<original micrograph> | The file containing the raw particles to be oriented |
<output image file> | output filename ofr newly reboxed particles. in IMAGIC format |
[box=<box file>] | Projections to be used as references |
[ptclfile=<IMAGIC file>] | the IMAGIC file with particles which stored the positions and center shifts in file header, this will override [box=<box file>] option |
[all] | rebox all particles, default is to ignore the bad particles (score<=0) |
[outbox=<box file>] | output the new box file, only effective when [ptclfile=<IMAGIC file>] is set |
[fixphase[=<CTF parafile>]] | flip the phases after reboxing using CTF parameters stored in file <CTF parafile>, or "ctfpara.txt" in current directory, or at last prompt for input |
[verbose] | if set, ouput some intermediate information |
rebox 7572.mrc 7572-rebox.img box=7572.box
rebox 7572.mrc 7572-rebox.img ptclfile=7572.img
This program could rebox the particles from a micrograph with information provided in two different ways, and serve two corresponding purposes.
1: when using boxer with focal pair or median filter mode, another round of loading the closer to focus or original unfiltered micrograph has to be reloaded and reboxed, this program will mimic this second round boxing by eliminating the graphic interaction.
2: when boxed for the first time, the particles might not have been centered well, the later processing step might find some particles are off centered by significant distance, then this program will try to rebox from the original micrograph so than to make the center shift less than ONE pixel, but not try to center them perfectly to avoid interpolation error, instead the remaining center shifts will be stored in the IMAGIC file header so the later processing steps will taken account.
The [fixphase[=
EMAN Manual page, generated Tue Feb 5 15:30:08 2002