id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15901 Crash on Mac waking from sleep bburendei@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.6.7-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. My mac went to sleep and ChimeraX had crashed when I came back Fatal Python error: Segmentation fault Thread 0x000000031f5fa000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031e5f7000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031d5f4000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031c5f1000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b5ee000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a5eb000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003195e8000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003185e5000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003175e2000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003165df000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003155dc000 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000202b3e280 (most recent call first): File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, 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nice cartoon suppressBackboneDisplay false; cartoon style width 1; > size stickRadius 0.12 > lighting soft > nice Changed 0 bond radii > alias voltr5 vol transparency 0.5 > alias voltroff vol transparency 0 > alias cylinders cartoon style protein modeh tube rad 2 sides 24 > alias cartoonDefaults cartoon style protein modeh default UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3418 messages similar to the above omitted Chain information for zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb #1 --- Chain | Description A B | No description available > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3270 messages similar to the above omitted Chain information for zfO1_NC2_10mM_bestModel_apo.pdb #2 --- Chain | Description A B | No description available > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/SWISSMODEL_results/mO1_dimer_on_zfO1_C2.2_apo_model_01.pdb"" mO1_dimer_on_zfO1_C2.2_apo_model_01.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) mO1_on_zfO1_C2.2_apo [more info...] Chain information for mO1_dimer_on_zfO1_C2.2_apo_model_01.pdb #3 --- Chain | Description A B | No description available > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF2_dockings/hOtop1_AF/hO1_aligned.pdb"" hO1_aligned.pdb title: Alphafold V2.0 prediction for proton channel OTOP1 (Q7RTM1) [more info...] Chain information for hO1_aligned.pdb #4 --- Chain | Description | UniProt A | proton channel OTOP1 | OTOP1_HUMAN 1-612 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF2_dockings/mOtop1_AF/mO1_aligned.pdb"" mO1_aligned.pdb title: Alphafold V2.0 prediction for proton channel OTOP1 (Q80VM9) [more info...] Chain information for mO1_aligned.pdb #5 --- Chain | Description | UniProt A | proton channel OTOP1 | OTOP1_MOUSE 1-600 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_4.cif"" Chain information for fold_mo1_monomer_model_4.cif #6 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_3.cif"" Chain information for fold_mo1_monomer_model_3.cif #7 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_2.cif"" Chain information for fold_mo1_monomer_model_2.cif #8 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_1.cif"" Chain information for fold_mo1_monomer_model_1.cif #9 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_0.cif"" Chain information for fold_mo1_monomer_model_0.cif #10 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_4.cif"" Chain information for fold_ho1_monomer_model_4.cif #11 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_3.cif"" Chain information for fold_ho1_monomer_model_3.cif #12 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_2.cif"" Chain information for fold_ho1_monomer_model_2.cif #13 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_1.cif"" Chain information for fold_ho1_monomer_model_1.cif #14 --- Chain | Description A | . > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_0.cif"" Chain information for fold_ho1_monomer_model_0.cif #15 --- Chain | Description A | . > hide models > show #!1 models > show #4 models > hide #!1 models > lighting soft > show > show #!1 models > mmaker #4,5 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with hO1_aligned.pdb, chain A (#4), sequence alignment score = 1156.9 RMSD between 181 pruned atom pairs is 1.108 angstroms; (across all 389 pairs: 5.671) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with mO1_aligned.pdb, chain A (#5), sequence alignment score = 1145.5 RMSD between 183 pruned atom pairs is 1.079 angstroms; (across all 389 pairs: 4.816) > hide #!1 models > show #!1 models > hide #4 models > show #4 models > hide #4 models > show #4 models > show #5 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #4 models > hide #5 models > show #10 models > mmaker #6-15to #1/A > matchmaker #6-15to #1/A Missing or invalid ""matchAtoms"" argument: only initial part ""#6-15"" of atom specifier valid > mmaker #6-15 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_mo1_monomer_model_4.cif, chain A (#6), sequence alignment score = 1148.5 RMSD between 270 pruned atom pairs is 1.222 angstroms; (across all 389 pairs: 4.343) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_mo1_monomer_model_3.cif, chain A (#7), sequence alignment score = 1146.1 RMSD between 230 pruned atom pairs is 1.153 angstroms; (across all 389 pairs: 4.456) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_mo1_monomer_model_2.cif, chain A (#8), sequence alignment score = 1142.5 RMSD between 283 pruned atom pairs is 1.240 angstroms; (across all 389 pairs: 4.179) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_mo1_monomer_model_1.cif, chain A (#9), sequence alignment score = 1142.5 RMSD between 241 pruned atom pairs is 1.153 angstroms; (across all 389 pairs: 4.308) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_mo1_monomer_model_0.cif, chain A (#10), sequence alignment score = 1135.3 RMSD between 223 pruned atom pairs is 1.079 angstroms; (across all 389 pairs: 4.409) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_ho1_monomer_model_4.cif, chain A (#11), sequence alignment score = 1165.7 RMSD between 310 pruned atom pairs is 1.150 angstroms; (across all 389 pairs: 4.983) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_ho1_monomer_model_3.cif, chain A (#12), sequence alignment score = 1169.3 RMSD between 304 pruned atom pairs is 1.185 angstroms; (across all 389 pairs: 