Can The Wget Command Be Used To Download Pdbs
2
2
Entering edit mode
12.5 years ago
Harpalss ▴ 310

I'm new to unix and I'm trying to use the wget command to download PDBs from the PDB database, can this be achieved?

I've tried the following:

wget http://www.pdb.org/pdb/download/downloadFile.dofileFormat=pdb&compression=NO&structureId=1PNK

but i get this in the console:

[mimas:/Users/ucbthsa/PDBs Similarity] ucbthsa% wget http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb & compression=NO & structureId=1PNK [3] 74828 [4] 74829 structureId=1PNK: Command not found. compression=NO: Command not found. [4] Exit 1
compression=NO [2] + Exit 1
compression=NO [1] - Exit 1
wget http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb wget: No match.

pdb • 9.5k views
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6
Entering edit mode
12.5 years ago

Make sure to enclose your URL with quotes otherwise the & character will be interpreted as a special character that makes the command before it run in the background:

This will work:

$ wget 'http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=cif&compression=NO&structureId=1PNK' -O 1PNK
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5
Entering edit mode
12.5 years ago
Philippe ★ 1.9k

Hi,

looking a bit at the source code of the PDB website (the Jmol page for example) I could see the files are accessible through URLs such as: http://www.pdb.org/pdb/files/1PNK.pdb

If you juste change 1PNK by any other PDB ID it seems to work.

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