I would like to plot a distribution of alpha-cabon to nitrogen bond distances of ubiquitin protein. So I downloaded the 1UBQ.pdb from RCSB website. Now using biopython, I am trying to find the distances between all alpha-cabon(CA) to nitrogen(N) bonds.
I have tried doing a code like below:
import sys
#from Bio.PDB import *
from Bio.PDB.PDBParser import PDBParser
from numpy import loadtxt
pdb1 ='/home/devanandt/Documents/VMD/1UBQ.pdb'
sys.stdout = open('file_ubq', 'w')
parser=PDBParser(PERMISSIVE=1)
#file=open('1UBQ.pdb','r')
#header_dict=parse_pdb_header(file)
#file.close()
i=1
structure = parser.get_structure('1UBQ',pdb1)
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
model = structure[0]
chain = model['A']
residue_1 = chain[i]
atom_1 = residue_1['N']
atom_2 = residue_1['CA']
distance = atom_1-atom_2
#print atom.get_vector(),atom.name,distance
print distance
i=i+1
#lines = loadtxt("file_ubq")
And I got the output in the file 'file_ubq' like below:
1.47369
1.4966
1.47547
1.51187
1.44885
1.50423
1.47052
1.48006
1.50265
.
.
.
.
1.48417
1.47194
1.45661
1.47023
But alongside this, I got error too like as below:
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
EXECUTING:
/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py
----------------------------------------------
Traceback (most recent call last):
File "/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py", line 38, in <module>
residue_1 = chain[i]
File "/usr/lib/pymodules/python2.7/Bio/PDB/Chain.py", line 67, in __getitem__
return Entity.__getitem__(self, id)
File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
EXECUTING:
/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py
----------------------------------------------
Traceback (most recent call last):
File "/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py", line 38, in <module>
residue_1 = chain[i]
File "/usr/lib/pymodules/python2.7/Bio/PDB/Chain.py", line 67, in __getitem__
return Entity.__getitem__(self, id)
File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
^CEXECUTING:
/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py
----------------------------------------------
Traceback (most recent call last):
File "/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py", line 38, in <module>
residue_1 = chain[i]
File "/usr/lib/pymodules/python2.7/Bio/PDB/Chain.py", line 67, in __getitem__
return Entity.__getitem__(self, id)
File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
EXECUTING:
/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py
----------------------------------------------
Traceback (most recent call last):
File "/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py", line 38, in <module>
residue_1 = chain[i]
File "/usr/lib/pymodules/python2.7/Bio/PDB/Chain.py", line 67, in __getitem__
return Entity.__getitem__(self, id)
File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
EXECUTING:
/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py
----------------------------------------------
Traceback (most recent call last):
File "/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py", line 38, in <module>
residue_1 = chain[i]
File "/usr/lib/pymodules/python2.7/Bio/PDB/Chain.py", line 67, in __getitem__
return Entity.__getitem__(self, id)
File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
EXECUTING:
/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py
----------------------------------------------
Traceback (most recent call last):
File "/home/devanandt/Documents/PYTHON/ubq/src/ubq_dist_pdf.py", line 38, in <module>
residue_1 = chain[i]
File "/usr/lib/pymodules/python2.7/Bio/PDB/Chain.py", line 67, in __getitem__
return Entity.__getitem__(self, id)
File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
return self.child_dict[id]
KeyError: (' ', 77, ' ')
----------------------------------------------
Program exited successfully with errcode (1)
Press the Enter key to close this terminal ...
Can any one help me understand and solve this error?
OK, this code fixes the error:
import sys
#from Bio.PDB import *
from Bio.PDB.PDBParser import PDBParser
from numpy import loadtxt
pdb1 ='1UBQ.pdb'
sys.stdout = open('file_ubq', 'w')
parser=PDBParser(PERMISSIVE=1)
#file=open('1UBQ.pdb','r')
#header_dict=parse_pdb_header(file)
#file.close()
i=1
structure = parser.get_structure('1UBQ',pdb1)
for model in structure:
for chain in model:
for residue in chain:
i = 1
for atom in residue:
model = structure[0]
chain = model['A']
residue_1 = chain[i]
atom_1 = residue_1['N']
atom_2 = residue_1['CA']
distance = atom_1-atom_2
#print atom.get_vector(),atom.name,distance
print distance
i=i+1
#lines = loadtxt("file_ubq")
However, it seems to contain lots of duplicate results, and may not cover the full chain. This code should not contain duplicates:
import sys
from Bio.PDB.PDBParser import PDBParser
from numpy import loadtxt
pdb1 ='1UBQ.pdb'
sys.stdout = open('file_ubq', 'w')
parser=PDBParser(PERMISSIVE=1)
structure = parser.get_structure('1UBQ',pdb1)
for model in structure:
for chain in model:
for residue in chain:
try:
atom_1 = residue['N']
atom_2 = residue['CA']
distance = atom_1-atom_2
print distance
except:
pass
It also produces just 76 results, which is the length of the chain. Tell me if there is anything wrong, as I haven't used biopython before.