CTF multiplying raw subtomograms from warp

[joe dobbs]

Hi all,

I'm looking at CTF correcting my warp subtomograms directly. When trying to multiply the subtomos with their ctf files via imod clip, I found that these are actually different sizes (eg. subtomos are 96x96x96 vs. ctf 49x96x96), so I assume direct multiplication might not be the best way to do it. Would anyone have any suggestions about the proper way to do this?

Thanks!

Joe

[Pranav Shah]

Hi Joe,

The CTF file is for multiplying an orient reference to best match the observation(your subtomo). The discrepancy in the file sizes is due to the symmetric nature of a fourier transform. If you are using warp generated subtomos you needn’t have to multiply the two files together.

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

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[joe dobbs]

Hi,

Thanks for your message, that's very good to know! 

Would you happen to know about any documentation that describes this? I wasn't able to find anything about it in the warp paper or original relion subtomo paper (unless I missed it!) and wrongly assumed that since ctf info is provided separately, and that some relion operations not implemented for subtomos (eg. signal subtraction) fail with an error message about images needing to be ctf-multipied, that the subtomos weren't already ctf multiplied.

In any case, thanks for the help!

[Pranav Shah]

Hi Joe,

The design of the 3d ctf model is explained here -

https://www.cell.com/structure/fulltext/S0969-2126(15)00279-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0969212615002798%3Fshowall%3Dtrue

In STA it is not necessary to perform subtraction, simple masking is sufficient.

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/53dc21fa-7655-4339-8417-ce32af9ad233n%40googlegroups.com.

[joe dobbs]

Hi Pranav,

Thanks for the link and the advice!! (I am not trying to do subtraction though, just an example :) )

Joe