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Hey Lorenzo,</div>
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<div class="elementToProof"><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">This was a 99% straightforward fix! The only thing I had to do after the conversion was to get rid of the data_optics section in it's
entirety and rename the "_experiment_id" in "_rlnTomoName" in the data_particles section and Relion liked the particles.star file very much!</span></div>
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<div class="elementToProof"><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Thanks everyone for pointing out the options!</span></div>
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<div class="elementToProof"><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Best,</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Willem</span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Van:</b> Lorenzo Gaifas <lorenzo.gaifas@gmail.com><br>
<b>Verzonden:</b> vrijdag 1 maart 2024 10:23<br>
<b>Aan:</b> Zongli Li <zongli.li@gmail.com><br>
<b>CC:</b> Willem Noteborn <willemnoteborn@outlook.com>; 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Onderwerp:</b> Re: [3dem] Converting cryolo tomogram particle coordinates to Relion4/5 friendly ones</font>
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<div>Hi Willem,</div>
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<div>If you want to simply convert to a star file you could use [cryohub](<a href="https://urldefense.com/v3/__https://github.com/teamtomo/cryohub/)'s__;!!Mih3wA!C6v5T9_ZYexscn6cAiYoRJZDxtWvWUs7KklxpNwrUp_h57R2A6KknJ6EqT6hLRvGWv19efLaHLCoQsJwxfF7zMxnPumE$">https://github.com/teamtomo/cryohub/)'s</a> `convert` command. It's been a while since I touched the cryolo part though, so please let
me know if things break :)</div>
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<div>Best,</div>
<div>Lorenzo<br>
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<div dir="ltr" class="x_gmail_attr">On Thu, Feb 29, 2024 at 8:11 PM Zongli Li <<a href="mailto:zongli.li@gmail.com">zongli.li@gmail.com</a>> wrote:<br>
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<div>Hi Willem,</div>
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<div>The EMAN format from cryolo can be directly used in Relion. I have been using this way for SPA all the time, but haven't used it in tomogram particles. I assume they should be the same.</div>
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<div>Best,</div>
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<div>Zongli<br>
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<div dir="ltr" class="x_gmail_attr">On Thu, Feb 29, 2024 at 1:44 PM Willem Noteborn <<a href="mailto:willemnoteborn@outlook.com" target="_blank">willemnoteborn@outlook.com</a>> wrote:<br>
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<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Dear list,</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><br>
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<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">I was wondering if anyone knows a way to convert cryolo picked tomogram coordinates (for instance the CBOX_3D or coords format) to a format that can be readily imported
into Relion. I've been playing around with cryolo_boxmanager_tools.py but can't seem to find a solution. Maybe I'm missing something obvious.</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><br>
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<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Any information on this would be highly appreciated!</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><br>
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<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Kind regards,</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Willem</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><br>
</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Dr. Willem Noteborn</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">CryoEM Scientist</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"> </span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">T: +31 (0)7 1527 1424</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><a href="mailto:w.e.m.noteborn@biology.leidenuniv.nl" target="_blank">w.e.m.noteborn@biology.leidenuniv.nl</a> </span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><a href="mailto:NeCEN@biology.leidenuniv.nl" target="_blank">NeCEN@biology.leidenuniv.nl</a></span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><a href="https://urldefense.com/v3/__http://www.NeCEN.nl__;!!Mih3wA!EZuage2pQokgJSH-i-JxI2i7DjK_QeRYVEWfI5sx2nh5hsrUkIg2nCI-JMcJHzkooSW_IoEeWqN0fpGQodQb_f5QHp2U$" id="x_m_3961501043176285810m_-8195834432432991172LPlnk949708" target="_blank">www.NeCEN.nl</a></span></div>
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