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brisvag / blik

Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
https://brisvag.github.io/blik/
GNU General Public License v3.0
23 stars 8 forks source link

I can't open a simple star #173

Closed kimdn closed 2 months ago

kimdn commented 3 months ago

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 https://github.com/brisvag/blik/issues/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
brisvag commented 3 months ago

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 ^^'