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Opened 2 hours ago
#19927 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-26.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000179d57000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000178d4b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x000000020a43f080 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.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-1.11.1.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.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 52)
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"procLaunch" : "2026-03-04 21:05:45.6928 +0800",
"procStartAbsTime" : 774665855591,
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"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "A1E950EC-7C27-3106-B903-CB6C78EE76C5",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage","selectedLanguageDoesNotMatchSelectedSiriLanguageInfo(system: en, siri: zh)","regionIneligible"]},
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 9821,
"sleepWakeUUID" : "5A9A03F0-813E-44EE-9C2B-E009E4F565B4",
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4374527992
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104be0000-104be4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3790},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4374527992
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jillzhou/Desktop/INBIOSIS/docking result for
> paper/3/notch3.jpg"
Opened image notch3.jpg
> close
> open "/Users/jillzhou/Desktop/INBIOSIS/docking result for
> paper/3/Notch.pdbqt" "/Users/jillzhou/Desktop/INBIOSIS/docking result for
> paper/3/notch3.pdbqt"
Summary of feedback from opening /Users/jillzhou/Desktop/INBIOSIS/docking
result for paper/3/notch3.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.6 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 0 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
ROOT
Ignored bad PDB record found on line 24
ENDROOT
49 messages similar to the above omitted
Chain information for Notch.pdb #1
---
Chain | Description
A | No description available
B | No description available
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
Opened Notch.pdbqt containing 1 structures (3610 atoms, 3648 bonds)
Opened notch3.pdbqt containing 9 structures (162 atoms, 180 bonds)
> select #1/B:131
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> set bgColor white
> select #1/B
1792 atoms, 1811 bonds, 189 residues, 1 model selected
> hide sel cartoons
> select #1/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
72 atoms, 72 bonds, 8 residues, 1 model selected
> select up
1818 atoms, 1837 bonds, 193 residues, 1 model selected
> color sel hot pink
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> color sel light gray
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> color sel magenta
> color sel cyan
> color sel forest green
> color sel hot pink
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
> select #1/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
57 atoms, 58 bonds, 7 residues, 1 model selected
