This is an old revision of the document!
3D Refinement: Performs 3D structure refinement using a quasi-Maximum Likelihood approach.
Usage in command line
sxmeridien.py stack output_directory initial_volume --do_final=MERIDIEN_ITERATION_ID --local_refinement --radius=particle_radius --mask3D=MASK3D --symmetry=SYMMETRY --inires=INITIAL_RESOLUTION --delta=DELTA --xr=XR --ts=TS --initialshifts --skip_prealignment --memory_per_node=MEMORY_PER_NODE --center_method=CENTER_METHOD --target_radius=TARGET_RADIUS --an=ANGULAR_NEIGHBORHOOD --shake=SHAKE --small_memory --ccfpercentage=CCFPERCENTAGE --nonorm --function=USER_FUNCTION
sxmeridien exists only in MPI version (Running MPI version does not require –MPI flag).
There are five ways to run the program:
1. Standard default run:
The standard refinement starts from exhaustive searches, uses initial reference structure
mpirun -np 64 --hostfile four_nodes.txt sxmeridien.py bdb:sparx_stack vton1 mask15.hdf --sym=c5 --initialshifts --radius=120 --mask3D=mask15.hdf >1ovotn &
2. Restart after the last fully finished iteration:
One can change some parameters (MPI settings have to be the same)
mpirun -np 64 --hostfile four_nodes.txt sxmeridien.py vton1 --radius=100 >2ovotn &
3. Local refinement:
Local refinement starts from user-provided orientation parameters, delta has to be ⇐ 3.75
mpirun -np 64 --hostfile four_nodes.txt sxmeridien.py --local_refinement bdb:sparx_stack vton3 --delta=1.875 --xr=2.0 --inires=5.5 --sym=c5 --radius=120 --mask3D=mask15.hdf >5ovotn &
4. Restart of local refinement after the last fully finished iteration.:
One can change some parameters (MPI settings have to be the same)
mpirun -np 64 --hostfile four_nodes.txt sxmeridien.py --local_refinement vton3 --xr=0.6 >6ovotn &
5. Final reconstruction only:
Do only final reconstruction using a fully finished iteration of meridien (here number 21).
mpirun -np 64 sxmeridien.py --do_final=21 meridien_outdir
Pawel A. Penczek
Category 1:: APPLICATIONS
sparx/bin/sxmeridien.py
References to relevant other routines.
Alpha:: Fully developed.
Glitches possible.