refine my filament
coordinates within the map. I generated
the coordinate map manually in Chimera by
building multiple chains with rigid body
refinement. Since I did not generate the
NCS operator file (I tried by doing map
symmetry, it did not give me the right
helical symmetry), I did not refine with
ncs restraints. I am wondering in this
case, how critical it is to refine a model
with helical symmetry applied. Is it a
must or can I go with the way I did? Hope
to hear from you soon!</p>
</div>
<div>
<p class="MsoNormal">Best,</p>
</div>
<div>
<p class="MsoNormal">Yangqi<br clear="all">
</p>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
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<p class="MsoNormal"><br clear="all">
</p>
<div>
<p class="MsoNormal"> </p>
</div>
<p class="MsoNormal">-- </p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Thomas C
Terwilliger</p>
<div>
<p class="MsoNormal">Laboratory
Fellow, Los Alamos National
Laboratory</p>
</div>
<div>
<p class="MsoNormal">Senior
Scientist, New Mexico
Consortium</p>
</div>
<div>
<p class="MsoNormal">100 Entrada
Dr, Los Alamos, NM 87544</p>
</div>
<div>
<p class="MsoNormal">Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></p>
</div>
<div>
<p class="MsoNormal">Tel:
505-431-0010</p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
</div>
</div>
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div><br>
</div>
Yangqi Gu
<div>Graduate Student</div>
<div>Malvankar Lab</div>
<div>Yale University, West Campus</div>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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</blockquote>
<br>
</div>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><br></div>Yangqi Gu<div>Graduate Student</div><div>Malvankar Lab</div><div>Yale University, West Campus</div></div></div></div></div>