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I can't open a simple star #173

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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

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@kimdn
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kimdn commented Jun 28, 2024

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
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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
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