Run-through example using simulated ribosome data 08/21/2007
Go to www.macro-em.org/download to download the package complete_3D_recon.tar and unzip it using the following command:
tar xvfz complete_3D_recon.tar
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 the 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, it should give the almost identical structure to R70S_small.spi.
Run-through example using cryo-EM ribosome data 02/04/2007
Download
Go to www.macro-em.org/download to download the data file DEMO.tar.gz and unzip it. The file is large (about 300 M) as it contains six micrographs. Also download and extract mics.tar.gz, which contains the scripts.
gunzip DEMO.tar.gz This will create a directory named DEMO, which contains following files and directory:
- clean_test : clean directory and intermediate files produced by run-through python script, run it before you start test.
- testsparxscript : single processor version run-through python script
- testsparxscriptmpi : multiple processor version (MPI) run-through python
- mergeparticles.py: python script to combine picked particles from each individual micrograph.
- set_dict_3D.py: convert 2D alignment paramters to 3D alignment parameters. ( map sx, sx into s2x s2y. This is a temporary step. In the future, it will be replaced by an application command )
- noisedoc.txt : noise image coordinates file, contains coordinates of noise image, which is used for image normalization. This file is used by auto_picking.py
- noisemic.hdf: image from which normalization noise image is windowed. This file is used by auto_picking.py
- model001.tcp: a reference structure for 3D reconstruction. This file is used by ali3d_d.py.
- mask.spi: a mask file for k_means classification. This file is used by k_means.py.
Download mics.tar.gz and unzip it in DEMO directory:
- mics directory, which contains six micrographs for run-through test.
Run single processor version
In directory DEMO type
sparx.shell # this might be required clean_test testsparxscript
Run MPI version
Edit file /sparx/libpy/global_def.py and change flag MPI from False to True by commenting out False (add symbol # in the first column of the line MPI = False) and remove symbol # from the front of line MPI = True. In directory DEMO type
sparx.shell # this might be required clean_test testsparxscriptmpi
Description
- The data comprises six downsampled micrographs of the 80S ribosome. The details of the full dataset are described in Blau, M., Mullapudi, S., Becker, T., Dudek, J., Zimmermann, R., Penczek, P.A. and Beckmann, R.: ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane. Nature Structural and Molecular Biology, 12:1015-1016, 2005.
- Here we provide a subset of six micrographs at a pixel size 4.7625 Angstroms.
- The run-through script goes through the basic steps of 3D EM single particle structure determination process. Each step can be run individually by typing line command when the previous step finished properly.