<div dir="ltr"><div class="gmail_default" style="font-size:small">Hi Julien,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">While we're plugging our favorite software solutions, I guess I should point you to the Results panel, available for analysis directly in the <b>cisTEM GUI</b>. This allows rapid visual feedback of each process (CTF determination shown in the attached screen grab) </div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">By selecting the "sort by" radio button a dialog opens (shown on right) which allows you to sort by CTF fit score among a large range of options.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Simply flip through using the "n" and "p" keys on your keyboard and delete those you don't like. This new group can be directly exported for further analysis in Relion. ( Or you could just continue on in cisTEM : )</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">HTH,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Ben H.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><div><img src="cid:ii_jouj4yhi0" alt="image.png" width="522" height="279"><br></div></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">------------------------<br><font color="black" size="2" face="Tahoma"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial">Benjamin Himes</font><font face="Arial"><br>
</font><font face="Arial"><br>cryoEM methods development</font><font face="Arial"><br>
</font><a href="https://mail.hhmi.org/owa/redir.aspx?C=SbsCefkcbOt75jDyr05lpd3OifVN_utmfvnhZrtXS7Bl2i2eOXXVCA..&URL=http%3a%2f%2fgrigoriefflab.janelia.org%2f" target="_blank"><font face="Arial">Grigorieff lab</font></a><font face="Arial">, HHMI Janelia Research Campus</font><font face="Arial"><br>
</font><font face="Arial"><br>cryoSTAC development @</font><a href="https://mail.hhmi.org/owa/redir.aspx?C=8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..&URL=https%3a%2f%2fgithub.com%2fbHimes%2femClarity%2fwiki" target="_blank"><font face="Arial">emClarity</font></a><font face="Arial"><br><br>-------------------------</font></span></font></span></font></div></div></div></div></div></div></div></div></div></div></div><br><br><div class="gmail_quote"><div dir="ltr">On Fri, Nov 23, 2018 at 11:11 AM <<a href="mailto:3dem-request@ncmir.ucsd.edu">3dem-request@ncmir.ucsd.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send 3dem mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: Micrographs manual sorting relion3 (Julien Bous)<br>
<br>
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<br>
Message: 1<br>
Date: Fri, 23 Nov 2018 17:10:29 +0100<br>
From: Julien Bous <<a href="mailto:julien.bous@etu.umontpellier.fr" target="_blank">julien.bous@etu.umontpellier.fr</a>><br>
To: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>><br>
Subject: Re: [3dem] Micrographs manual sorting relion3<br>
Message-ID: <<a href="mailto:d011b391-ddcb-7272-f2ff-1766e95709a3@etu.umontpellier.fr" target="_blank">d011b391-ddcb-7272-f2ff-1766e95709a3@etu.umontpellier.fr</a>><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Dear all,<br>
<br>
<br>
Thank you all very much for your nice suggestions.<br>
<br>
I tried to sort it with the motion estimation as suggested mazdak <br>
radjainia and it work quite well in my case so I'll gofor this solution.<br>
<br>
Another sugestion was to do it in scipion and it looks really <br>
convenient, as well as the FOCUS software.<br>
<br>
Thank you very much for all your answers.<br>
<br>
Cheers,<br>
<br>
Julien<br>
<br>
<br>
Le 23/11/2018 ? 11:57, Henning Stahlberg a ?crit?:<br>
> Dear Julien,<br>
><br>
> You could try FOCUS for this, see<br>
> <a href="https://www.youtube.com/watch?v=fKees50shgY&list=PLteVxMX-rlQspNczCoWrLyamWHgrhTMGv&index=6" rel="noreferrer" target="_blank">https://www.youtube.com/watch?v=fKees50shgY&list=PLteVxMX-rlQspNczCoWrLyamWHgrhTMGv&index=6</a><br>
><br>
> Henning.<br>
><br>
> Henning Stahlberg, PhD<br>
> Prof. for Structural Biology, C-CINA, Biozentrum, University of Basel<br>
> Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland<br>
> <a href="http://c-cina.org?%7C" rel="noreferrer" target="_blank">http://c-cina.org?|</a> Tel. +41-61-387 32 62<br>
><br>
><br>
><br>
><br>
> Dear Julien,<br>
><br>
> You can use Scipion to do that.<br>
> When running movie alignment (motioncor2, unblur, xmipp3, etc) you can <br>
> active an option<br>
> to generate a thumbnail and then after CTF estimation (gctf, ctffind4, <br>
> etc) you will have a GUI (see<br>
> figure below) where you can sort by any column (estimated resoltion, <br>
> quality fit, defocus, etc)<br>
> and select/deselect micrographs and create a new subset. You can also <br>
> change to a view to see<br>
> a gallery of all thumbnails (real space micrograph) or a gallery of <br>
> all PSDs images, this also helps<br>
> to screen the micrographs quickly in some cases. If you don't want to <br>
> continue processing<br>
> inside Scipion, you could easily export micrographs?+ CTF (protocol <br>
> 'relion - export ctf') and then<br>
> proceed in Relion.<br>
><br>
> Please let me know if you want to give it a?try and have any further <br>
> questions.<br>
><br>
> Kind?regards,<br>
> Jose Miguel<br>
><br>
><br>
><br>
> image.png<br>
<br>
<br>
<br>
><br>
><br>
> On Thu, Nov 22, 2018 at 6:18 PM Julien Bous <br>
> <<a href="mailto:julien.bous@etu.umontpellier.fr" target="_blank">julien.bous@etu.umontpellier.fr</a> <br>
> <mailto:<a href="mailto:julien.bous@etu.umontpellier.fr" target="_blank">julien.bous@etu.umontpellier.fr</a>>> wrote:<br>
><br>
> Dear All,<br>
><br>
> I wish to realise a sorting of my realigned micrographs in<br>
> Relion3, in<br>
> order to get rid of broken ice area. I wanted to do it in the subset<br>
> selection mode but I was not able to set a lowpass filter in this<br>
> mode<br>
> and it was challenging to asses the micrographs quality. I thougt<br>
> to do<br>
> it in the manual picking mode or manually, with eman , but in this<br>
> way I<br>
> can just display the micrographs one by one and it'll be very time<br>
> consuming. Therefore if anyone? knows how to realise this task<br>
> effectively I'll be glad to know your opinion.<br>
><br>
> Cheers,<br>
><br>
> Julien<br>
><br>
><br>
><br>
><br>
>> On 22 Nov 2018, at 18:18, Julien Bous <br>
>> <<a href="mailto:julien.bous@etu.umontpellier.fr" target="_blank">julien.bous@etu.umontpellier.fr</a> <br>
>> <mailto:<a href="mailto:julien.bous@etu.umontpellier.fr" target="_blank">julien.bous@etu.umontpellier.fr</a>>> wrote:<br>
>><br>
>> Dear All,<br>
>><br>
>> I wish to realise a sorting of my realigned micrographs in Relion3, <br>
>> in order to get rid of broken ice area. I wanted to do it in the <br>
>> subset selection mode but I was not able to set a lowpass filter in <br>
>> this mode and it was challenging to asses the micrographs quality. I <br>
>> thougt to do it in the manual picking mode or manually, with eman , <br>
>> but in this way I can just display the micrographs one by one and <br>
>> it'll be very time consuming. Therefore if anyone? knows how to <br>
>> realise this task effectively I'll be glad to know your opinion.<br>
>><br>
>> Cheers,<br>
>><br>
>> Julien<br>
>><br>
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