<div dir="ltr"><br><div>The error means the program could not find your box file. You'd better copy your box file into the directory where you store the mrc file. Then the input in relion interface should be yourdirectory/.box</div><div><br></div><div>Weimin</div><div><br></div><div>LSBR/NIAMS/NIH</div><div>____________________________________________________________________________________</div><div><span style="font-size:12.8px">Message: 2</span><br style="font-size:12.8px"><span style="font-size:12.8px">Date: Thu, 25 Jan 2018 17:16:07 -0500</span><br style="font-size:12.8px"><span style="font-size:12.8px">From: Vishaka Santosh <</span><a href="mailto:vs4p@virginia.edu" style="font-size:12.8px">vs4p@virginia.edu</a><span style="font-size:12.8px">></span><br style="font-size:12.8px"><span style="font-size:12.8px">To: </span><a href="mailto:3dem@ncmir.ucsd.edu" style="font-size:12.8px">3dem@ncmir.ucsd.edu</a><br style="font-size:12.8px"><span style="font-size:12.8px">Subject: [3dem] Problem using .box files from EMAN2 in relion</span><br style="font-size:12.8px"><span style="font-size:12.8px">Message-ID:</span><br style="font-size:12.8px"><span style="font-size:12.8px"> <CAH55gAxRn-qCRDbpWJe+</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">c3rBTy3H3xt__N8B8okBLe8kbM=</span><a href="mailto:47w@mail.gmail.com" style="font-size:12.8px">47w<wbr>@mail.gmail.com</a><span style="font-size:12.8px">></span><br style="font-size:12.8px"><span style="font-size:12.8px">Content-Type: text/plain; charset="utf-8"</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">I used EMAN2's particle picker and was able to generate some box files.</span><br style="font-size:12.8px"><span style="font-size:12.8px">When I open them, they do seem to display coordinates, but when I try to</span><br style="font-size:12.8px"><span style="font-size:12.8px">extract the particles from the micrographs using relion, I get the</span><br style="font-size:12.8px"><span style="font-size:12.8px">following error:</span><br style="font-size:12.8px"><span style="font-size:12.8px">Warning: coordinate file</span><br style="font-size:12.8px"><span style="font-size:12.8px">Import/job014/../FoilHole_</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">27906377_Data_27903491_</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">27903492_20171128_0547_</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">Fractions.box</span><br style="font-size:12.8px"><span style="font-size:12.8px">does not exist...</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">I was able to create a .star file with all of the box files, so I am not</span><br style="font-size:12.8px"><span style="font-size:12.8px">sure what could be going wrong. Anyone have any suggestions?</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">--</span><br style="font-size:12.8px"><span style="font-size:12.8px">Vishaka Santosh</span><br style="font-size:12.8px"><span style="font-size:12.8px">UVA Class of 2011, BS in Chemistry with a specialization in Biochemistry</span><br style="font-size:12.8px"><span style="font-size:12.8px">VCU Class of 2013, MS in Biochemistry</span><br style="font-size:12.8px"><span style="font-size:12.8px">-------------- next part --------------</span><br style="font-size:12.8px"><span style="font-size:12.8px">An HTML attachment was scrubbed...</span><br style="font-size:12.8px"><span style="font-size:12.8px">URL: <</span><a href="http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180125/856f6217/attachment-0001.html" rel="noreferrer" target="_blank" style="font-size:12.8px">http://mail.ncmir.ucsd.edu/<wbr>pipermail/3dem/attachments/<wbr>20180125/856f6217/attachment-<wbr>0001.html</a><span style="font-size:12.8px">></span><br style="font-size:12.8px"></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 26, 2018 at 7:05 AM, <span dir="ltr"><<a href="mailto:3dem-request@ncmir.ucsd.edu" target="_blank">3dem-request@ncmir.ucsd.edu</a>></span> wrote:<br><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>
<br>
