Defocus value substitution


I was wondering about the way your refinements function, so I wanted to ask here before proceeding.
I wanted to substitute defocus values in my files. To this end I have a choice, depending on how cryosparc reads values:

  • First is substituting the values in the original data file I used to create the set - it will only work, if parameters are read anew from this file during refinement, with the csv files acting as sel-ection files
  • Second is generating a new set from the minimized set of particles, in which I substitute-d parameters
  • Third option would work with the older version of cryosparc - when one was able to provide one’s own entry file per refinement - as far as I am aware, this no longer is an option ?

Could you please weigh in on this and suggest the mode of action ?



Hi Jean-Paul,

Both the first and second options would work I believe. cryoSPARC always reads the defocus values straight from the original data (i.e. star) files every time a dataset is loaded, so if you modify that file then the defocus values will change.
Alternatively for the second option, you can take the output csv from an experiment, convert it back to .star with Daniel’s script, change the defocus values, then load that as a new cryoSPARC dataset.

Hope that helps!

Hi Ali,

Thanks, that solves it ! I appreciate the input.