Hi Rex,
I like this simple and quick server to extract pdb seq.
http://swift.cmbi.ru.nl/servers/html/soupir.html
Manish
--
Manish Chandra Pathak, Ph.D.
Department of Biochemistry
Emory University School of Medicine
1510 Clifton Road, NE, Room G235
Atlanta, GA 30322 USA
Tel: +1-404-727-2563 Fax: +1-404-727-2738
----- Original Message ----
> From: Miri Hirshberg <[log in to unmask]>
> To: [log in to unmask]
> Sent: Tue, April 6, 2010 3:24:57 AM
> Subject: Re: [ccp4bb] sequence from pdb
>
> several options with no need for extra software:
(1) goto
> http://www.ebi.ac.uk/pdbe/
left handside under "Get PDB by ID" enter a pdb
> idcode for example 1mh1
you
> get
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary
goto Structure
> primary and click Fasta
cut and paste the sequence
(2) pickup the
> file, it contains all fasta sequences
> href="ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/derived_data/pdb_seqres.txt"
> target=_blank>ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/derived_data/pdb_seqres.txt
(3)
> or pickup this file which is a better format of JUST proteins
> href="ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_aa.fasta"
> target=_blank>ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_aa.fasta
(all
> peptide sequences in released PDB)
Miri
PDBe EBI
On Sun, 4 Apr
> 2010, Rex Palmer wrote:
> Is there software that will extract a protein
> sequence in either 3 letter
> or single letter code from a given pdb
> file?
>
> Rex Palmer
> Birkbeck College
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