Issues importing a mask made in ChimeraX

Import and Export
1

Hi all,

I’m having issues importing a mask into cryoSPARC version 3.3.2. I made the mask using the following commands in ChimeraX:

vop threshold #volume minimum 0.18 set 0
vop threshold #volume maximum 0.1 setMaximum 1
save cryosparc_P18_J187_007_volume_mask_0.1.mrc #volume

In CryoSPARC, I try to import this mask using Import 3D volumes and changing the type of volume being imported to mask. However, I keep getting the error:

[CPU: 209.0 MB]  Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 85, in cryosparc_compute.run.main
  File "/home/satori-csparc/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 580, in run_import_volumes
    hdr, data = mrc.read_mrc(far_import_path)
  File "/home/satori-csparc/cryosparc/cryosparc_master/cryosparc_compute/blobio/mrc.py", line 124, in read_mrc
    header = read_mrc_header(file_obj, debug_fname=fname)
  File "/home/satori-csparc/cryosparc/cryosparc_master/cryosparc_compute/blobio/mrc.py", line 43, in read_mrc_header
    assert len(header_int32) == 256, f"Could not read mrc header from {debug_fname}"
AssertionError: Could not read mrc header from /nobackup/users/vasquezs/cryosparc/P18/imports/cryosparc_P18_J187_007_volume_mask.mrc

Does anyone know how to resolve this issue? Can it be how I created the mask? Thank you in advance!

-Sheena

3

I know this will sound silly, but as a sanity check, if you download the mask from your server can you open it in chimeraX?

scp {username}@{host}:/nobackup/users/vasquezs/cryosparc/P18/imports/cryosparc_P18_J187_007_volume_mask.mrc ~/Desktop/server_mask.mrc

and then try to open server_mask.mrc from your Desktop