<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">Hi all,</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">I recenly used relion_refine_mpi and ran into the error below when the refinement converged and try to make the final model.</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">idx= 3170799282 packed_size= -1124168014</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">MlWsumModel::unpack: idx != idx_stop-idx_start</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">File: src/ml_model.cpp line: 930</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">I went to this file and figured this error seemed to say that I am out of memory, in my out.txt it says this before making the final model:</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><div class=""><br class=""></div><div class="">Estimated required memory for expectation step= 39.469 Gb, maximum allowed memory = 128 Gb.</div><div class=""><br class=""></div>I just wonder if anyone ran into this error before and what would be the solution. I am willing to provide error details if anyone is interested to help. Thanks!</div><p style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""></p><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div id="Signature" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><div class="BodyFragment"><font size="2" class=""><div class="PlainText">Best,<br class=""><br class="">Zhaoming Su, Ph.D.<br class="">Postdoctoral Associate<br class="">National Center of Macromolecular Imaging (NCMI)<br class="">Baylor College of Medicine<br class="">(713)-798-6989</div></font></div></div><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">Regards<br class=""><br class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><br class=""></div></div>
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<br class=""><div style=""><blockquote type="cite" class=""><div class="">On Apr 28, 2016, at 2:00 PM, <a href="mailto:3dem-request@ncmir.ucsd.edu" class="">3dem-request@ncmir.ucsd.edu</a> wrote:</div><br class="Apple-interchange-newline"><div class="">Send 3dem mailing list submissions to<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a><br class=""><br class="">To subscribe or unsubscribe via the World Wide Web, visit<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<br class="">or, via email, send a message with subject or body 'help' to<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>3dem-request@ncmir.ucsd.edu<br class=""><br class="">You can reach the person managing the list at<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>3dem-owner@ncmir.ucsd.edu<br class=""><br class="">When replying, please edit your Subject line so it is more specific<br class="">than "Re: Contents of 3dem digest..."<br class=""><br class=""><br class="">Today's Topics:<br class=""><br class=""> 1. video on making graphene oxide grids (Sjors Scheres)<br class=""> 2. Re: video on making graphene oxide grids (Henning Stahlberg)<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">Message: 1<br class="">Date: Thu, 28 Apr 2016 15:17:10 +0100<br class="">From: Sjors Scheres <scheres@mrc-lmb.cam.ac.uk><br class="">To: "ccpem@jiscmail.ac.uk" <ccpem@jiscmail.ac.uk>, 3dem@ncmir.ucsd.edu<br class="">Cc: Andreas Boland <aboland@mrc-lmb.cam.ac.uk>, Anthony Fitzpatrick<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><afitzpat@mrc-lmb.cam.ac.uk><br class="">Subject: [3dem] video on making graphene oxide grids<br class="">Message-ID: <57221B66.10105@mrc-lmb.cam.ac.uk><br class="">Content-Type: text/plain; charset=utf-8; format=flowed<br class=""><br class="">Dear colleagues,<br class=""><br class="">Recently, Thomas Martin and Anthony Fitzpatrick in my group, together <br class="">with Andreas Boland from the Barford group, have successfully used <br class="">graphene oxide as a support layer for cryo-EM grids on various projects <br class="">(e.g. see http://dx.doi.org/10.1038/ncomms11293). Graphene oxide may be <br class="">used, much like a thin film of amorphous carbon, to concentrate <br class="">particles on the grid, to modify orientational distributions, or to <br class="">convince particles to go over the holes. However, the background signal <br class="">from a single layer of graphene oxide is significantly less than for a <br class="">thin film of amorphous carbon, making it better suited for small complexes.<br class=""><br class="">The use of graphene oxide for this purpose was first proposed by Rado <br class="">Pantelic et al. in the Plitzko group (see <br class="">http://dx.doi.org/10.1016/j.jsb.2009.12.020). Thomas, Andreas and <br class="">Anthony made minor modifications to their procedure, i.e. they <br class="">introduced washing steps to have a more reproducible coverage of single <br class="">graphene oxide layers. In the hope that this procedure is useful for <br class="">others, Thomas has kindly prepared a video on how to prepare these <br class="">grids. This procedure takes only a few minutes and is generally <br class="">perceived as much easier than making and depositing a thin film of <br class="">amorphous carbon. The video is available through figshare: <br class="">http://dx.doi.org/10.6084/m9.figshare.3178669. Please direct questions <br class="">about the practicalities of this method directly to Thomas (CC), and <br class="">don't forget to cite the Pantelic paper when using graphene oxide grids.