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Revision as of 13:24, 1 March 2013 by Tlinnet (talk | contribs) (Example 3 - multistate)
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Fetch retrieves a protein structure from the PDB and loads it into PyMOL. The PDB file is saved in the current working directory for PyMOL.

You can now fetch electron density maps using type=fofc or type=2fofc. The map will be loaded if the electron density map exists on the EDS server. You can also fetch the so-called biological assembly or biological unit files from PDB using type=pdb1, type=pdb2 and so on.


fetch PDB_ID [ ID2 ... IDN ] [,type=[fofc,2fofc,pdb1]] [,multiplex= [0,1]] [,async = [0,1]]

To specify more than one PDB, just add its ID to the command line (separated by spaces).

Proxy Setting

If your network requires a proxy server, you can specify it by 'http_proxy' and 'ftp_proxy' environmental variables.

At least in Mac OS X, these values are setup automatically. Otherwise, add

export http_proxy='http://proxy.server.name:port/'
export ftp_proxy='http://proxy.server.name:port/' # shouldn't start with ftp://...

to your start up shell script.


# fetch them singly
fetch 1kao
fetch 1ctq

# fetch them at once
fetch 1kao 1ctq

# fetch them at once, load them into PyMOL all at once (synchronously)
fetch 1kao 1ctq, async=0

# multiple commands in one line is accepted
fetch 1kao, async=0; as cartoon

# Example loading a protein and its electron density map
fetch 1cll
fetch 1cll, type=2fofc
# focus on residues 30-40
map_trim *, i. 30-40, 4
zoom i. 30-40

Example 2

# fetch PDB files and process each of them
# using async=0, PyMOL will wait for fetch to finish before executing the next command
fetch 1kao, async=0
remove not (alt ''+A)
alter all, alt=''
save 1koa_clean.pdb,1koa
delete 1koa
fetch 1ctq, async=0
remove not (alt ''+A)
alter all, alt=''
save 1ctq_clean.pdb,1ctq

Example 3 - pdb1

# fetch the biological assembly of 1avd
# the assembly is composed of asymmetric units (ASUs) stored in different MODELs
# split the biological assembly using split_state
fetch 1avd, type=pdb1
split_state 1avd

Example 4 - multistate

This will fetch the biological assembly (type=pdb1) from the pdb, split the 60 states into separate objects (multiplex=1), and tell PyMOL to wait for all this to be completed before moving to the next command in a .pml script (async=0).

# fetch the biological assembly of 2buk
fetch 2buk, type=pdb1, multiplex=1, async=0

See Also

Fetch_Path, Fetch_Host, FetchLocal