5.005) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_ho1_monomer_model_2.cif, chain A (#13), sequence alignment score = 1165.1 RMSD between 240 pruned atom pairs is 1.204 angstroms; (across all 389 pairs: 5.086) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_ho1_monomer_model_1.cif, chain A (#14), sequence alignment score = 1168.7 RMSD between 232 pruned atom pairs is 1.180 angstroms; (across all 389 pairs: 5.162) Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1) with fold_ho1_monomer_model_0.cif, chain A (#15), sequence alignment score = 1168.7 RMSD between 211 pruned atom pairs is 1.217 angstroms; (across all 389 pairs: 5.209) > lighting simple > show #9 models > show #8 models > show #7 models > show #6 models > show #11 models > show #12 models > show #13 models > show #14 models > show #15 models > hide #!1 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #15 models > show #15 models > hide #15 models > show #15 models > hide #15 models > show #15 models > hide #11 models > hide #12 models > hide #13 models > hide #14 models > show #4 models > hide #15 models > show #15 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #4 models > hide #15 models > show #10 models > hide #!1 models > show #9 models > show #8 models > show #7 models > show #6 models > show #!1 models > hide #!1 models > hide #10 models > show #10 models > hide #10 models > show #10 models > hide #10 models > show #10 models > hide #10 models > show #10 models > hide #6 models > hide #7 models > hide #9 models > hide #8 models > show #5 models > hide #5 models > show #5 models > show #!1 models > hide #10 models > show #10 models > show #15 models > hide #15 models > show #15 models > hide #15 models > hide #5 models > hide #10 models > show #3 models > hide #3 models > show #!2 models > hide #!1 models > view 1/A:267 Expected an objects specifier or a view name or a keyword > view #1/A:267 > ui tool show ""Add Hydrogens"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > addh #!2 hbond false Summary of feedback from adding hydrogens to zfO1_NC2_10mM_bestModel_apo.pdb #2 --- notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo.pdb (#2) chain A; guessing termini instead No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo.pdb (#2) chain B; guessing termini instead Chain-initial residues that are actual N termini: zfO1_NC2_10mM_bestModel_apo.pdb #2/A TYR 47, zfO1_NC2_10mM_bestModel_apo.pdb #2/B TYR 47 Chain-initial residues that are not actual N termini: zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 124, zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 158, zfO1_NC2_10mM_bestModel_apo.pdb #2/A LYS 187, zfO1_NC2_10mM_bestModel_apo.pdb #2/A SER 252, zfO1_NC2_10mM_bestModel_apo.pdb #2/A LEU 305, zfO1_NC2_10mM_bestModel_apo.pdb #2/A MET 334, zfO1_NC2_10mM_bestModel_apo.pdb #2/A ASN 376, zfO1_NC2_10mM_bestModel_apo.pdb #2/A GLY 511, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ALA 124, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ALA 158, zfO1_NC2_10mM_bestModel_apo.pdb #2/B LYS 187, zfO1_NC2_10mM_bestModel_apo.pdb #2/B SER 252, zfO1_NC2_10mM_bestModel_apo.pdb #2/B LEU 305, zfO1_NC2_10mM_bestModel_apo.pdb #2/B MET 334, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ASN 376, zfO1_NC2_10mM_bestModel_apo.pdb #2/B GLY 511 Chain-final residues that are actual C termini: zfO1_NC2_10mM_bestModel_apo.pdb #2/A LYS 585, zfO1_NC2_10mM_bestModel_apo.pdb #2/B LYS 585 Chain-final residues that are not actual C termini: zfO1_NC2_10mM_bestModel_apo.pdb #2/A ARG 110, zfO1_NC2_10mM_bestModel_apo.pdb #2/A HIS 153, zfO1_NC2_10mM_bestModel_apo.pdb #2/A ASP 184, zfO1_NC2_10mM_bestModel_apo.pdb #2/A THR 216, zfO1_NC2_10mM_bestModel_apo.pdb #2/A ARG 285, zfO1_NC2_10mM_bestModel_apo.pdb #2/A HIS 327, zfO1_NC2_10mM_bestModel_apo.pdb #2/A THR 373, zfO1_NC2_10mM_bestModel_apo.pdb #2/A ARG 443, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ARG 110, zfO1_NC2_10mM_bestModel_apo.pdb #2/B HIS 153, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ASP 184, zfO1_NC2_10mM_bestModel_apo.pdb #2/B THR 216, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ARG 285, zfO1_NC2_10mM_bestModel_apo.pdb #2/B HIS 327, zfO1_NC2_10mM_bestModel_apo.pdb #2/B THR 373, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ARG 443 Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 124 Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 158 Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A LYS 187 Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A SER 252 Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A LEU 305 11 messages similar to the above omitted 6828 hydrogens added > hide #!2 models > show #!2 models > ui tool show ""Add Charges"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Add Hydrogens"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16 --- Chain | Description A | No description available > hide #!2 models > show > ui tool show ""Add Hydrogens"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > addh #!16 Summary of feedback from adding hydrogens to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16 --- notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb (#16) chain A; guessing termini instead Chain-initial residues that are actual N termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A TYR 47 Chain-initial residues that are not actual N termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 124, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 158, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LYS 187, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A SER 252, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LEU 305, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A MET 334, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ASN 376, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A GLY 511 Chain-final residues that are actual C termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LYS 585 Chain-final residues that are not actual C termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ARG 110, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A HIS 153, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ASP 184, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A THR 216, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ARG 285, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A HIS 327, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A THR 373, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ARG 443 440 hydrogen bonds Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 124 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 158 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LYS 187 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A SER 252 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LEU 305 3 messages similar to the above omitted 3171 hydrogens added > pwd Current working directory is: /Users/bburendei/Desktop > cd ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking"" Current working directory is: /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking > save zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_addH.pdb models #16 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE_E267protTest.