> select up
1818 atoms, 1837 bonds, 193 residues, 1 model selected
No Surface models open
> surface sel
> transparency (#!1 & sel) 60
> select clear
> color #1 #ff69b448
> color #1 #ff69b44f
> color #1 #ff69b495
> color #1 #ff69b498
> color #1 #ff69b499
> undo
> transparency #1#2.1#!2 60
> redo
> close #1
> open "/Users/jillzhou/Desktop/INBIOSIS/docking result for
> paper/3/Notch.pdbqt"
Chain information for Notch.pdb #1
---
Chain | Description
A | No description available
B | No description available
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Opened Notch.pdbqt containing 1 structures (3610 atoms, 3648 bonds)
Computing secondary structure
> select #1/B
1792 atoms, 1811 bonds, 189 residues, 1 model selected
> hide sel cartoons
> select #1/A:107
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
93 atoms, 93 bonds, 9 residues, 1 model selected
> select up
1818 atoms, 1837 bonds, 193 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> color (#!1 & sel) hot pink
> color #1 #ff69b4b4
> color #1 #ff69b4bb
> color #1 #ff69b4d0
> color #1 #ff69b4cc
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
18 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel ignoreHiddenModels true makePseudobonds false showDist true
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
32 contacts
atom1 atom2 overlap distance
notch3.pdb #2.1/? UNL 1 Cl2 Notch.pdb #1/A ALA 135 CB 0.511 3.249
notch3.pdb #2.1/? UNL 1 C13 Notch.pdb #1/A LEU 140 CD2 0.293 3.347
notch3.pdb #2.1/? UNL 1 C11 Notch.pdb #1/A GLU 141 CB 0.229 3.411
notch3.pdb #2.1/? UNL 1 Cl1 Notch.pdb #1/A GLY 138 CA 0.065 3.695
notch3.pdb #2.1/? UNL 1 O2 Notch.pdb #1/A ASN 169 OD1 0.012 2.888
notch3.pdb #2.1/? UNL 1 Cl2 Notch.pdb #1/A ASN 169 OD1 0.007 3.353
notch3.pdb #2.1/? UNL 1 Cl2 Notch.pdb #1/A ALA 135 CA 0.001 3.759
notch3.pdb #2.1/? UNL 1 C5 Notch.pdb #1/A GLY 138 HN -0.067 2.677
notch3.pdb #2.1/? UNL 1 C1 Notch.pdb #1/A GLY 138 HN -0.084 2.694
notch3.pdb #2.1/? UNL 1 C10 Notch.pdb #1/A GLU 137 CD -0.093 3.553
notch3.pdb #2.1/? UNL 1 C13 Notch.pdb #1/A VAL 175 CG2 -0.100 3.740
notch3.pdb #2.1/? UNL 1 C10 Notch.pdb #1/A GLU 137 CB -0.125 3.765
notch3.pdb #2.1/? UNL 1 Cl1 Notch.pdb #1/A GLU 141 OE1 -0.129 3.489
notch3.pdb #2.1/? UNL 1 Cl2 Notch.pdb #1/A ALA 135 O -0.140 3.500
notch3.pdb #2.1/? UNL 1 C9 Notch.pdb #1/A ALA 172 CA -0.146 3.786
notch3.pdb #2.1/? UNL 1 C13 Notch.pdb #1/A LEU 140 CB -0.158 3.798
notch3.pdb #2.1/? UNL 1 C10 Notch.pdb #1/A GLU 137 CG -0.169 3.809
notch3.pdb #2.1/? UNL 1 C10 Notch.pdb #1/A GLU 137 OE2 -0.197 3.437
notch3.pdb #2.1/? UNL 1 C11 Notch.pdb #1/A VAL 175 CG2 -0.200 3.840
notch3.pdb #2.1/? UNL 1 O1 Notch.pdb #1/A GLU 137 CG -0.238 3.538
notch3.pdb #2.1/? UNL 1 C7 Notch.pdb #1/A GLY 138 HN -0.283 2.893
notch3.pdb #2.1/? UNL 1 C9 Notch.pdb #1/A LEU 140 CD2 -0.293 3.933
notch3.pdb #2.1/? UNL 1 C6 Notch.pdb #1/A ASP 171 CB -0.294 3.784
notch3.pdb #2.1/? UNL 1 C4 Notch.pdb #1/A GLU 137 CA -0.303 3.793
notch3.pdb #2.1/? UNL 1 C11 Notch.pdb #1/A GLU 141 HN -0.308 3.068
notch3.pdb #2.1/? UNL 1 C10 Notch.pdb #1/A GLU 137 CA -0.313 3.953
