aretomo3 not reading tilt-axis angle from mdoc

[McHaillet]

I noticed that my reconstruction had incorrect handedness and found that AreTomo3 does not seem to read the tilt-axis angle from the Mdoc file (at least I think that is the problem). Here are my notes on the issue and how you could reproduce it:

Raw data downloaded from https://doi.org/10.34894/OLYEFI, placed in this folder structure:

match_pick_data/
+- raw/
¦  +- tomo200528_100.mrc.mdoc
¦  +- tomo200528_100_0.0_May30_22.19.28.tif
¦  +- tomo200528_100_-12.0_May30_22.22.24.tif
¦  +- ...
+- at_proc/

The mdocs file has this header (i.e. tilt axis angle is -88.7):

>>> head -n 10 raw/tomo200528_100.mrc.mdoc 
PixelSpacing = 1.724
Voltage = 200
ImageFile = tomo200528_100.mrc
ImageSize = 3836 3710
Montage = 1
DataMode = 1

[T = SerialEM: Acquired on Utrecht University Talos          30-May-21  22:34:28    ]

[T =     Tilt axis angle = -88.7, binning = 1  spot = 6  camera = 1 bidir = 0.0]

I ran this command for the reconstruction:

aretomo3 -InMdoc raw/tomo200528_100.mrc.mdoc -OutDir at_proc  -PixSize 1.724 -kV 200 -Cs 2.7 -AtBin 8 -FlipVol 1 -Gpu 0 -AlignZ 1200 -VolZ 2000 -Wbp 1 -CorrCtf 1

However, a visual inspection shows the tomogram is mirrored to previous reconstructions I made with aretomo (v1.3) (available here: https://doi.org/10.34894/TLGJCM). For template matching I also had to mirror the template to localize the particles back.

Looking at the .aln file from aretomo3 the in-plane rotation (ROT) is also 90.0 degrees:

>>> head -n 10 at_proc/tomo200528_100.mrc.aln
# AreTomo Alignment / Priims bprmMn 
# RawSize = 3838 3710 34
# NumPatches = 0
# AlphaOffset =    -0.00
# BetaOffset =     0.00
# SEC     ROT         GMAG       TX          TY      SMEAN     SFIT    SCALE     BASE     TILT
    0    89.3098    1.00000      9.039    -26.936     1.00     1.00     1.00     0.00    -50.99
    1    89.3098    1.00000     16.175     -8.258     1.00     1.00     1.00     0.00    -47.99
    2    89.3098    1.00000     -8.308     -7.383     1.00     1.00     1.00     0.00    -44.99
    3    89.3098    1.00000      4.197    -82.245     1.00     1.00     1.00     0.00    -41.99

After providing the -TiltAxis -90:

aretomo3 -InMdoc raw/tomo200528_100.mrc.mdoc -OutDir at_proc  -PixSize 1.724 -kV 200 -Cs 2.7 -AtBin 8 -FlipVol 1 -Gpu 0 -AlignZ 1200 -VolZ 2000 -Wbp 1 -CorrCtf 1 -TiltAxis -90

I do get the correct in-plane rotation (ROT) (as well as reconstruction handedness):

# AreTomo Alignment / Priims bprmMn 
# RawSize = 3838 3710 34
# NumPatches = 0
# AlphaOffset =    -0.00
# BetaOffset =     0.00
# SEC     ROT         GMAG       TX          TY      SMEAN     SFIT    SCALE     BASE     TILT
    0   -90.3329    1.00000      8.971    -28.769     1.00     1.00     1.00     0.00    -50.99
    1   -90.3329    1.00000     16.023    -10.354     1.00     1.00     1.00     0.00    -47.99
    2   -90.3329    1.00000     -8.398     -8.329     1.00     1.00     1.00     0.00    -44.99
    3   -90.3329    1.00000      4.071    -82.676     1.00     1.00     1.00     0.00    -41.99

[szhengczii]

AreTomo3 does not read it because of the incompatible coordinate systems.

[McHaillet]

Sorry, what do you mean exactly?