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ncbi / icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode
https://www.ncbi.nlm.nih.gov/Structure/icn3d
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Style changes aren't applied to selection #71

Open digitalbio opened 2 years ago

digitalbio commented 2 years ago

Structure 7BZ5

  1. I used Select by Distance to identify amino acids that are in the epitope. I chose the H and L chains in the first set and the spike protein in the second set.
  2. Opened Select > Save selection and named the selected residues "epitope"
  3. Opened Analysis > Interactions
  4. Deselected all interactions except for Hydrogen bonds, Salt bridges, and pi stacking.
  5. Chose 3D Display Interactions.
  6. Chose 2D Interaction map.
  7. Clicked the data point for the salt bridge (K471 and E98).
  8. Open View > View Selection.
  9. Opened Style > Protein > Ball and Stick.

Expectation: I expected that the amino acids would be shown with a Ball and Stick drawing style.

Result: The amino acids are shown with a drawing style that is not Ball and Stick. As a general rule, I think, whenever something has been selected, the change in style or color should be applied to the selected item.

Screen Shot 2021-11-24 at 9 21 14 AM
jiywang3 commented 2 years ago

When the interactions are shown, the style is always "Stick". You can click "Reset" in the "Interaction" popup to clear the dashed lines and change style as you want.

digitalbio commented 2 years ago

I want to keep the dashed line. That part is fine.

I think in general, if I have selected two amino acids and they are highlighted, then I should be able to apply changes in drawing style and coloring style to the selection.

I was able to change the coloring style. But when I tried to change the drawing style, I got the wrong style. I didn't get the style that I chose from the menu.

Also - I think this drawing style might be tubes. It's not "Stick."

jiywang3 commented 2 years ago

We used fixed style when showing interactions because we want to show the interacting atoms. Some styles don't have the atoms shown and the interaction dashed lines will look mysterious.

digitalbio commented 2 years ago

I think I'm not communicating the problem clearly.

The initial view of the interacting atoms is fine. That is not the problem.

The problem is that I'm not able to change the drawing style to the style that I selected. I think I should be able to do that.

jiywang3 commented 2 years ago

Currently we can change the style wen the interactions are not shown, or stick with the "stick" style when the interactions are shown. We could improve this in the future.

digitalbio commented 2 years ago

Thanks, it would be nice to have the option to change the style of any item that has been selected and not exclude amino acids because they show an interaction.