Hello guys,
I'm using the ligand docking protocol, and when I put the command below it does not generate the expected output file "2ou0_threaded.pdb"
command:
/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py --template=2anv_A --target=2ou0_ --chain=A --align_format=clustal alignment.aln 2anv_A.pdb 2ou0_threaded.pdbD
Error:
Traceback (most recent call last):
File "/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py", line 63, in <module>
template_gaps = alignment.find_gaps(alignment_data,options.template)
File "/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/rosettautil/protein/alignment.py", line 18, in find_gaps
if sequence == None:
File "/home/carlos/.local/lib/python2.7/site-packages/Bio/SeqRecord.py", line 737, in __eq__
raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
NotImplementedError: SeqRecord comparison is deliberately not implemented. Explicitly compare the attributes of interest.
Please, help me?
I think you can try editing /home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/rosettautil/protein/alignment.py, at line 18 where it has
if sequence == None:
change that to
if sequence is None:
That will fix the proximal error, though I'm not sure if other errors might pop up. There are reports that recent updates to Biopython have changed how certain tools behave, which causes many of the scripts in Rosetta which use it to break. You may or may not run into that issue.
I did not find the part "if sequence == None:"
But I found at least 3 regions with "find_gaps"
I still do not know what to do.
My script printscreen
https://uploaddeimagens.com.br/imagens/captura_de_tela_de_2018-03-09_16-28-58-png
The "if sequence == None:" is not in the thread_pdb_from_alignment.py script itself, it's in a script that the thread_pdb_from_alignment.py script is calling. (alignment.py in tools/protein_tools/rosettautil/protein/)
Thank you rmoretti
It worked after the modification.
Sorted out.