[3dem] 3dem Digest, Vol 125, Issue 35

Weimin Wu ppxwwtaking at gmail.com
Fri Jan 26 06:35:14 PST 2018


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

Weimin

LSBR/NIAMS/NIH
____________________________________________________________________________________
Message: 2
Date: Thu, 25 Jan 2018 17:16:07 -0500
From: Vishaka Santosh <vs4p at virginia.edu>
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Problem using .box files from EMAN2 in relion
Message-ID:
        <CAH55gAxRn-qCRDbpWJe+c3rBTy3H3xt__N8B8okBLe8kbM=47w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I used EMAN2's particle picker and was able to generate some box files.
When I open them, they do seem to display coordinates, but when I try to
extract the particles from the micrographs using relion, I get the
following error:
Warning: coordinate file
Import/job014/../FoilHole_27906377_Data_27903491_27903492_20171128_0547_
Fractions.box
does not exist...

I was able to create a .star file with all of the box files, so I am not
sure what could be going wrong.  Anyone have any suggestions?

--
Vishaka Santosh
UVA Class of 2011, BS in Chemistry with a specialization in Biochemistry
VCU Class of 2013, MS in Biochemistry
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On Fri, Jan 26, 2018 at 7:05 AM, <3dem-request at ncmir.ucsd.edu> wrote:

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> Today's Topics:
>
>    1. Recovery of Autoloader Clip Rings (Paolo Swuec)
>    2. Problem using .box files from EMAN2 in relion (Vishaka Santosh)
>    3. position at institut Pasteur (Jacomina  KRIJNSE LOCKER)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 25 Jan 2018 22:12:47 +0100
> From: Paolo Swuec <paolo.swuec at gmail.com>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Recovery of Autoloader Clip Rings
> Message-ID: <4C87D5D9-4D40-482B-B2B5-9E2FA3C6AD68 at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> 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,
>
> Thanks,
>
> Paolo
>
> ------------------------------------------------
> Paolo Swuec, PhD
> Cryo-Electron Microscopy Lab ? Facility Manager
> Dep. BioSciences
> University of Milano
> Via Celoria 26 - 20133 (Italy)
> Tel. +39 02 503 147 78
>
> Follow on twitter @PS_CryoEM
>
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> ------------------------------
>
> Message: 2
> Date: Thu, 25 Jan 2018 17:16:07 -0500
> From: Vishaka Santosh <vs4p at virginia.edu>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Problem using .box files from EMAN2 in relion
> Message-ID:
>         <CAH55gAxRn-qCRDbpWJe+c3rBTy3H3xt__N8B8okBLe8kbM=47w
> @mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I used EMAN2's particle picker and was able to generate some box files.
> When I open them, they do seem to display coordinates, but when I try to
> extract the particles from the micrographs using relion, I get the
> following error:
> Warning: coordinate file
> Import/job014/../FoilHole_27906377_Data_27903491_27903492_20171128_0547_
> Fractions.box
> does not exist...
>
> I was able to create a .star file with all of the box files, so I am not
> sure what could be going wrong.  Anyone have any suggestions?
>
> --
> Vishaka Santosh
> UVA Class of 2011, BS in Chemistry with a specialization in Biochemistry
> VCU Class of 2013, MS in Biochemistry
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 26 Jan 2018 12:05:01 +0000
> From: "Jacomina  KRIJNSE LOCKER" <jacomina.krijnse-locker at pasteur.fr>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Cc: Cidalia  DA AGRA <cidalia.da-agra at pasteur.fr>
> Subject: [3dem] position at institut Pasteur
> Message-ID: <9b6dd04532a04f0889c1a52645af2137 at pasteur.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear colleagues,
>
>
> we have a position available for an engineer in electron tomography and
> image processing.
>
> 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.
>
> To strengthen our team we are looking for an enthusiastic PhD with
> background in cryo-EM and image analysis.
>
> The tasks and requirements for this position are detailed in the
> attachment.
>
>
> Informations can be obtained from me and applications should be send to:
>
>
> cidalia.da-agra at pasteur.fr
>
>
>
> Jacomine Krijnse Locker
>
> unit for technology and service ultra-structural bio-imaging
>
> Center for innovation and technological research
>
> Institut Pasteur
>
> 28, rue du Dr. Roux
>
> 75015 Paris, France
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