[Biopython] Key Error

[Mark Livingstone]

Hi Guys,

I am about 3 days into learning BioPython using the current EPD 32 bit
Mac OS X academic distribution . When I run the included code, it
works fine if I do

num_atoms_to_do = 36

but if I try to do any more, I get a key error.

I am using the 1fat.pdb since that is what your tutes seem to use. The
only thing that I note is that when comparing residues in model A & C,
it is at residue 37 that the letters are no longer the same. However,
since I only look at Model A in the first part of the code, I can't
see that this should be a factor?

Program output:

<snipped>

>From residue 0
0.000000 3.795453 5.663135 9.420295 12.296334 15.957790 19.201048
22.622383 25.621159 27.803837 27.483303 28.365652 28.663099 27.070955
23.441793 24.625151 26.016047 29.257225 31.299105 34.907970 36.100464
32.837784 33.310841 32.332653 35.280716 36.668713 35.319839 31.738102
31.607626 30.115669 33.220890 32.487370 36.199894 39.507755 42.668190
46.333019
Traceback (most recent call last):
  File "./inter_atom_distance.py", line 47, in <module>
    residue2 = chain[y+1]
  File "/Library/Frameworks/Python.framework/Versions/7.2/lib/python2.7/site-packages/Bio/PDB/Chain.py",
line 67, in __getitem__
    return Entity.__getitem__(self, id)
  File "/Library/Frameworks/Python.framework/Versions/7.2/lib/python2.7/site-packages/Bio/PDB/Entity.py",
line 38, in __getitem__
    return self.child_dict[id]
KeyError: (' ', 37, ' ')

<code>


#! /usr/bin/env python

# Initial idea for this code from
http://stackoverflow.com/questions/6437391/how-to-get-distance-between-two-atoms-using-for-loop

print "\n\n\033[95mMark's PDB Geometry experimentation code\033[0m\n\n"
print "This code prints a set of c-alpha to c-alpha distances which
are colourised so that distances < 5.0 are green\n"
print "otherwise are colourised red. If you are using Microsoft
Windows, you may need to load an ansi.sys driver in your
config.sys\n\n"

print "Any errors below in yellow are due to the .pdb file not being
properly well formed.\n\n\033[93m"

from Bio.PDB.PDBParser import PDBParser
pdb_filename ='./1fat.pdb'
parser = PDBParser(PERMISSIVE=1)
structure = parser.get_structure("1fat", pdb_filename)
model = structure[0]
chain = model["A"]
residue1 = chain[1]
print "\033[0m"
print residue1.get_resname() # SER
residue2 = chain[2]
print residue2.get_resname() # ASN

atom1 = residue1['CA']
print atom1.get_name()
print atom1.get_coord()
atom2 = residue2['CA']
print atom2.get_name()
print atom2.get_coord()
distance = atom1-atom2 # minus is overloaded to do 3D vector math - how clever!!
print"%s to %s euclidean distance = %f Angstroms"  %
(residue1.get_resname(), residue2.get_resname(), distance)
print "%d models in pdb file named %s" % (len(model), pdb_filename) #
4 models in pdb
print "%d residues in model 1" % len(chain) # 239 residues
print "%s has %d atoms" % (residue1.get_resname(), len(residue1)) #
SER has 6 atoms

print "Length of Model 'A' is %d and Model 'C' is %d" %
(len(model['A']), len(model['C']))

print ("\n\033[93mDistances between C-alpha atoms of residues in model 1 \n")

num_atoms_to_do = 37

for x in range(num_atoms_to_do):
    print "\033[0mFrom residue %d" % x
    residue1 = chain[x+1]
    atom1 = residue1['CA']

    for y in range(num_atoms_to_do):
        residue2 = chain[y+1]
        atom2 = residue2['CA']
        distance = (atom1 - atom2)
        if distance < 5.0:
            print("\033[92m%f" % distance),
        else:
            print("\033[91m%f" % distance),
    print "\n"

print "\n\033[93mDistances between C-alpha atoms of residues in model
1 to model 3 \n"
print "NB: These have NOT been superimposed - thus the large distances
between matched atoms\033[0m\n"


num_atoms_to_do = 37

for x in range(num_atoms_to_do):
    print "\033[0mFrom residue %d" % x
    model = structure[0]
    chain = model["A"]
    residue1 = chain[x+1]
    atom1 = residue1['CA']

    for y in range(num_atoms_to_do):
        model = structure[0]
        chain = model["C"]
        residue2 = chain[y+1]
        atom2 = residue2['CA']

        distance = (atom1 - atom2)
        if distance < 5.0:
            print("\033[92m%f" % distance),
        else:
            print("\033[91m%f" % distance),
    print "\n"


print "\033[0m"

</code>

Thanks in advance,

MarkL