notch3.pdb #2.1/? UNL 1 Cl2 Notch.pdb #1/A ASN 169 CG -0.324 3.904
notch3.pdb #2.1/? UNL 1 Cl2 Notch.pdb #1/A ALA 135 C -0.326 3.906
notch3.pdb #2.1/? UNL 1 Cl1 Notch.pdb #1/A GLY 138 N -0.341 3.846
notch3.pdb #2.1/? UNL 1 O1 Notch.pdb #1/A GLU 137 OE2 -0.353 3.253
notch3.pdb #2.1/? UNL 1 Cl1 Notch.pdb #1/A GLY 138 HN -0.378 3.258
notch3.pdb #2.1/? UNL 1 O2 Notch.pdb #1/A ASN 169 CG -0.397 3.517
32 contacts
> ui tool show H-Bonds
> hbonds sel makePseudobonds false color #faf01e showDist true reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2.1 notch3.pdb
2.2 notch3.pdb
2.3 notch3.pdb
2.4 notch3.pdb
2.5 notch3.pdb
2.6 notch3.pdb
2.7 notch3.pdb
2.8 notch3.pdb
2.9 notch3.pdb
1 Notch.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
Notch.pdb #1/A ASN 169 ND2 notch3.pdb #2.1/? UNL 1 O2 Notch.pdb #1/A ASN 169 2HD2 3.360 2.528
1 hydrogen bonds found
> hbonds sel makePseudobonds false color #faf01e showDist true reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2.1 notch3.pdb
2.2 notch3.pdb
2.3 notch3.pdb
2.4 notch3.pdb
2.5 notch3.pdb
2.6 notch3.pdb
2.7 notch3.pdb
2.8 notch3.pdb
2.9 notch3.pdb
1 Notch.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
Notch.pdb #1/A ASN 169 ND2 notch3.pdb #2.1/? UNL 1 O2 Notch.pdb #1/A ASN 169 2HD2 3.360 2.528
1 hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> undo
> select #1/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
22 atoms, 21 bonds, 2 residues, 2 models selected
> undo
> color (#!1 & sel) byelement
> select clear
> show #2.1#!1 surfaces
> hide #2.1#!1 surfaces
> select #1/A:200
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
76 atoms, 77 bonds, 8 residues, 2 models selected
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 60
> select clear
> hide #2.1#!1 surfaces
> show #2.1#!1 surfaces
> hide #2.1#!1 surfaces
> select #1/A:191
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
133 atoms, 132 bonds, 13 residues, 2 models selected
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> surface style #1.1 mesh
> undo
> surface style #1.1 solid
> transparency (#!1 & sel) 80
> transparency (#!1 & sel) 60
> color #1 hotpink
> select #1/A:170@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
54 atoms, 53 bonds, 7 residues, 2 models selected
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> select up
3610 atoms, 3648 bonds, 382 residues, 2 models selected
> select up
3610 atoms, 3648 bonds, 382 residues, 3 models selected
> select #1/A:200@CB
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 2 models selected
> select up
76 atoms, 77 bonds, 8 residues, 2 models selected
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> select up
3610 atoms, 3648 bonds, 382 residues, 2 models selected
> undo
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> transparency (#!1 & sel) 60
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> undo
> hide sel surfaces
> select clear
> hide #2.1#!1 surfaces
> select #1/A:196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
76 atoms, 77 bonds, 8 residues, 2 models selected
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> show sel surfaces
