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:

• 3MFP_1SU.tar.gz contains the pdb file for one unit of helical structure.

• saved_pos.tar.gz contains the coordinate file of helix box. Based on its information, we can cut the filament from the micrograph and rotate the filament to a nearly vertical position. We provide this file to help you to run the demo faster by skipping the manual boxing step. However, you still need GUI enviroment to run the pre-processing steps.

• answer.tar.gz cotains the result of our previous run. reuslt_a is the first run without considering the out-of-plane angle. result_b is the continuous run based on result_a but with out-of-plane angle. The logifle, parameter files and pixer file are stored in both folders.

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: Pawel.A.Penczek@uth.tmc.edu