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE_E267protTest.pdb --- warnings | Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 3154 messages similar to the above omitted Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE_E267protTest.pdb #17 --- Chain | Description A | No description available > hide #!16 models > show > show #!16 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_REDUCE.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_REDUCE.pdb --- warnings | Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 3147 messages similar to the above omitted Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_REDUCE.pdb #18 --- Chain | Description A | No description available > hide #!17 models > hide #!16 models > hide #!18 models > show #!18 models > showq Unknown command: showq > show > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > addH Unknown command: addH > AddH Unknown command: AddH > hide #!18 models > show #!16 models > show #!17 models > hide #!16 models > hide #!17 models > show #!16 models > hide #!16 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19 --- Chain | Description A | No description available > show > addh #19 Summary of feedback from adding hydrogens to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19 --- notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb (#19) chain A; guessing termini instead Chain-initial residues that are actual N termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A TYR 47 Chain-initial residues that are not actual N termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 124, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 158, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LYS 187, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A SER 252, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LEU 305, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A MET 334, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ASN 376, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A GLY 511 Chain-final residues that are actual C termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LYS 585 Chain-final residues that are not actual C termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ARG 110, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A HIS 153, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ASP 184, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A THR 216, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ARG 285, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A HIS 327, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A THR 373, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ARG 443 440 hydrogen bonds Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 124 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 158 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LYS 187 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A SER 252 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LEU 305 3 messages similar to the above omitted 3171 hydrogens added > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20 --- Chain | Description A | No description available > hide #!19 models > hide #!20 models > show #!20 models > show > addh #20/A:267 Summary of feedback from adding hydrogens to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20 --- notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb (#20) chain A; guessing termini instead Chain-initial residues that are actual N termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A TYR 47 Chain-initial residues that are not actual N termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 124, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 158, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LYS 187, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A SER 252, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LEU 305, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A MET 334, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ASN 376, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A GLY 511 Chain-final residues that are actual C termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LYS 585 Chain-final residues that are not actual C termini: zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ARG 110, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A HIS 153, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ASP 184, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A THR 216, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ARG 285, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A HIS 327, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A THR 373, zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ARG 443 440 hydrogen bonds Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 124 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 158 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LYS 187 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A SER 252 Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LEU 305 3 messages similar to the above omitted 3171 hydrogens added > settatr Unknown command: settatr > setatr Unknown command: setatr > setattr Missing or invalid ""target"" argument: Expected a text string The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!20 models > show #!20 models > setattr #20/A:267 residue name GLU Assigning name attribute to 1 item > setattr #20/A:267 residue name GLH Assigning name attribute to 1 item > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb --- warnings | Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 Duplicate atom serial number found: 0 3154 messages similar to the above omitted Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb #21 --- Chain | Description A | No description available > hide #!20 models > hide #!21 models > show #!21 models > show > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb #22 --- Chain | Description A | No description available Opened zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt containing 1 structures (3755 atoms, 3831 bonds) > hide #!21 models > show > clip off > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE.pdbqt"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE.pdb #23 --- Chain | Description A | No description available Opened zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE.pdbqt containing 1 structures (3754 atoms, 3830 bonds) > hide #!22 models > show > hide #!23 models > show #!22 models > show #!23 models > hide #!23 models > hide #!22 models > show #!16 models > hide #!16 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean.pdb"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean.pdb #24 --- Chain | Description A | No description available > show > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/zfO1_NC2_10mM_F570outerSite_TRP126FLEX_reDocks/zfO1_F570_outer_site_bare_BOX.