Hi @hansenbry,
If you are just looking to multiply the mask with an input volume, then I don’t believe that the Volume Tools job has this functionality; the Volume Tools job is intended more for processing and creating masks, which can then be inputted into refinement jobs.
If you already have the mask that has the central region removed, and you want to launch a new refinement with this mask, you can input the mask into a refinement job along with the volume and particles. Note that the mask used in refinement is never applied to the output volume; it is only used when generating the volume that particles are aligned to. The output volume is always the filtered reconstruction directly from the particles.
Alternatively, if you just want to get a map that is the same as the refined structure with the mask multiplied into it, I don’t believe this can be done in a standalone job in cryoSPARC. You can, however, use the vop multiply command in UCSF Chimera. For example if you opened both the mask and the volume as model specifier 0 and 1 respectively then you can run vop multiply #0,#1 onGrid #1 and save the output map as an .mrc file.
Michael