Run-through example using simulated ribosome data 12/10/2010

Download file demo.tar and unzip it using the following command:

tar -xvf demo.tar

There are the following files in this directory

• tteftu_with_tRNA.pdb.gz as the name suggested is 70S ribosome with ttEFTU and tRNA in PDB format.

• mpi_bdb/run_through_example test for bdb format without CTF and with MPI

• mpi_bdb_ctf/run_through_example test for bdb format with CTF and MPI

Unzip tteftu_with_tRNA.pdb.gz:

gunzip tteftu_with_tRNA.pdb.gz

To run a particular example, simply go to the directory you want and type

./run_through_example &

The program will begin to run in the batch mode. The estimated runtime of this program is 2 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, it should give the almost identical structure to model_structure.hdf located in the demo directory (most likely the resolution will be lower).