Running focused 3D classification using local mask



Hi cryoSPARC team,
I’m using v2.4.6 version of cryoSPARC. I’m wondering if there’s a way to run a focused 3D classification using a local mask in cryoSPARC? my particles have heterogeneity on specific sites and I’d like to try refining them using a focused map.
Would appreciate your help,


Hi Atousa,

There is not. There is a local refinement module but no masked classification yet. You can perform local refinement and then convert to STAR and perform masked classification outside cryoSPARC though, e.g. in RELION.



Hi Oil,

Thanks so much for your suggestion. I tried local refinement and it works better well. Regarding the STAR conversion, Daniel Asarnow’s script worked perfectly to convert csv after to star after 2D classification. However, I’m badly failing to do the conversion after any of 3D classifications. It just doesn’t work for me. I Will keep trying though to understand what I’m doing wrong.