[Biopython-dev] [Bug 2290] Not reading 1YVE.pdb

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2290





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2007-05-10 10:06 EST -------
Which version of Biopython do you have?

The "no parent bug" was fixed as bug 1936, make sure you have Biopython 1.43 or
later.

Mine installation of Biopython works but spits out a LOT of
PDBConstructionException warnings about multiply defined water atoms (aka
"Residue HOH").

Looking at the raw PDB file, there is a problem with multiply defined waters. 
As you can see below, the identifier jumps from 799 back to 1 (i.e. there are
two waters with residue number 1).

...
HETATM16581  O   HOH   793      36.450  15.564  -9.023  1.00 39.79           O  
HETATM16582  O   HOH   794      33.448  13.711 -11.019  1.00 40.42           O  
HETATM16583  O   HOH   796      28.414  11.908 -16.047  1.00 48.15           O  
HETATM16584  O   HOH   797      29.445   8.114 -11.059  1.00 55.49           O  
HETATM16585  O   HOH   799      28.383   5.173  -8.998  1.00 33.85           O  
HETATM16586  O   HOH     1      26.615   4.599  -6.718  1.00 24.95           O  
HETATM16587  O   HOH     2      23.353   4.948  -7.137  1.00 34.47           O  
HETATM16588  O   HOH     3      17.401  11.710   0.938  1.00 35.16           O  
HETATM16589  O   HOH     4      21.326  11.092   8.215  1.00 22.51           O  
HETATM16590  O   HOH     5      13.703   2.159  11.421  1.00 24.87           O  
...

Are you happy for me to mark this as a duplicate of bug 1936


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