[3dem] EMAN2

[Eric Hanssen]

Hi Steve,
Thank you. These tif stacks are not compressed. I will install the latest version of EMAN2 as I only have 2.2 installed.
All the files I tried seems problematic. Running tiffinfo works fine and gives me all the standard info for each frame.
Eric



Assoc. Prof Eric Hanssen
Head - Advanced Microscopy Facility
Honorary Principal Fellow – Department of Biochemistry and Molecular Biology

Bio21 Molecular Science and Biotechnology Institute - 30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia
email: ehanssen at unimelb.edu.au<mailto:ehanssen at unimelb.edu.au> | Office: +61 3 83442449 | Microscope: +61 3 83442509
Web: www.microscopy.unimelb.edu.au<http://www.microscopy.unimelb.edu.au/>


On 19 Sep 2018, at 22:33, Ludtke, Steven J <sludtke at bcm.edu<mailto:sludtke at bcm.edu>> wrote:

Hi Eric,
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.

So, there are 2 things to check:
1) if you have it, run "tiffinfo" on one of the problematic files
2) run e2version.py and make sure you have at least EMAN2.21



--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<http://cryoem.bcm.edu>)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)



On Sep 19, 2018, at 2:40 AM, Eric Hanssen <ehanssen at unimelb.edu.au<mailto:ehanssen at unimelb.edu.au>> wrote:

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Hi all,
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 .
I ran:
e2proc2d.py *.tiff @.mrc

but then get this error message:

1 images, processing 0-0 stepping by 1
Traceback (most recent call last):
  File "/home/bio21em1/EMAN2/bin/e2proc2d.py", line 1158, in <module>
    main()
  File "/home/bio21em1/EMAN2/bin/e2proc2d.py", line 583, in main
    d.read_image(infile, i)
  File "/home/bio21em1/EMAN2/lib/EMAN2db.py", line 439, in db_read_image
    return self.read_image_c(fsp,*parms, **kparms)
RuntimeError: InvalidValueException at /home/bio21em1/Downloads/eman2-master/libEM/emdata_metadata.cpp:844: error with '0': 'y size <= 0' caught

Thoughts?
Regards
Eric

-----------------
Assoc. Prof Eric Hanssen

Head - Advanced Microscopy Facility
Honorary Principal Fellow – Department of Biochemistry and Molecular Biology

Bio21 Molecular Science and Biotechnology Institute
30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia
email: ehanssen at unimelb.edu.au<mailto:ehanssen at unimelb.edu.au> | Office: +61 3 83442449 | Microscope: +61 3 83442509
Web: www.microscopy.unimelb.edu.au<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=>
<image001.png>


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