任何人都可以幫助我理解並解決這個錯誤嗎？

Question

我想繪製一個分佈alpha-cabon到nitrogen鍵距離的泛素蛋白。所以我下載了1UBQ.pdb from RCSB website。現在使用biopython，我試圖找到所有alpha-cabon(CA)到nitrogen(N)債券之間的距離。

我試圖做類似下面代碼：

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") 

而且我得到的文件「file_ubq」輸出象下面這樣：

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 

但是旁邊這一點，我有錯誤太像如下：

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 ... 

任何人都可以幫助我理解和解決這個錯誤嗎？

Answer 1

OK，這個代碼修正錯誤：

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") 

但是，它似乎包含大量重複的結果，並且可能無法覆蓋整個鏈條。此代碼不應包含重複項：

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 

它也只產生76個結果，這是鏈的長度。告訴我是否有任何問題，因爲我之前沒有使用過biopython。

Answer 2

您的代碼有幾個問題。

1. 您正在使用文件句柄重載sys.stdout，以便您可以寫入文件。你可以簡單地做：

f_handle = open('random.pdb', 'w') 
print >>f_handle, "This will be written to the file, followed by a newline character" 

您對結構對象和相應的兒童（鏈，殘渣等）接入可以做的更好，讀了一下常見問題解答更好地瞭解圖書館。您可能達到了鏈的極限（76個殘基），並嘗試尋找第77個殘基，因爲您正在使用計數器來訪問殘基。 Biopython在結構，鏈接等對象中實現了迭代器，因此您可以只說'用於對象中的x'並覆蓋其子元素。要打印在每個N和Ca原子之間的距離連鎖你這樣做：

parser = PDBParser() 
structure = parser.get_structure('randomPDB', 'randomPDB.pdb') 
for model in structure: 
    for chain in model: 
     for residue in chain: 
      if residue.id[1] == ' ': # filters heteroatoms 
       resid = residue.id[0] 
       n_ca_dist = residue['N'] - residue['CA'] 
       print >>f_handle, "Distance N-Ca bond of residue {0}: {1}".format(resid, n_ca_dist)