Co-refining Different Species in M Together

[Dylan Noone]

Hey all,

I’m a relative newcomer to Warp Tools/M, so please correct me if I’ve misunderstood something conceptually.

My understanding is that different particle species can be refined together in M, allowing them to effectively benefit from shared improvements in alignment and data quality. In my case, I have a low-abundance species alongside a much more abundant species (ribosomes), so I thought this approach might be advantageous.

However, I’m not entirely sure how to implement this in practice. My assumption was that I would:

1. Create a single population that would be shared between both particle sets.
2. Create two separate sources and species, both referencing the same population.

Is it really as straightforward as this, or are there additional steps or considerations required to refine multiple species together in M?

Thank you in advance for any advice or clarification.

Dylan

[Mathew McLaren]

Hi Dylan,

You would probably want one population, one source and two species. Populations are basically projects, so for one organism (for example) you would likely group many datasets together. Sources are individual datasets that are grouped by population, so if you've collected two sets of particles from one dataset then you wouldn't need to specify this twice.

In theory you should see an improvement although from my experience if the resolution of the low-abundance species is poor (20A or worse), you may not see a resolution improvement by including it in M. However, the last time I did this I had much less experience with Warp/M so I may have been doing it all wrong! It would be interesting to hear how it goes, I think from what I've seen on here and in papers people like to use ribosomes in M first, then use the improved tomograms to pick and refine their low-abundance particles.

Cheers,

Mat

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[Dylan Noone]

Hey Mathew,

Thanks for the detailed response.

I found this thread describing using ribosomes as fiducials, I think I will press ahead with that:

https://groups.google.com/g/warp-em/c/0rdmC9CU1L4

Thanks!

Dylan

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