Subtomogram export (warp)

[Marius Knauf]

Dear all, 

Im currently working on a tilt series dataset of the SERCA pump in its native membrane and want to export subtomograms of the SERCA protein from my cells, but when i try to use the export tomogram function in Warp i get the following error:

System.Exception: Couldn't find rlnCoordinateZ column.

  

Does anybody know what the rlncoordinateZ column is?

I have been training my tilt series with boxnet_20180602

Hopefully someone know what causes this error and how to eventuelly fix it 

Best wishes,
Marius Knauf
Aarhus University, Denmark

[Pranav Shah]

Hi Marius,
Your particle coordinates need to specify rlnCoordinateX,
rlnCoordinateY, rlnCoordinateZ columns which your starfile does not
have based on the description of the error. You need to pick the 3D
coords using cryolo(3d) or manually using tools such as imod. Many
tutorials online.
Good luck!


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

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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[Matthias Vorländer]

Just to add to that, you can also use the template matching routine in Warp (this is a seperate job from the usual particle picking using boxnet as you might be familiar with from single particle data analysis). You will need to provide a 3D map of your structure as a reference for template matching, and you can visualize the picked coordinates later on in the seperate program "Cube". I find it very helpful to denoise your tomograms using Noise2Map, which is distributed with Warp, before you inspect the picks. In cube, when you load the star file that is the output of Warps template matching, make sure to specify the dimensions of your input volume as 1x1x1 px for correct display. Let me know if you have further questions!

Best, Matthias 

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[Marius Knauf]

Hi Matthias & Pranav, 

my thesis revolves around spefic pipeline development of Etomo (Imod) , Warp and M - Do any of you know which feature i have to use in Etomo to eliminate the RlnCoordinate error that i get in Warp?

If any of you know and potentially would be interested in a meeting, please dont hesitate to contact me 

Best,
Marius

[Alister Burt]

Hi Marius,

It looks like you’re missing a few key concepts - rather than steaming ahead with your own data just now you would probably learn most quickly by working through an existing tutorial to gain experience.

You can then start to work through your own data processing more efficiently, applying different approaches where necessary

*self promotion follows*

Lorenzo and I put together this tutorial which can take you from raw data to a high resolution reconstruction, working between warp, dynamo, RELION (3.0/3.1) - it was explicitly written with the intention of exposing new users to a variety of tools which may be useful in their own projects beyond the tutorial, spanning multiple software packages :)

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

*end*

Within individual software packages dynamo, warp/M, emclarity, relion4 and eman offer nice tutorials covering their own functionality.

Good luck, the learning curve for cryo-ET and subsequent averaging is very steep and things aren’t as easy as they could be for people new to the field. Keep asking questions!

Cheers,

Alister

On 3 Dec 2021, at 16:03, Marius Knauf <knauf...@gmail.com> wrote:

Hi Matthias & Pranav, 

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/f1058bd1-27eb-40d3-ad9e-dc41b1f9c4e8n%40googlegroups.com.