CTF correction in WARP

[Julien Maufront]

Hi everyone,

I have a naive question concerning the use of CTF fitting from WARP :

Are the micrographs from the "average" folder CTF corrected ? Or are they just raw frames alignment results ?

Indeed, I processed a dataset made of 2D movies in WARP (frames alignment/CTF fitting).

I then picked/extracted particles out of the micrographs contained in the average folder to use the generated stack for 2D alignment/classification.

Do I need to had a CTF correction step of my particles ?

Similarly, can the tomograms generated by IMOD out of tilt series pre-processed in WARP be considered as CTF corrected ?

If not, how should we use the powerspectrum files to do the CTF correction step ?

Thanks in advance for your help,

Julien Maufront

[Julien Maufront]

(Note : I picked/extracted the particles out of WARP with EMAN)

[Julien Maufront]

Sorry to ask again but does anyone know if images from average folder are phase flipped ? wiener filtered ? or just raw frames aligned ?

Thank you

[teg...@gmail.com]

Hi Julien,

The CTF of the images in the average folder is not modified, so they're not phase-flipped and not Wiener-filtered. There is no easy way to get such images out of Warp. A hack that might work for this is to create a fake tilt series from every individual micrograph (1 tilt per series), go through the tilt series pipeline, and then reconstruct very thin tomograms. You'd still have to flatten the resulting volumes along Z manually since the smallest Z dimension Warp will let you choose is 2. Phase flipping is applied based on local defocus values during tomogram reconstruction, and you can get Wiener filtering by enabling deconvolution.

However, I'm not sure this is the best way to go for the pipeline you envision. If you want to reconstruct in IMOD, it's best to also let it handle the CTF. If you're using IMOD for reconstruction because Warp up-weights high frequencies in a weird way in its reconstructions, you might want to try the new 1.1.0 where this bug is fixed (not really a bug, more of a side effect of the algorithm used).

Cheers,

Dimitry

[Julien Maufront]

Hi Dimitry,

Thank you for this answer and the proposed trick !

I will move to WARP 1.1.0, thank you for all your amazing work with WARP !

Cheers,

Julien