How to create a new dataset with one "star" file, but two sperated "mrc" files

Troubleshooting
1

Hi,
I have 2 data set and I have merged them with RELION “join star file”.
Now I have one “star” file, and the relative “mrcs” are in two different directory.
Can we select 2 “mrc” folders for one star file?
I know we can copy the files together, but is there a better way to do this?

Thank you.

3

Glad that worked! It’s a lesser known feature (and lesser tested)

4

Hi,
I’m having difficulty accomplishing this. cryoSPARC version 0.4.1.

Combined_cryoSPARC.star has the meta data for 3 mrcs stacks
16oct31b_cryoSPARC.mrcs
17apr26e_cryoSPARC.mrcs
17feb14c_cryoSPARC.mrcs

I upload the same star file and associate it with a difference mrcs each time via the “Add New File Set” option. I receive the following error:
Launched job eNLfFjbvyeqh69KMD
License is valid.
Job Type: visualize_dataset Job ID: eNLfFjbvyeqh69KMD
Assigned Slots: RAM: None GPU: None
Visualizing Dataset ID sCoJ8zk2pFT5EfGhg
Loading Dataset …
---- Loading File Set. Type: star Path: /mnt/Data_01/cryosparc/run/bulk/./Data/rkhayat/Brown/Combined_cryoSPARC.star
Loaded meta data for 186070 images.
Traceback (most recent call last):
File “/mnt/Data_01/cryosparc/cryosparc-compute/sparcjob.py”, line 115, in
dataset = dataio.dataset_factory(current_dataset_params, do_cache=False, do_datasign_estimation=False)
File “/mnt/Data_01/cryosparc/cryosparc-compute/dataio/init.py”, line 18, in dataset_factory
do_cache=do_cache)
File “/mnt/Data_01/cryosparc/cryosparc-compute/dataio/load.py”, line 60, in filesets_into_dataset
get_abs_input_paths(dataset, images, data_input)
File “/mnt/Data_01/cryosparc/cryosparc-compute/dataio/load.py”, line 97, in get_abs_input_paths
assert len(all_relpaths) == 1, “Single data input file specified, but images have multiple different relative paths!”
AssertionError: Single data input file specified, but images have multiple different relative paths!

5

Hi Reza,

You shouldn’t have to add a new file set (that is you shouldn’t have to explicitly specify the mrcs files) - what happens if you just import the star file?

Otherwise, have you tried just combining the three sets with relion_stack_create?

Cheers
Oli

6

Hi Oli.
There are too many particles to combine into a single stack through relion_stack_create (I run out of my 128GB of RAM). I haven’t tried just importing the star file, but I just found that uploading the three stacks with their individual meta files as a single data set results in cryoSPARC combining everything internally. The refinement works just fine this way. Thanks for the help.

Best wishes,
Reza

1 Like
7