Load pdb files from the NCBI

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Sandra Porter
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I'm uploading a pdb formatted file downloaded from the NCBI.

It would only be necessary to use this if mmdb files aren't an option.

Sandra Porter
User offline. Last seen 12 years 17 weeks ago. Offline
Joined: 11/24/2008
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Okay, I tried to upload the file but I got a message saying that the .pdb extension isn't allowed.

So, here is a link to the file: 1NAJ

When you get to the page, click "Structure view in Rasmol" to download a pdb formatted file or Structure view in Cn3D to download an mmdb formatted file.

Thanks!

Brad Larson
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Joined: 05/14/2008
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I downloaded the file manually, placed it on my server, and was able to download it via the following link: molecules://www.sunsetlakesoftware.com/sites/default/files/mmdb.pdb, so it's not a problem with the PDB file itself (although I do see that I'm not creating the bonds correctly, so I might need to fix that).

However, when I go to the NCBI link in the built-in browser, it starts the download and displays a blank molecule. Examining the file it downloads, it appears that the NCBI uses a redirect for the download link and Molecules is not following that redirect to get to the actual file. I'll see if I can fix that.

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