[ccp4bb] Summary of Extracting Amino Acid Sequence from PDB File

[Buz Barstow]

Dear All,

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

2. Use Pymol 1.2

load $TUT/1hpv.pdb

save 1hpv.fasta

# or by selection

save 1hpv_A.fasta, chain A


3. With Phenix, you can use the "phenix.print_sequence" tool to output  
the sequence in FASTA format.

4. If the PDB file is in the PDB, you can download the primary  
sequence from here.

5. Use MOLEMAN2

6. Use PDBSET (part of CCP4)

All the best,

---Buz