id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20557 Find Cavities crash in constitutional charles.midgett@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-26.5.1-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000312a2f000 (most recent call first): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030c743000 (most recent call first): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/zmq/utils/garbage.py"", line 46 in run File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017f35f000 (most recent call first): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 566 in select File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 1898 in _run_once File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 608 in run_forever File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tornado/platform/asyncio.py"", line 211 in start File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/iostream.py"", line 93 in _thread_main File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017ad5f000 (most recent call first): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 327 in wait File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py"", line 1111 in run File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py"", line 99 in only_when_enabled File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/decorator/__init__.py"", line 247 in fun File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000001f1cede80 (most recent call first): File ""/Users/charlesmidgett/Library/Application Support/ChimeraX/1.12/lib/python/site-packages/pyKVFinder/grid/constitutional.py"", line 291 in constitutional File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/kvfinder/cmd.py"", line 83 in cmd_kvfinder File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3245 in run File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/kvfinder/tool.py"", line 172 in find_cavities File 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""factorPackIds"" : [ ], ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > set bgColor aliceblue > windowsize 570 570 > ui mousemode right zoom > camera ortho > color name bluishwhite rgb(201, 218,222) Color 'bluishwhite' is opaque: rgb(78.8%, 85.5%, 87.1%) hex: #c9dade > ~label UCSF ChimeraX version: 1.12 (2026-06-12) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX-Clipper==0.27' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting ChimeraX-Clipper==0.27 Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.27/chimerax_clipper-0.27-cp311-cp311-macosx_11_0_universal2.whl (11.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 7.7 MB/s 0:00:01 Requirement already satisfied: ChimeraX-Core==1.12.*,>=1.12.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Clipper==0.27) (1.12) Requirement already satisfied: ChimeraX-Atomic~=1.67 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Clipper==0.27) (1.67.1) Requirement already satisfied: ChimeraX-AtomicLibrary~=14.4 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Clipper==0.27) (14.4) Requirement already satisfied: ChimeraX-Arrays~=1.1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Clipper==0.27) (1.1) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.0.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (1.3) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (1.4.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.16) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.0.3) Requirement already satisfied: ChimeraX-PDB~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.7.13) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (1.0.5) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.67->ChimeraX- Clipper==0.27) (1.2.4) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.67->ChimeraX- Clipper==0.27) (1.15.4) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.67->ChimeraX- Clipper==0.27) (1.5.2) Requirement already satisfied: ChimeraX-IO~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX- Atomic~=1.67->ChimeraX-Clipper==0.27) (1.0.4) Requirement already satisfied: ChimeraX-Surface~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX- Clipper==0.27) (1.0.1) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX- Clipper==0.27) (1.50.8) Requirement already satisfied: ChimeraX-Map~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.67->ChimeraX-Clipper==0.27) (1.3) Requirement already