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 <[email protected]> > To: [email protected] > 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
