[Bioperl-l] PDB file parser (Separates chain-sequence and chain-structure)

Animesh Sharma sharma.animesh at gmail.com
Tue Jul 18 07:58:41 UTC 2006


Hi Chris,
I have written a small script to separate the Chain in a PDB file. It stores
the sequence (fasta format) and structure (pdb format) in separate files
with middle name according to the Chain it contains. If the PDB file has
only one chain, it creates a file with default as middle name.
Eg,
             perl pdb_chain_extract.pl 1HCO.pdb
Will create 4 files with names:
1HCO.A.fas  ( Sequence of Chain A in fasta format)
1HCO.A.pdb ( Structure of Chain A in pdb format)
1HCO.B.fas  ( Sequence of Chain B in fasta format)
1HCO.B.pdb ( Sequence of Chain B in pdb format)
.I wrote it in the spirit of your example script given @
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/examples/structure/structure-io.pl?rev=1.2&content-type=text/vnd.viewcvs-markupCan
this be included in the example scripts too?
Thanks and regards,
Animesh




-- 
______________________"The Answer Lies in Genome"______________________
http://fuzzylife.org/animesh/
+919868580004
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pdb_chain_extract.pl
Type: application/octet-stream
Size: 2593 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20060718/9e98ece2/attachment-0004.obj>


More information about the Bioperl-l mailing list