[Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method

Jian Huang hjian at kuicr.kyoto-u.ac.jp
Wed Jan 24 19:31:20 EST 2007


Dear all,

When two or more continuous residues have insertion codes and they are with the same residue name, get_residues() method of Bio::Structure::Entry can only get the first residue. Other residue(s) will be omitted. For example, in PDB structure 1tal, SER-120H will be omitted, although the previous SER-120G will be returned properly. I have reported this bug. See http://bugzilla.open-bio.org/show_bug.cgi?id=2192

It seems that this bug is then actually due to add_residue() method and then and then...Is there any solution to this problem?

Jian Huang
hjian at kuicr.kyoto-u.ac.jp
 
Bioinformatics Center,
Kyoto University
Gokasho, Uji, Kyoto 611-0011, JAPAN 
Phone: +81-774-38-3296, Fax: +81-774-38-3269


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