<br class=""><br class="">Best wishes,<br class="">Sjors<br class=""><br class="">-- <br class="">Sjors Scheres<br class="">MRC Laboratory of Molecular Biology<br class="">Francis Crick Avenue, Cambridge Biomedical Campus<br class="">Cambridge CB2 0QH, U.K.<br class="">tel: +44 (0)1223 267061<br class="">http://www2.mrc-lmb.cam.ac.uk/groups/scheres<br class=""><br class=""><br class=""><br class="">------------------------------<br class=""><br class="">Message: 2<br class="">Date: Thu, 28 Apr 2016 14:37:39 +0000<br class="">From: Henning Stahlberg <henning.stahlberg@unibas.ch><br class="">To: Sjors Scheres <scheres@mrc-lmb.cam.ac.uk><br class="">Cc: Anthony Fitzpatrick <afitzpat@mrc-lmb.cam.ac.uk>,<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu>, Andreas Boland<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><aboland@mrc-lmb.cam.ac.uk>, "ccpem@jiscmail.ac.uk"<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><ccpem@jiscmail.ac.uk><br class="">Subject: Re: [3dem] video on making graphene oxide grids<br class="">Message-ID: <D27C1CF5-7F08-4B61-A9C6-C388C98001CE@unibas.ch><br class="">Content-Type: text/plain; charset="utf-8"<br class=""><br class="">Dear Sjors,<br class=""><br class="">Very nice video, indeed. And thanks for referring to Rado?s paper.<br class=""><br class="">Rado Pantelic still followed up with a later publication that might also be of interest. That appeared in Applied Physics Letters, which is a good journal in Nanosciences, but unfortunately not indexed in PubMed.<br class="">Appl. Phys. Lett. 104, 134103 (2014), http://dx.doi.org/10.1063/1.4870531<br class=""><br class="">Rado there describes that merely dipping a grid with pristine graphene into pyrene solution makes it hydrophilic, without loosing any of the amazing capabilities of graphene (extremely high electric conductivity, almost zero image background, etc.).<br class=""><br class="">All the best,<br class=""><br class="">Henning.<br class=""><br class="">Henning Stahlberg, PhD<br class="">Prof. for Structural Biology, C-CINA, Biozentrum, University Basel<br class="">Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland<br class="">http://c-cina.org | Tel. +41-61-387 32 62<br class=""><br class=""><br class=""><br class="">On Apr 28, 2016, at 16:17, Sjors Scheres <scheres@mrc-lmb.cam.ac.uk<mailto:scheres@mrc-lmb.cam.ac.uk>> wrote:<br class=""><br class="">Dear colleagues,<br class=""><br class="">Recently, Thomas Martin and Anthony Fitzpatrick in my group, together with Andreas Boland from the Barford group, have successfully used graphene oxide as a support layer for cryo-EM grids on various projects (e.g. see http://dx.doi.org/10.1038/ncomms11293). Graphene oxide may be used, much like a thin film of amorphous carbon, to concentrate particles on the grid, to modify orientational distributions, or to convince particles to go over the holes. However, the background signal from a single layer of graphene oxide is significantly less than for a thin film of amorphous carbon, making it better suited for small complexes.<br class=""><br class="">The use of graphene oxide for this purpose was first proposed by Rado Pantelic et al. in the Plitzko group (see http://dx.doi.org/10.1016/j.jsb.2009.12.020). Thomas, Andreas and Anthony made minor modifications to their procedure, i.e. they introduced washing steps to have a more reproducible coverage of single graphene oxide layers. In the hope that this procedure is useful for others, Thomas has kindly prepared a video on how to prepare these grids. This procedure takes only a few minutes and is generally perceived as much easier than making and depositing a thin film of amorphous carbon. The video is available through figshare: http://dx.doi.org/10.6084/m9.figshare.3178669. Please direct questions about the practicalities of this method directly to Thomas (CC), and don't forget to cite the Pantelic paper when using graphene oxide grids.<br class=""><br class="">Best wishes,<br class="">Sjors<br class=""><br class="">--<br class="">Sjors Scheres<br class="">MRC Laboratory of Molecular Biology<br class="">Francis Crick Avenue, Cambridge Biomedical Campus<br class="">Cambridge CB2 0QH, U.K.<br class="">tel: +44 (0)1223 267061<br class="">http://www2.mrc-lmb.cam.ac.uk/groups/scheres<br class=""><br class="">_______________________________________________<br class="">3dem mailing list<br class="">3dem@ncmir.ucsd.edu<br class="">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<br class=""><br class="">-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160428/cb43c5a2/attachment-0001.html><br class=""><br class="">------------------------------<br class=""><br class="">Subject: Digest Footer<br class=""><br class="">_______________________________________________<br class="">3dem mailing list<br class="">3dem@ncmir.ucsd.edu<br class="">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<br class=""><br class=""><br class="">------------------------------<br class=""><br class="">End of 3dem Digest, Vol 104, Issue 22<br class="">*************************************<br class=""></div></blockquote></div><br class=""></body></html>