satisfied: ChimeraX-MapData~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.67->ChimeraX-Clipper==0.27) (2.0) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.67->ChimeraX-Clipper==0.27) (1.19.3) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.0.1) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.1.1) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (1.2) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX- Clipper==0.27) (2.0) Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (1.4.2) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (2.0) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.67->ChimeraX-Clipper==0.27) (1.0) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.67->ChimeraX-Clipper==0.27) (1.0.1) Installing collected packages: ChimeraX-Clipper Attempting uninstall: ChimeraX-Clipper Found existing installation: ChimeraX-Clipper 0.23.0 Uninstalling ChimeraX-Clipper-0.23.0: Successfully uninstalled ChimeraX-Clipper-0.23.0 Successfully installed ChimeraX-Clipper-0.27 [notice] A new release of pip is available: 25.2 -> 26.1.2 [notice] To update, run: /Applications/ChimeraX-1.12.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip > open /Users/charlesmidgett/Downloads/HomologSessPocketSurfaces.cxs Populating font family aliases took 155 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > view name session-start opened ChimeraX session > view #2.1.2.1 @ zoom 0.75 moved plane near -42.220261646888936 [-0.89898692 -0.19874886 0.39028372] moved plane far -42.220261646888936 [-0.89898692 -0.19874886 0.39028372] > surface #2.1.2.1 transparency 50 > ~surface #2.1.2 > surface #2.1.2.1 > select #!2.1 & (#2.1.2.1 @ show > #!2.1/A:14,17-23,25,32,34,49,51,53-57,59,61,71,75-76,78,81-82,108,157-159,161,163-164,167,174,201-203,207-208,211-212,215-216,218-219,222,251,258,262 > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > hide #!2 models > show #!2 models > hide #!5 models > show #!5 models > show #!4 models > hide #!5 models > show #!5 models > hide #!4 models > select add #2 11841 atoms, 4126 bonds, 2 pseudobonds, 498 residues, 10 models selected > select subtract #2 3 models selected > hide #!2 models > hide #!5 models > show #!2 models > select add #2 11841 atoms, 4126 bonds, 2 pseudobonds, 498 residues, 9 models selected > show #!2.1 models > clsoe Unknown command: clsoe > close > open ""/Users/charlesmidgett/Library/CloudStorage/OneDrive- > DartmouthCollege/writing-one-drive/2025 RegA paper/RegA cavity > part/HomologSessPocketSurfaces.cxs"" > view name session-start opened ChimeraX session > save ""/Users/charlesmidgett/Library/CloudStorage/OneDrive- > DartmouthCollege/writing-one-drive/2025 RegA paper/RegA cavity > part/HomologSessPocketSurfaces.cxs"" > view > save ""/Users/charlesmidgett/Library/CloudStorage/OneDrive- > DartmouthCollege/writing-one-drive/2025 RegA paper/RegA cavity > part/HomologSessPocketSurfaces.cxs"" > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Errors may have occurred when running pip: pip standard error: \--- ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you have numpy 2.4.6 which is incompatible. scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.6 which is incompatible. \--- pip standard output: \--- \--- pyKVFinder module installed from PyPi repository. > kvfinder volumeCutoff 200 2 cavities found for 3gbg #3 3gbg Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 3.2.2 | | 577.37 | 451.44 | 2673 | 10.8 | 5.63 3.2.1 | | 320.11 | 341.54 | 1482 | 3.84 | 1.2 1 cavities found for 6xiu A #2.1 6xiu A Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.1.2.1 | | 1105.27 | 860.98 | 5117 | 7.61 | 2.16 1 cavities found for 6xiu B #2.2 6xiu B Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.2.2.1 | | 1367.06 | 1000.55 | 6329 | 8.36 | 2.18 1 cavities found for GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb C #4.3 GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb C Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 4.3.2.1 | | 768.96 | 563.41 | 3560 | 11.8 | 5.18 1 cavities found for GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb D #4.4 GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb D Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 4.4.2.1 | | 804.82 | 587.96 | 3726 | 11.27 | 5.04 2 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.3.1 | | 992.3 | 747.9 | 4594 | 12.78 | 4.18 1.3.2 | | 984.53 | 756.46 | 4558 | 12.88 | 4.35 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.2.1 | | 724.25 | 609.4 | 3353 | 13.81 | 5.03 > show #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #1.1 models > show #1.1 models > hide #1.1 models > hide #1.2 models > show #1.2 models > show #1 target r > delete target s Missing or invalid ""atoms"" argument: invalid atoms specifier > delete surface Missing or invalid ""atoms"" argument: invalid atoms specifier > close #1.1-2 > hide #!4.3 models > show #!4.3 models > show #!4.4 models > hide #!4.4 models > show #!4.4 models > hide #5.1 models > show #5.1 models > hide #5.1 models > show #5.1 models > close #5.1 > close #3.3 > close #2.1.3 > close #2.2.3 > close #4.3.1 > kvfinder volumeCutoff 200 2 cavities found for 3gbg #3 3gbg Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 3.2.2 | | 577.37 | 451.44 | 2673 | 10.8 | 5.63 3.2.1 | | 320.11 | 341.54 | 1482 | 3.84 | 1.2 1 cavities found for 6xiu A #2.1 6xiu A Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.1.2.1 | | 1105.27 | 860.98 | 5117 | 7.61 | 2.16 1 cavities found for 6xiu B #2.2 6xiu B Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.2.2.1 | | 1367.06 | 1000.55 | 6329 | 8.36 | 2.18 1 cavities found for GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb C #4.3 GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb C Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 4.3.1.1 | | 768.96 | 563.41 | 3560 | 11.8 | 5.18 1 cavities found for GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb D #4.4 GVL_230724_3_4_selfautoProc_cut_refine_165LigandInChainsFinal.pdb D Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 4.4.2.1 | | 804.82 | 587.96 | 3726 | 11.27 | 5.04 2 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.1.1 | | 992.3 | 747.9 | 4594 | 12.78 | 4.18 1.1.2 | | 984.53 | 756.46 | 4558 | 12.88 | 4.35 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 724.25 | 609.4 | 3353 | 13.81 | 5.03 > hide #1,2,3,4 > hide #1,2,3,4 target ar > kvfinder #5 removalDistance 2 volumeCutoff 200 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 724.25 | 609.4 | 3353 | 13.81 | 5.03 > view #5.1.1 @ zoom 0.75 moved plane near -41.67920777672473 [-0.61369997 -0.06579128 0.78679336] moved plane far -41.67920777672473 [-0.61369997 -0.06579128 0.78679336] > surface #5.1.1 transparency 50 > ~surface #5.1 > surface #5.1.1 > select #!5 & (#5.1.1 @ show > #!5/A:5,7,10-14,16,18,25,27,42,44,50,52,54,63-69,72,115,118-119,121-122,177,181,184,222,225-226,228-229,232-233,268,271-272 > select clear > select add #!5/A:62 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #!5/A:230 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #!5/A:5 23 atoms, 20 bonds, 3 residues, 1 model selected > select add #!5/A:53 30 atoms, 26 bonds, 4 residues, 1 model selected > select add #!5/A:25 38 atoms, 33 bonds, 5 residues, 1 model selected > select add #!5/A:19 44 atoms, 38 bonds, 6 residues, 1 model selected > select add #!5/A:24 53 atoms, 46 bonds, 7 residues, 1 model selected > select add #!5/A:58 61 atoms, 53 bonds, 8 residues, 1 model selected > select add #!5/A:46 70 atoms, 61 bonds, 9 residues, 1 model selected > select add #!5/A:15 81 atoms, 72 bonds, 10 residues, 1 model selected > select add #!5/A:100 93 atoms, 84 bonds, 11 residues, 1 model selected > select add #!5/A:33 100 atoms, 90 bonds, 12 residues, 1 model selected > select up 540 atoms, 542 bonds, 66 residues, 1 model selected > kvfinder #5 removalDistance 2 volumeCutoff 200 boxAtoms sel > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpn12rnmpg.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 740.45 | 612.7 | 3428 | 12.61 | 4.85 > kvfinder #5 removalDistance 2 volumeCutoff 200 boxAtoms sel boxPad 0.5 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp8zlaezw1.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 733.54 | 613.38 | 3396 | 13.44 | 5.23 > kvfinder #5 removalDistance 2 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpht8lvfqj.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 735.7 | 597.25 | 3406 | 13.1 | 5.17 > kvfinder #5 probeOut 7 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpyop8py8c.