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/zfO1_NC2_10mM_F570outerSite_TRP126FLEX_reDocks/zfO1_F570_outer_site_bare_BOX.pdb --- warning | Ignored bad PDB record found on line 1 REMARK This is the box from the file : zfO1_F570_outer_site_bare.gpf > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/cryosparc_P120_J3424_008_volume_map_sharp.mrc"" Opened cryosparc_P120_J3424_008_volume_map_sharp.mrc as #26, grid size 200,200,200, pixel 1.07, shown at level 0.371, step 1, values float32 > volume #26 level 0.939 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/control_zfO1_C2.2_chA_reDocking/GLH267_only_vina/CB68710218_C2.36_to_zfO1_C2.2_GLH267_out.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/control_zfO1_C2.2_chA_reDocking/GLH267_only_vina/CB68710218_C2.36_to_zfO1_C2.2_GLH267_out.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.037 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -10.132 Ignored bad PDB record found on line 4 REMARK INTER: -10.011 Ignored bad PDB record found on line 5 REMARK INTRA: -0.121 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.303 166 messages similar to the above omitted Opened CB68710218_C2.36_to_zfO1_C2.2_GLH267_out.pdbqt containing 9 structures (198 atoms, 225 bonds) > viewdockx #27.1-9 > voltr5 > view #27 > hide #27.2 models > hide #27.3 models > hide #27.4 models > hide #27.1,5-9 models > show #27.6 models > show #27.5 models > hide #27.5-6 models > show #27.6 models > show #27.5 models > hide #27.5 models > hide #27.6 models > show #27.6 models > hide #27.6 models > show #27.1 models > hide #27.1 models > show #27.1 models > hide #27.1 models > show #27.1 models > hide #27.1 models > show #27.1 models > ui tool show ""Side View"" > hide #27.1 models > show #27.2 models > hide #27.2 models > show #27.2 models > hide #27.2 models > show #27.3 models > hide #27.3 models > show #27.2 models > hide #27.2 models > show #27.3 models > hide #27.3 models > show #27.4 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/cryosparc_P120_J2922_005_volume_map_sharp.mrc"" Opened cryosparc_P120_J2922_005_volume_map_sharp.mrc as #28, grid size 200,200,200, pixel 1.04, shown at level 0.0781, step 1, values float32 > view > volume #28 level 0.2402 > fitmap #28 inMap #26 Fit map cryosparc_P120_J2922_005_volume_map_sharp.mrc in map cryosparc_P120_J3424_008_volume_map_sharp.mrc using 22339 points correlation = 0.2658, correlation about mean = 0.09642, overlap = 4230 steps = 104, shift = 0.849, angle = 9.49 degrees Position of cryosparc_P120_J2922_005_volume_map_sharp.mrc (#28) relative to cryosparc_P120_J3424_008_volume_map_sharp.mrc (#26) coordinates: Matrix rotation and translation 0.98764353 0.07825688 -0.13577969 7.55735375 -0.07110994 0.99585461 0.05671837 1.17503716 0.13965543 -0.04636224 0.98911420 -8.98840843 Axis -0.31250818 -0.83503318 -0.45283354 Axis point 66.00373887 0.00000000 51.32634286 Rotation angle (degrees) 9.49285738 Shift along axis 0.72732290 > ui mousemode right translate > select add #28 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #28,0.98764,0.078257,-0.13578,11.111,-0.07111,0.99585,0.056718,3.802,0.13966,-0.046362,0.98911,-8.916 > view matrix models > #28,0.98764,0.078257,-0.13578,11.45,-0.07111,0.99585,0.056718,6.0462,0.13966,-0.046362,0.98911,-9.5918 > fitmap #28 inMap #26 Fit map cryosparc_P120_J2922_005_volume_map_sharp.mrc in map cryosparc_P120_J3424_008_volume_map_sharp.mrc using 22339 points correlation = 0.8531, correlation about mean = 0.5538, overlap = 1.979e+04 steps = 96, shift = 4.04, angle = 9.61 degrees Position of cryosparc_P120_J2922_005_volume_map_sharp.mrc (#28) relative to cryosparc_P120_J3424_008_volume_map_sharp.mrc (#26) coordinates: Matrix rotation and translation 0.99999108 -0.00422418 0.00001892 2.66215676 0.00422418 0.99999108 -0.00000358 1.78465294 -0.00001890 0.00000366 1.00000000 2.04039659 Axis 0.00085787 0.00447662 0.99998961 Axis point -418.97955466 630.68673302 0.00000000 Rotation angle (degrees) 0.24203105 Shift along axis 2.05064839 > select subtract #28 Nothing selected > ui mousemode right ""next docked"" > viewdockx down > hide #27.4 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx down > hide #27.7 models > show #27.8 models > viewdockx down > hide #27.8 models > show #27.9 models > viewdockx down > viewdockx up > hide #27.9 models > show #27.8 models > viewdockx up > hide #27.8 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > viewdockx up > hide #27.6 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx down > hide #27.7 models > show #27.8 models > viewdockx down > hide #27.8 models > show #27.9 models > viewdockx down > viewdockx up > hide #27.9 models > show #27.8 models > viewdockx up > hide #27.8 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > viewdockx up > hide #27.6 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx down > hide #27.7 models > show #27.8 models > viewdockx down > hide #27.8 models > show #27.9 models > viewdockx up > hide #27.9 models > show #27.8 models > viewdockx down > hide #27.8 models > show #27.9 models > viewdockx down > viewdockx up > hide #27.9 models > show #27.8 models > viewdockx up > hide #27.8 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > viewdockx up > hide #27.6 models > show #27.5 models > viewdockx up > hide #27.5 models > show #27.4 models > viewdockx up > hide #27.4 models > show #27.3 models > viewdockx up > hide #27.3 models > show #27.2 models > viewdockx up > hide #27.2 models > show #27.1 models > viewdockx up > voltr5 > view #27.1 > viewdockx down > hide #27.1 models > show #27.2 models > viewdockx down > hide #27.2 