Re: WarpTools create_settings --folder_data problem

[Alister Burt]

Hey! In your processing directory there should be a logs folder, check in there for logs which should tell you why things have failed

Cheers,

Alister

Sent from mobile - apologies for brevity

On Mar 17, 2025, at 23:53, yoko “yokomaz” maz <chenxia...@gmail.com> wrote:



Hey there! 

I'm new to cryo-em and I'm now following the tutorial <Quick Start: Tilt Series

From the tutorial>, when I used 

"WarpTools create_settings --folder_data ./frames --folder_processing  --output warp_frameseries.settings --extension "*.tif" --angpix 3.3702 --exposure 2.35" 

to create a .settings file, and I continued with 

"WarpTools fs_motion_and_ctf --settings warp_frameseries.settings --out_averages"

 the programe was looking for data at warp_frameseries/*.tif. The error is

Failed to process xx/xx/xx/DEF_TOMO2/warp_frameseries/TS_034_040_-40.0.tif, marked as unselected

As far as I understand, --folder_data is the location where we have *.tif and --folder_processing is the location where we store the result of the processing. Can anybody help me this? Thanks a lot!

The organization of my file system is:

xx/xx/xx/DEF_TOMO2/warp_frameseries.settings

xx/xx/xx/DEF_TOMO2/frames/*.tif

xx/xx/xx/DEF_TOMO2/metadata/mdocs_modified/*.mdoc

xx/xx/xx/DEF_TOMO2/warp_frameseries

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[yoko “yokomaz” maz]

Thank you, Alister! I've solved this problem and continued my learning along the "Quick Start: Tilt Series" guide. Since I started with .tif files, I used ts_stack to create a .st file and used AreTomo2 to estimate alignment files. Then, I imported the alignment files (.xf and .tlt) into warp_tiltseries.settings using ts_import_alignment. Now, I have reached the step of checking the handedness of defocus. When I ran ts_defocus_hand --check, I got a value of -0.954. To set the correct handedness, I used --set_flip, but after rerunning ts_defocus_hand, it still shows -0.954. I suspect that ts_defocus_hand --set_flip didn't work because in the output, there is no message saying "Finished processing in xx:xx:xx", only with "Setting defocus handedness to 'flip' for all tilt series...    10/10", is that means that filp has been set?

[Alister Burt]

Hi Yoko,

This has come up before and it’s a bit different from how warp desktop worked: 

- defocus handedness for a tilt series can be in one of two states referred to as “flip” and “no-flip”

- ts_defocus_hand reports what this state should be set to for a dataset

- it is not expected that changing the state would change the outcome of the defocus handedness check, the check is telling you an absolute state that you should set to for your dataset 

To confirm whether the flag has been set you can check in your tilt series xml files but if the program ran to completion I wouldn’t worry!

Cheers,

Alister

c.f https://github.com/warpem/warp/issues/145#issuecomment-2168057181

Sent from mobile - apologies for brevity

On Mar 26, 2025, at 22:02, yoko “yokomaz” maz <chenxia...@gmail.com> wrote:

 Thank you, Alister! I've solved this problem and continued my learning along the "Quick Start: Tilt Series" guide. Since I started with .tif files, I used ts_stack to create a .st file and used AreTomo2 to estimate alignment files. Then, I imported the alignment files (.xf and .tlt) into warp_tiltseries.settings using ts_import_alignment. Now, I have reached the step of checking the handedness of defocus. When I ran ts_defocus_hand --check, I got a value of -0.954. To set the correct handedness, I used --set_flip, but after rerunning ts_defocus_hand, it still shows -0.954. I suspect that ts_defocus_hand --set_flip didn't work because in the output, there is no message saying "Finished processing in xx:xx:xx", only with "Setting defocus handedness to 'flip' for all tilt series...    10/10", is that means that filp has been set?

To view this discussion visit https://groups.google.com/d/msgid/warp-em/3315b58b-a857-49bc-8fc6-d9bbdbd38d7bn%40googlegroups.com.

[yoko “yokomaz” maz]

Thank you, Alister! That's much clearer for me to understand how warp works!