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<p>Hi Tom,<br>
</p>
<p><br>
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<p>Thanks for the help. I fixed the problem by assigning model_1= to a structure that was refined into the original cryo-EM map. </p>
<p><br>
</p>
<p>The nightly build (Aug 24th dev-3965) does not read the sequence file. It errors with sequence file not found. <br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
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Reza Khayat, PhD
<div>Associate Professor <br>
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<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Tom Terwilliger <tterwilliger@newmexicoconsortium.org><br>
<b>Sent:</b> Sunday, August 23, 2020 7:31 PM<br>
<b>To:</b> Reza Khayat<br>
<b>Cc:</b> PHENIX user mailing list; Tom Terwilliger<br>
<b>Subject:</b> [EXTERNAL] Re: [phenixbb] phenix.resolve_cryo_em</font>
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<div dir="ltr">Hi Reza,
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<div>Yes, I'm sorry about that. The current nightly build fixes one clipping issue (wrong boxing done by default). If that doesn't work, please let me know and I'll try to help.</div>
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</div>
<div>Another option is to box your map before running resolve_cryo_em and then specify "box_before_analysis=False" and then you can control the clipping yourself. (You can use map_box to do this)</div>
<div><br>
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<div>All the best,</div>
<div>Tom T</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sun, Aug 23, 2020 at 4:13 PM Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu">rkhayat@ccny.cuny.edu</a>> wrote:<br>
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<p>​Hi,<br>
</p>
<p><br>
</p>
<p>I'm running into a clipping issue with phenix.resolve_cryo_em. The program seems to be improving the map; however, portions of the map get clipped. Any suggestion would be appreciated. <br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="gmail-m_1040080235152018716Signature">
<div name="divtagdefaultwrapper">Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
</div>
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<div dir="ltr">Thomas C Terwilliger
<div>Laboratory Fellow, Los Alamos National Laboratory</div>
<div>Senior Scientist, New Mexico Consortium</div>
<div>100 Entrada Dr, Los Alamos, NM 87544</div>
<div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">
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