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pipeline:meridien:sp_beamtilt [2021/02/19 16:19] shaikh |
pipeline:meridien:sp_beamtilt [2021/02/19 16:34] shaikh old revision restored (2021/02/19 14:19) |
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Correct Beam Tilt : Applies beam-tilt correction to particles. | Correct Beam Tilt : Applies beam-tilt correction to particles. | ||
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===== Usage ===== | ===== Usage ===== | ||
Usage in command line | Usage in command line | ||
- | < | + | sp_beamtilt.py output_directory --input_stack=INPUT_STACK --star_file=STAR_FILE --kv=KV --cs=CS --apix=APIX --tiltx=TILTX --tilty=TILTY --micdir=MICDIR --box_size=BOX_SIZE --coordsdir=COORDSDIR --partdir=PARTDIR --verbosity=verbosity_level --debug |
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- | </ | ||
+ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sp_beamtilt exists in both MPI and non-MPI versions (Running MPI version does not require | + | sp_beamtilt exists in both MPI and non-MPI versions (Running MPI version does not require |
The purpose of sp_beamtilt.py is to: | The purpose of sp_beamtilt.py is to: | ||
- | < | + | |
- | : read beam-tilt information, | + | : corrects images for beam tilt |
- | : corrects images for beam tilt | + | : applies those corrections to either an input stack or extracts them from particles |
- | : applies those corrections to either an input stack or extracts them from particles | + | : write the correct particle stack to disk |
- | : write the correct particle stack to disk | + | |
+ | \\ __1. Standard usage: Read beam-tilt data from STAR file and particles from stack__: | ||
- | </ | + | |
- | + | ||
- | + | ||
- | __1. Standard usage: Read beam-tilt data from STAR file and particles from stack__: | + | |
- | < | + | |
- | mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb: | + | |
- | + | ||
- | </ | + | |
STAR files from RELION v3.0 and v3.1 have been tested and should work. | STAR files from RELION v3.0 and v3.1 have been tested and should work. | ||
- | \\ | + | \\ __2. Provide the beam-tilt parameters directly from the command line__: |
- | __2. Provide the beam-tilt parameters directly from the command line__: | + | |
- | < | + | |
- | mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb: | + | |
- | </ | + | mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb: |
Beam tilt is to be provided in units of milliradians. Other required parameters are accelerating voltage, spherical aberration constant, and pixel size. | Beam tilt is to be provided in units of milliradians. Other required parameters are accelerating voltage, spherical aberration constant, and pixel size. | ||
+ | | ||
+ | \\ __3. Particles are to be extract directly from micrographs__ | ||
- | \\ | + | |
- | __3. Particles are to be extract directly from micrographs__ | + | |
- | < | + | |
- | mpirun -np 16 sp_beamtilt.py output_directory --star_file particles.star --micdir=input_micrograph_directory | + | |
- | + | ||
- | </ | + | |
This option has not been tested thoroughly. | This option has not been tested thoroughly. | ||
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+ | \\ | ||
===== Input ===== | ===== Input ===== | ||
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=== Main Parameters === | === Main Parameters === | ||
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=== Advanced Parameters === | === Advanced Parameters === | ||
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- | ; ; < | + | |
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===== Output ===== | ===== Output ===== | ||
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- | ; ; bdb: | + | |
+ | \\ | ||
===== Description ===== | ===== Description ===== | ||
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==== Method ==== | ==== Method ==== | ||
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==== Reference ==== | ==== Reference ==== | ||
Zivanov J., Nakane T., Forsberg B.O., Kimanius D., Hagen W.J.H., Lindahl E, Scheres S.H.W. (2018) "New tools for automated high-resolution cryo-EM structure determination in RELION." | Zivanov J., Nakane T., Forsberg B.O., Kimanius D., Hagen W.J.H., Lindahl E, Scheres S.H.W. (2018) "New tools for automated high-resolution cryo-EM structure determination in RELION." | ||
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==== Developer Notes ==== | ==== Developer Notes ==== | ||
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Eventually, we want to correct for beam tilt on the fly, and not write the corrected images to disk. | Eventually, we want to correct for beam tilt on the fly, and not write the corrected images to disk. | ||
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==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
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Tapu Shaikh | Tapu Shaikh | ||
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==== Keywords ==== | ==== Keywords ==== | ||
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Category 1:: APPLICATIONS | Category 1:: APPLICATIONS | ||
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==== Files ==== | ==== Files ==== | ||
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sphire/ | sphire/ | ||
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==== See also ==== | ==== See also ==== | ||
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==== Maturity ==== | ==== Maturity ==== | ||
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Beta:: Under evaluation and testing. Please let us know if there are any bugs. | Beta:: Under evaluation and testing. Please let us know if there are any bugs. | ||
+ | \\ | ||
==== Bugs ==== | ==== Bugs ==== | ||
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