models > show #27.3 models > viewdockx down > hide #27.3 models > show #27.4 models > viewdockx down > hide #27.4 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx up > hide #27.6 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > viewdockx up > hide #27.6 models > show #27.5 models > viewdockx up > hide #27.5 models > show #27.4 models > viewdockx down > hide #27.4 models > show #27.5 models > viewdockx up > hide #27.5 models > show #27.4 models > viewdockx up > hide #27.4 models > show #27.3 models > viewdockx up > hide #27.3 models > show #27.2 models > viewdockx up > hide #27.2 models > show #27.1 models > viewdockx up > volume #28 level 0.3802 > volume #28 level 0.2549 > viewdockx up > viewdockx down > hide #27.1 models > show #27.2 models > viewdockx down > hide #27.2 models > show #27.3 models > viewdockx down > hide #27.3 models > show #27.4 models > viewdockx down > hide #27.4 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx down > hide #27.7 models > show #27.8 models > viewdockx up > hide #27.8 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > viewdockx up > hide #27.6 models > show #27.5 models > viewdockx up > hide #27.5 models > show #27.4 models > viewdockx up > hide #27.4 models > show #27.3 models > viewdockx up > hide #27.3 models > show #27.2 models > viewdockx up > hide #27.2 models > show #27.1 models > viewdockx up > show #!28 models > viewdockx down > hide #27.1 models > show #27.2 models > viewdockx up > hide #27.2 models > show #27.1 models > viewdockx up > viewdockx down > hide #27.1 models > show #27.2 models > viewdockx down > hide #27.2 models > show #27.3 models > viewdockx down > hide #27.3 models > show #27.4 models > viewdockx down > hide #27.4 models > show #27.5 models > viewdockx down > hide #27.5 models > show #27.6 models > viewdockx down > hide #27.6 models > show #27.7 models > viewdockx down > hide #27.7 models > show #27.8 models > viewdockx down > hide #27.8 models > show #27.9 models > viewdockx down > viewdockx up > hide #27.9 models > show #27.8 models > viewdockx up > hide #27.8 models > show #27.7 models > viewdockx up > hide #27.7 models > show #27.6 models > hide #27.6 models > show #27.9 models > hide #27.9 models > show #27.8 models > hide #27.8 models > show #27.7 models > show #27.6 models > show #27.5 models > hide #27.5 models > hide #27.6 models > hide #27.7 models > show #27.7 models > show #27.5 models > hide #27.7 models > hide #27.5 models > show #27.4 models > hide #27.4 models > show #27.3 models > show #27.1 models > hide #27.3 models > hide #27.1 models > show #27.2 models > hide #27.2 models > show #27.1 models > hide #27.1 models > show #27.2 models > hide #27.2 models > show #27.1 models > hide #27.1 models > show #27.2 models > hide #27.2 models > show #27.1 models > hide #27.1 models > show #27.2 models > hide #27.2 models > show #27.3 models > hide #27.3 models > show #27.1 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #27 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"" > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt containing 1 structures (22 atoms, 23 bonds) > hide #27 models > show #27 models > color #29 #d58258ff > color #29 byhetero > rmsd Missing or invalid ""atoms"" argument: empty atom specifier > rmsd #27 #29 Missing required ""to"" argument > rmsd #27 tot #29 Expected a keyword > rmsd #27 to #29 RMSD between 22 atom pairs is 3.588 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #29 models > show #29 models > rmsd #29 to #1/A:609 Number of atoms from first atom spec (22) differs from number in second (37) > rmsd #29 to #1/A:609@~H Invalid ""to"" argument: only initial part ""#1/A:609"" of atom specifier valid > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central.pdb"" > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt containing 1 structures (22 atoms, 23 bonds) > hide #!1 models > hide #!24 models > show #!24 models > hide #!24 models > hide #!25 models > hide #27 models > show #27 models > hide #27 models > hide #29 models > hide #30 models > hide #32 models > hide #31 models > hide #33 models > hide #34 models > hide #35 models > show #27 models > show #29 models > rmsd #27 to #29 RMSD between 22 atom pairs is 3.588 > rmsd #27 to #31 RMSD between 22 atom pairs is 3.666 > show #31 models > hide #29 models > show #29 models > hide #31 models > show #31 models > hide #31 models > show #31 models > show #32 models > rmsd #27 to #32 RMSD between 22 atom pairs is 3.639 > hide #31 models > hide #32 models > hide #29 models > hide #27 models > show #27 models > show #29 models > hide #27 models > show #31 models > rmsd #29 to #31 RMSD between 22 atom pairs is 2.213 > show #27 models > hide #27 models > hide #29 models > show #32 models > show #27 models > hide #32 models > hide #31 models > show #29 models > hide #29 models > show #29 models > show #31 models > hide #31 models > show #31 models > hide #31 models > hide #27 models > show #27 models > show #31 models > hide #31 models > hide #27 models > show #27 models > hide #29 models > show #29 models > show #31 models > hide #31 models > show #31 models > show #32 models > hide #32 models > show #32 models > hide #31 models > show #31 models > hide #32 models > show #32 models > hide #29 models > show #29 models > hide #27 models > hide #32 models > show #27 models > hide #27 models > show #27 models > hide #27 models > show #27 models > hide #27 models > show #27 models > hide #27 models > show #27 models > hide #27 models > align #27 toAtoms #29 move nothing RMSD between 22 atom pairs is 2.489 angstroms > hide #29 models > show #29 models > align #29 toAtoms #27 RMSD between 22 atom pairs is 2.489 angstroms > show #27 models > show #32 models > hide #31 models > hide #32 models > align #29 toAtoms #27 matchAtomNames true Pairing dropped 22 atoms and 22 reference atoms No atoms paired for alignment > align #29 toAtoms #27 matchAtomNames true Pairing dropped 22 atoms and 22 reference atoms No atoms paired for alignment > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"" > hide #27 models > hide #29 models > hide #36 models > show #36 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"" > hide #36 models > hide #37 models > show #37 models > align #29 toAtoms #37 matchAtomNames true RMSD between 22 atom pairs is 2.489 angstroms > hide #37 models > show #37 models > show #27 models > hide #27 models > show #29 models > align #29 toAtoms #37 RMSD between 22 atom pairs is 2.489 angstroms > rmsd #29 to #37 RMSD between 22 atom pairs is 2.489 > hide #29 models > show #31 models > rmsd #29 to #31 RMSD between 22 atom pairs is 3.989 > align 329 to #1 Missing or invalid ""atoms"" argument: invalid atoms specifier > align #29 toAtoms #1 Unequal number of atoms to pair, 22 and 6846 > align #29 toAtoms #31 RMSD between 22 atom pairs is 0.978 angstroms > show #29 models > hide #37 models > view #27-37 initial Expected an integer >= 1 or a keyword > view initial #27-37 initial Expected a keyword > view initial #27-37 > align #29 toAtoms #31 RMSD between 22 atom pairs is 0.978 angstroms > hide #31 models > show #27 models > hide #29 models > show #29 models > hide #27 models > show #37 models > label #22,29,37 atoms attribute name > show #27 models > hide #!29 models > hide #!37 models > label #22,27 atoms attribute name > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/docked_C2.2_renamed_atoms.