[3dem] 3dem Digest, Vol 104, Issue 22

kmzhang zhangkaiming11 at 163.com
Mon May 2 08:43:53 PDT 2016


Hi all,

I recenly used relion_refine_mpi and ran into the error below when the refinement converged and try to make the final model.
idx= 3170799282 packed_size= -1124168014
MlWsumModel::unpack: idx != idx_stop-idx_start
File: src/ml_model.cpp line: 930

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:

Estimated required memory for expectation step= 39.469 Gb, maximum allowed memory = 128 Gb.

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!

Best,

Zhaoming Su, Ph.D.
Postdoctoral Associate
National Center of Macromolecular Imaging (NCMI)
Baylor College of Medicine
(713)-798-6989
Regards



> On Apr 28, 2016, at 2:00 PM, 3dem-request at ncmir.ucsd.edu wrote:
> 
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> Today's Topics:
> 
>   1. video on making graphene oxide grids (Sjors Scheres)
>   2. Re: video on making graphene oxide grids (Henning Stahlberg)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 28 Apr 2016 15:17:10 +0100
> From: Sjors Scheres <scheres at mrc-lmb.cam.ac.uk>
> To: "ccpem at jiscmail.ac.uk" <ccpem at jiscmail.ac.uk>, 3dem at ncmir.ucsd.edu
> Cc: Andreas Boland <aboland at mrc-lmb.cam.ac.uk>, Anthony Fitzpatrick
> 	<afitzpat at mrc-lmb.cam.ac.uk>
> Subject: [3dem] video on making graphene oxide grids
> Message-ID: <57221B66.10105 at mrc-lmb.cam.ac.uk>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> Dear colleagues,
> 
> 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.
> 
> 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.
> 
> Best wishes,
> Sjors
> 
> -- 
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 28 Apr 2016 14:37:39 +0000
> From: Henning Stahlberg <henning.stahlberg at unibas.ch>
> To: Sjors Scheres <scheres at mrc-lmb.cam.ac.uk>
> Cc: Anthony Fitzpatrick <afitzpat at mrc-lmb.cam.ac.uk>,
> 	"3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>, Andreas Boland
> 	<aboland at mrc-lmb.cam.ac.uk>, "ccpem at jiscmail.ac.uk"
> 	<ccpem at jiscmail.ac.uk>
> Subject: Re: [3dem] video on making graphene oxide grids
> Message-ID: <D27C1CF5-7F08-4B61-A9C6-C388C98001CE at unibas.ch>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Sjors,
> 
> Very nice video, indeed. And thanks for referring to Rado?s paper.
> 
> 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.
> Appl. Phys. Lett. 104, 134103 (2014),  http://dx.doi.org/10.1063/1.4870531
> 
> 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.).
> 
> All the best,
> 
> Henning.
> 
> Henning Stahlberg, PhD
> Prof. for Structural Biology, C-CINA, Biozentrum, University Basel
> Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
> http://c-cina.org | Tel. +41-61-387 32 62
> 
> 
> 
> On Apr 28, 2016, at 16:17, Sjors Scheres <scheres at mrc-lmb.cam.ac.uk<mailto:scheres at mrc-lmb.cam.ac.uk>> wrote:
> 
> Dear colleagues,
> 
> 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.
> 
> 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.
> 
> Best wishes,
> Sjors
> 
> --
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
> 
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