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<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Dear Bastiaan and All here interested:<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><br></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">A more subtle two-stage particle picking procedure for
highly concentrated samples is implemented in IMAGIC which is illustrated in:<span></span></p>
<p class="MsoNormal" style="margin:0cm;text-align:justify;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><a name="_Hlk142811625"><span style="font-family:"Times New Roman",serif">Afanasyev</span></a><span style="font-family:"Times New Roman",serif"> P, Seer-Linnemayr C, Ravelli RBG,
Matadeen R, De Carlo S, Alewijnse B, Portugal RV, Pannu NS, Schatz M, Van Heel
M (2017). Single-particle cryo-EM using alignment by classification (ABC): the
structure of Lumbricus terrestris haemoglobin. <i>IUCrJ.</i> <b>4</b>, 678–694.<span> </span></span>(free download)<span style="font-family:"Times New Roman",serif"><span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span> </span></p>
<img src="cid:ii_lpib3p4t1" alt="image.png" width="481" height="488"><br><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Cheers<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Marin van Heel<span></span></p>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Nov 27, 2023 at 3:32 PM Bastiaan Bergman <<a href="mailto:bastiaan@modelmedicines.com">bastiaan@modelmedicines.com</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">All,<div><br></div><div>I'm reprocessing this data from <a href="https://urldefense.com/v3/__https://www.ebi.ac.uk/empiar/EMPIAR-11176/__;!!Mih3wA!CUyE02u7zsgfaew-RbTyNrOq6oGiT2gUKjW0bIRXWVGHTDfNrRK_22uSkfU72hnZOQFy1aEZ2ZvBgA9YfmsgNNaMbV_bow$" target="_blank">Empiar</a> with Relion (4.0.1 commit: 8e4597), clearly it's possible to get a highres structure with it, <a href="https://urldefense.com/v3/__https://journals.plos.org/plospathogens/article?id=10.1371*journal.ppat.1011206__;Lw!!Mih3wA!CUyE02u7zsgfaew-RbTyNrOq6oGiT2gUKjW0bIRXWVGHTDfNrRK_22uSkfU72hnZOQFy1aEZ2ZvBgA9YfmsgNNZePmjmjw$" target="_blank">they</a> did it with Cryospark.<br clear="all"><div><br></div><div>I'm having trouble picking particles. I tried autopicking with Topaz and I tried manual picking. The first did not result in any good particles (as judged by the 2D classes). Looking at it manually it seems too crowded or aggregated to really pick individual particles.</div><div><br></div><div>There are 7000 micrographs, I looked manually at about 700 (10%) of them, the one below is one of the best 10 I could find. I have trouble picking single particles in this, most structures here seem to be larger than a single particle.</div><div><img src="cid:ii_lpgznz560" alt="Screenshot 2023-11-27 at 14.55.44.png" width="542" height="484"><br></div><div><br></div><div>Are there any expert directions I can get? How do I pick particles, is there hope with this micrograph or should I use different displaying settings? (Above was done with Topaz denoising). Or are there any tools to go through all 7000 and look for some better ones?</div><div><br></div><div>Thanks for all your insights! I attached the <a href="https://urldefense.com/v3/__https://drive.google.com/file/d/1mbEepGxoCt2zCEw3mc1HfDt6r5MWYlJ_/view?usp=sharing__;!!Mih3wA!CUyE02u7zsgfaew-RbTyNrOq6oGiT2gUKjW0bIRXWVGHTDfNrRK_22uSkfU72hnZOQFy1aEZ2ZvBgA9YfmsgNNaqqo6XeQ$" target="_blank">micrograph.mrc</a> here as well.</div><div>Bastiaan.</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div></div></div>
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