Re: [PyMOL] Summary of Extracting Amino Acid Sequence from PDB File

[David M. <ma...@ca...>]

Buz Barstow <bu...@ma...> wrote:

> Thanks to everyone who replied to my query about extracting an amino  
> acid sequence from a PDB file!
> 
> Here is a summary of responses of my query;
> 
> 1. Use SwissPDBViewer
...
> 6. Use PDBSET (part of CCP4)

t_coffee comes with s perl script "unpack_extract_from_pdb".  For
instance, in the following it extracts all of the sequences from the
entire PDB dataset:

nice -15 find /u4/pdb -name '*.pdb' \
  -exec ./extract_from_pdb -chain ALL \
  -infile '{}' -mode fasta -seq_field ATOM \;  > all_pdb_seq.aa

Note, this takes a long time!  It would probably be significantly faster
if a persistent perl was used, instead of restarting the perl script
from scratch for each file.

Regards,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech