[Biopython] Bio.PDB.ResidueDepth help

[Daniel Chubb]

Hi, I'm trying to calculate residue depth using this module and I'd really
appreciate it if someone could help me make some sense out of the output.


Here is some code:

>>> from Bio.PDB import *
>>> parser=PDBParser()
>>> structure=parser.get_structure("scr",'/.../d1t3ta3.pdb')
>>> model=structure[0]
>>> rd=ResidueDepth(model, '/.../d1t3ta3.pdb')
>>> for i in rd:
...     print i

I then get this output:

...

 ...
(<Residue MET het=  resseq=1 icode= >, (941.50269996685836,
938.52026632473292))
(<Residue MET het=  resseq=2 icode= >, (943.30248293205898,
935.73449250166789))
(<Residue GLU het=  resseq=3 icode= >, (956.22610923774971,
929.58401500468858))
(<Residue ILE het=  resseq=4 icode= >, (946.39762766474189,
929.1969204628009))
(<Residue LEU het=  resseq=5 icode= >, (980.35736194344759,
952.50174666095472))
(<Residue ARG het=  resseq=6 icode= >, (943.33749438200709,
941.41471544399076))
(<Residue GLY het=  resseq=7 icode= >, (1005.0456481617543,
1021.4687548192563))
(<Residue SER het=  resseq=8 icode= >, (998.26228815878574,
1014.7065537464257))
(<Residue PRO het=  resseq=9 icode= >, (954.34720196525564,
933.69587405187428))
(<Residue ALA het=  resseq=10 icode= >, (865.68049599904009,
859.80537822913527))
(<Residue LEU het=  resseq=11 icode= >, (888.74360153732255,
871.36588689619543))
(<Residue SER het=  resseq=12 icode= >, (887.82610875300952,
870.97697239966283))
(<Residue ALA het=  resseq=13 icode= >, (882.65307575266002,
870.71143243803749))
(<Residue PHE het=  resseq=14 icode= >, (1038.6138896432872,
986.73921610486354))
(<Residue ARG het=  resseq=15 icode= >, (1036.0337702261368,
984.51578671438835))

....

As I understand it, the two values in the tuple (e.g. (941.50269996685836,
938.52026632473292)) for residue 1) are residue depth and Ca depth. But
those values don't seem to make sense to me. Are they not supposed to be in
Angstroms? They range in my output from about 865 to 1200, I would expect
some to be 0 (or around that).

Could anyone point out what has gone wrong/what I'm doing wrong?


Thanks a lot for the help

Daniel Chubb


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