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extpdb

A perl script for cutting up PDB files.

extpdb


A perl script for cutting up pdb files. This is one of my favorite utilities that I've written because of its simplicity and utility. If you cut up pdb files, this is the one for you. Also, I will build on this very simple selection syntax in future utilities that require residue selection.

You need perl installed, of course.

Home page: http://www.jamesstroud.com/software/extpdb/

 


 

Download latest version.

 


© 2006 James C. Stroud

Licensed under the GNU Public License.

 


Instructions

Usage: "extpdb [-hs] pdbfile.pdb < ranges.txt > new-pdbfile.pdb"

-h  flag gets this help message
-s  flag strips all but atoms

ranges.txt is a text file specifying ranges to be cut. EG:

a 200 300
b 330 335
b 201 205

where "a", "b" is the chain, and "200 300" is the range in the chain
Use the exact spacing of the example above in ranges.txt

Hint: Use just chain, like this

a

to extract a whole chain (here, chain a)
if you don't remember the exact residues

a 4

gets just residue 4 from chain a, and

a 4 -

gets residues 4 through the end from chain a

You can also use the "*" wildcard for chains:

* 200 300

gets residues 200 through 300 from all chains.

Use the "~" character for chains without an chainID:

~ 330 335

gets residues 330 through 335 from a chain with no ID.