RuntimeError: Astigmatism angle is outside [-2 pi, 2 pi]

Troubleshooting
1

Hello,
I am running an ab intitio reconstruction of my own dataset and I keep getting the following error:
Traceback (most recent call last):
File “/home/exx/cryosparc/cryosparc-compute/sparcjob.py”, line 288, in
cuda_devs = current_experiment_params[‘cuda_devs’])
File “/home/exx/cryosparc/cryosparc-compute/abinit.py”, line 342, in abinit
class_anneal_beta = class_anneal_beta)
File “/home/exx/cryosparc/cryosparc-compute/reconstruct.py”, line 281, in reconstruction_kernel
work(img)
File “/home/exx/cryosparc/cryosparc-compute/reconstruct.py”, line 187, in work
C = img.get_parametric_ctf()
File “/home/exx/cryosparc/cryosparc-compute/dataio/data.py”, line 155, in get_parametric_ctf
self.parametric_ctf = ctf.ParametricCTF(params=p)
File “/home/exx/cryosparc/cryosparc-compute/ctf/ctf.py”, line 73, in init
raise exceptions.RuntimeError(‘Astigmatism angle is outside [-2 pi, 2 pi]: {0} rad, {1} deg. Likely a missing degrees to radians conversion.’.format(angast,180*angast/n.pi))
RuntimeError: Astigmatism angle is outside [-2 pi, 2 pi]: -9.81032166377 rad, -562.090027 deg. Likely a missing degrees to radians conversion.

This error appears early in the reconstruction, usually after iteration 4 or 5. I have tried this with a single class and multiple classes and the same error occurs. Is this a problem with the data set? Is there a way to manually convert degrees to radians in my dataset?

Thank you.

2

Hi Taylor,

Thanks for reporting. This is most likely a bad value in your star file (assuming you used a star file as input?). CryoSPARC expects astigmatism angles to be in degrees in the star file, but in the range [-360,360]. Your star file has at least one particle that is being seen at later iterations that has an astigmatism angle = -562.09. Perhaps you can look in your star file to find the offending particle? There may actually be a parsing issue (if there is no whitespace between two columns in some line for example).

Ali

3

Thank you. In my .star file there was one micrograph with that astigmatism value. Once I removed it from the dataset everything ran smoothly.

4

Great, glad it’s sorted out.

5