Trying to get an oriented 2D projection image of a 3d Volume

[Bullitt, Esther]

Hi,

I have a class average for which I would like to get a 2D projection, oriented for computing a useful FT.

The numbers from doing the rotation myself and looking at the ‘basics’ tab in e2display.py for the rotation angles do not give the expected orientation.

My e2project3d.py command is

e2project3d.py sptsgd_07/output_cls2.hdf  --outfile=testprj2.hdf --orientgen=single:alt=60. --orientgen=single:az=24.2  --orientgen=single:phi=-38.7 --projector standard --verbose 2

Documentation for the command says:

Defining rotations:

single : Generate a single orientation with the specified EMAN style Euler angles. Symmetry is ignored.

alt(FLOAT) - Altitude (X rotation in deg)

az(FLOAT) - Azimuthal angle (Z rotation in deg)

phi(FLOAT) - Phi angle (Z' rotation in deg

I know that the order within the command matters, so is there a trick with respect to the order I place the numbers in the command? Or a systematic difference ?

 e2version.py

EMAN 2.99.72 ( GITHUB: 2026-03-06 14:19 - commit: NOT-INSTALLED-FROM-GIT-REPO )

Your EMAN2 is running on: Linux-4.18.0-553.89.1.el8_10.x86_64-x86_64-with-glibc2.28 4.18.0-553.89.1.el8_10.x86_64

Your Python version is: 3.12.13

Thanks,

Esther

[Steve Ludtke]

If I'm understanding correctly, I think you're after this:

e2project3d.py sptsgd_07/output_cls2.hdf  --outfile=testprj2.hdf --orientgen=single:alt=60:az=24.2:phi=-38.7 --projector standard --verbose 2

Is that what you're trying to achieve?  With multiple --orientgen options, you're just overriding the earlier ones...

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

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[Bullitt, Esther]

Yes!  That works (commas or spaces did not)

Thank you!

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