Difference between revisions of "Fetch"

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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.
 
'''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 [http://eds.bmc.uu.se/eds/ EDS] server.
  
 
=== Syntax ===
 
=== Syntax ===
 
<source lang="python">
 
<source lang="python">
fetch PDB_ID [ ID2...IDN ] [, async = [0,1] ]
+
fetch PDB_ID [ ID2...IDN ] [, async = [0,1] , [ type=[fofc,2fofc] ]
 
</source>
 
</source>
  
To specify more than one PDB, just add its ID to the command line (without adding spaces).
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To specify more than one PDB, just add its ID to the command line (without adding spaces).
 +
 
  
 
=== Example ===
 
=== Example ===
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# fetch them at once, load them into PyMOL all at once (synchronously)
 
# fetch them at once, load them into PyMOL all at once (synchronously)
 
fetch 1kao 1ctq, async=0
 
fetch 1kao 1ctq, async=0
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 +
# Example loading a protein and its electron density map
 +
fetch 1cll
 +
fetch 1cll, type=2fofc
 +
# focus on residues 30-40
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map_trim *, i. 30-40, 4
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zoom i. 30-40
 
</source>
 
</source>
  

Revision as of 17:37, 24 March 2010

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.

Syntax

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

To specify more than one PDB, just add its ID to the command line (without adding spaces).


Example

# 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

# 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

See Also

Fetch_Path