<jupyter_start><jupyter_text>SummaryEvaluate structures produced by I-Tasser.**100k sequences generated with `test_14`:**- Best sequence identity: https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S394102/ (`S394102_results.tar.bz2`).- Best secondary structure identity: https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S394316/ (`S394316_results.tar.bz2 `).----  Imports<jupyter_code>%run _imports.ipynb
import nglview as nv<jupyter_output><empty_output><jupyter_text>Parameters<jupyter_code>NOTEBOOK_NAME = 'itasser'
NOTEBOOK_PATH = Path(NOTEBOOK_NAME)
NOTEBOOK_PATH.mkdir(exist_ok=True)
!ls {NOTEBOOK_NAME}
!ls {NOTEBOOK_NAME}/S394102_results<jupyter_output>1vkf.cif		  model1_1f5nA.pdb  model5.pdb
1vkf.pdb1		  model1_1jadA.pdb  prob.txt
BFP.png			  model1_2v0oA.pdb  RSQ_1.png
Bsites.clr		  model1_4dylA.pdb  RSQ_2.png
Bsites.inf		  model1_4gnkE.pdb  RSQ_3.png
CH_CF_2w6dA_BS09_CPL.pdb  model1_4ke2A.pdb  RSQ_4.png
CH_CF_2w6dA_BS12_CPL.pdb  model1_4mu6A.pdb  RSQ_5.png
CH_complex1.pdb		  model1_4tqlA.pdb  threading10.pdb
CH_complex2.pdb		  model1_4widA.pdb  threading1.pdb
CH_complex3.pdb		  model1_5c1fA.pdb  threading2.pdb
CH_complex4.pdb		  model1.gif	    threading3.pdb
CH_complex5.pdb		  model1.pdb	    threading4.pdb
CH_TM_1m56B_BS01_HEA.pdb  model2.gif	    threading5.pdb
CH_TM_1y66B_BS02_DIO.pdb  model2.pdb	    threading6.pdb
CH_TM_3eykB_BS01_EYK.pdb  model3.gif	    threading7.pdb
cscore.txt		  model3.pdb	    threading8.pdb
index.html		  model4.gif	    threading9.pdb
lscore.html		  model4.pdb
lscore.txt		  model5.gif<jupyter_text>View structures  Reference (`1vkf`)<jupyter_code>structure = kmbio.PDB.load(NOTEBOOK_PATH.joinpath('1vkf.cif'))
ref = kmbio.PDB.Structure('1vkf0A')
ref.add(kmbio.PDB.Model(0))
ref[0].add(structure[0]['A'])
ref_view = kmbio.PDB.show(ref)
ref_view
time.sleep(2)
nv.write_html(NOTEBOOK_PATH.joinpath('ref.html'), [ref_view])<jupyter_output><empty_output><jupyter_text>Best sequence (`S394102`)<jupyter_code>best_seq = kmbio.PDB.load(NOTEBOOK_PATH.joinpath('S394102_results').joinpath('model2.pdb'))
best_seq_view = kmbio.PDB.show(best_seq)
best_seq_view
nv.write_html(NOTEBOOK_PATH.joinpath('best_seq.html'), [best_seq_view])<jupyter_output><empty_output><jupyter_text>Best secondary structure (`S394316`)<jupyter_code>best_ss = kmbio.PDB.load(NOTEBOOK_PATH.joinpath('S394316_results').joinpath('model1.pdb'))
best_ss_view = kmbio.PDB.show(best_ss)
best_ss_view
nv.write_html(NOTEBOOK_PATH.joinpath('best_ss.html'), [best_ss_view])<jupyter_output><empty_output>
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{'chain_length': '5', 'dir': 'jupyter-structured-clean-dedup', 'id': '479702', 'license': 'MIT', 'n_tokens_mistral': 1265, 'n_tokens_neox': 1172, 'n_words': 119, 'path': 'notebooks/07-itasser.ipynb', 'repo_name': 'ostrokach/protein-adjacency-net', 'size': '2530'}