如何在 python 的 pdb 文件中重新编号残基（从 1 开始在链中继续）？
How to renumber residues (start from 1 in continuation among chains) in pdb file in python?
我想对具有多个链（A、H、L）的 pdb 文件进行连续重新编号。一些链的残基位置附有插入代码（例如 190A 等）。谁能帮我写这段代码？
Example of pdb file with insertion
我使用 Biopython 的尝试：
输入文件：testA.pdb：
ATOM 25 N ALA E 5 48.087 97.950 74.514 1.00 9.33 N
ATOM 26 CA ALA E 5 48.052 99.292 73.904 1.00 9.37 C
ATOM 27 C ALA E 5 47.483 100.285 74.935 1.00 9.65 C
ATOM 28 O ALA E 5 47.693 101.493 74.908 1.00 9.11 O
ATOM 29 CB ALA E 5 47.247 99.339 72.623 1.00 8.31 C
ATOM 30 N ILE E 6 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 6 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 6 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 6 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 6 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 6 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 6 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 6 42.926 100.408 74.814 1.00 11.29 C
ATOM 30 N ILE E 6A 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 6A 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 6A 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 6A 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 6A 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 6A 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 6A 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 6A 42.926 100.408 74.814 1.00 11.29 C
ATOM 38 N GLN E 7 47.184 100.177 79.159 1.00 10.08 N
ATOM 39 CA GLN E 7 47.750 99.648 80.383 1.00 10.85 C
ATOM 40 C GLN E 7 46.749 99.311 81.476 1.00 10.94 C
ATOM 41 O GLN E 7 45.812 100.068 81.762 1.00 10.33 O
ATOM 42 CB GLN E 7 48.855 100.550 80.962 1.00 11.19 C
ATOM 43 CG GLN E 7 50.227 100.292 80.353 1.00 11.71 C
ATOM 44 CD GLN E 7 50.656 101.322 79.346 1.00 12.04 C
ATOM 45 OE1 GLN E 7 50.015 101.625 78.348 1.00 11.94 O
ATOM 46 NE2 GLN E 7 51.811 101.943 79.591 1.00 12.40 N
ATOM 47 N PRO E 8 46.990 98.145 82.066 1.00 11.13 N
ATOM 48 CA PRO E 8 46.204 97.689 83.212 1.00 11.66 C
ATOM 49 C PRO E 8 46.688 98.594 84.352 1.00 11.77 C
ATOM 50 O PRO E 8 47.885 98.899 84.409 1.00 11.72 O
ATOM 51 CB PRO E 8 46.586 96.236 83.432 1.00 11.66 C
ATOM 52 CG PRO E 8 47.935 96.031 82.787 1.00 11.65 C
ATOM 53 CD PRO E 8 48.114 97.207 81.829 1.00 11.20 C
我的代码：
from Bio.PDB import PDBIO, PDBParser
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
# to work with some non orthodox pdbs
import warnings
warnings.filterwarnings('ignore')
io = PDBIO()
parser = PDBParser()
# my_pdb_structure = parser.get_structure('test', 'test.pdb')
my_pdb_structure = parser.get_structure('test', 'testA.pdb')
print(my_pdb_structure)
# renumber residue in my_pdb_structure
residue_N = 1
for model in my_pdb_structure:
for chain in model:
for residue in chain:
print(residue.id)
if 'A' in residue.id[2]:
residue.id = (residue.id[0], residue_N-1, residue.id[2])
print('----',residue.id)
else:
residue.id = (residue.id[0], residue_N, residue.id[2])
print('----',residue.id)
residue_N += 1
# this bit just print the renumbered my_pdb_structure
print('\n stucture with renumbered atoms : \n___________________________________')
for model in my_pdb_structure:
