transforming star file

[pherepanov]

Dear Daniel,

I am trying to transform a star file (from a single particle project, Relion 5.0) to superpose subparticles based on Chimera transformation matrix. I used both star.py and subparticles.py, which produce different results but neither allow reconstruction of correctly oriented and positioned particle. Here are two commands I used:

star.py --transform "[[-0.990457,-0.00727857,0.137627,352.06],[-0.00724027,0.999973,0.000778896,-45.7555],[-0.137629,-0.000224997,-0.990484,426.689]]" cryosparc_P3_J13_010_particles_mindist35A.star cryosparc_P3_J13_010_particles_mindist35A_moved1.star

subparticles.py --transform "[[-0.990457,-0.00727857,0.137627,352.06],[-0.00724027,0.999973,0.000778896,-45.7555],[-0.137629,-0.000224997,-0.990484,426.689]]" cryosparc_P3_J13_010_particles_mindist35A.star cryosparc_P3_J13_010_particles_mindist35A_moved1c.star --boxsize 400 --apix 0.95

I noticed that in either case, positions of particles in star file (rlnCoordinateX,Y and rlnOriginX/YAngst) did not change, so shifts were not applied. Moreover, reconstructed orientations did not match one another. With the second method, it seems that a 180 degree rotation around Y, plus a translation is required to bring the new volume in the correct position.

I double-checked my transformation matrix in Chimera using matrixset, which placed the volume precisely where it needs to be. So the problem is with the script or with the way I am trying to use it (?). BTW, are these two scripts expected to produce different results with the same transformation matrix? My guess is that star.py expects a matrix from ZYZ Euler sequence and subpartilcles.py expected a matrix from ZXZ (Chimera) - is this interpretation correct?

Our pyem installation is recent, from June this year (after star.py update). I did try an older version also, with the same result.

Peter

[pherepanov]

I think I found a workaround using star.py:

1. convert the Chimera-computed matrix from ZXZ (Chimera) to ZYZ (Relion) convention.
2. rotate particles with star.py:

star.py --transform "[[0.9999734855418153, 0.007240271878779304, -0.0007788943920751361],[0.007278570633670146, -0.9904573829780646, 0.1376270137501123],[0.0002249952962242808, -0.13762903388226003, -0.9904838203674767]]" cryosparc_P3_J13_010_particles_mindist35A.star cryosparc_P3_J13_010_particles_mindist35A_lower_subparticle.star

3. reconstruct rotated volume
4. measure required shift in Chimera (disable any rotations during fitting)
5. shift rotated particles with relion_star_handler via reciprocal shift of origins:

relion_star_handler --i cryosparc_P3_J13_010_particles_mindist35A_lower_subparticle.star --o cryosparc_P3_J13_010_particles_mindist35A_lower_subparticle_shifted_down.star --center --center_X 8.28719 --center_Y 53.3376 --center_Z -23.0831

Since this approach worked, I think there has to be a bug in subparticles.star, which does not get the right rotation around Y (either adds an extra 180 or does not do the main rotation).

Also, I noticed star.py adds extra columns to output star file (ucsfImageOriginalIndex, etc). Is there any use for them?