[3dem] Error with RELION, autopick for filaments

[Takanori Nakane]

Hi,

Are you using RELION 4.0 or 5.0 beta?

Helical picking by Topaz needs a special, forked and modified
version of Topaz. This is installed via conda in RELION 5.0.

In RELION 4.0, you have to install it manually from
https://urldefense.com/v3/__https://github.com/3dem/topaz__;!!Mih3wA!ExttUvFyxOvxUjSxlaYm7U3nkDEZ7KOs8atss6iNAZPCn3sTGRw6roLYGadfeYInpI5fnVHnS35w5C0TeykSU8NqyibhNNPBY0M$ , not from the original repository
at https://urldefense.com/v3/__https://github.com/tbepler/topaz__;!!Mih3wA!ExttUvFyxOvxUjSxlaYm7U3nkDEZ7KOs8atss6iNAZPCn3sTGRw6roLYGadfeYInpI5fnVHnS35w5C0TeykSU8NqyibhpLKuU1E$ .

Best regards,

Takanori Nakane

On 2024/05/28 17:11, Irene Del Mar Farinas Lucas wrote:
> Hello!
> 
> I'm kind of new to Relion, so I've been learning bit by bit, but now I'm 
> stuck. I've picked particles using the Helix feature until I got pretty 
> good classes. I used those to train a model in Topaz and then used that 
> model to do autopicking. However, when I try to extract those particles, 
> the job terminates with errors. First, I was getting the error: “ERROR: 
> helix.cpp::convertHelicalTubeCoordsToMetaDataTable(): Input coordinates 
> should be in pairs!”
> 
> I switched off the option for "Coordinates are start-end only?" and now 
> I'm getting the error: “ERROR: 
> helix.cpp::convertHelicalSegmentCoordsToMetaDataTable(): Prior 
> information of helical segments is missing in micrographs.” The problem 
> is probably due to the settings in Topaz and not the extraction, but I'm 
> not sure what the exact issue is.
> 
> Any help is welcomed!
> 
> Thanks,
> 
> Irene Farinas
> 
> 
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