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NGL Viewer Displays Hydrogen Instead of Chlorine Atoms #229

Closed wverastegui closed 3 months ago

wverastegui commented 5 months ago

Describe the bug The NGL viewer plugin in Galaxy is visualizing hydrogen atoms instead of chlorine atoms.

Galaxy Version and/or server at which you observed the bug Galaxy Version: 23.1.5.dev0

To Reproduce Steps to reproduce the behavior:

  1. Load the molecule in pdb format from the attached zip file (mirex.zip).
  2. Go to the "Visualize" section and select the NGL viewer plugin.

Expected behavior The tool should display the chlorine atoms instead of hydrogen atoms (white) as shown in the screenshots.

Screenshots

  1. [Correct visualization with NGL viewer]ngl_viewer

  2. [Incorrect visualization with NGL tool]ngl_galaxyeu

Additional context

bgruening commented 5 months ago

@wverastegui can it be that the old version we are shipping is doing it wrong? Maybe an update to the new version can fix that?

hechth commented 4 months ago

It seems like the new version seems to handle this correctly, assumed that the web version has the latest version.

bgruening commented 4 months ago

@itisAliRH can you please look at this and update the plugin in Galaxy?

itisAliRH commented 4 months ago

@bgruening Sure, I'll take a look!

itisAliRH commented 4 months ago

There is an error in rendering options for this visualisation and default values are not loaded. I opened galaxyproject#18030 which is related.

bgruening commented 4 months ago

@itisAliRH something you can fix?

itisAliRH commented 4 months ago

@itisAliRH something you can fix?

Working on it...

hechth commented 4 months ago

@itisAliRH let me know if there is anything we can help with and ping me or @wverastegui !

itisAliRH commented 3 months ago

It's fixed on galaxyproject#18299. Feel free to reopen this issue if the problem is still there @hechth @wverastegui

hechth commented 3 months ago

Thanks Alireza :) @wverastegui can you check if this is correct on usegalaxy.org or eu? Not sure if EU is running version 24.1 already though.

wverastegui commented 3 months ago

Thanks Alireza !. @hechth, neither of them is running version 24.1. The problem still persists in version 24.0.3.

itisAliRH commented 3 months ago

@hechth You're welcome✌🏻 The 24.1 has not been released yet and will be available soon on EU.