Run-through example using simulated ribosome data 08/21/2007

Go to http://www.macro-em.org/download to download the package complete_3D_recon.tar and unzip it. There are three files in this package:

• R70S_small.spi is the X-ray crystal structure of a 70S ribosome tRNA complex. It was converted from the combination of PDB file 1VS9 and 2I1C using the SPIDER software package and the pixel size is 3.0 Angstroms.
• generate_projections.py is a program to generate a set of 849 quasi-even projections of the structure.
• run_through_example is a set of command lines that will go through the whole 3-D reconstruction process.

To run this example, simply type

run_through_example &

The program will begin to run in batch mode. The estimated runtime of this program is 12 hours for a 2.4GHz CPU. Upon finishing, the program will leave many intermediate results and log file in the directory, please refer to help page of each command for their individual meanings.

The final reconstruction result is ali3d_e/vol0005.spi. If finished successfully, its structure should be almost identical to R70S_small.spi.