Importing particles from a .mrcs particle stack

Import and Export
1

Hi all,

I’m trying to import a single .mrcs particle stack into CryoSPARC to no success.

Does anybody have experience with this? (I don’t have a .star file, only the .mrcs file).

Armando

2

can you make a star file? what format is the metadata in (describing defocus, other optical parameters)

3

I tried making the .mrcs to a .star using pyem’s stack.py but I get the following error:

Traceback (most recent call last):
  File "/Users/armandopach/pyem/stack.py", line 77, in main
    for img in reader:
TypeError: iter() returned non-iterator of type 'ZSliceReader'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/armandopach/pyem/stack.py", line 126, in <module>
    sys.exit(main(parser.parse_args()))
  File "/Users/armandopach/pyem/stack.py", line 95, in main
    first_ptcl += df.shape[0]
  File "/Users/armandopach/pyem/pyem/mrc.py", line 326, in __exit__
    self.close()
  File "/Users/armandopach/pyem/pyem/mrc.py", line 316, in close
    header = mrc_header(shape=(self.shape[1], self.shape[0], self.i),
TypeError: 'NoneType' object is not subscriptable

I generated the .mrcs file from cryoDRGN.

Best,
Armando