Question: (Closed) How to use biopython for finding distance between N - CA (nitrogen - C alpha) bonds in proteins from PDB file?
0
gravatar for devanand.t.1986
4.5 years ago by
India
devanand.t.19860 wrote:

Hi all,

         I would like to plot a histogram 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 to nitrogen bonds. Can some one help me with biopython commands?

I have tried doing a code like below:

import sys
from Bio.PDB import *
sys.stdout = open('file_ubq', 'w')
parser=PDBParser()

structure = parser.get_structure('1UBQ','1UBQ.pdb')

for model in structure:
    for chain in model:
        for residue in chain:
            for atom in residue:
                print atom.get_vector(),atom.name

And I got the output in the file 'file_ubq' like below :

<Vector 27.34, 24.43, 2.61> N
<Vector 26.27, 25.41, 2.84> CA
<Vector 26.91, 26.64, 3.53> C
<Vector 27.89, 26.46, 4.26> O
<Vector 25.11, 24.88, 3.65> CB
<Vector 25.35, 24.86, 5.13> CG
<Vector 23.93, 23.96, 5.90> SD
<Vector 24.45, 23.98, 7.62> CE
<Vector 26.33, 27.77, 3.26> N
<Vector 26.85, 29.02, 3.90> CA
.
.
.
.
<Vector 27.84, 46.06, 17.59> O
<Vector 37.67, 43.42, 17.00> O

You might have noticed characters like N , CA etc. This is what I mentioned before. I wanted their data alone by stripping away anything else. My aim is to find the distance between these consecutive N and CA atoms and make a frequency distribution. Any help is appreciated.

 

 

ADD COMMENTlink modified 4.5 years ago by linus330 • written 4.5 years ago by devanand.t.19860

post was deleted. Re-opened + closed.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Pierre Lindenbaum119k
0
gravatar for linus
4.5 years ago by
linus330
Germany
linus330 wrote:

same question and solved here:

http://stackoverflow.com/questions/26193034/can-any-one-help-me-understand-and-solve-this-error

 

ADD COMMENTlink written 4.5 years ago by linus330
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