3D classes - pixel size - masking

Dear colleagues,

I want to make a mask for the classes after 3D classes using the tool outside CS.

I noticed that the outcome 3D classes have different pixel sizes from the original particle.

My question is – how to unbin the classes or find out their current pixel size to make a correct mask outside the CS?

Thank you in advance.


Hi @Dmitry,

Have you tried Homogeneous Reconstruction Only job on the classes you would like to “unbin”? This will output the reconstruction in the original pixel size using the angular assignment determined in the upstream refinement job.

You might wanna try info map e.g. info #1 in ChimeraX. This will show you the size (box size) and the voxel size (pixel size) of a map in the log window.


1 Like

dear Kookjoo @kookjookeem,

Thank you. I will try those options.

Kind regards,

Hi @Dmitry! I have one last tip for you: if you ever find yourself in this situation again, you can use the volume resample function in ChimeraX to move a mask from one box/pixel size to another.

For example, in your case, if you have a mask you’ve made from your 3D classification job as volume #1 in chimeraX and your original volume (with the full box size) as volume #2, you can fix your mask’s box size using

volume resample #1 onGrid #2

That saves you the step of performing a reconstruction just to build a mask!


hi @rposert , thank you for the nice solution!

Kind regards,