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Error: Dssp With Biopython

Hello I having some trouble when i use biopython to compute dssp

    p.get_structure("x",pdb_file)       #read pdb struture
    model = s[0]
    s_chain = model[chain_name]                   #choose chain
    res_list = PDB.Selection.unfold_entities(s_chain, 'R')  
    dssp = DSSP(model, pdb_file, dssp='mkdssp')

but there are some erro

enter code here
/home/sen/.local/lib/python3.5/site-packages/Bio/PDB/DSSP.py:251: UserWarning: DSSP could not be created due to an error:basic_string::substr: __pos (which is 60) > this->size() (which is 54)
warnings.warn(err)

Traceback (most recent call last):
 File "cal_pdb_feature_with_dssp.py", line 274, in <module>
 test_cal_dssp()
  File "cal_pdb_feature_with_dssp.py", line 271, in test_cal_dssp
  just_cal_dssp(pdb_store_path, feat_store_path, pdb_id)
  File "cal_pdb_feature_with_dssp.py", line 122, in just_cal_dssp
  dssp = DSSP(model, pdb_file, dssp='mkdssp')
  File "/home/sen/.local/lib/python3.5/site-packages/Bio/PDB/DSSP.py", line 430, in __init__
  dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
  File "/home/sen/.local/lib/python3.5/site-packages/Bio/PDB/DSSP.py", line 253, in dssp_dict_from_pdb_file
  raise Exception("DSSP failed to produce an output")
  Exception: DSSP failed to produce an output
software error
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written by 846980754 • 846980754

Can you provide your example input, as well as what version of python and biopython you are using?

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written by Joe Joe

Thanks a lot. The python version is 3.5.2. The version of dssp is 2.2.1 ,which installed by "apt-get install dssp". And the version of biopython is 1.76. I get dssp from 1abv_.pdb( ITASSER decoy set which most pdb structure have the similar condition), and also for T0418.pdb in CASP5-8.

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written by 846980754 • 846980754

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