[go: nahoru, domu]
Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

I can't open a simple star #173

Closed
kimdn opened this issue Jun 28, 2024 · 1 comment
Closed

I can't open a simple star #173

kimdn opened this issue Jun 28, 2024 · 1 comment

Comments

@kimdn
Copy link
kimdn commented Jun 28, 2024 •
edited
Loading

I installed blik
by
pip install "blik[all]"
at local python3.10 conda environment in my linux.

I didn't see any error message in this installation as
Screenshot 2024-06-28 at 1 25 19 PM

However, I see an error message as
Screenshot 2024-06-28 at 1 24 08 PM

when I ran
napari -w blik -- /home/kimd999/brave/DN/model/segmentation/blik/input.star /home/kimd999/brave/DN/model/segmentation/blik/MED4_TS_14_srec10_rec_scores_threshold_-6.0.mrc

This message is similar to the one from
#142

My input.star is simple as


data_

loop_
_rlnIndex #1
_rlnMicrographName #2
_rlnPixelSize #3
_rlnDefocus #4
_rlnNumberSubtomo #5
_rlnSnrFalloff #6
_rlnDeconvStrength #7

1 	/home/kimd999/brave/DN/model/segmentation/blik/MED4_TS_14_srec10_rec_scores_threshold_-6.0.mrc 	10.400000 	0.000000 	300 	1.000000 	1.000000
@kimdn kimdn closed this as completed Jun 28, 2024
@kimdn kimdn reopened this Jun 28, 2024
@brisvag
Copy link
Owner
brisvag commented Jul 4, 2024

Hi @kimdn! Yeah, this error is not very informative, sorry. If I use cryohub directly, I get the following (more useful) error:

ParseError: coordinate information missing

Indeed, you have no coordinate columns in your star file... So particles cannot be read from it ^^'

@brisvag brisvag closed this as completed Jul 15, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@kimdn @brisvag