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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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secondary structures are not being expressed in web page #102

Closed danny2551515 closed 1 year ago

danny2551515 commented 2 years ago

Hello,

We are currently checking Alphafold prediction results by including iCn3D in our lab’s web server. When opening the pdb file created by Alphafold’s prediction in iCn3D, secondary structures such as α-helix are not being expressed. We would like to know why they are not being expressed and whether there is a way to solve the problem.

Thank you.

youkha commented 2 years ago

The secondary structure is annotated automatically. Please read the documentation example: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?6BioUubm5ccFRwP46

On Mon, Nov 28, 2022 at 6:30 AM 최원종 @.***> wrote:

Hello,

We are currently checking Alphafold prediction results by including iCn3D in our lab’s web server. When opening the pdb file created by Alphafold’s prediction in iCn3D, secondary structures such as α-helix are not being expressed. We would like to know why they are not being expressed and whether there is a way to solve the problem.

Thank you.

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jiywang3 commented 2 years ago

I understood the issue. When a PDB file is posted (instead of get) to NCBI servers, somehow jsonp didn't work. That's why iCn3D from your server can not get the secondary structure information. I will try to make jsonp work for the post method at NCBI. Meanwhile, you can use DSSP servers elsewhere to get the secondary structure information and add it to your PDB file.

danny2551515 commented 1 year ago

I'm always grateful for your help and advice

jiywang3 commented 1 year ago

I modified the backend service and it should work now. You can get the most recent copy from icn3d npm and try it again. Please let me know if you see any further problems.