1. Recovery of Autoloader Clip Rings (Paolo Swuec)<br>
2. Problem using .box files from EMAN2 in relion (Vishaka Santosh)<br>
3. position at institut Pasteur (Jacomina KRIJNSE LOCKER)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Thu, 25 Jan 2018 22:12:47 +0100<br>
From: Paolo Swuec <<a href="mailto:paolo.swuec@gmail.com">paolo.swuec@gmail.com</a>><br>
To: <a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>
Subject: [3dem] Recovery of Autoloader Clip Rings<br>
Message-ID: <<a href="mailto:4C87D5D9-4D40-482B-B2B5-9E2FA3C6AD68@gmail.com">4C87D5D9-4D40-482B-B2B5-<wbr>9E2FA3C6AD68@gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I was wondering whether anyone can recommend a way to recover the C-clip ring of the autoloader. The cost of the ring (100x pack sold by FEI\Thermo) is unjustifiably high, at least to me, and I would like to get rid of the C-clip and keep the ring,<br>
<br>
Thanks,<br>
<br>
Paolo<br>
<br>
------------------------------<wbr>------------------<br>
Paolo Swuec, PhD<br>
Cryo-Electron Microscopy Lab ? Facility Manager<br>
Dep. BioSciences<br>
University of Milano<br>
Via Celoria 26 - 20133 (Italy)<br>
Tel. +39 02 503 147 78<br>
<br>
Follow on twitter @PS_CryoEM<br>
<br>
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Message: 2<br>
Date: Thu, 25 Jan 2018 17:16:07 -0500<br>
From: Vishaka Santosh <<a href="mailto:vs4p@virginia.edu">vs4p@virginia.edu</a>><br>
To: <a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>
Subject: [3dem] Problem using .box files from EMAN2 in relion<br>
Message-ID:<br>
<CAH55gAxRn-qCRDbpWJe+<wbr>c3rBTy3H3xt__N8B8okBLe8kbM=<a href="mailto:47w@mail.gmail.com">47w<wbr>@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
I used EMAN2's particle picker and was able to generate some box files.<br>
When I open them, they do seem to display coordinates, but when I try to<br>
extract the particles from the micrographs using relion, I get the<br>
following error:<br>
Warning: coordinate file<br>
Import/job014/../FoilHole_<wbr>27906377_Data_27903491_<wbr>27903492_20171128_0547_<wbr>Fractions.box<br>
does not exist...<br>
<br>
I was able to create a .star file with all of the box files, so I am not<br>
sure what could be going wrong. Anyone have any suggestions?<br>
<br>
--<br>
Vishaka Santosh<br>
UVA Class of 2011, BS in Chemistry with a specialization in Biochemistry<br>
VCU Class of 2013, MS in Biochemistry<br>
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Message: 3<br>
Date: Fri, 26 Jan 2018 12:05:01 +0000<br>
From: "Jacomina KRIJNSE LOCKER" <<a href="mailto:jacomina.krijnse-locker@pasteur.fr">jacomina.krijnse-locker@<wbr>pasteur.fr</a>><br>
To: "<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
Cc: Cidalia DA AGRA <<a href="mailto:cidalia.da-agra@pasteur.fr">cidalia.da-agra@pasteur.fr</a>><br>
Subject: [3dem] position at institut Pasteur<br>
Message-ID: <<a href="mailto:9b6dd04532a04f0889c1a52645af2137@pasteur.fr">9b6dd04532a04f0889c1a52645af2<wbr>137@pasteur.fr</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear colleagues,<br>
<br>
<br>
we have a position available for an engineer in electron tomography and image processing.<br>
<br>
The unit for technology and service in ultra-structural bio-imaging at Institut Pasteur in Paris is a state of the art EM platform run by a team of 10 members.<br>
<br>
To strengthen our team we are looking for an enthusiastic PhD with background in cryo-EM and image analysis.<br>
<br>
The tasks and requirements for this position are detailed in the attachment.<br>
<br>
<br>
Informations can be obtained from me and applications should be send to:<br>
<br>
<br>
<a href="mailto:cidalia.da-agra@pasteur.fr">cidalia.da-agra@pasteur.fr</a><br>
<br>
<br>
<br>
Jacomine Krijnse Locker<br>
<br>
unit for technology and service ultra-structural bio-imaging<br>
<br>
Center for innovation and technological research<br>
<br>
Institut Pasteur<br>
<br>
28, rue du Dr. Roux<br>
<br>
75015 Paris, France<br>
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</blockquote></div><br></div>