for chain in model:
for residue in chain:
print(residue, residue.id)
io.set_structure(my_pdb_structure)
# io.save('renumbered.pdb')
io.save('renumberedA.pdb', preserve_atom_numbering=True)
输出renumberedA.pdb:
ATOM 25 N ALA E 1 48.087 97.950 74.514 1.00 9.33 N
ATOM 26 CA ALA E 1 48.052 99.292 73.904 1.00 9.37 C
ATOM 27 C ALA E 1 47.483 100.285 74.935 1.00 9.65 C
ATOM 28 O ALA E 1 47.693 101.493 74.908 1.00 9.11 O
ATOM 29 CB ALA E 1 47.247 99.339 72.623 1.00 8.31 C
ATOM 30 N ILE E 2 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 2 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 2 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 2 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 2 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 2 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 2 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 2 42.926 100.408 74.814 1.00 11.29 C
ATOM 30 N ILE E 2A 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 2A 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 2A 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 2A 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 2A 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 2A 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 2A 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 2A 42.926 100.408 74.814 1.00 11.29 C
ATOM 38 N GLN E 3 47.184 100.177 79.159 1.00 10.08 N
ATOM 39 CA GLN E 3 47.750 99.648 80.383 1.00 10.85 C
ATOM 40 C GLN E 3 46.749 99.311 81.476 1.00 10.94 C
ATOM 41 O GLN E 3 45.812 100.068 81.762 1.00 10.33 O
ATOM 42 CB GLN E 3 48.855 100.550 80.962 1.00 11.19 C
ATOM 43 CG GLN E 3 50.227 100.292 80.353 1.00 11.71 C
ATOM 44 CD GLN E 3 50.656 101.322 79.346 1.00 12.04 C
ATOM 45 OE1 GLN E 3 50.015 101.625 78.348 1.00 11.94 O
ATOM 46 NE2 GLN E 3 51.811 101.943 79.591 1.00 12.40 N
ATOM 47 N PRO E 4 46.990 98.145 82.066 1.00 11.13 N
ATOM 48 CA PRO E 4 46.204 97.689 83.212 1.00 11.66 C
ATOM 49 C PRO E 4 46.688 98.594 84.352 1.00 11.77 C
ATOM 50 O PRO E 4 47.885 98.899 84.409 1.00 11.72 O
ATOM 51 CB PRO E 4 46.586 96.236 83.432 1.00 11.66 C
ATOM 52 CG PRO E 4 47.935 96.031 82.787 1.00 11.65 C
ATOM 53 CD PRO E 4 48.114 97.207 81.829 1.00 11.20 C
TER 53 PRO E 4
END
代码只是通过 PDBParser() 加载 pdb 文件并遍历 pdb 结构对象，从 1 开始更改残基的 id，并在每个循环中添加 +1，然后通过 PDBIO() 保存 renubered_structure （先设置结构再保存）
我不知道 Biopython 的 PDB 解析和 PDB 结构对象的内部结构，我的代码只适用于你的测试输入，即有 A 的残基总是在没有 A 的相同残基之后，你可以 运行 使用不同的输入 pdb 进行测试以检查出来
根据您的评论和我上面的输入，您可以获得以下输出：
ATOM 25 N ALA E 1 48.087 97.950 74.514 1.00 9.33 N
ATOM 26 CA ALA E 1 48.052 99.292 73.904 1.00 9.37 C
ATOM 27 C ALA E 1 47.483 100.285 74.935 1.00 9.65 C
ATOM 28 O ALA E 1 47.693 101.493 74.908 1.00 9.11 O
ATOM 29 CB ALA E 1 47.247 99.339 72.623 1.00 8.31 C
ATOM 30 N ILE E 2 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 2 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 2 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 2 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 2 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 2 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 2 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 2 42.926 100.408 74.814 1.00 11.29 C
