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Opened 3 hours ago
#20557 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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 "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/kvfinder/tool.py", line 131 in
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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.pdb_lib._load_libs, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imaging, PIL._imagingmath, chimerax.core._mac_util, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lxml._elementpath, lxml.etree, pyKVFinder._pyKVFinder, zmq.backend.cython._zmq, tornado.speedups, PyQt6.QtSvg (total: 60)
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"procLaunch" : "2026-06-30 12:56:47.1775 -0400",
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"bundleInfo" : {"CFBundleShortVersionString":"1.12.0","CFBundleVersion":"1.12.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn"]},
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4366909440
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 10449c000-1044a0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.12.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":65502},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4366909440
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 10449c000-1044a0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.12.app\/Contents\/MacOS\/ChimeraX",
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===== 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
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