Volume Tools job: resample error?

Troubleshooting
1

Hi! :slight_smile:

This could probably be also a good question for the Chimera forum, but I try it here first.

Today I was struggling with something that usually would take me 15 minutes to do: mask creation.
I have after long time realized what was the problem. I created a simulated map from model using Chimera molmap with the onGrid option to have the same box size as the reconstruction map from cryoSPARC. I then imported the new volume on cryoSPARC successfully and attempted to use Volume Tools job to covert map to mask.

I was then surprised by this error:

[CPU: 223.9 MB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 85, in cryosparc_compute.run.main
File “/home/angr5008/Software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/utilities/run_volume_tools.py”, line 90, in run
vol_f = fourier.fft(vol)
File “/home/angr5008/Software/cryosparc/cryosparc_worker/cryosparc_compute/fourier.py”, line 110, in fft
return fftcenter3(x, fft_threads)
File “/home/angr5008/Software/cryosparc/cryosparc_worker/cryosparc_compute/fourier.py”, line 69, in fftcenter3
assert all([d%2 == 0 for d in vol.shape])
AssertionError

I tried to figure the error, but it is not very self-explanatory.

I then returned to chimera and performed a vop resample onGrid command on the simulated map I originally imported on cryoSPARC. Turns out that when I followed this ‘traditional’ way there was no error.
Why does cryoSPARC require resampled volumes? At least in real space, the volume looked as it should (right box size, centered), but I am curious to understand the concept/reason for resampling, especially because Volume tools job should be able to resample the volume right?

Cheers,
André

2

It doesn’t - I use molmap with ongrid all the time for exactly the same thing and it works fine. There must be some issue more specific to this particular map

3

Thanks @olibclarke, your vast experience is always valuable and saving me :slight_smile:

Hummm
 very ‘unusual’, I see. Good that I was simply not satisfied that vop resample worked.
Any ideas about what I could further explore? Anything I can provide the community that can be helpful, just let me know.

4

These lines in the log indicate that at least one of the input volume’s dimensions was not divisible by 2, which caused the job to fail.

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