Using RELION coordinates in SPRING segment

[Isabelle Gordon]

Hi Carsten, 

I am currently having some issues using the coordinates produced from ManualPick in RELION for segmentation in SPRING. I have managed to produce *.box coordinate files from the particles.star file using SPHIREs conversion function. However, the output particle stack for SPRINGs segment seems to not be applying the coordinates correctly. Although all the particles are in the correct, vertical orientation, the majority of the particles seem to not be centered appropriately. It seems the particles have been shifted so far to the left or right that they are almost entirely out of the window, with only approximately 1/4 of the particles width remaining in the extracted image.

Could this be due to EMAN2s function of using the bottom left corner of the box for its coordinates, rather than the center of the box used in RELION? If so, how could I go about fixing this issue? Would I have to manually make a change in the coding? Please let me know what suggestions you have for correcting this issue.

Thank you for your time and help! 

Best,

Isabelle Gordon

Washington University in St. Louis- School of Medicine

Neurology Department- Kotzbauer Lab

[Carsten Sachse]

Hi Isabelle,

We found an older python conversion script.

You can import the star coordinates by converting them to .box files with the attached script.

Modify the name of your input and output files at the end of the script.

% springenv python starcoord2box.py

Let us know if this works.

Best wishes,

Carsten