segmentexam on extracted particles from RELION

[jrj...@gmail.com]

Hi Carsten, 

I have extracted particles from micrographs using RELION, and would like to use segmentexam in order to determine the width profile of the helices. 

I have imported the particles using e2import.py, and they are in the hdf format. 

How do I use the RELION output partlicles.star, and the micrographs in segmentexam? 

Thanks,

-John J.

[Carsten Sachse]

Dear John,

Unfortunately, there is currently no simple way to convert the particles.star into the spring.db format, which is what is technically required. One would need to write a converter, which is possible if you know the structure of the star and db files.

Minimally, you will need to run the program SEGMENT to generate a Spring hdf stack and a spring.db with the help of the *.box coordinates. Afterwards you can run SEGMENTEXAM. The power of SEGMENTEXAM is using different selection criteria, which you can easily make use using the spring.db

I hope this information helps.

Best wishes,

Carsten

On Tuesday, 14 August 2018 14:28:18 UTC+2