AssertionError during CTF Refinement job: Field ctf/cs_nm is not constant in group 0

[niu]

Hi, all

Do you have a error like attached below during CTF refinement in a process of Homogeneous Refinement (NEW!)? I have checked that the cs_mm is set with a value of 2.7.

[stephan]

Hi @niu,

This is an odd issue- these values should be consistent, unless particles were joined that didn’t have the same values.

You can circumvent this by running your particles through the Exposure Group Utilities job:

Tutorial: CTF Refinement

Set the combine strategy to take_median, explained here: Job: Exposure Group Utilities - CryoSPARC Guide

Please let me know if this works. Otherwise, you’ll have to manually open the .cs file, and set the value.
For more information on how to do this, see this guide:

Guide: Manipulating .cs Files Created By CryoSPARC

And this post:

Delete excluded micrographs

Hi @AndreGraca, You can do this by first downloading the movie_blob .cs file output from the exposures_rejected output result group of the Manually Curate Exposures job. [Screen Shot 2020-09-15 at 3.58.21 PM] You can also just get the path to the .cs file on the master node by navigating to the Outputs tab and pressing the “copy path” button on the movie_blob output: [Screen Shot 2020-09-15 at 4.02.34 PM] Once you have the .cs file, you can then open it up using the instructions from our g…

You can assign values like so:
CryoSPARC v4.0 and earlier

particle_dset.data['ctf/cs_mm'] = 2.7

CryoSPARC v4.1 and later

particle_dset['ctf/cs_mm'] = 2.7

[niu]

Hi, @stephan

After setting the combine strategy to take_median, the ctF/cs_mm value for all particles recovered to 2.7 as before and I can seccesfully run Homogeneous Refinement (NEW) using a particles combination of several 3D classes.

thanks again.

Niu