Type in the topmost directory:
./init_new_recon.py.
This makes the binaries needed for the package and links them into a new reconstruction directory named "recon_nnnn". For help on customizing this setup script (e.g. custom folder name or counter):
./init_new_recon.py -h.
Go to your newly created recon directory
cd recon_nnnn.
Change the experiment parameters in config.ini to your liking.
Here are some things that you might like to change:
- in_pdb_file: relative path to your own PDB file
- scattering setup (detector distance, photon wavelength, etc)
- parameter unit:
- detd (detector distance): millimeter
- lambda (photon wavelength): Angstrom
- detsize (linear size of detector): pixels in integer
- pixsize: millimeter
- stoprad (radius of beamstop): pixels in float
- parameter unit:
- num_data: the number of diffraction patterns
- fluence: the incident beam intensity in photons per micron squared
- log_file: name of log file
When ready to start creating synthetic data, type:
./sim_setup.py.
Again, you can get help to customize this using the command:
./sim_setup.py -h.
You can use the convenience script run_emc.py that we provided to start the reconstruction:
Typing
./run_emc.py,
will start the reconstruction with the default of 10 iterations.
You can continue to refine the last reconstruction by typing
./run_emc.py -r,
or if you wanted to increase the quaternion sampling by one,
./run_emc.py -R.
If you have enough processors to do an MPI reconstruction:
./run_emc.py -m <number of MPI processes>.
For more information, type:
./run_emc.py -h.
Or you can start a single process reconstruction in the recon directory with more control way:
./emc <num_iterations> <path to config file> [threads per process],
where <necessary arguments> and [optional arguments]. The default number of threads per process is defined by the system parameter OMP_NUM_THREADS.
By default, the intermediate output of the reconstruction is stored in the recon directory's data subdirectory.
To spawn multiple MPI reconstructions from your recon directory:
mpirun -n <num_mpi_processes> ./emc <num_iterations> <path to config file> [threads per process].
By default, images from the reconstruction that are generated by this script are saved to the data/images subdirectory.
In the recon directory type:
./autoplot.py.
Checking the "keep checking" box will automagically look for new reconstructed 3D volumes in the default data directories.
For a more verbose, and maybe informative, view of the underlying setup and reconstruction processes, look at the log files recon.log and EMC.log files respectively.