Buz Barstow <[email protected]> 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
[email protected]
Manager, Sequence Analysis Facility, Biology Division, Caltech
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