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4.0 years ago
846980754
•
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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
Can you provide your example input, as well as what version of python and biopython you are using?
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.