2D Class Average Particles

[Colin Deniston]

Hello again. I know you've answered questions like this before but they usually involved the person doing further processing in SPRING. I wanted to ask if there is a away to find out which particles belong to a certain 2D class average so that I can process those particles either in another software or in another round of 2D class averaging in SPRING. I'm use to doing things like this in Relion for example and I'm wondering how to go about it in SPRING. Thanks.

[Carsten Sachse]

Dear Colin,

Yes, there are several ways of making use of this feature in Spring. First of all the member segments of the classes can be found in a table at the end of the report.log file. Second, all class assignments are being recorded in the spring.db saved to the running directory. The spring.db is a binary file but can be read in text format by:

% sqlite3 spring.db .dump | more

There are currently no conversion tools to RELION or other programs but I am sure one can reformat text files if needed.

For all subsequent runs within Spring that should make use of this class information, you need to pick up that spring.db as a database input file. For example, if you want to make use of this selection in SEGMENTREFINE3D you can just include or exclude relevant classes in your refinement. I believe further subclassification using SEGMENTCLASS is currently not implemented. In the current implementation, Spring always keeps segments together as much as possible as otherwise the algorithm cannot assess any of the helical properties anymore that arise from simple continuity. This puts a practical limit on being too selective. 

Best wishes,

Carsten

[Colin Deniston]

Thanks for the info!