Re-extract particles with shifting original position


If I want to re-extract particles slightly down to the current position,
how can I deal with the output of Volume Alignment Tools?

Images below are generated from Volume Alignment Tools.


Hi @yuhx0914,

To use Volume alignment tools to shift the particles, you will need to provide the particles and volume as input to the job. Once the center of the volume has been shifted to the desired center as shown in the second plot, you can take the output particles and input them to Extract from Micrographs (along with the original micrographs) to re-extract. Ensure that the “re-centering using aligned shift” parameter in Extract from Micrographs is activated.

For more information in this workflow, check out our guide page on Volume Alignment Tools.


Greeting there,

I’m using Volume alignment tools now to re-center and re-extract particles: my target new position is far from the original center and close to the edge, then I want to re-extract particles with same or larger box size (not smaller or sub-particles) in which means the re-extracted particles are only partly overlap with original particles. I want to know whether it will be working or not before I try it.

Thanks and cheers,

In my opinion, it works no matter overlaps or is bigger, just try to test if the center is what you want.

1 Like