> show sel cartoons
> hide sel cartoons
> close #1
> close #2
> close #
Expected a models specifier or a keyword
> open "/Users/jillzhou/Desktop/INBIOSIS/docking result for
> paper/3/notch3.pdbqt" "/Users/jillzhou/Desktop/INBIOSIS/docking result for
> paper/3/Notch.pdbqt"
Summary of feedback from opening /Users/jillzhou/Desktop/INBIOSIS/docking
result for paper/3/notch3.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.6 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 0 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
ROOT
Ignored bad PDB record found on line 24
ENDROOT
49 messages similar to the above omitted
Chain information for Notch.pdb #2
---
Chain | Description
A | No description available
B | No description available
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
Opened notch3.pdbqt containing 9 structures (162 atoms, 180 bonds)
Opened Notch.pdbqt containing 1 structures (3610 atoms, 3648 bonds)
> select #2/B
1792 atoms, 1811 bonds, 189 residues, 1 model selected
> hide sel cartoons
> cartoon suppressBackboneDisplay false
> hide sel surfaces
> hide sel cartoons
> select #2/A:132
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
72 atoms, 72 bonds, 8 residues, 1 model selected
> select up
1818 atoms, 1837 bonds, 193 residues, 1 model selected
> cartoon suppressBackboneDisplay false
> select clear
> select #2/B:96
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
57 atoms, 58 bonds, 7 residues, 1 model selected
> select up
1792 atoms, 1811 bonds, 189 residues, 1 model selected
> hide sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
18 atoms, 20 bonds, 1 residue, 1 model selected
> cartoon suppressBackboneDisplay false
> select clear\
Expected an objects specifier or a keyword
> select clear
> select #2/B:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
66 atoms, 66 bonds, 7 residues, 1 model selected
> select up
1792 atoms, 1811 bonds, 189 residues, 1 model selected
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
18 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel ignoreHiddenModels true makePseudobonds false showDist true
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
32 contacts
atom1 atom2 overlap distance
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 CB 0.511 3.249
notch3.pdb #1.1/? UNL 1 C13 Notch.pdb #2/A LEU 140 CD2 0.293 3.347
notch3.pdb #1.1/? UNL 1 C11 Notch.pdb #2/A GLU 141 CB 0.229 3.411
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLY 138 CA 0.065 3.695
notch3.pdb #1.1/? UNL 1 O2 Notch.pdb #2/A ASN 169 OD1 0.012 2.888
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ASN 169 OD1 0.007 3.353
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 CA 0.001 3.759
notch3.pdb #1.1/? UNL 1 C5 Notch.pdb #2/A GLY 138 HN -0.067 2.677
notch3.pdb #1.1/? UNL 1 C1 Notch.pdb #2/A GLY 138 HN -0.084 2.694
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CD -0.093 3.553
notch3.pdb #1.1/? UNL 1 C13 Notch.pdb #2/A VAL 175 CG2 -0.100 3.740
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CB -0.125 3.765
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLU 141 OE1 -0.129 3.489