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/docked_C2.2_renamed_atoms.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened docked_C2.2_renamed_atoms.pdbqt containing 1 structures (22 atoms, 23 bonds) > hide #!27 models > hide #38 models > show #38 models > hide #38 models > show #38 models > label #22,38 atoms attribute name > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"" > hide #!38 models > show #!38 models > color #39 #415bffff > label #22,38-39 atoms attribute name > hide #!38 models > show #!38 models > hide #!39 models > show #!39 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!22 models > color byhetero > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > hide #!38 models > show #!38 models > hide #!39 models > show #!39 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!38 models > hide #!39 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb --- warning | Ignored bad PDB record found on line 23 > label #40 atoms attribute name > hide #!40 models > show #!40 models > show #!29 models > show #!27 models > hide #!27 models > rmsd #40 to 329 Invalid ""to"" argument: invalid atoms specifier > rmsd #40 to #29 RMSD between 22 atom pairs is 1.561 > align #29 toAtoms #40 RMSD between 22 atom pairs is 0.880 angstroms > view initial #29 > hide #!29 models > show #!29 models > rmsd #40 to #29 RMSD between 22 atom pairs is 1.250 > rmsd #40 to #31 RMSD between 22 atom pairs is 1.789 > show #31 models > show #32 models > view initial #29,31,32,40 > rmsd #40 to #32 RMSD between 22 atom pairs is 1.912 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central.pdb --- warnings | Ignored bad PDB record found on line 5 Ignored bad PDB record found on line 7 Ignored bad PDB record found on line 14 > align #41 toAtoms #40 RMSD between 22 atom pairs is 2.442 angstroms > hide #31 models > hide #32 models > hide #!29 models > hide #!40 models > show #!40 models > hide #!40 models > label #41 atoms attribute name > ui mousemode right translate > show #!40 models > hide #!40 models > show #!39 models > hide #!39 models > show #!39 models > ui mousemode right ""rotate selected models"" > select add #41 22 atoms, 23 bonds, 1 residue, 2 models selected > view matrix models > #41,0.94928,0.14026,-0.28142,19.492,-0.15443,0.98759,-0.028715,23.961,0.2739,0.07072,0.95915,-39.717 > view matrix models > #41,0.94765,0.016102,-0.31891,36.963,0.020875,0.99347,0.1122,-13.564,0.31863,-0.11298,0.94112,-23.739 > view matrix models > #41,0.99805,-0.059362,0.01954,4.9264,0.058007,0.99627,0.063845,-13.898,-0.023257,-0.062586,0.99777,9.7105 > hide #!39 models > show #!39 models > select subtract #41 Nothing selected > ui mousemode right translate > hide #!39 models > show #!38 models > hide #!38 models > show #!38 models > hide #!41 models > show #!41 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!41 models > show #!41 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!41 models > hide #!38 models > show #!38 models > show #!41 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed > copy.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed copy.pdb --- warning | Ignored bad PDB record found on line 23 > hide #!38 models > rmsd #41 to #32 RMSD between 22 atom pairs is 3.628 > show #32 models > hide #32 models > hide #!41 models > show #!41 models > hide #!41 models > show #!41 models > rmsd #42 to #32 RMSD between 22 atom pairs is 1.755 > rmsd #42 to #29 RMSD between 22 atom pairs is 1.236 > rmsd #42 to #31 RMSD between 22 atom pairs is 1.775 > rmsd #42 to #32 RMSD between 22 atom pairs is 1.755 > hide #!41 models > hide #42 models > show #32 models > show #31 models > show #42 models > hide #32 models > hide #31 models > show #!40 models > hide #!40 models > show #!39 models > show #!41 models > hide #42 models > hide #!39 models > hide #!41 models > show #!41 models > show #!39 models > hide #!39 models > show #!38 models > hide #!38 models > show #!38 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central_renamed.pdb"" > hide #43 models > show #43 models > hide #43 models > show #43 models > hide #43 models > show #43 models > hide #!41 models > show #!41 models > view #41 initial Expected an integer >= 1 or a keyword > view initial #1 > view initial #41 > hide #43 models > show #43 models > show #!1 models > hide #43 models > show #43 models > hide #!41 models > hide #!38 models > hide #43 models > show #43 models > hide #!1 models > show #!1 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central_renamed.pdb"" > hide #43 models > show #43 models > hide #43 models > view #43 > view #44 > close #43 > show #42 models > view #42 > hide #!1 models > close #40 > close #41 > close #39 > show #!38 models > hide #!38 models > view #44 > show #33 models > show #34 models > show #35 models > rmsd #44 to #33 RMSD between 22 atom pairs is 0.656 > rmsd #44 to #34 RMSD between 22 atom pairs is 1.290 > rmsd #44 to #35 RMSD between 22 atom pairs is 1.481 > hide #34 models > hide #35 models > show #35 models > show #34 models > hide #33 models > hide #34 models > show #34 models > hide #35 models > show #35 models > hide #34 models > show #34 models > hide #35 models > show #35 models > hide #34 models > hide #35 models > show #!1 models > hide #!1 models > show #!2 models > hide #44 models > show #44 models > hide #42 models > show #42 models > show #!29 models > show #31 models > show #32 models > hide #31 models > hide #32 models > label delete > view #29 > hide HC > view lst Expected an objects specifier or a view name or a keyword > view lstview ist Expected an objects specifier or a view name or a keyword > view list No named views. > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240830_zfO1_final_structures_maps_comparison_15_mutagen_extraDensity.cxs"" Opened