Error during Homogenous Refinment

3D Refinement
1

Good afternoon,

I have got an error during when I tried to run Homogeneous Refinement. Please find the Error log below.

I have tried to use the MRC map that I have generated using crystallography PDB converted with “molmap” command in Chimera and saved as MRC from volume viewer.

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/refine/newrun.py”, line 327, in cryosparc_compute.jobs.refine.newrun.run_homo_refine**
** File “/home/giovgonz/software/cryosparc/v3/cryosparc_worker/cryosparc_compute/newfourier.py”, line 416, in resample_resize_real**
** return ZT( ifft( ZT(fft(x, stack=stack), N_resample, stack=stack), stack=stack), M, stack=stack), psize_final**
** File “/home/giovgonz/software/cryosparc/v3/cryosparc_worker/cryosparc_compute/newfourier.py”, line 107, in fft**
** return fftcenter3(x, fft_threads)**
** File “/home/giovgonz/software/cryosparc/v3/cryosparc_worker/cryosparc_compute/newfourier.py”, line 72, in fftcenter3**
** assert all([d%2 == 0 for d in vol.shape])**
AssertionError

Please let me know if the error appearance may depend on the input file and if so what I am doing wrong.

Thank you

Best regards

Dmytro

2

Did you resample the molmap’d pdb volume on the same grid as your data? I think you could “vop resample #molmap ongrid #ab_initio_or_refinement” then save the volume and import as starting volume.

1 Like
3

Yes, when doing this you will find the shape of the box changes from irregular rectangle to perfect square matching your volume. Can slide threshold bar to see the effect. All 3D jobs require a square box reference and to use a volume as reference they should be in the exact same box size and position

4

@dmytrokompani To add to the other users’ suggestions: This error indicates that at least one of the box dimensions is not divisible by two, and could be the indirect consequence of some inconsistency in the preparation of your inputs.

5

Thank you very much.

Yes the box shape was not cubical and resampling helped.

Dima