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Fetching datasets from the Internet. Downloading Datasets. Let\'s Get Data. http://www.emboss.org. Downloading From The Web. $ man wget. Using wget to download PDB data-files. $ mkdir structures $ cd structures $ wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1m7t.ent.Z

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Presentation Transcript
let s get data
Let\'s Get Data

http://www.emboss.org

using wget to download pdb data files
Using wget to download PDB data-files

$ mkdir structures

$ cd structures

$ wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1m7t.ent.Z

$ wget ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb1lqt.ent.Z

$ gzip -d pdb1m7t.ent.Z pdb1lqt.ent.Z

slide5

Mirroring a dataset

$ wget --mirror ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb

slide7

Smarter mirroring

structures/ftp.rcsb.org/pub/pdb/data/structures/all/pdb

$ wget --output-file=log --mirror --http-user=anonymous

[email protected]

--directory-prefix=structures/mmCIF

--no-host-directories

--cut-dirs=6 ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb

slide8

Downloading a subset of a dataset

$ wget ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/all/1ger.cif.Z

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