[3dem] Tilt axis angle

[Sylvain Trepout]

Hi Zongli and Ricardo, and tomo enthusiasts,

Same here, on a Krios G4 with Falcon 4i and Tomo software version
5.16.0.6389, the orientation of the tilt axis is not reported correctly.
TiltAxisAngle = -174.72
RotationAngle = 84.72

But the correct tilt axis angle found by IMOD is 95.07
It does not fit the formula you gave Ricardo though... off by just 10
degrees.
Or maybe this is a flip and then the orientation would be ok, but this
would change the handedness.

For comparison, on the Krios G1 (with a K3 and an older version of Tomo
software)
TiltAxisAngle = -174.47
RotationAngle = -84.72
The correct tilt axis orientation (as found by IMOD) is around 87 (this
fits your formula, Ricardo).

Best wishes,
Sylvain

PhD
Research Fellow - Microscopy Australia

*Monash University*
Ramaciotti Centre for Cryo-EM
G92, 15 Innovation Walk, Clayton Campus
Victoria, 3800 Australia

E: sylvain.trepout at monash.edu


On Sun, 17 Mar 2024 at 07:53, Zongli Li <zongli.li at gmail.com> wrote:

> 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!Hpk_Da05ULp8VSDgCGDsUn4lxlUYtLSBQcdl-AumgluDZ0DfzRUu0vBVT4ETXJOa9ZjzKhYlIBKictUVVxFob3BkJ-5voQgo$ 
>> <https://urldefense.com/v3/__https://groups.google.com/g/eman2/c/piux0GdX_7M/m/ScQNh9TNAQAJ__;!!Mih3wA!Go-c8e-QwJVBsU0qttyzgSDv-knvzqN6KJbTdN11SKI-RKgQ9dktWrwtqL_J9HC10IqJx5KxDD2MNvPZcrYB$>
>>
>> TiltAxisAngle and RotationAngle should always be 90 degrees apart in any
>> mdoc:
>> https://urldefense.com/v3/__https://bio3d.colorado.edu/SerialEM/hlp/html/about_formats.htm__;!!Mih3wA!Hpk_Da05ULp8VSDgCGDsUn4lxlUYtLSBQcdl-AumgluDZ0DfzRUu0vBVT4ETXJOa9ZjzKhYlIBKictUVVxFob3BkJ6545NyN$ 
>> <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
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>
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