[Biopython-dev] [Bug 3096] PPBuilder build_peptides bugs

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jun 9 08:43:02 UTC 2010


------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-09 04:43 EST -------
(In reply to comment #0)
> Given a chain of backbone connected residues 'IXRGXTGL' that contains two
> non-standard amino acids 'X' in between, building peptide with only standard
> amino acid builder should return two peptides 'RG' and 'TGL'. 'I' should not
> be returned as a peptide since it is just one residue. Currently biopython
> would return 'IXGXGL', with two bugs in between:

What is wrong with returning 'IXGXGL'? The PDB contains a peptide of six
linked residues doesn't it? It looks like Bio.PDB is doing something sensible.

P.S. You didn't fill in which version of Biopython you are using.

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