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Hi Matt, Qingping Xu wrote a python script that will compare a PDB file with a fasta file and corrects ala/gly to the correct amino acid on output. The script depends on biopython and clustalw. If you are interested I made a copy available, http://smb.slac.stanford.edu/~mmiller/seqcheck.py http://biopython.org/ http://www.ebi.ac.uk/clustalw/ Regards, Mitch -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bottomley, Matthew Sent: Tuesday, October 03, 2006 1:01 PM To: [EMAIL PROTECTED] Subject: [ccp4bb]: PDB to 1 letter code *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hello, could anyone tell me how to get the single-letter amino acid sequence out of a PDB file, e.g. in fasta format? I would like to do this so that I can compare it with the 'expected' sequence, since e.g. arp/warp sometimes puts an Ala when there is a Lys with poor side-chain density.... Thanks. Matt ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ------------------------------------------------------------------------------