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 13 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.7 | | 1840.75 | 1163.77 | 8522 | 12.95 | 4.36 5.1.8 | | 599.62 | 380.58 | 2776 | 5.47 | 1.48 5.1.12 | | 101.52 | 114.91 | 470 | 4.95 | 1.21 5.1.5 | | 75.6 | 92.16 | 350 | 2.4 | 0.71 5.1.13 | | 65.45 | 77.11 | 303 | 2.55 | 0.54 5.1.4 | | 45.36 | 49.11 | 210 | 2.24 | 0.73 5.1.1 | | 33.48 | 58.05 | 155 | 0 | 0 5.1.3 | | 18.79 | 33.27 | 87 | 1.04 | 0.38 5.1.9 | | 15.77 | 22.21 | 73 | 1.34 | 0.52 5.1.6 | | 12.31 | 29.54 | 57 | 0 | 0 5.1.10 | | 12.31 | 29.54 | 57 | 0 | 0 5.1.2 | | 6.7 | 15.73 | 31 | 1.04 | 0.38 5.1.11 | | 5.83 | 14 | 27 | 0.85 | 0.29 > kvfinder #5 probeOut 7 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpeo1ws25e.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 2 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 1840.75 | 1163.77 | 8522 | 12.95 | 4.36 5.1.2 | | 599.62 | 380.58 | 2776 | 5.47 | 1.48 > view #5.1.2 @ zoom 0.75 moved plane near -33.00241444444664 [ 0.75116358 -0.09957168 0.65256318] moved plane far -33.00241444444664 [ 0.75116358 -0.09957168 0.65256318] > surface #5.1.1-2 transparency 50 > ~surface #5.1 > surface #5.1.2 > select #!5 & (#5.1.2 @ show #!5/A:11,29-32,45-49,91-97,166-167,169,171,173,211-213 > kvfinder #5 probeOut 2 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpvxj_ke_z.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 > kvfinder #5 probeOut 2 volumeCutoff 200 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 > kvfinder #5 volumeCutoff 200 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 724.25 | 609.4 | 3353 | 13.81 | 5.03 > select add #!5/A:64 145 atoms, 128 bonds, 28 residues, 1 model selected > select add #!5/A:66 153 atoms, 135 bonds, 29 residues, 1 model selected > select add #!5/A:229 162 atoms, 143 bonds, 30 residues, 1 model selected > kvfinder #5 volumeCutoff 200 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 724.25 | 609.4 | 3353 | 13.81 | 5.03 > select clear > select #!5/A:63 11 atoms, 11 bonds, 1 residue, 1 model selected > kvfinder #5 volumeCutoff 200 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 724.25 | 609.4 | 3353 | 13.81 | 5.03 > select #5/A:63@ca 1 atom, 1 residue, 1 model selected > select add #5/A:14@ca 2 atoms, 2 residues, 1 model selected > select add #5/A:267@ca 3 atoms, 3 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0.5 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpxm1h85iu.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 613.01 | 478.59 | 2838 | 7.61 | 2.41 > select #5/A:54@ca 1 atom, 1 residue, 1 model selected > select #5/A:54,63,47,14@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0.5 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpf50yuwto.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 613.66 | 503.8 | 2841 | 11.08 | 4.18 > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpkl90juey.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 585.79 | 468.07 | 2712 | 11.06 | 3.87 > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp0zifwp2b.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 585.79 | 468.07 | 2712 | 11.06 | 3.87 > select #5/A:5,63,47,68@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp9x8qn_0l.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 587.74 | 469.62 | 2721 | 11.06 | 4.54 > select #5/A:5,63,47,70@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpci4mvafg.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 578.02 | 465.59 | 2676 | 11.06 | 4.51 > select #5/A:5,63,173,70@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpwk6_s28c.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 662.26 | 571.71 | 3066 | 13.48 | 5.59 > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmptokewc3x.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 662.26 | 571.71 | 3066 | 13.48 | 5.59 > select #5/A:5,63,47,70@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmphcnnw762.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 578.02 | 465.59 | 2676 | 11.06 | 4.51 > select #5/A:5,63,11,70@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp2fmtjanb.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 636.77 | 535.66 | 2948 | 13.19 | 5.66 > select #5/A:5,63,11,14@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpvcdsltkp.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 618.62 | 504.47 | 2864 | 13.39 | 5.91 > select #5/A:5,63,11,67@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpvekd32w0.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 600.7 | 485.56 | 2781 | 12.88 | 5.76 > select #5/A:5,63,48,67@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp9t2lhy_m.