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 O -0.140 3.500
notch3.pdb #1.1/? UNL 1 C9 Notch.pdb #2/A ALA 172 CA -0.146 3.786
notch3.pdb #1.1/? UNL 1 C13 Notch.pdb #2/A LEU 140 CB -0.158 3.798
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CG -0.169 3.809
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 OE2 -0.197 3.437
notch3.pdb #1.1/? UNL 1 C11 Notch.pdb #2/A VAL 175 CG2 -0.200 3.840
notch3.pdb #1.1/? UNL 1 O1 Notch.pdb #2/A GLU 137 CG -0.238 3.538
notch3.pdb #1.1/? UNL 1 C7 Notch.pdb #2/A GLY 138 HN -0.283 2.893
notch3.pdb #1.1/? UNL 1 C9 Notch.pdb #2/A LEU 140 CD2 -0.293 3.933
notch3.pdb #1.1/? UNL 1 C6 Notch.pdb #2/A ASP 171 CB -0.294 3.784
notch3.pdb #1.1/? UNL 1 C4 Notch.pdb #2/A GLU 137 CA -0.303 3.793
notch3.pdb #1.1/? UNL 1 C11 Notch.pdb #2/A GLU 141 HN -0.308 3.068
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CA -0.313 3.953
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ASN 169 CG -0.324 3.904
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 C -0.326 3.906
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLY 138 N -0.341 3.846
notch3.pdb #1.1/? UNL 1 O1 Notch.pdb #2/A GLU 137 OE2 -0.353 3.253
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLY 138 HN -0.378 3.258
notch3.pdb #1.1/? UNL 1 O2 Notch.pdb #2/A ASN 169 CG -0.397 3.517
32 contacts
> contacts sel ignoreHiddenModels true makePseudobonds false showDist true
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
32 contacts
atom1 atom2 overlap distance
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 CB 0.511 3.249
notch3.pdb #1.1/? UNL 1 C13 Notch.pdb #2/A LEU 140 CD2 0.293 3.347
notch3.pdb #1.1/? UNL 1 C11 Notch.pdb #2/A GLU 141 CB 0.229 3.411
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLY 138 CA 0.065 3.695
notch3.pdb #1.1/? UNL 1 O2 Notch.pdb #2/A ASN 169 OD1 0.012 2.888
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ASN 169 OD1 0.007 3.353
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 CA 0.001 3.759
notch3.pdb #1.1/? UNL 1 C5 Notch.pdb #2/A GLY 138 HN -0.067 2.677
notch3.pdb #1.1/? UNL 1 C1 Notch.pdb #2/A GLY 138 HN -0.084 2.694
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CD -0.093 3.553
notch3.pdb #1.1/? UNL 1 C13 Notch.pdb #2/A VAL 175 CG2 -0.100 3.740
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CB -0.125 3.765
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLU 141 OE1 -0.129 3.489
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 O -0.140 3.500
notch3.pdb #1.1/? UNL 1 C9 Notch.pdb #2/A ALA 172 CA -0.146 3.786
notch3.pdb #1.1/? UNL 1 C13 Notch.pdb #2/A LEU 140 CB -0.158 3.798
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CG -0.169 3.809
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 OE2 -0.197 3.437
notch3.pdb #1.1/? UNL 1 C11 Notch.pdb #2/A VAL 175 CG2 -0.200 3.840
notch3.pdb #1.1/? UNL 1 O1 Notch.pdb #2/A GLU 137 CG -0.238 3.538
notch3.pdb #1.1/? UNL 1 C7 Notch.pdb #2/A GLY 138 HN -0.283 2.893
notch3.pdb #1.1/? UNL 1 C9 Notch.pdb #2/A LEU 140 CD2 -0.293 3.933
notch3.pdb #1.1/? UNL 1 C6 Notch.pdb #2/A ASP 171 CB -0.294 3.784
notch3.pdb #1.1/? UNL 1 C4 Notch.pdb #2/A GLU 137 CA -0.303 3.793
