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Hi Steve,
<div>Thank you. These tif stacks are not compressed. I will install the latest version of EMAN2 as I only have 2.2 installed.</div>
<div>All the files I tried seems problematic. Running tiffinfo works fine and gives me all the standard info for each frame.</div>
<div>Eric</div>
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<div id="AppleMailSignature">Assoc. Prof Eric Hanssen
<div><b style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">Head - Advanced Microscopy Facility</b></div>
<div><b style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">Honorary Principal Fellow – Department of Biochemistry and Molecular Biology</b></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"><br>
</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">Bio21 Molecular Science and Biotechnology Institute - </span><span style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">30 Flemington Road - The University of Melbourne
- Victoria 3010 - Australia</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">email:</span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span><a href="mailto:ehanssen@unimelb.edu.au" style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">ehanssen@unimelb.edu.au</a><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">|
Office: +61 3 83442449 | Microscope: +61 3 83442509</span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">Web:</span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span><a href="http://www.microscopy.unimelb.edu.au/" style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">www.microscopy.unimelb.edu.au</a></div>
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<div><br>
On 19 Sep 2018, at 22:33, Ludtke, Steven J <<a href="mailto:sludtke@bcm.edu">sludtke@bcm.edu</a>> wrote:<br>
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<div>Hi Eric,
<div class="">there are extremely good reasons for raw data (particularly counting mode data) to be stored in the TIFF format. The command you used should be fine.The message you're getting is an indication that the image you are trying to convert is corrupt
or unreadable for some reason. One possibility is that the version of EMAN2 you are using is too old and does not support (for example) lossless compression, which is the primary reason TIFF is now being adopted for raw data.</div>
<div class=""><br class="">
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<div class="">So, there are 2 things to check:</div>
<div class="">1) if you have it, run "tiffinfo" on one of the problematic files</div>
<div class="">2) run e2version.py and make sure you have at least EMAN2.21</div>
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<font face="Courier" class=""><span style="font-size: 14px;" class="">--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D. <<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a>> Baylor College of Medicine <br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology (<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)<br class="">
Academic Director, CryoEM Core (<a href="http://cryoem.bcm.edu" class="">cryoem.bcm.edu</a>)<br class="">
Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)<br class="">
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<div class="">On Sep 19, 2018, at 2:40 AM, Eric Hanssen <<a href="mailto:ehanssen@unimelb.edu.au" class="">ehanssen@unimelb.edu.au</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><font size="2" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><b class="">***CAUTION:***
This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span>
<hr style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hi all,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
I am trying to convert a bunch of .tif file (each a stack of 25 frames) to .mrc files. why would anyone save as tif instead of mrc I beyond me but lets not dwelve in this .<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
I ran:<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
e2proc2d.py *.tiff @.mrc<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
but then get this error message:<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
1 images, processing 0-0 stepping by 1<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Traceback (most recent call last):<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
File "/home/bio21em1/EMAN2/bin/e2proc2d.py", line 1158, in <module><o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
main()<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
File "/home/bio21em1/EMAN2/bin/e2proc2d.py", line 583, in main<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
d.read_image(infile, i)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
File "/home/bio21em1/EMAN2/lib/EMAN2db.py", line 439, in db_read_image<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
return self.read_image_c(fsp,*parms, **kparms)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
RuntimeError: InvalidValueException at /home/bio21em1/Downloads/eman2-master/libEM/emdata_metadata.cpp:844: error with '0': 'y size <= 0' caught<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Thoughts?<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Regards<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Eric<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: navy;" class="">-----------------<o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: navy;" class="">Assoc. Prof Eric Hanssen<o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: navy;" class=""><o:p class=""> </o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: rgb(31, 73, 125);" class="">Head - Advanced Microscopy Facility</span></b><b class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: rgb(31, 73, 125);" class="">Honorary Principal Fellow – Department of Biochemistry and Molecular Biology<o:p class=""></o:p></span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: "Comic Sans MS"; color: rgb(31, 73, 125);" class=""><br class="">
Bio21 Molecular Science and Biotechnology Institute<br class="">
</span><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: gray;" class="">30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia<br class="">
email:<span class="Apple-converted-space"> </span></span><span style="color: rgb(31, 73, 125);" class=""><a href="mailto:ehanssen@unimelb.edu.au" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: gray;" class="">ehanssen@unimelb.edu.au</span></a></span><span style="font-size: 10pt; font-family: "Comic Sans MS"; color: gray;" class=""><span class="Apple-converted-space"> </span>|
Office: +61 3 83442449 | Microscope: +61 3 83442509<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: "Comic Sans MS"; color: gray;" class="">Web:<span class="Apple-converted-space"> </span><a style="color: purple; text-decoration: underline;" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.microscopy.unimelb.edu.au_&d=DwMF-g&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=Vpcdx_A-gzNrOlFP7mH4V4Ib1yWQj9S1N94sT9P6rCo&s=qZPonGcNnqP3LVzzGnz2M2FVjzKBCq1ZC0dBUXNwM9M&e=" class="">www.microscopy.unimelb.edu.au</a><o:p class=""></o:p></span></div>
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<span class=""><span id="cid:image001.png@01D4503F.D282DBA0"><image001.png></span><o:p class=""></o:p></span></div>
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