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 491.18 | 388.13 | 2274 | 9.75 | 3.17 > select #5/A:5,63,11,67@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpi1q1lfzl.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.1.1 | | 600.7 | 485.56 | 2781 | 12.88 | 5.76 > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpamtnpfd4.bild id > 5.3 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.4.1 | | 600.7 | 485.56 | 2781 | 12.88 | 5.76 > select #5/B:5,63,11,48@ca Nothing selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false No atoms specified by 'box_atoms' argument > select #5/B:5,63,11,48@ca Nothing selected > select #5/A:5,63,11,48@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpy1ehkuj7.bild id > 5.5 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.6.1 | | 623.59 | 504.68 | 2887 | 13.39 | 5.79 > select #5/A:5,13,11,48@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp7wm3mafu.bild id > 5.7 name ""cavity search box"" Opened BILD data containing 15 objects 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp_vj1v2v9.bild id > 5.2 name ""cavity search box"" Opened BILD data containing 15 objects 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 > select #5/A:5,11,63,48@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp6ojhctmu.bild id > 5.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.2.1 | | 623.59 | 504.68 | 2887 | 13.39 | 5.79 > ui tool show Shell > select #5/A:5,11,63,48@ca 4 atoms, 4 residues, 1 model selected > hide #5 target ars > show #1 target r > ~show #1/B target r > select #1/A:71,52,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp5kea5wpt.bild id > 5.3 name ""cavity search box"" Opened BILD data containing 15 objects 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 > select #1/A:71,52,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpms_e6v5i.bild id > 5.4 name ""cavity search box"" Opened BILD data containing 15 objects 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 > close #1.1.1-2 > close #1.1 > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpl65nvwqx.bild id > 5.5 name ""cavity search box"" Opened BILD data containing 15 objects 0 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 > hide #5.3 models > hide #5.4 models > hide #5.5 models > hide #!5.2 models > show #!5.2 models > close #2.1.2 > close #2.2.2 > close #3.2 > close #4.4.2 > hide #5.1 models > show #5.1 models > close #5.3-5 > select #1/A:71,52,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp8p91dqfu.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 282.53 | 255.39 | 1308 | 7.22 | 1.75 > select #1/A:71,208,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmparfa873l.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 798.34 | 597.67 | 3696 | 12.73 | 4.87 > select #1/A:73,208,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpv251hwva.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 949.54 | 713.66 | 4396 | 12.54 | 4.35 > select #1/A:72,208,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp_58wamjq.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 842.62 | 652.64 | 3901 | 12.78 | 4.6 > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpx5lnc2as.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 842.62 | 652.64 | 3901 | 12.78 | 4.6 > select #1/A:71,208,27,64@ca 4 atoms, 4 residues, 1 model selected > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpvuqp5n1k.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 798.34 | 597.67 | 3696 | 12.73 | 4.87 > hide #1.1 models > show #1.1 models > hide #5.1 models > select #1:71,208,27,64@ca 8 atoms, 8 residues, 1 model selected > kvfinder #5 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmput2bdvmj.bild id > 5.3 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for fold_hild_delta1_35_palmacid_monomer_model_0.cif #!5 fold_hild_delta1_35_palmacid_monomer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 5.4.1 | | 734.83 | 620.36 | 3402 | 10.48 | 3.97 > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpxvao21d0.bild id > 1.3 name ""cavity search box"" Opened BILD data containing 15 objects 2 cavities found for fold_virf_myristic_dimer_model_0.cif #!1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.4.1 | | 1003.1 | 764.11 | 4644 | 12.78 | 4.28 1.4.2 | | 927.72 | 696.7 | 4295 | 12.6 | 4.47 > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpncxcwyxl.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 2 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 1003.1 | 764.11 | 4644 | 12.78 | 4.28 1.2.2 | | 927.72 | 696.7 | 4295 | 12.6 | 4.47 > close #4.3.1 > close #1.2 > close #1.1 > close #5.1 > close #5.3 > select #1/:71,208,27,64@ca Expected an objects specifier or a keyword > select #1:71,208,27,64@ca 8 atoms, 8 residues, 1 model selected > kvfinder #1 volumeCutoff 200 boxAtoms sel boxPad 0 replace false > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmpjri38oev.bild id > 1.1 name ""cavity search box"" Opened BILD data containing 15 objects 2 cavities found for fold_virf_myristic_dimer_model_0.cif #1 fold_virf_myristic_dimer_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.1 | | 1003.1 | 764.11 | 4644 | 12.78 | 4.28 1.2.2 | | 927.72 | 696.7 | 4295 | 12.6 | 4.47 > close #1.1 > close #1.2 > close #5.2,4 > hide #1 models > show #2/A target r > show #2.1 target r > show #!2.1 models > select #2.1:70,63,19,76@ca 4 atoms, 4 residues, 1 model selected > kvfinder #2.1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp2co34wxt.bild id > 2.1.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for 6xiu A #2.1 6xiu A Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.1.3.1 | | 330.48 | 224.99 | 1530 | 4.28 | 1.56 > select #2.1:70,63,19,216@ca 4 atoms, 4 residues, 1 model selected > kvfinder #2.1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp_okbogqy.bild id > 2.1.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for 6xiu A #2.1 6xiu A Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.1.3.1 | | 494.64 | 326.6 | 2290 | 5.4 | 2.06 > select #2.1:70,43,19,216@ca 4 atoms, 4 residues, 1 model selected > kvfinder #2.1 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp42ffhxb3.bild id > 2.1.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for 6xiu A #2.1 6xiu A Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.1.3.1 | | 505.01 | 361.53 | 2338 | 7.59 | 2.82 > hide 2.1 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #2.1 > hide #2.1 target ar > show #3 target r > select #3:53,230,26,113@ca 4 atoms, 4 residues, 1 model selected > kvfinder #3 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp6974uwmi.bild id > 3.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for 3gbg #3 3gbg Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 3.3.1 | | 476.93 | 343.42 | 2208 | 7.42 | 3.25 > select #3:74,230,26,113@ca 4 atoms, 4 residues, 1 model selected > kvfinder #3 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp2206fkay.bild id > 3.2 name ""cavity search box"" Opened BILD data containing 15 objects 1 cavities found for 3gbg #3 3gbg Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 3.3.1 | | 587.74 | 456.66 | 2721 | 14.07 | 7.51 > close #3.2#3.3 > close #2.1.2#2.1.3 > hide #3 target r > show #4 target r > hide #4/C target r > show #4/C target r > ~show #4/D target r > select #4/D:232,42,88,28@ca 4 atoms, 4 residues, 1 model selected > hide #!4 models > hide #4.3 models > show #4.3 models > hide #4.3 models > hide #!4.4 models > hide #!4 models > show #!4 models > select #4/D:232,42,88,28@ca 4 atoms, 4 residues, 1 model selected > kvfinder #4.3 volumeCutoff 200 boxAtoms sel boxPad 0 > open /var/folders/5h/hr_gkrdx6yz7g31vtv0815pc0000gn/T/tmp512qffcn.bild id > 4.3.1 name ""cavity search box"" Opened BILD data containing 15 objects ===== Log before crash end ===== Log: > set bgColor aliceblue > windowsize 570 570 > ui mousemode right zoom > camera ortho > color name bluishwhite rgb(201, 218,222) Color 'bluishwhite' is opaque: rgb(78.8%, 85.5%, 87.1%) hex: #c9dade > ~label UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15H00105LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 Performance and 2 Efficiency) Memory: 32 GB System Firmware Version: 18000.120.36 OS Loader Version: 18000.120.36 Software: System Software Overview: System Version: macOS 26.5.1 (25F80) Kernel Version: Darwin 25.5.0 Time since boot: 26 days, 13 hours, 1 minute Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 MolecularDynamicsViewer: 1.6 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.16.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 2.4.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 plotly: 6.5.2 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.14.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect feedback normal Surface/Binding Analysis all ChimeraX