Thank you, Randy and Elad, for your reply!
I learned that I didn't change the box size in the same command (--new_box 128, similar to the one in relion tutorial)
But after I did that, when I checked the resized particle in Chimera, it looks like one end of the particle is slightly outside the new box and thus is missing. Randy suggested alternative ways: eman (https://groups.google.com/forum/#!topic/eman2/WQLQVe8OGrs) and using vop resample in chimera, which will make any 3d map have the same pix/box as another 3d map.
I used e2proc3d.py to do the job: e2proc3d.py run_class001.mrc run_class001_box128.mrc --scale=0.703 --clip=128,128,128.
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