Load pdb files from the NCBI
Mon, 11/24/2008 - 22:20
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.
Tue, 11/25/2008 - 13:23
#2
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.
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!