Hi @LTP,
The difference between the two pixel sizes is significant, and unfortunately combining datasets of different pixel sizes isn’t easily handled in cryoSPARC right now. Ali posted an insightful comment on another thread about the practical utility of merging dataset of different pixel sizes, which may be of interest. More formal support of this workflow in cryoSPARC is coming when magnification anisotropy is released, but in the meantime, the only other way to do this is quite cumbersome (and in practice may not result in much of a benefit – see Ali’s comment).
If you believe that it is worth trying to do in your case, the long answer is that you will need to follow a very similar procedure as the one outlined on this CCPEM forum post by Max Wilkinson. (See also the RELION wiki page on pixel size issues). First you would have to find exactly the relative pixel size of one dataset to the other, which Max Wilkinson suggests using Chimera “fit in map” command for. You’d have to use the script linked in the forum post to find a ratio of two even box sizes that is very nearly equal to the ratio between the two pixel sizes. Once that is done, you would need to re-extract particles from the larger pixel size dataset at the smaller box size, and re-extract particles from the smaller pixel size dataset at the larger box size. Then, you’ll need to use “Downsample Particles” to downsample the larger box particles to match the smaller box size.
In case the pixel sizes are still different by > 10^-4, you’ll need to modify the .cs files of the particle sets to override the pixel size of each set to be exactly equal, and then save and re-import the modified particle stack using “Import Result Group”. It’s fine to do this only if the error is very small. Stephan made an excellent tutorial explaining how to do this for a different case of modifying the shifts in a dataset.
Best,
Michael