Quick start

Spawn a reconstruction directory

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.

Configure experiment

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
• 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.

Start your EMC reconstruction

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.

Monitor the progress of your reconstruction

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.

Additional information

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.