Hi Jane, Qingping Xu wrote a python script that will extract the sequence from the PDB file and align it with a fasta file. The script depends on biopython and clustalw. Regards, Mitch -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miller, Mitchell D. Sent: Tuesday, October 03, 2006 1:57 PM To: Bottomley, Matthew; [EMAIL PROTECTED] Subject: RE: [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 *** 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 ________________________________ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jane Bailey Sent: Wednesday, October 01, 2008 1:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] to extract protein sequence from a rebuilt pdb file Hi, all I am currently rebuilting my structure in coot, and the protein sequence is around 98% rebuilt yet. I am looking for a way to extract protein sequence from the rebuilt.pdb so that I could see clearly which part need to be rebuilt by sequence alignment. Any ideas about this? thanks Best Jane