emd_9360.map as #1, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_cryosparc_P120_J2190_007_volume_map.mrc as #4, grid size 256,256,256, pixel 1.15, shown at level 0.176, step 1, values float32 Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map.mrc as #7, grid size 200,200,200, pixel 1.07, shown at level 0.34, step 1, values float32 Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map_sharp.mrc as #8, grid size 200,200,200, pixel 1.07, shown at level 0.272, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map.mrc as #11, grid size 200,200,200, pixel 1.07, shown at level 0.289, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc as #12, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map.mrc as #15, grid size 200,200,200, pixel 1.04, shown at level 0.0979, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc as #16, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 0 as #25.1, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 1 as #25.2, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 2 as #25.3, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 3 as #25.4, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 4 as #25.5, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 5 as #25.6, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened emd_9360.map 0 as #24.1, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 1 as #24.2, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 2 as #24.3, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 3 as #24.4, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 4 as #24.5, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 0 as #31.1, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 1 as #31.2, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 2 as #31.3, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 3 as #31.4, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 4 as #31.5, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 5 as #31.6, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 0 as #30.1, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 1 as #30.2, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 2 as #30.3, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 3 as #30.4, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 4 as #30.5, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 5 as #30.6, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 opened ChimeraX session > show #!3 models > hide #!3 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240807_zfO1_final_structures_maps_comparison_14.cxs"" Opened emd_9360.map as #1, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_cryosparc_P120_J2190_007_volume_map.mrc as #4, grid size 256,256,256, pixel 1.15, shown at level 0.176, step 1, values float32 Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map.mrc as #7, grid size 200,200,200, pixel 1.07, shown at level 0.34, step 1, values float32 Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map_sharp.mrc as #8, grid size 200,200,200, pixel 1.07, shown at level 0.272, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map.mrc as #11, grid size 200,200,200, pixel 1.07, shown at level 0.242, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc as #12, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map.mrc as #15, grid size 200,200,200, pixel 1.04, shown at level 0.0979, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc as #16, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 0 as #25.1, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 1 as #25.2, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 2 as #25.3, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 3 as #25.4, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 4 as #25.5, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 5 as #25.6, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values float32 Opened emd_9360.map 0 as #24.1, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 1 as #24.2, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 2 as #24.3, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 3 as #24.4, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened emd_9360.map 4 as #24.5, grid size 200,200,200, pixel 1.03, shown at level 3.67, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 0 as #31.1, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 1 as #31.2, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 2 as #31.3, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 3 as #31.4, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 4 as #31.5, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32 Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 5 as #31.6, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 0 as #30.1, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 1 as #30.2, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 2 as #30.3, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 3 as #30.4, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 4 as #30.5, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 5 as #30.6, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values float32 opened ChimeraX session > transparency 0 target ca > select clear > style #!13,34 stick Changed 13056 atom styles > hide #!13 models > show #!13 models > view > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb --- warning | Ignored bad PDB record found on line 23 > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central_renamed.pdb"" > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt containing 1 structures (22 atoms, 23 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C Ignored bad PDB record found on line 2 REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 Ignored bad PDB record found on line 3 REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21 Ignored bad PDB record found on line 4 REMARK H PARENT 12 14 18 22 Ignored bad PDB record found on line 5 REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13 15 messages similar to the above omitted Opened CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt containing 1 structures (22 atoms, 23 bonds) > hide #39 models > show #39 models > view initial #13 > hide #!34 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/mO1_on_zfO1C2.2_clean_REDUCE_GLH274.pdbqt"" Chain information for mO1_on_zfO1C2.2_clean_REDUCE_GLH274.pdb #44 --- Chain | Description A | No description available Opened mO1_on_zfO1C2.2_clean_REDUCE_GLH274.pdbqt containing 1 structures (5211 atoms, 5317 