WarpTools ts_reconstruct map mode

[Lucas Morley]

Hi,

I was wondering if anyone knows if there is a setting that can be changed to produce tomograms in a map mode compatible with Dynamo. The tomograms generated by WarpTools are in mode 12 (16-bit float) which causes the error in Dynamo: Unknown file mrc_file_type 12. 

I am used to reconstructing tomograms using Etomo which produces mrc files in map mode 1 (16-bit integer).

My plan was to use IMOD's newstack to change the mode but it just produced a white tomogram.

Any help would be appreciated, thanks!

[Alister Burt]

Hi Lucas,

You can force writing 32 bit MRC files - https://warpem.github.io/warp/reference/warptools/environment_variables/

I remember asking Daniel about this a while ago and he said he had added 16 bit float support - might be worth upgrading your dynamo installation :-)

Cheers,

Alister

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[Lucas Morley]

Hi Alister

I found the force 32 bit after I sent that, thank you. Unfortunately, I updated to the most recent Dynamo version and still get the error.

Best,

Lucas

[Reika Watanabe]

Hi Alister and Lucas,

I could not use Dynamo extraction exactly Lucas faced. 

How could I use this force writing 32 bit as suggested by Alister? 

Should I change tiltseries.settings? If so where?

I need a bit more guidance.

Thank you very much!

Reika 

[Reika Watanabe]

Dear all,

I got this kind instruction from Hamid! 

And now the tomogram is mode 2 (32-bit float). 

Thanks!!!

Reika 

 

Hi Reika,

For changing to float32 this is what I ran:
export WARP_FORCE_MRC_FLOAT32=1; WarpTools ts_reconstruct --settings warp_tiltseries.settings --angpix 9.98 --device_list 2 3 --perdevice 8 --dont_invert --deconv

export WARP_FORCE_MRC_FLOAT32=1 sets a bash env variable that is passed to WarpTools
(sorry alister for answering on your behalf, I thought I could help!)

Best,

Hamid

[Alister Burt]

Hi Reika,

Copying the command from the website into your shell before running any warptools program will make it write out 32 bit mrc files - if you only want to enable it for a specific command you can prepend your warptools command with WARP_FORCE_MRC_FLOAT32=1

Cheers,

Alister

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[Reika Watanabe]

Hi Alister,

Thank you very much for clarifying it! 

Reika