notch3.pdb #1.1/? UNL 1 C11 Notch.pdb #2/A GLU 141 HN -0.308 3.068
notch3.pdb #1.1/? UNL 1 C10 Notch.pdb #2/A GLU 137 CA -0.313 3.953
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ASN 169 CG -0.324 3.904
notch3.pdb #1.1/? UNL 1 Cl2 Notch.pdb #2/A ALA 135 C -0.326 3.906
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLY 138 N -0.341 3.846
notch3.pdb #1.1/? UNL 1 O1 Notch.pdb #2/A GLU 137 OE2 -0.353 3.253
notch3.pdb #1.1/? UNL 1 Cl1 Notch.pdb #2/A GLY 138 HN -0.378 3.258
notch3.pdb #1.1/? UNL 1 O2 Notch.pdb #2/A ASN 169 CG -0.397 3.517
32 contacts
> select clear
> select #2/A:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
70 atoms, 72 bonds, 8 residues, 1 model selected
> select up
1818 atoms, 1837 bonds, 193 residues, 1 model selected
> show sel surfaces
> transparency (#!2 & sel) 60
> select clear
> select #2/A:99@CB
1 atom, 1 residue, 1 model selected
> select clear
> transparency #2#1.1#!1 50
> transparency #2#1.1#!1 90
> transparency #2#1.1#!1 80
> select #2/A:170@N
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:141@OE1
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:135@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:134@C
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:134@C
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:135@CB
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #2/A:163@CH2
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:163@CH2
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 17 bonds, 1 residue, 2 models selected
> select up
70 atoms, 72 bonds, 8 residues, 2 models selected
> select up
1818 atoms, 1837 bonds, 193 residues, 2 models selected
> hide sel surfaces
> select clear
> select #2/A:135@HN
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!2 & sel) blue
> color (#!2 & sel) medium blue
> color (#!2 & sel) byhetero
> color (#!2 & sel) cyan
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select #2/B:64
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
66 atoms, 66 bonds, 7 residues, 1 model selected
> select up
1792 atoms, 1811 bonds, 189 residues, 1 model selected
> hide sel cartoons
> ui tool show H-Bonds
> hbonds sel makePseudobonds false color #faf01e showDist true reveal true log
> true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1.1 notch3.pdb
1.2 notch3.pdb
1.3 notch3.pdb
1.4 notch3.pdb
1.5 notch3.pdb
1.6 notch3.pdb
1.7 notch3.pdb
1.8 notch3.pdb
1.9 notch3.pdb
2 Notch.pdb
180 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
Notch.pdb #2/A HIS 236 N Notch.pdb #2/B ASP 71 OD2 Notch.pdb #2/A HIS 236 HN 3.290 2.518
Notch.pdb #2/A ARG 240 NH1 Notch.pdb #2/B SER 68 O Notch.pdb #2/A ARG 240 2HH1 3.050 2.346
Notch.pdb #2/B HIS 62 ND1 Notch.pdb #2/B THR 59 OG1 Notch.pdb #2/B HIS 62 HD1 2.954 2.048
Notch.pdb #2/B HIS 62 NE2 Notch.pdb #2/B ARG 91 O Notch.pdb #2/B HIS 62 HE2 2.736 1.738
Notch.pdb #2/B LEU 63 N Notch.pdb #2/B THR 59 O Notch.pdb #2/B LEU 63 HN 3.136 2.149
Notch.pdb #2/B ALA 64 N Notch.pdb #2/B ALA 60 O Notch.pdb #2/B ALA 64 HN 2.929 2.029
Notch.pdb #2/B ALA 65 N Notch.pdb #2/B LEU 61 O Notch.pdb #2/B ALA 65 HN 3.030 2.034