ATOM 30 N ILE E 3 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 3 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 3 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 3 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 3 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 3 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 3 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 3 42.926 100.408 74.814 1.00 11.29 C
ATOM 38 N GLN E 4 47.184 100.177 79.159 1.00 10.08 N
ATOM 39 CA GLN E 4 47.750 99.648 80.383 1.00 10.85 C
ATOM 40 C GLN E 4 46.749 99.311 81.476 1.00 10.94 C
ATOM 41 O GLN E 4 45.812 100.068 81.762 1.00 10.33 O
ATOM 42 CB GLN E 4 48.855 100.550 80.962 1.00 11.19 C
ATOM 43 CG GLN E 4 50.227 100.292 80.353 1.00 11.71 C
ATOM 44 CD GLN E 4 50.656 101.322 79.346 1.00 12.04 C
ATOM 45 OE1 GLN E 4 50.015 101.625 78.348 1.00 11.94 O
ATOM 46 NE2 GLN E 4 51.811 101.943 79.591 1.00 12.40 N
ATOM 47 N PRO E 5 46.990 98.145 82.066 1.00 11.13 N
ATOM 48 CA PRO E 5 46.204 97.689 83.212 1.00 11.66 C
ATOM 49 C PRO E 5 46.688 98.594 84.352 1.00 11.77 C
ATOM 50 O PRO E 5 47.885 98.899 84.409 1.00 11.72 O
ATOM 51 CB PRO E 5 46.586 96.236 83.432 1.00 11.66 C
ATOM 52 CG PRO E 5 47.935 96.031 82.787 1.00 11.65 C
ATOM 53 CD PRO E 5 48.114 97.207 81.829 1.00 11.20 C
TER 53 PRO E 5
END
只是更改重新编号的代码块，下一个：
# renumber residue in my_pdb_structure
residue_N = 1
for model in my_pdb_structure:
for chain in model:
for residue in chain:
print(residue.id)
residue.id = (residue.id[0], residue_N, " ")
print('----',residue.id)
residue_N += 1
这将对所有从 1 开始计数的残基重新编号并删除 pdb 中的所有 As 或其他字母
我想对具有多个链（A、H、L）的 pdb 文件进行连续重新编号。一些链的残基位置附有插入代码（例如 190A 等）。谁能帮我写这段代码？
Example of pdb file with insertion
我使用 Biopython 的尝试：
输入文件：testA.pdb：
ATOM 25 N ALA E 5 48.087 97.950 74.514 1.00 9.33 N
ATOM 26 CA ALA E 5 48.052 99.292 73.904 1.00 9.37 C
ATOM 27 C ALA E 5 47.483 100.285 74.935 1.00 9.65 C
ATOM 28 O ALA E 5 47.693 101.493 74.908 1.00 9.11 O
ATOM 29 CB ALA E 5 47.247 99.339 72.623 1.00 8.31 C
ATOM 30 N ILE E 6 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 6 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 6 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 6 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 6 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 6 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 6 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 6 42.926 100.408 74.814 1.00 11.29 C
ATOM 30 N ILE E 6A 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 6A 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 6A 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 6A 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 6A 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 6A 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 6A 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 6A 42.926 100.408 74.814 1.00 11.29 C
ATOM 38 N GLN E 7 47.184 100.177 79.159 1.00 10.08 N
ATOM 39 CA GLN E 7 47.750 99.648 80.383 1.00 10.85 C
ATOM 40 C GLN E 7 46.749 99.311 81.476 1.00 10.94 C
ATOM 41 O GLN E 7 45.812 100.068 81.762 1.00 10.33 O
