Run-through example for helical structure using simulated data 4/23/2013

This is a demo to show the workflow of helical refinement.

Download file helical_mpi.tgz and unzip it using the following command:

tar -zxvf helical_mpi.tgz

You need to copy the commands from run_through_example and paste them on your terminal to run them. For helical refinement, we only provide MPI version. Depending on your computational environment, you need to change the mpirun command.

There are six files in this directory. The function of some of the files are explained below:

The preprocessing steps can be completed within ten minutes on a Mac workstation. The first run of helical refinement without out-of-plane angle may take half an hour on 3 or 4 CPUs. The second run that includes the out-of-plane tilt angle will take much longer time on 3 or 4 CPUs. tmp.hdf is the ideal volume generated from pdb file, but is much longer than the volume produced by our program. For comparison, you will need window and pad tmp.hdf to the same size with the volume generated by our program.


Author / Maintainer

Pawel Penczek, email: [email protected]

Runthrough_helical_example (last edited 2023-07-01 13:12:47 by localhost)