Thanks Peter. The file is standard ATOM record straight from PDB. I will check on that.
Best regards, perdeep -----Original Message----- From: Peter Rice [mailto:[EMAIL PROTECTED] Sent: Tuesday, November 04, 2008 12:04 PM To: [EMAIL PROTECTED] Cc: Mehta, Perdeep Subject: Re: [EMBOSS] extracting sequence from a pdb file Mehta, Perdeep wrote: > Hi, > > Does anyone know if there is a program in EMBOSS that can extract protein > sequence from a pdb format file? It depends on the pdb file format. There is a "pdb" sequence format that reads from the ATOM records, but fails on some pdb entries. There is also a "pdbseq" sequence format (-sf pdbseq on the command line) that reads the SEQRES records. If you find a PDB file that fails to read, please let us know. I just tested on an old 2ins entry file and it found zero sequences and failed (it was designed for a cleaned up PDB format). regards, Peter Rice _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