Notch.pdb #2/B ARG 66 N Notch.pdb #2/B HIS 62 O Notch.pdb #2/B ARG 66 HN 2.860 1.866
Notch.pdb #2/B ARG 66 NE Notch.pdb #2/B GLU 58 OE2 Notch.pdb #2/B ARG 66 HE 2.873 1.951
Notch.pdb #2/B ARG 66 NH2 Notch.pdb #2/B GLU 58 OE2 Notch.pdb #2/B ARG 66 2HH2 2.985 2.121
Notch.pdb #2/B TYR 67 N Notch.pdb #2/B LEU 63 O Notch.pdb #2/B TYR 67 HN 2.985 2.073
Notch.pdb #2/B SER 68 N Notch.pdb #2/B ALA 65 O Notch.pdb #2/B SER 68 HN 3.211 2.206
Notch.pdb #2/B ARG 69 N Notch.pdb #2/B ALA 64 O Notch.pdb #2/B ARG 69 HN 2.803 1.801
Notch.pdb #2/B ARG 69 NH1 Notch.pdb #2/A GLU 204 OE2 Notch.pdb #2/B ARG 69 1HH1 2.858 1.915
Notch.pdb #2/B ASP 71 N Notch.pdb #2/A ASP 237 OD1 Notch.pdb #2/B ASP 71 HN 2.850 1.865
Notch.pdb #2/B ALA 72 N Notch.pdb #2/A ASP 237 OD2 Notch.pdb #2/B ALA 72 HN 3.001 2.044
Notch.pdb #2/B ALA 73 N Notch.pdb #2/B ARG 69 O Notch.pdb #2/B ALA 73 HN 3.081 2.088
Notch.pdb #2/B LYS 74 N Notch.pdb #2/B SER 70 O Notch.pdb #2/B LYS 74 HN 3.054 2.041
Notch.pdb #2/B ARG 75 N Notch.pdb #2/B ASP 71 O Notch.pdb #2/B ARG 75 HN 3.028 2.032
Notch.pdb #2/B LEU 76 N Notch.pdb #2/B ALA 72 O Notch.pdb #2/B LEU 76 HN 2.931 1.996
Notch.pdb #2/B LEU 77 N Notch.pdb #2/B ALA 73 O Notch.pdb #2/B LEU 77 HN 3.089 2.084
Notch.pdb #2/B GLU 78 N Notch.pdb #2/B LYS 74 O Notch.pdb #2/B GLU 78 HN 2.811 1.845
Notch.pdb #2/B ALA 79 N Notch.pdb #2/B ARG 75 O Notch.pdb #2/B ALA 79 HN 3.118 2.376
Notch.pdb #2/B ALA 79 N Notch.pdb #2/B LEU 76 O Notch.pdb #2/B ALA 79 HN 3.154 2.400
Notch.pdb #2/B SER 80 N Notch.pdb #2/B LEU 77 O Notch.pdb #2/B SER 80 HN 2.888 2.003
Notch.pdb #2/B ALA 81 N Notch.pdb #2/B LEU 76 O Notch.pdb #2/B ALA 81 HN 2.902 1.933
Notch.pdb #2/B ASN 84 N Notch.pdb #2/B ASP 82 OD1 Notch.pdb #2/B ASN 84 HN 2.922 1.935
Notch.pdb #2/B ASN 84 ND2 Notch.pdb #2/B ALA 114 O Notch.pdb #2/B ASN 84 2HD2 2.914 1.928
Notch.pdb #2/B GLN 86 NE2 Notch.pdb #2/B GLY 90 O Notch.pdb #2/B GLN 86 1HE2 3.202 2.343
Notch.pdb #2/B GLN 86 NE2 Notch.pdb #2/B ARG 120 O Notch.pdb #2/B GLN 86 1HE2 3.159 2.539
Notch.pdb #2/B ASP 87 N Notch.pdb #2/B ARG 91 O Notch.pdb #2/B ASP 87 HN 2.751 1.782
Notch.pdb #2/B ASN 88 N Notch.pdb #2/B THR 56 O Notch.pdb #2/B ASN 88 HN 2.912 1.928
Notch.pdb #2/B MET 89 N Notch.pdb #2/B ASP 87 OD1 Notch.pdb #2/B MET 89 HN 2.849 2.031
Notch.pdb #2/B GLY 90 N Notch.pdb #2/B ASP 87 O Notch.pdb #2/B GLY 90 HN 3.017 2.057
Notch.pdb #2/B ARG 91 N Notch.pdb #2/B ASP 87 OD1 Notch.pdb #2/B ARG 91 HN 2.972 2.110
Notch.pdb #2/B ARG 91 NE Notch.pdb #2/B ASP 87 OD1 Notch.pdb #2/B ARG 91 HE 3.535 2.572
Notch.pdb #2/B ARG 91 NE Notch.pdb #2/B ASP 87 OD2 Notch.pdb #2/B ARG 91 HE 2.654 1.751
Notch.pdb #2/B ARG 91 NH2 Notch.pdb #2/B ASP 87 OD2 Notch.pdb #2/B ARG 91 2HH2 3.095 2.366
Notch.pdb #2/B HIS 95 NE2 Notch.pdb #2/B THR 125 O Notch.pdb #2/B HIS 95 HE2 2.978 2.163
Notch.pdb #2/B ALA 96 N Notch.pdb #2/B THR 92 O Notch.pdb #2/B ALA 96 HN 3.149 2.167
Notch.pdb #2/B ALA 97 N Notch.pdb #2/B PRO 93 O Notch.pdb #2/B ALA 97 HN 2.869 1.966
Notch.pdb #2/B VAL 98 N Notch.pdb #2/B LEU 94 O Notch.pdb #2/B VAL 98 HN 3.119 2.134
Notch.pdb #2/B SER 99 N Notch.pdb #2/B HIS 95 O Notch.pdb #2/B SER 99 HN 2.858 1.859