bonds) > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/hO1_on_zfO1C2.2_clean_REDUCE_GLH276_HIE600.pdbqt"" Chain information for hO1_on_zfO1C2.2_clean_REDUCE_GLH276_HIE600.pdb #45 --- Chain | Description A | No description available Opened hO1_on_zfO1C2.2_clean_REDUCE_GLH276_HIE600.pdbqt containing 1 structures (5330 atoms, 5442 bonds) > hide #44 models > show #44 models > hide #45 models > hide #44 models > hide #!13 models > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb"" Summary of feedback from opening /Users/bburendei/Dropbox (Scripps Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3270 messages similar to the above omitted Chain information for zfO1_NC2_10mM_bestModel_apo.pdb #46 --- Chain | Description A B | No description available > hide #40 models > hide #41 models > hide #42 models > hide #43 models > hide #!46 models > show #!46 models > color #46 #aa5ee8 > show #46/A:126,130,133,134,267,574,573,532,570 > hide /B target ca > hide :CLR.Y01 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide :CLR,Y01 > color byhet' Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byhetero > hide #39 models > show #39 models > hide #37 models > hide #36 models > show #36 models > hide #39 models > show #40 models > hide #38 models > hide #36 models > show #36 models > color #36,37 cyan > show #39 models > color #36,37 cyanview list Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > view list Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly, C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket, F570_central_NC36_2copies_modelComp_view, F570central_densityComp, F570central_modelComp, F570central_modelComp2, F570central_resi_comp, F570central_site_allModels, F570outer, F570outer_resi_comp, F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly, NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison, N_domonly_side_comparison, all_models_aligned_Cdompocket_models, all_models_aligned_F570central_models, all_models_aligned_F570outer_site_models, bottom_view, c11_in_dens_Cdom, c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45, outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models, top_view > view F570outer > view F570outer_site_modelComp2 > hide #39 models > hide #40 models > show #40 models > show #38 models > hide #38 models > show #44 models > hide #44 models > show #44 models > hide #44 models > show #45 models > color #45 #cf7c15ff > color #45 #cfca15ff > color #45 #cfa815ff > color #45 #ada815ff > color #45 #ada81cff > color #45 #d7a81cff > color #45 #e9a81cff > color #45 #eca81cff > hide #40 models > show #40 models > color #40 #eca81cff > color #40 #ec621cff > hide #36 models > show #36 models > hide #45 models > hide #!46 models > show #!46 models > show #45 models > hide #!46 models > select #45/A:132 16 atoms, 17 bonds, 1 residue, 1 model selected > select add #45/A:135 21 atoms, 21 bonds, 2 residues, 1 model selected > select add #45/A:136 29 atoms, 28 bonds, 3 residues, 1 model selected > select add #45/A:280 38 atoms, 36 bonds, 4 residues, 1 model selected > select add #45/A:139 47 atoms, 44 bonds, 5 residues, 1 model selected > select add #45/A:276 58 atoms, 54 bonds, 6 residues, 1 model selected > select add #45/A:596 70 atoms, 66 bonds, 7 residues, 1 model selected > select add #45/A:599 79 atoms, 74 bonds, 8 residues, 1 model selected > select add #45/A:600 91 atoms, 86 bonds, 9 residues, 1 model selected > select add #45/A:603 97 atoms, 91 bonds, 10 residues, 1 model selected > show sel > select clear > select #45/A:135 5 atoms, 4 bonds, 1 residue, 1 model selected > show #!46 models > hide #!46 models > show #!46 models > hide #!46 models > select #45/A:140 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #45/A:143 21 atoms, 20 bonds, 2 residues, 1 model selected > show #!46 models > hide #46 > show #46/A:126,130,133,134,267,574,573,532,570 > select clear > select #45/A:140 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel > hide #45 models > show #45 models > select #45/A:603@CB 1 atom, 1 residue, 1 model selected > hide sle Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel > select clear > select #45/A:558 16 atoms, 17 bonds, 1 residue, 1 model selected > show sel > open ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt"" Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb #47 --- Chain | Description A | No description available Opened zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt containing 1 structures (3755 atoms, 3831 bonds) > hide #!47 models > show #!47 models > hide #47 > show #47/A:126,130,133,134,267,574,573,532,570 > color #aa5ee8 > undo > color #47 #aa5ee8 > select clear > hide #!46 models > close #46 > color byhetero > select clear > color #40 #ecbd1cff > color #40 #ec991cff > color byhetero > select clear > size #36,40 stickRadius 0.2 Changed 46 bond radii > size #36,40 stickRadius 0.4 Changed 46 bond radii > size #36,40 stickRadius 0.3 Changed 46 bond radii > color #40 #00991cff > color #40 #00ff1cff > color #40 lime > color #40 #00d700ff > color byhetero > size #36,40 stickRadius 0.2 Changed 46 bond radii > select clear > size #36,40 stickRadius 0.25 Changed 46 bond radii > size #36,40 stickRadius 0.2 Changed 46 bond radii > select clear > ui tool show ""Side View"" > hide #!47 models > show #!47 models > hide #47:573 > hide #45:590 > hide #45:599 > show #38 models > hide #38 models > show #38 models > hide #38 models > show #38 models > hide #36 models > save ""/Users/bburendei/Dropbox (Scripps > Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/240906_best_poses_comparison_session.cxs"" > show #42 models > hide #42 models > hide #45 models > hide #!47 models > hide #40 models > hide #38 models > show #!1 models > show #45 models > hide #45 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > alias nice cartoon suppressBackboneDisplay false; cartoon style width 1; > size stickRadius 0.12 > lighting soft > nice Changed 0 bond radii > alias voltr5 vol transparency 0.5 > alias voltroff vol transparency 0 > alias cylinders cartoon style protein modeh tube rad 2 sides 24 > alias cartoonDefaults cartoon style protein modeh default UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,2 Model Number: Z15S000D5LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.121.1 OS Loader Version: 8422.141.2.700.1 Software: System Software Overview: System Version: macOS 13.6.7 (22G720) Kernel Version: Darwin 22.6.0 Time since boot: 2 days, 10 hours, 47 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL P2721Q: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX