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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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Label by atom hides everything but the label #53

Closed digitalbio closed 3 years ago

digitalbio commented 3 years ago

I wanted to label each atom in a nucleotide so that students could identify them.

Here's what I did:

  1. Selected a single nucleotide in 7ODF.
  2. Choose View Selection to hide everything else.
  3. Chose Nucleotide > Ball and Stick.
  4. Chose Color > Atom.
  5. Opened the Analysis menu and chose Label per Atom.

The nucleotide disappeared and I got large square labels that aren't attached to any atoms. I put the image below. This is not very useful. I should be able to see both the labels and the atoms. The labels should be on top of the atoms and should be smaller than the atoms.

Screen Shot 2021-10-18 at 3 34 17 PM

Here's what I would like to see (I didn't add the position numbers, just the letters).

labeled_atoms

digitalbio commented 3 years ago

I did find a way to make labels smaller but I could only make one label the size the that I wanted (P). All the rest of the labels were too large. I think the labels should all the same size and the background color for the labels should be white, not grey.

label scale
jiywang3 commented 3 years ago

I added a new label type "per Atom Element". You can try it out: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?MRAbCZNrv2jnUtPFA image

digitalbio commented 3 years ago

I like this! thanks!