Difference between revisions of "Fetch"

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alter all, alt=''
 
alter all, alt=''
 
save 1ctq_clean.pdb,1ctq
 
save 1ctq_clean.pdb,1ctq
 +
</source>
  
 
= See Also =
 
= See Also =

Revision as of 17:30, 4 May 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

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

See Also

Fetch_Path, Fetch_Host