matching IMOD clip flipyz tomogram handness

[Oleksiy Kovtun]

Hi all, 

Need your help with figuring out how to recreate tomogram orientation from IMOD in WarpTool 2.0 

Established IMOD pipeline:  -85 Rotation Angle does not require flipping for defocus estimation,  and clip flipyz produce tomograms with correct molecular handiness.   

WarpTool pipeline without tilt angle inversion:  ts_import with  --override_axis -85 and omitted --dont_invert flags. Check with  ts_defocus_hand if tilt angle hand need flipping. If does, use --dont_invert flag for ts_import. Problem: tomograms from ts_reconstruct will be of a wrong molecular handness, assuming their default orientation matches IMODs clip rotx.

WarpTool pipeline with tilt angle inversion:  set Rotation Angle to 95 (native angle +180).  ts_import. with --override_axis 95, --dont_invert flags. Problem:  not sure if this will result in correct tilt angle hand and molecular handness of the tomograms.  

Thank you and best, 

Oleksiy

 

[Alister Burt]

Hi Oleksiy,

I recommend picking in tomograms generated by the package you intend to use for refinement to avoid the ordeal you’re currently going through :-) otherwise, trial and error.

Cheers,

Alister

Sent from mobile - apologies for brevity

On Mar 2, 2025, at 08:45, Oleksiy Kovtun <memt...@gmail.com> wrote:

Hi all, 

--
You received this message because you are subscribed to the Google Groups "Warp" group.
To unsubscribe from this group and stop receiving emails from it, send an email to warp-em+u...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/warp-em/36c34a91-c6b0-438d-a928-abb0006f41c1n%40googlegroups.com.

[Oleksiy Kovtun]

Hi Alister,

Thank you for the fast reply. 

Yes, I remember the importance of using the same software tomogram projector for particles. Here I wanted to copy just a handness from the Imod protocol.

SDo you have plans to include an analogue of clip flipyz in the warptool tomo reconstruction?

Best wishes,

Oleksiy 

To view this discussion visit https://groups.google.com/d/msgid/warp-em/E8F3C544-A351-429F-8B6A-32ADACA083FA%40gmail.com.

[Alister Burt]

Hi Oleksiy,

flipYZ vs rotX90 in Etomo is only relevant for tomograms  reconstructed by the IMOD program tilt which generates XZ planes one at a time and saves them as XY planes in the output file by default. 

Flipping handedness in Warp is achieved by inverting tilt angles, which has the side effect of flipping the reconstruction through the XY plane

Cheers,

Alister

Sent from mobile - apologies for brevity

On Mar 2, 2025, at 11:46, Oleksiy Kovtun <gqv...@gmail.com> wrote:



[Oleksiy Kovtun]

Hi Alister and all, 

In case it will be helpful to someone, here I attach a table showing how tilt angle hand and tomogram hand behaves in warptool 2.0 comparing to the IMOD.

Reference IMOD settings:  -85 Rotation Angle. No need for hand flipping for ctf correction. Clip flipyz reorientation is required for tomograms with correct molecular handiness.

Thank you very much for your help. 

Best, 

Oleksiy