How to rotate and project a volume along a specific axis in EMAN2?

[Steve Chou]

Hi EMAN2/SPARX developers and users,

I downloaded a tubelike PDB file from RCSB PDB. The tube axis has been aligned along the Z-axis already. I want to (1) convert the PDB into a volume, (2) rotate the tubelike volume around the Z-axis every 10 degrees, and (3) project each rotated volume along the Y-axis into 2D particles. How to do that?

Many thanks in advance!

Steven
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Steven Chou

[Ludtke, Steven J.]

Hi,

you'd want to use e2pdb2mrc.py to generate the volume. Make sure to read the options (e2pdb2mrc.py --help). The box size you select should be a cube, and you will likely want to center it. 

You can generate projections with e2project3d.py (e2project3d.py --help)

That program is generally designed to generate a bunch of projections at once, normally filling the asymmetric triangle. 

The orientations are generated using an orientation generator (e2help.py orientgen or e2help.py orientgen -v 2). The orientation generator is specified as an option on the e2project3d.py command-line. To generate a single projection, you would likely use the "single" orientation generator. 

Finally, you need to specify the orientations you want. The default projection (az=0, alt=0, phi=0) is a view along the Z axis. To generate a range of side views like you describe, you would want alt=90, and az=0,5,10,15,... (whatever step you like). phi is in-plane rotation of the final image.

See also:

http://eman2.org/Symmetry

https://blake.bcm.edu/emanwiki/Eman2TransformInPython

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Steve Chou]

Thank you Prof. Ludtke,

Following your advice, I created a script, and it worked well for me.

===========================================================

csh

e2pdb2mrc.py  tube.pdb  tube.mrc  --apix=2.1  --res=4  --box=500  --center
set twist = 0
while ($twist < 360)
     echo "project at twist angle: " $twist
     set twist_formatted = `echo $twist | awk '{printf "%3d", $0}'`
e2project3d.py tube.mrc --sym=c1 --orientgen=single:alt=90:az=${twist}:phi=0 --outfile=projection_${twist_formatted}.hdf --projector=standard --verbose=2
     @ twist = $twist + 10
end
e2proc2d.py  projection_*.hdf  projections.hdf

===========================================================

All the best,

Steven

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/5AD6E6A3-2405-4F1F-8301-02CDB4E79FAE%40bcm.edu.