Could not Import micrographs

Import and Export
1

Type of Issue: Import Error

Hi

I imported movies, however, I could not import negative stain data as micrographs.

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 95, in cryosparc_compute.run.main
  File "/home/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py", line 864, in run_import_movies_or_micrographs
    assert datashape[0] == 1, "Data file %s has more than 1 frame - import as movie instead" % (abs_path)
AssertionError: Data file /home/cryosparcuser/cryosparc/cryosparc_master/container/negative stain/data/102x60000.mrc has more than 1 frame - import as movie instead

I was able to import tutorial data.

I used JEM-1230 and Orius camera, and converted dm3 to mrc files using digital micrograph software. They were single frame micrographs. I use CryoSPARC ver 4.3.1 on WSL-Ubuntu 20.04.
How can I import these micrographs to CryoSPARC?

Naoki

2

Hi @nkasahata! Welcome to the forum!

Have you double-checked that the files are indeed micrographs with only a single frame? If you have IMOD installed somewhere on your workstation you could try

header "/home/cryosparcuser/cryosparc/cryosparc_master/container/negative stain/data/102x60000.mrc"

which should produce a result like this for micrographs with a single frame:

                   This file has an old-style MRC header.

 Number of columns, rows, sections .....    3838    3710       1
 Map mode ..............................    2   (32-bit real)              
 Start cols, rows, sects, grid x,y,z ...    0     0     0       1      1      1
 Pixel spacing (Angstroms)..............   1.000      1.000      1.000    
 Cell angles ...........................   90.000   90.000   90.000
 Fast, medium, slow axes ...............    X    Y    Z
 Origin on x,y,z .......................    0.000       0.000       0.000    
 Minimum density .......................   0.0000    
 Maximum density .......................   0.0000    
 Mean density ..........................   0.0000    
 tilt angles (original,current) ........   0.0   0.0   0.0  90.0  90.0  90.0
 Space group,# extra bytes,idtype,lens .        0      128        5        0

Note that the Number of columns, rows, sections has a 1 in the third column, indicating a single frame.

If you do not have IMOD installed, you could try importing the files as if they are movies (using Import Movies) and seeing how many frames that job reports in the log. For instance, if I import micrographs using the Import Movies job, I get an error telling me the files only have 1 frame:

Traceback (most recent call last):
  File "/u/cryosparcdev/develop_all/cryosparc2_package/cryosparc_worker/cryosparc_compute/run.py", line 115, in main
    run_function(job_doc)    # this will do the work and output specific outputs from this job
  File "/u/cryosparcdev/develop_all/cryosparc2_package/cryosparc_worker/cryosparc_compute/jobs/imports/run.py", line 920, in run_import_movies_or_micrographs
    assert datashape[0] > 1, "Data file %s has only 1 frame - import as micrograph instead" % (abs_path)
AssertionError: Data file /u/rposert/mic_path space/000001209646069743173_FoilHole_24980087_Data_24016511_24016513_20200225_1447_Fractions_mrc.mrc has only 1 frame - import as micrograph instead
3

Thank you Dr. Rich Posert for detailed answer. I installed IMOD and try it. The results are followings.

This is a byte-swapped file.

Number of columns, rows, sections 2048 2048 1
Map mode 2 (23-bit real)
Start cols, rows, sect, grid x, y, z 0 0 0 2048 2048 1
Pixel spacing (Angstroms) 0.9269 0.9269 0.9269
Cell angles 90.000 90.000 90.000
Fast, medium, slow axes X Y Z
Origin on x, y, z 0.000 0.000 0.000
Minimum density 1197.0
Maximum density 10138.
Mean density 4495.2
tilt angles (original, current) 0.0 0.0 0.0 0.0 0.0 0.0
Space group, # extra bytes, idtype, lens 0 0 0 0

1 Titles:
Digital Micrograph ™, GMS, v2.20

Number of columns, rows, sections has a 1 in the third column, indicating a single frame?
This error may be associated with byte-swapped file?

If you have any suggestion or answer, please let me know.

Thank you for your answer.

4

Alright, so you definitely just have 1 frame!

Do you still have access to the original .dm3 files? If so, could you try using IMOD’s dm2mrc program or EMAN2’s e2proc2d.py to convert them to MRC files? You could just try one to check whether it will work.

5

[quote=“nkasahata, post:3, topic:14295”]
Thank you Dr. Rich Posert.
[/quote] I converted a .dm3 file to a .mrc file using IMOD’s dm2mrc program.
Thereafter, I successfully imported this file as a micrograph.
I will use dm2mrc program, convert other files and go ahead.
Thank you for your assistance.

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