I am still working on the Cao protocol. And I ran into another problem. When I ran step 15: Motif extraction. I ran the following command:
/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py -in:file:silent /home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/fd_output_splits/xaa.silent -ref_pdb /home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb -out_prefix mot_
It reported this error:
core.conformation.Conformation: Found disulfide between residues 117 145
length of the binder 65
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/gaon/miniconda3/lib/python3.11/site-packages/pyrosetta/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/gaon/miniconda3/lib/python3.11/site-packages/pyrosetta/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.169196 seconds to load from binary
total score of the complex: -442.187
Traceback (most recent call last):
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 302, in <module>
graph = get_my_interface_graph(pose)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 94, in get_my_interface_graph
edge = it.__mul__()
^^^^^^^^^^
AttributeError: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'. Did you mean: '__module__'?
Could anyone please help me solve this problem?
Having a `it.__mul__()` method was a bug that has since been fixed.
Edit the script to use `
it.dereference()` instead.
Hi!I edit the script to use “it.dereference()” instead, but another problem was reported.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/gaon/miniconda3/lib/python3.11/site-packages/pyrosetta/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/gaon/miniconda3/lib/python3.11/site-packages/pyrosetta/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.17178 seconds to load from binary
total score of the complex: -442.187
Traceback (most recent call last):
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 302, in <module>
graph = get_my_interface_graph(pose)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 95, in get_my_interface_graph
it.plus_plus()
^^^^^^^^^^^^
AttributeError: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute 'plus_plus'
Could you please help me with that? Thank you!
And are there any other words needed to be fixed in this module?
Thank you for your help!
I believe you should replace `it.plus_plus()` with `it.pre_increment()`
I think that should be all you need to do, but I can't say for certain.
It worked now!Thank you for your answer!