Apply trapped CTF : Multiplies images by the contrast transfer function only after the first extremum.
Usage in command line:
sp_ctf_punish.py input_stack output_directory --plot --singlehdf --verbosity --debug
The purpose of sp_ctf_punish.py is to:
: multiply images by the contrast transfer function (CTF) only after the first extremum
The general choices for CTF-correction include (among others):
: doing nothing : phase-flipping : multiplying by the CTF
Multiplying by the CTF has the effect of flipping the phases where the CTF is negative, while avoiding the sharp filter edges during phase-flipping. (See 1D profile plot.)
However, multiplying by the CTF also dampens the data near the origin, which often adversely affects particle-recognition and alignment.
This program multiplies by the CTF, but only after the first extremum of the CTF. Before this extremum, the amplitudes are preserved. This strategy was referred to as a “trapped CTF” in SPIDER, or “ignore CTF until first peak” in RELION.
sp_ctf_punish.py input_stack output_directory
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. Nat Protoc. 2008;3(12):1941-74. doi: 10.1038/nprot.2008.156.
Category 1:: APPLICATIONS
Beta:: Under evaluation and testing. Please let us know if there are any bugs.
On some machines, the 1D profiles cannot be plotted.