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NOMAD lets you manage and share your materials science data in a way that makes it truly useful to you, your group, and the community.
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Element detection in material visualization is wrong #85

Closed CalCraven closed 9 months ago

CalCraven commented 9 months ago

Was just browsing the recent additions for MD NPT simulation workflows. The doi for this work is https://doi.org/10.1101/2021.02.26.433010, with id of b9Ln-OKXsZQlUt5cdHN93dArYHB6.

The image below shows the representation of a sodium atom in solution with a PDZ3 protein. The atom is labeled as GROUP_NA, but look to potentially be a nitrogen atom, potentially being identified by just the N in NA. Image below to show structure, as well as the identification as a Nitrogen atom. Not sure if this is an issue that will crop up with future atoms, such as silicon and sulfur.

Screenshot 2023-09-26 at 10 15 06 AM
lauri-codes commented 9 months ago

Hi @CalCraven!

Thanks for the report. This indeed looks like a problem in parsing the chemical elements, I'm pretty sure it should be a Na atom, and we are for some reason only picking up the first letter of the element.

I will see to fix this and report back here.

lauri-codes commented 9 months ago

@ladinesa provided a fix for this. The fixed version will end up in our beta site within a few weeks and once we reprocess this entry the problem will go away.

Thanks again for the report!

CalCraven commented 9 months ago

Thank you @lauri-codes!