GitHub - leschzinerlab/EMAN2recon: Scripts for running EMAN2/Sparx refinement written by Pawel Penczek

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Scripts for running EMAN2/Sparx refinement written by Pawel Penczek

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
README		README
functions.py		functions.py
hfunctions.py		hfunctions.py
mpi.so		mpi.so
reconstruction_rjh.py		reconstruction_rjh.py
refine.py		refine.py

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3D reconstruction script that uses libraries from SPARX and EMAN2
To use the --CTF option, particles must contain CTF info in the stack header

example job file for an asymmetric reconstruction:
-------------------
#!/bin/csh -f

mpirun -np 8 /path/to/refine.py start.hdf init.mrc refine --ou=56 --rs=1 --xr='10 6 5 4 3 2 2 2' --ts='2 1 1 1 1 1 1 1' --delta='20 15 10 8 5 4 3 2' --an='-1 -1 90 80 70 60 40 20' --snr=0.07 --maxit=5 --ref_a=S --sym=c1 --cutoff=1 --MPI --full_output


example job file for a microtubule reconstruction (13 & 14 protofilament):
-------------------
#!/bin/csh -f

mpirun -np 8 /path/to/refine.py start.hdf init.hdf refine --ou=56 --rs=1 --xr='10 6 5 4 3 2 1' --ts='2 1 1 1 1 1 1' --delta='5 4 3 2 1 0.8 0.5' --an='-1 90 40 20 10 5 2' --snr=0.08 --maxit=3 --ref_a=S --cutoff=1 --MPI --proto='13 14' --oplane=5 --sort --findseam --recon_pad=2 --full_output --hpars='-27.6 9.2 -25.7 9.0'