corelation between stack and particle

Hi Jay,

I'm sorry, but there is currently no way to do this from within the GUI.  However you can work this out yourself if you want.  In the refinement package the Ori. Pos. ID should refer to the original position in the imported refinement package.

You first need to know the IDs of the refinement packages you want.  If you type the following :-

sqlite3 name_of_database.db "select * from refinement_package_assets;"

it will list all refinement packages - you can find the refinement packages you want, and the first column is the id.

To return a list of all the original position asset ids for a given refinement_package_id use :-

sqlite3 name_of_database.db "select original_particle_position_asset_id from refinement_package_contained_particles_$wanted_id;"

e.g. to return all the positions for the refinement package with the id 1 :-

sqlite3 name_of_database.db "select original_particle_position_asset_id from refinement_package_contained_particles_1;"

If you had 2 refinement packages, created from the same initial refinement package and you want to see which particles are in both then the following command would return them :-

sqlite3 name_of_database.db "select refinement_package_contained_particles_$first_id.original_particle_position_asset_id from refinement_package_contained_particles_$first_id,refinement_package_contained_particles_$second_id where refinement_package_contained_particles_$first_id.original_particle_position_asset_id = refinement_package_contained_particles_$second_id.original_particle_position_asset_id;"

e.g. To return all particles in both the refinement package with an id of 7, and the refinement package with an id of 9 :-

sqlite3 name_of_database.db "select refinement_package_contained_particles_7.original_particle_position_asset_id from refinement_package_contained_particles_7,refinement_package_contained_particles_9 where refinement_package_contained_particles_7.original_particle_position_asset_id = refinement_package_contained_particles_9.original_particle_position_asset_id;"

Thanks!

Tim

How to import a stack file from RELION that can be used directly in a 2D classification in cisTEM?

The stack file has been created with "relion_stack_create" command from a star file in RELION.

Hi,

If you have a stack and a star file, you should be able to import it by going to Assets->Refinement Packages->Import.

Hope that is what you were after.

Thanks,

Tim

Hi Tim,

Thank you. I imported the stack and the star files as indicated.
I do not understand why in the Refinement package (Relion import) for the image ID I have -1 for the entire stack and the X&Y positions are 0.00?

Hi,

I have imported some RELION data using Assets->Refinement Packages->Import. The new Refinement package contains 104021 particles.
I follow this with a "2D classification". However in "Actions/2D Classify" the fields for the 2D class averages are EMPY.

I wonder what it is wrong? When I look at the newly created "Refinement package" at the "Image ID" I have -1 for all the 104,021 positions, and the XPos is 0.00A and YPos is 0.00A for all the 104,021 positions.

Thank you very much.

The fact that the Image ID is -1 and the positions are 0 is expected.  Those fields refer to the original image, and you are importing a stack, so there is no info about the original image.

If you click on display stack in the refinement package assets panel - does the stack look ok?

Are your defocus values as listed in the refinement package assets panel ok? Are they all the same?

Cheers,

Tim

Hi Tim,

The defocus values are not the same, they are OK. In the stack the protein in white. Do I have to change the density to negative values?

Thank you.

Actually for "Protein Density in Stack Is"   I had "White (RELION Default)"

I wonder whether I have to switch to " BLACK  (Frealign Default)"

Thank you.

Hi Tim,

Switching to "Back (Frealign default)" during the IMPORT process did not solve the problem.

Hi Tim,

Yes; that was the problem. Things work. Thank you.

Changing the particle diameter worked.