tool for cropping tomogram

[xulabs]

We can use numpy to crop a volume, but if we save the volume into a mrc file, the header information is incorrect. To solve this problem there are two possible ways:

1. try to find a command line tool to do such cropping. This command line tool may exist in bsoft package
2. write our own code to correct the header and write into the mrc file using the mrcfile package.

Following is how to crop a tomogram using bshow: To cut a subvolume using bshow: 1) choose micrograph / pick particles 2) set box size 3) in boxes menu, choose extract particles 4) may check individual output files. 5) use micrograph / write parameter file. You can first cut according to the low passed filtered map, save the cutted subvolume and star file, then modified star file and load it with the unfiltered tomogram. Then cut the unfiltered tomogram and save the subvolume.

[xulabs]

@wendingp please add the tool under
aitom/aitom/io/mrc/

please also add to the particle picking tutorial