Error broadcasting two matrices together when running Create Templates

Troubleshooting
1

Hello,

I am trying to create projections of an electron density map that I’ve generated in Chimera with molmap.

I have done the following:

  1. Fetched the appropriate pdb, and ran molmap #0.1 4 in Chimera to generate a map of resolution 4A.
  2. Saved this as an .mrc file
  3. Imported the .mrc file using the Import Volume job with a resolution of 1.06:
    image
  4. Ran the Create Templates job with a resolution of 1.06

Then, I receive the following error:

[CPU: 212.8 MB]  Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "cryosparc_worker/cryosparc_compute/jobs/create_templates/run.py", line 47, in cryosparc_compute.jobs.create_templates.run.run
  File "/home/nick/CryoSPARC/install/cryosparc_worker/cryosparc_compute/fourier.py", line 152, in zeropad
    new_X[a:b,a:b,a:b] = X
ValueError: could not broadcast input array from shape (60,61,74) into shape (74,74,74)

How can I get the ogrid of my map and the one to be generated by CryoSPARC to match?

2

Hi @NKHO,

The map needs to have the same shape along all three axes for cryoSPARC to process it. If you have an already existing volume from cryoSPARC that is on a cubic grid, I think this can be accomplished by using the vop resample command with the onGrid option – check out this thread: Creating templates from imported 3D volume using Chimera

Best,
Michael

1 Like
3

yep you can do that, or use onGrid directly as an argument to molmap, assuming you have both maps loaded