Is it possible to export all these selected particles into independent separate image files for 3D reconstruction of protein from 2D images?
Please let me know how can I store these segmented particles for further processing to construct 3D from these 2D images using own algorithm.
Should be as simple as hitting the “Export” button on the relevant job (e.g.: selected templates, and it’ll offer to save them as an .mrc file “blob”).
I’d suggest increasing the box size by at least 50%, you’re clipping your particles with a box that tight.
When I download the “blob”, it downloads a .cs file. What shall we do in this case?
Once you have decided on the correct box size (based on @rbs_sci’s suggestion) and rerun 2D classification/class selection, you may connect selected particles to a Downsample Particles job. If you run the job (leaving Crop to box size and Fourier crop to box size unset), you should end up with mrc-format particle stacks including only selected particles inside that job’s downsample subdirectory.