Biopython to compute the distance between residues
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2.0 years ago
lisa • 0

Hello,

I am trying to use Biopython to find the distance between the alpha carbons for a pair of residues in a model:

from Bio.PDB.PDBParser import PDBParser
parser = PDBParser()
structure = parser.get_structure("4HHB", "4HHB.pdb")
# Create a list of all the residues
residues = []
for model in structure.get_list():
    for chain in model.get_list():
        for residue in chain.get_list():
            residues.append(residue)
# Calculate the distance between the alpha carbons for a pair of residues
firstResidue = residues[0]
secondResidue = residues[1]
diff = firstResidue["CA"].get_coord() - secondResidue["CA"].get_coord()
distance = numpy.sqrt(numpy.sum(diff * diff))

However, I get the error, KeyError: 'CA'. I'm new to Biopython and was hoping someone with more experience can help me understand how to correctly reference atoms in the residues.

Thank you.

Biopython • 3.0k views
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Hello lisa,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Also, post your complete code here with some background information about the input; best way is to host the file somewhere and provide a link for that here at biostars or provide first few/ relevant lines here.

Thank you!

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Hello, thank you for your response. I have updated my question to include the complete code.

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Can you please post the exact error? I can’t see anything obviously wrong with your approach so far.

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2.0 years ago
Joe 19k

I can’t see where the exact error is coming from, but from playing with it, it seems that firstResidue and secondResidue aren’t what they seem to be. I think it has something to do with your use of get_list(), which isn’t the ‘normal’ way of dealing with these objects in my experience.

This code works (I haven’t checked the maths though). I’m using a dummy structure (1A80). See a similar question/answer here: Creating a distance matrix from PDB file coordinates (Python)

import numpy
from Bio.PDB.PDBParser import PDBParser

parser = PDBParser()
structure = parser.get_structure("1A80", "1A80.pdb")

residues = [r for r in structure.get_residues()]        # You don’t need the extensive list traversal you were doing before because there are many get_*() methods
# Calculate the distance between the alpha carbons for a pair of residues
one  = residues[0]["CA"].get_coord()
two = residues[1]["CA"].get_coord()
print('{} - {} = {}'.format(one,two, numpy.linalg.norm(one-two)))

A linear algebra ‘normal’ should be equivalent to the Euclidean distance between the arrays, but check my maths by all means.

I get ~4A, which sounds sensible though:

[-3.606  8.443  4.224] - [-3.507  6.781  7.627] = 3.78846311569
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Hello, thank you for your help. The residues[0]["CA"].get_coord() works on its own. It seems the key error arises when I try to do this for all the residues. For example:

residues = [r for r in structure.get_residues()]
distances = numpy.empty(len(residues), len(residues))
for x in range(len(residues)):
    for y in range(len(residues)):
        one = residues[x]["CA].get_coord()
        two = residues[y]["CA"].get_coord()
        distances[x, y] =  numpy.linalg.norm(one-two)
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Fairly sure this is caused by non-amino acid elements in the list as they wont have alpha carbons.

Try the following:

import numpy
import itertools
from Bio.PDB.PDBParser import PDBParser

parser = PDBParser()
structure = parser.get_structure("1A80", "1A80.pdb")

residues = [r for r in structure.get_residues() if r.get_id()[0] == " "]
for each in itertools.combinations(residues, 2):
    one  = each[0]["CA"].get_coord()
    two = each[1]["CA"].get_coord()
    print('{} - {} = {}'.format(one,two, numpy.linalg.norm(one-two)))
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