ATOM 42 CB GLN E 7 48.855 100.550 80.962 1.00 11.19 C
ATOM 43 CG GLN E 7 50.227 100.292 80.353 1.00 11.71 C
ATOM 44 CD GLN E 7 50.656 101.322 79.346 1.00 12.04 C
ATOM 45 OE1 GLN E 7 50.015 101.625 78.348 1.00 11.94 O
ATOM 46 NE2 GLN E 7 51.811 101.943 79.591 1.00 12.40 N
ATOM 47 N PRO E 8 46.990 98.145 82.066 1.00 11.13 N
ATOM 48 CA PRO E 8 46.204 97.689 83.212 1.00 11.66 C
ATOM 49 C PRO E 8 46.688 98.594 84.352 1.00 11.77 C
ATOM 50 O PRO E 8 47.885 98.899 84.409 1.00 11.72 O
ATOM 51 CB PRO E 8 46.586 96.236 83.432 1.00 11.66 C
ATOM 52 CG PRO E 8 47.935 96.031 82.787 1.00 11.65 C
ATOM 53 CD PRO E 8 48.114 97.207 81.829 1.00 11.20 C
我的代码：
from Bio.PDB import PDBIO, PDBParser
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
# to work with some non orthodox pdbs
import warnings
warnings.filterwarnings('ignore')
io = PDBIO()
parser = PDBParser()
# my_pdb_structure = parser.get_structure('test', 'test.pdb')
my_pdb_structure = parser.get_structure('test', 'testA.pdb')
print(my_pdb_structure)
# renumber residue in my_pdb_structure
residue_N = 1
for model in my_pdb_structure:
for chain in model:
for residue in chain:
print(residue.id)
if 'A' in residue.id[2]:
residue.id = (residue.id[0], residue_N-1, residue.id[2])
print('----',residue.id)
else:
residue.id = (residue.id[0], residue_N, residue.id[2])
print('----',residue.id)
residue_N += 1
# this bit just print the renumbered my_pdb_structure
print('\n stucture with renumbered atoms : \n___________________________________')
for model in my_pdb_structure:
for chain in model:
for residue in chain:
print(residue, residue.id)
io.set_structure(my_pdb_structure)
# io.save('renumbered.pdb')
io.save('renumberedA.pdb', preserve_atom_numbering=True)
输出renumberedA.pdb:
ATOM 25 N ALA E 1 48.087 97.950 74.514 1.00 9.33 N
ATOM 26 CA ALA E 1 48.052 99.292 73.904 1.00 9.37 C
ATOM 27 C ALA E 1 47.483 100.285 74.935 1.00 9.65 C
ATOM 28 O ALA E 1 47.693 101.493 74.908 1.00 9.11 O
ATOM 29 CB ALA E 1 47.247 99.339 72.623 1.00 8.31 C
ATOM 30 N ILE E 2 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 2 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 2 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 2 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 2 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 2 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 2 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 2 42.926 100.408 74.814 1.00 11.29 C
ATOM 30 N ILE E 2A 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 2A 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 2A 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 2A 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 2A 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 2A 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 2A 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 2A 42.926 100.408 74.814 1.00 11.29 C
ATOM 38 N GLN E 3 47.184 100.177 79.159 1.00 10.08 N
ATOM 39 CA GLN E 3 47.750 99.648 80.383 1.00 10.85 C
ATOM 40 C GLN E 3 46.749 99.311 81.476 1.00 10.94 C
ATOM 41 O GLN E 3 45.812 100.068 81.762 1.00 10.33 O
ATOM 42 CB GLN E 3 48.855 100.550 80.962 1.00 11.19 C
