can't import tilt series from IMOD

[Juha Huiskonen]

Hi All,

I have been able to follow the Warp tutorial to the point where the tomostar files are created based on IMOD alignment:

-  I import the tilt series and alignment information to Warp

- I see the tick box appearing, indicating that alignment was found from the IMOD folders.

- The Tomostar files are created and they point to raw frames that are in the same directory.  

However, nothing happens when I click start processing (the circle indicating the number of items to process does not appear).

Any idea why this could happen and what should I do next?

best wishes,

Juha

[Genis Valentin Gese]

Hi Juha

I got stuck at the same point, but I found out that if I manually edit the tomostar files to remove the decimal numbers in the tilt angle and dose columns, then WARP can read the tomostar files.

For example, this file is ignored (I just copied the first rows as an example)

data_

loop_

_wrpMovieName #1

_wrpAngleTilt #2

_wrpAxisAngle #3

_wrpAxisOffsetX #4

_wrpAxisOffsetY #5

_wrpDose #6

  TS_01_038_-57.0.mrc   57.09  85.01966    35.42966   113.2249  115

  TS_01_035_-54.0.mrc   54.11  85.04208     20.4199   93.81467  106

  TS_01_034_-51.0.mrc   51.13   85.0446    30.81794   117.7421  103

....

But this file is properly read by WARP

data_

loop_

_wrpMovieName #1

_wrpAngleTilt #2

_wrpAxisAngle #3

_wrpAxisOffsetX #4

_wrpAxisOffsetY 

_wrpDose #6

  TS_01_038_-57.0.mrc   57  85.01966    35.42966   113.2249  115

  TS_01_035_-54.0.mrc   54  85.04208     20.4199   93.81467  106

  TS_01_034_-51.0.mrc   51   85.0446    30.81794   117.7421  103

...

However, the reconstructed tomograms still do not look good, as it seems that the tilt angles are not taken into account for the reconstruction.

This is a more detailed tutorial for processing the EMPIAR-10164 dataset made by Alister Burt and Lorenzo Gaifas from the Gutsche lab (I did not try it out yet, though)

https://teamtomo.org/walkthroughs/EMPIAR-10164/introduction.html

Best

Genis

[Alister Burt]

Hi both,

I just checked my tomostar files and they all have decimals in them and things run fine here (sorry, probably not what you want to hear!). I remember debugging a different issue a while ago with a friend https://groups.google.com/g/warp-em/c/wHgFAG1ftuI/m/QLOlP76iAQAJ which turned out to be a regional decimal separator settings problem - I’m not sure where you’re both located but it might be worth looking into this as a possible cause?

Good luck!

Alister

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[Ortiz, Julio]

Hi Juha,

I had similar problems before.

Indeed, it is better to change the metric system of your Windows, to the American standard. Then decimals are separated by points and thousands by commas.

Many WARP problems just disappear after the change,

Saludos,

Julio

Dr. Julio Ortiz

EM Facility Manager

Forschungszentrum Jülich GmbH

Ernst Ruska-Centrum für Mikroskopie und Spektroskopie

mit Elektronen

ER-C-3: Strukturbiologie

52425 Jülich

Germany

Phone: +49 2461 61-2032

Fax:       +49 2461 61-1448

EMAIL: j.o...@fz-juelich.de

Am 26.02.2021 um 09:08 schrieb Juha Huiskonen <juha.hu...@gmail.com>:



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[Genis Valentin Gese]

Hi Alister and Julio

Indeed changing my computer from Swedish to US English solved the issue.

Thanks so much for the feedback!

Genis

[Juha Huiskonen]

Same here. Changing from Finnish to US English solved the issue.

[Behruz Ghazi]

Hi

I have the same issue, when I import to WARP it creates the tomostar file (it looks ok, I am using the US(English) system. But when I click to start processing, it does not do anything and after a while, on the graphic shell it gives this error (on the screenshot) and the shell gets closed while the WARP is still rotating its thing. Please let me know if you experienced such a thing or have any idea what's going on.
You can also space characters before movie names in the tomostar file, I edited this manually to remove the space, but the same thing happened.



Best 
Behrouz