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<p>Dear Charlotte:</p>
<p><br>
</p>
<p>An easy way to do this is in EMAN2,</p>
<p><br>
</p>
<p>for i in seriesname*.tif</p>
<p>do e2proc2d.py ${i} new-stack.mrcs #default behaviour is to append to the stack</p>
<p>done</p>
<p>mv new-stacks.mrcs new-stack.mrc (or new-stack.st)</p>
<p><br>
</p>
<p>The reason for the mrcs extension is that EMAN2 thinks about mrc STACK (.mrcs) and mrc single image (.mrc) files separately based on file extension, even though an mrcs renamed to mrc is read fine by all the other software.</p>
<p><br>
</p>
<p>Note that if you do it in EMAN2 the default will be to output the data as floating point unless you tell it not to (which is not a problem for your subsequent processing in this case, but just FYI).</p>
<p><br>
</p>
<p>As for how to do it in IMOD, I haven't used tif2mrc so I can't comment on your particular error, but if you are only able to create single image mrc, you can just combine them with newstack afterward, i.e.</p>
<p><br>
</p>
<p>for i in seriesname*.tif</p>
<p>do j=`basename ${i} .tif`</p>
<p>tif2mrc ${i} ${j}.mrc</p>
<p>done</p>
<p>newstack seriesname*.mrc new-stack.mrc</p>
<p>rm seriesname*.mrc</p>
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Jason<br>
<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of 3dem-request@ncmir.ucsd.edu <3dem-request@ncmir.ucsd.edu><br>
<b>Sent:</b> Friday, April 7, 2017 7:47 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> 3dem Digest, Vol 116, Issue 8</font>
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Today's Topics:<br>
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1. Re: How to merge tif-files into an *.mrc-file<br>
(Charlotte Hamngren Blomqvist)<br>
<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 7 Apr 2017 12:46:51 +0000<br>
From: Charlotte Hamngren Blomqvist<br>
<charlotte.hamngren.blomqvist@chalmers.se><br>
To: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] How to merge tif-files into an *.mrc-file<br>
Message-ID: <524F2E26-A5B4-490B-80A7-15F1BF4F2FF6@chalmers.se><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello again,<br>
<br>
I have some questions about the tf2mrc command which is a part of the iMOD package. The specifications say this:<br>
<br>
NAME<br>
tif2mrc - Make a MRC file from TIFF image files.<br>
<br>
SYNOPSIS<br>
tif2mrc [options] TIFF_input_files... MRC_output_file<br>
<br>
DESCRIPTION<br>
tif2mrc takes a series of TIFF files and converts them into an MRC<br>
stack. tif2mrc can also convert a single multi-page TIFF file to an<br>
MRC stack.<br>
?.<br>
<br>
I have 67 files named: seriesname_001.tif to seriesname_067.tif. How do I write for creating the mrc file? I tried writing in the file names of all the files at the ?TIFF_input_files... ?-position, but it only seem to accept one name at the position. I also
tried using the ?cat? command for creating a tiff-stack of the images and then the mrc-file, but the resulting mrc-file is very small and doesn?t open in inspect3D.<br>
<br>
Does this ring a bell?<br>
<br>
Best,<br>
Charlotte<br>
<br>
Fr?n: 3dem <3dem-bounces@ncmir.ucsd.edu> p? uppdrag av Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se><br>
Datum: fredag 7 april 2017 11:01<br>
Till: Sacha De Carlo <sachadecarlo@yahoo.com>, "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
?mne: Re: [3dem] How to merge tif-files into an *.mrc-file in Inspect3D<br>
<br>
Sounds like a good idea.<br>
I will try the tif2mrc command.<br>
<br>
Thanks!<br>
/Charlotte<br>
<br>
Fr?n: Sacha De Carlo <sachadecarlo@yahoo.com><br>
Datum: fredag 7 april 2017 10:57<br>
Till: Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se>, "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
?mne: Re: [3dem] How to merge tif-files into an *.mrc-file in Inspect3D<br>
<br>
Why not use imod or em2em to convert your tif files into an MRC stack that can then be imported into inspect 3D?<br>
<br>
Best<br>
Sacha<br>
<br>
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On Friday, April 7, 2017, 10:41 AM, Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se> wrote:<br>
<br>
Dear Hivemind,<br>
<br>
<br>
<br>
I want to use computer-generated projections in order to quantify our ET method. Now I want to load the projected images (tif) into the software using the concert/merge files option. I get the error message: "Operation failed Reason: Error reading file". What
do I need to change in order for this to work? My version is v. 3.0.0.3494REL of Inspect3D.<br>
<br>
<br>
<br>
Best regards<br>
<br>
Charlotte Hamngren Blomqvist<br>
<br>
<br>
<br>
<br>
<br>
_______________________<br>
<br>
Charlotte Hamngren Blomqvist, PhD<br>
<br>
Researcher<br>
<br>
<br>
<br>
Department of Physics<br>
<br>
Eva Olsson group<br>
<br>
Chalmers University of Technology<br>
<br>
SE-41296 Gothenburg, Sweden<br>
<br>
Tel +46-(0)31 772 51 80<tel:+46-31%20772%2051%2080><br>
<br>
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