[3dem] Tilt axis angle

[Ricardo Righetto]

Dear Zongli,

Thanks for bringing this up. As far as I know this is a bug (?) in Tomo5.
This is how you convert the TiltAxisAngle from the Tomo5 mdoc to match the
IMOD/SerialEM convention (followed by RELION and other packages):

TiltAxisAngle_SerialEM = TiltAxisAngle_Tomo5 * (-1) - 90

Thanks to Grigory Sharov for reporting this conversion previously on the
EMAN2 mailing list:
https://urldefense.com/v3/__https://groups.google.com/g/eman2/c/piux0GdX_7M/m/ScQNh9TNAQAJ__;!!Mih3wA!GVNODk79TdJOM39MkZyCm_rvKZNLipdpiBvWB21fpWyrjyDvr4XqEo_dYpU6qzD0wqYVWclQix7y0-QNY6pdCiKCe1ND$ 

TiltAxisAngle and RotationAngle should always be 90 degrees apart in any
mdoc:
https://urldefense.com/v3/__https://bio3d.colorado.edu/SerialEM/hlp/html/about_formats.htm__;!!Mih3wA!GVNODk79TdJOM39MkZyCm_rvKZNLipdpiBvWB21fpWyrjyDvr4XqEo_dYpU6qzD0wqYVWclQix7y0-QNY6pdCjrgD61Z$ 
That's why you got the "correct" result when using the value from
RotationAngle as the tilt axis. Beware though that you may have inverted
handedness in your reconstructions. In my experience, the conversion above
should give the correct results.

Would be great if others can comment if this is indeed the case, and why
this bug persists for so long...

Best wishes,

--
Ricardo Diogo Righetto


Em sex., 15 de mar. de 2024 às 21:33, Zongli Li <zongli.li at gmail.com>
escreveu:

> Dear colleagues,
>
> We recently collected some tilt series data on vitrified ribosome sample
> using ThermoFisher Scientifc's Tomo5 software. The data were collected on
> Falcon 4i. When trying to process the data using the new version of relion
> tomo workflow (relion 5.0-beta), we are wondering what parameter we should
> use from the dmoc file for tilt axis angle (TiltAxisAngle or
> RotationAngle). If the TiltAxisAngle is used in our test run, the
> reconstructed tomogram is nonsense, but the reconstructed tomogram looks
> okay if RotationAngle is used. Any suggestions or explanations on this
> would be highly appreciated.
>
> Best,
>
> Zongli
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