[Biopython-dev] [Bug 2910] Bio.PDB build_peptides sometimes gives shorter peptide sequences than expected

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2910





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-09-23 10:47 EST -------
I've looked at PDB file 13GS in more detail, and this doesn't look like a bug
in Biopython, but rather just another odd PDB file.

Chains C and D are only three residue peptides, e.g.

ATOM   3301  N   GLU D   1      16.854  13.061  10.252  1.00 65.68           N  
ATOM   3302  CA  GLU D   1      17.100  13.860   9.018  1.00 66.23           C  
ATOM   3303  C   GLU D   1      17.937  15.095   9.363  1.00 65.02           C  
ATOM   3304  O   GLU D   1      18.510  15.724   8.439  1.00 56.86           O  
ATOM   3305  CB  GLU D   1      15.764  14.279   8.389  1.00 66.35           C  
ATOM   3306  CG  GLU D   1      15.913  14.994   7.062  1.00 67.41           C  
ATOM   3307  CD  GLU D   1      14.584  15.456   6.508  1.00 68.72           C  
ATOM   3308  OE1 GLU D   1      13.547  15.340   7.163  1.00 69.08           O  
ATOM   3309  OXT GLU D   1      17.998  15.420  10.569  1.00 66.12           O  
ATOM   3310  N   CYS D   2      14.618  15.966   5.283  1.00 69.97           N  
ATOM   3311  CA  CYS D   2      13.431  16.483   4.614  1.00 70.18           C  
ATOM   3312  C   CYS D   2      13.374  15.898   3.213  1.00 69.53           C  
ATOM   3313  O   CYS D   2      14.409  15.625   2.610  1.00 65.61           O  
ATOM   3314  CB  CYS D   2      13.502  18.008   4.507  1.00 73.18           C  
ATOM   3315  SG  CYS D   2      14.485  18.841   5.796  1.00 76.47           S  
ATOM   3316  N   GLY D   3      12.166  15.713   2.693  1.00 71.49           N  
ATOM   3317  CA  GLY D   3      12.023  15.155   1.360  1.00 75.33           C  
ATOM   3318  C   GLY D   3      11.489  13.733   1.399  1.00 78.72           C  
ATOM   3319  O   GLY D   3      10.840  13.313   0.413  1.00 79.95           O  
ATOM   3320  OXT GLY D   3      11.717  13.031   2.412  1.00 80.37           O  
TER    3321      GLY D   3

Look at the C-alpha distances, (17.100, 13.860, 9.018) to (13.431, 16.483,
4.614) to (12.023, 15.155, 1.360) giving distances of 6.3 and 3.8:

>>> from math import sqrt
>>> import numpy
>>> a = numpy.array((17.100, 13.860, 9.018))
>>> b = numpy.array((13.431, 16.483, 4.614))
>>> c = numpy.array((12.023, 15.155, 1.360))
>>> sqrt(sum((a-b)**2))
6.3037215991825049
>>> sqrt(sum((b-c)**2))
3.7861014249488876

Clearly the first two residues in this "peptide" are very far apart, regardless
of if you do a simple C-alpha distance (as here), or look at the backbone's N
to C bonds.

The "problem" for 13GS goes away if you relax the default distance threshold,
e.g. use PPBuilder(10.0) instead of PPBuilder().

However, whatever affects 1A2D seems to be a different issue...

Peter


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