Interactive Shifting of particle alignment center in 2D

Features and Functionality
1

Hi CryoSPARC Team,

This may just be more brainstorming than feasible but who knows. More often with proteins I am working with due to odd shape or being localized on a nanodisc/tube or liposome, centering the pick is an issue. While Topaz and cryolo do a good job, it is really challenging. What happen usually is the membrane bound or odd shaped molecule defines a center based on some high detail/bright spot. If I increase box size to be big enough and some other strategies, I can eventually center it and train better models.

Would it be possible to have an interactive 2D classification job in which the circular mask can be shifted across the 2D square. The output of that jobs would be particle stack with coordinates shifted to reflect the back calculated new pick center.

Thanks,
Bassem

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Hi @Bassem,

We have made note of your feature request.

Additionally, would you be able to share here or via DM details about the specific case that you are struggling with?

Thanks,
Kye

3

I would also be very interested in such a feature. Often I need to recenter particles in 2D (in the absence of a 3D volume) and the automated recentering is failing for some of my cases. What I typically end up doing is migrating to relion where an arbitrary extraction center can be manually defined in the extraction job. The interactive feature suggested above would be really cool, but the possibility to define a new shifted extraction center would already be much appreciated.

Looking forward to this,

Mike

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4

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