why i can not use dssp in python

[tomlongcool]

my os is windows, `from Bio.PDB import PDBParser from Bio.PDB.DSSP import DSSP import matplotlib.pyplot as plt

解析PDB文件

p = PDBParser() structure = p.get_structure("protein_name", "01.pdb")

使用DSSP分析二级结构

model = structure[0] dssp = DSSP(model, "01.pdb")

提取阿尔法螺旋和贝塔折叠的片段

helices = [res for res in dssp if res[2] == 'H'] # 阿尔法螺旋 sheets = [res for res in dssp if res[2] == 'E'] # 贝塔折叠

打印片段信息

print("Alpha helices:") for res in helices: print(f"Residue {res[0]}: {res[1]}")

print("\nBeta sheets:") for res in sheets: print(f"Residue {res[0]}: {res[1]}")

可视化

plt.figure(figsize=(10, 6)) plt.plot([res[1] for res in dssp], label='DSSP index') plt.scatter([res[0] for res in helices], [res[1] for res in helices], color='r', label='Alpha helices') plt.scatter([res[0] for res in sheets], [res[1] for res in sheets], color='b', label='Beta sheets') plt.xlabel('Residue number') plt.ylabel('DSSP index') plt.legend() plt.show() `

and some error : C:\Users\zhaol.conda\envs\tom\python.exe D:\CodePro\py\pdb\01.py Traceback (most recent call last): File "C:\Users\zhaol.conda\envs\tom\lib\site-packages\Bio\PDB\DSSP.py", line 386, in init [dssp, "--version"], universal_newlines=True File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 411, in check_output *kwargs).stdout File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 488, in run with Popen(popenargs, **kwargs) as process: File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 800, in init restore_signals, start_new_session) File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 1207, in _execute_child startupinfo) FileNotFoundError: [WinError 2] 系统找不到指定的文件。

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "D:\CodePro\py\pdb\01.py", line 11, in dssp = DSSP(model, "01.pdb") File "C:\Users\zhaol.conda\envs\tom\lib\site-packages\Bio\PDB\DSSP.py", line 400, in init [dssp, "--version"], universal_newlines=True File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 411, in check_output *kwargs).stdout File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 488, in run with Popen(popenargs, **kwargs) as process: File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 800, in init restore_signals, start_new_session) File "C:\Users\zhaol.conda\envs\tom\lib\subprocess.py", line 1207, in _execute_child startupinfo) FileNotFoundError: [WinError 2] 系统找不到指定的文件。

Process finished with exit code 1

[drlemmus]

The Python package is not ours but let's have a look anyway. The error message says file not found. Do you actually have the dssp executable installed? If so, is it in your Python environment?