Hi,
I have imported the extract folder from RELION with a box size of 240.Now while running refinement in cryosparc, can I increase the box size like we are able to do this in RELION.Instead of processing whole dataset from starting with larger box size.
Thanks,
Regards,
priyanka
Hi @PRIYANKA,
Are you looking to re-extract the same particles from micrographs, just with a larger box size? This can be done by taking the imported particle stack (which must contain location information for the extraction coordinates) and passing it through an Extract from Micrographs (CPU) job with your desired box size. Without re-extracting, your current box size of 240 is the maximum box size that can be used by any of the 3D refinement jobs. Some of the legacy refinement jobs (Homogeneous and Non-Uniform) allow you to specify a box size, but this is intended for the purposes of downsampling images rather than zeropadding, i.e. for the case when you don’t expect the resolution to approach the nyquist limit.
Best,
Michael
Hi @ mmclean,
In Extract from Micrographs, I have to import micrographs also?
But I don’t have micrographs.
Hi @PRIYANKA,
To re-extract particles at a different box size, you would need access to the original micrographs, which would have to be imported from an Import Micrograph job
Best,
Michael
Hi,
Thank you for your concern.
I am wondering if there is any way like downsampling during refinement for increasing the box size.
Regards,
Priyanka
Hi Priyanka,
There’s no way of “upsampling” your particles without re-extracting them again from the original micrographs with a larger box size.
To do that, as Michael said, you need the original micrographs and your particle stack to contain the appropiate location information.
Best,
Armando
Hi,
Thanks for your help and concern.
Regards,
Priyanka
Hi,
I have imported the micrographs also.But I am facing problem.It is showing error related Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “/home/priyanka/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/extract/run.py”, line 51, in run_extract_micrographs_cpu_parallel
particles_dset = rc.load_input_group(input_group_name='particles’)
File “/home/priyanka/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 554, in load_input_group
assert is_connected, “Slot %s.%s must be connected!” % (input_group_name, slot[‘name’])
AssertionError: Slot particles.location must be connected!
Can you please help me for the same.
Regards,
Priyanka