[3dem] Tilt axis angle

[Zongli Li]

Dear Ricardo,

Thank you so much! This makes a lot of sense.
Best wishes,

Zongli

On Sat, Mar 16, 2024 at 12:37 PM Ricardo Righetto <ricardorighetto at gmail.com>
wrote:

> 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!Go-c8e-QwJVBsU0qttyzgSDv-knvzqN6KJbTdN11SKI-RKgQ9dktWrwtqL_J9HC10IqJx5KxDD2MNvPZcrYB$ 
>
> 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!Go-c8e-QwJVBsU0qttyzgSDv-knvzqN6KJbTdN11SKI-RKgQ9dktWrwtqL_J9HC10IqJx5KxDD2MNiJtThea$ 
> 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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>>
>
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