ATOM 43 CG GLN E 3 50.227 100.292 80.353 1.00 11.71 C
ATOM 44 CD GLN E 3 50.656 101.322 79.346 1.00 12.04 C
ATOM 45 OE1 GLN E 3 50.015 101.625 78.348 1.00 11.94 O
ATOM 46 NE2 GLN E 3 51.811 101.943 79.591 1.00 12.40 N
ATOM 47 N PRO E 4 46.990 98.145 82.066 1.00 11.13 N
ATOM 48 CA PRO E 4 46.204 97.689 83.212 1.00 11.66 C
ATOM 49 C PRO E 4 46.688 98.594 84.352 1.00 11.77 C
ATOM 50 O PRO E 4 47.885 98.899 84.409 1.00 11.72 O
ATOM 51 CB PRO E 4 46.586 96.236 83.432 1.00 11.66 C
ATOM 52 CG PRO E 4 47.935 96.031 82.787 1.00 11.65 C
ATOM 53 CD PRO E 4 48.114 97.207 81.829 1.00 11.20 C
TER 53 PRO E 4
END
代码只是通过 PDBParser() 加载 pdb 文件并遍历 pdb 结构对象，从 1 开始更改残基的 id，并在每个循环中添加 +1，然后通过 PDBIO() 保存 renubered_structure （先设置结构再保存）
我不知道 Biopython 的 PDB 解析和 PDB 结构对象的内部结构，我的代码只适用于你的测试输入，即有 A 的残基总是在没有 A 的相同残基之后，你可以 运行 使用不同的输入 pdb 进行测试以检查出来
根据您的评论和我上面的输入，您可以获得以下输出：
ATOM 25 N ALA E 1 48.087 97.950 74.514 1.00 9.33 N
ATOM 26 CA ALA E 1 48.052 99.292 73.904 1.00 9.37 C
ATOM 27 C ALA E 1 47.483 100.285 74.935 1.00 9.65 C
ATOM 28 O ALA E 1 47.693 101.493 74.908 1.00 9.11 O
ATOM 29 CB ALA E 1 47.247 99.339 72.623 1.00 8.31 C
ATOM 30 N ILE E 2 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 2 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 2 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 2 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 2 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 2 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 2 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 2 42.926 100.408 74.814 1.00 11.29 C
ATOM 30 N ILE E 3 46.802 99.657 75.862 1.00 9.99 N
ATOM 31 CA ILE E 3 46.118 100.279 77.004 1.00 10.34 C
ATOM 32 C ILE E 3 46.521 99.491 78.253 1.00 10.35 C
ATOM 33 O ILE E 3 46.292 98.274 78.348 1.00 9.61 O
ATOM 34 CB ILE E 3 44.613 100.230 76.772 1.00 11.05 C
ATOM 35 CG1 ILE E 3 44.269 100.841 75.413 1.00 11.39 C
ATOM 36 CG2 ILE E 3 43.845 100.913 77.879 1.00 11.06 C
ATOM 37 CD1 ILE E 3 42.926 100.408 74.814 1.00 11.29 C
ATOM 38 N GLN E 4 47.184 100.177 79.159 1.00 10.08 N
ATOM 39 CA GLN E 4 47.750 99.648 80.383 1.00 10.85 C
ATOM 40 C GLN E 4 46.749 99.311 81.476 1.00 10.94 C
ATOM 41 O GLN E 4 45.812 100.068 81.762 1.00 10.33 O
ATOM 42 CB GLN E 4 48.855 100.550 80.962 1.00 11.19 C
ATOM 43 CG GLN E 4 50.227 100.292 80.353 1.00 11.71 C
ATOM 44 CD GLN E 4 50.656 101.322 79.346 1.00 12.04 C
ATOM 45 OE1 GLN E 4 50.015 101.625 78.348 1.00 11.94 O
ATOM 46 NE2 GLN E 4 51.811 101.943 79.591 1.00 12.40 N
ATOM 47 N PRO E 5 46.990 98.145 82.066 1.00 11.13 N
ATOM 48 CA PRO E 5 46.204 97.689 83.212 1.00 11.66 C
ATOM 49 C PRO E 5 46.688 98.594 84.352 1.00 11.77 C
ATOM 50 O PRO E 5 47.885 98.899 84.409 1.00 11.72 O
ATOM 51 CB PRO E 5 46.586 96.236 83.432 1.00 11.66 C
ATOM 52 CG PRO E 5 47.935 96.031 82.787 1.00 11.65 C
ATOM 53 CD PRO E 5 48.114 97.207 81.829 1.00 11.20 C
TER 53 PRO E 5
END
只是更改重新编号的代码块，下一个：
# renumber residue in my_pdb_structure
residue_N = 1
for model in my_pdb_structure:
for chain in model:
for residue in chain:
print(residue.id)
residue.id = (residue.id[0], residue_N, " ")
print('----',residue.id)
residue_N += 1
这将对所有从 1 开始计数的残基重新编号并删除 pdb 中的所有 As 或其他字母