Notch.pdb #2/B ALA 100 N Notch.pdb #2/B ALA 96 O Notch.pdb #2/B ALA 100 HN 2.843 1.921
Notch.pdb #2/B ASP 101 N Notch.pdb #2/B VAL 98 O Notch.pdb #2/B ASP 101 HN 3.019 2.068
Notch.pdb #2/B ALA 102 N Notch.pdb #2/B ALA 97 O Notch.pdb #2/B ALA 102 HN 2.845 1.850
Notch.pdb #2/B PHE 106 N Notch.pdb #2/B ALA 102 O Notch.pdb #2/B PHE 106 HN 2.858 1.881
Notch.pdb #2/B GLN 107 N Notch.pdb #2/B GLN 103 O Notch.pdb #2/B GLN 107 HN 2.947 1.953
Notch.pdb #2/B GLN 107 NE2 Notch.pdb #2/B GLN 103 OE1 (alt loc B, occupancy 0.5) Notch.pdb #2/B GLN 107 2HE2 2.749 1.769
Notch.pdb #2/B GLN 107 NE2 Notch.pdb #2/B ASP 142 OD2 Notch.pdb #2/B GLN 107 1HE2 2.751 1.886
Notch.pdb #2/B ILE 108 N Notch.pdb #2/B GLY 104 O Notch.pdb #2/B ILE 108 HN 3.143 2.143
Notch.pdb #2/B LEU 109 N Notch.pdb #2/B VAL 105 O Notch.pdb #2/B LEU 109 HN 2.855 1.881
Notch.pdb #2/B ILE 110 N Notch.pdb #2/B PHE 106 O Notch.pdb #2/B ILE 110 HN 2.918 1.942
Notch.pdb #2/B ARG 111 N Notch.pdb #2/B GLN 107 O Notch.pdb #2/B ARG 111 HN 3.018 2.142
Notch.pdb #2/B ASN 112 N Notch.pdb #2/B LEU 109 O Notch.pdb #2/B ASN 112 HN 3.270 2.437
Notch.pdb #2/B ASN 112 ND2 Notch.pdb #2/B THR 115 OG1 Notch.pdb #2/B ASN 112 2HD2 3.125 2.146
Notch.pdb #2/B THR 115 N Notch.pdb #2/B ASN 112 O Notch.pdb #2/B THR 115 HN 3.124 2.181
Notch.pdb #2/B THR 115 OG1 Notch.pdb #2/B ASN 112 O Notch.pdb #2/B THR 115 HG1 3.266 2.612
Notch.pdb #2/B ASP 116 N Notch.pdb #2/B ASN 84 OD1 Notch.pdb #2/B ASP 116 HN 2.777 1.765
Notch.pdb #2/B ASP 118 N Notch.pdb #2/B ASP 116 OD1 Notch.pdb #2/B ASP 118 HN 2.877 1.981
Notch.pdb #2/B ALA 119 N Notch.pdb #2/B ASP 116 O Notch.pdb #2/B ALA 119 HN 3.421 2.478
Notch.pdb #2/B ARG 120 NH1 Notch.pdb #2/B VAL 153 O Notch.pdb #2/B ARG 120 2HH1 2.796 1.923
Notch.pdb #2/B ARG 120 NH2 Notch.pdb #2/B VAL 153 O Notch.pdb #2/B ARG 120 2HH2 2.807 1.931
Notch.pdb #2/B ARG 120 NH2 Notch.pdb #2/B ASP 155 OD1 Notch.pdb #2/B ARG 120 1HH2 3.265 2.324
Notch.pdb #2/B MET 121 N Notch.pdb #2/B THR 125 O Notch.pdb #2/B MET 121 HN 2.805 1.793
Notch.pdb #2/B HIS 122 N Notch.pdb #2/B MET 89 O Notch.pdb #2/B HIS 122 HN 3.050 2.036
Notch.pdb #2/B GLY 124 N Notch.pdb #2/B MET 121 O Notch.pdb #2/B GLY 124 HN 2.885 1.941
Notch.pdb #2/B THR 125 N Notch.pdb #2/B ASP 123 OD1 Notch.pdb #2/B THR 125 HN 3.083 2.138
Notch.pdb #2/B THR 125 OG1 Notch.pdb #2/B ASP 123 OD1 Notch.pdb #2/B THR 125 HG1 2.771 1.932
Notch.pdb #2/B LEU 130 N Notch.pdb #2/B THR 126 O Notch.pdb #2/B LEU 130 HN 2.949 1.941
Notch.pdb #2/B ALA 131 N Notch.pdb #2/B PRO 127 O Notch.pdb #2/B ALA 131 HN 2.838 1.876
Notch.pdb #2/B ALA 132 N Notch.pdb #2/B LEU 128 O Notch.pdb #2/B ALA 132 HN 3.031 2.051
Notch.pdb #2/B ARG 133 N Notch.pdb #2/B ILE 129 O Notch.pdb #2/B ARG 133 HN 2.890 1.881
Notch.pdb #2/B LEU 134 N Notch.pdb #2/B LEU 130 O Notch.pdb #2/B LEU 134 HN 2.918 1.960
Notch.pdb #2/B MET 139 N Notch.pdb #2/B GLU 137 O Notch.pdb #2/B MET 139 HN 2.850 2.095
Notch.pdb #2/B ASP 142 N Notch.pdb #2/B GLY 138 O Notch.pdb #2/B ASP 142 HN 3.103 2.105
Notch.pdb #2/B LEU 143 N Notch.pdb #2/B MET 139 O Notch.pdb #2/B LEU 143 HN 2.835 1.834
Notch.pdb #2/B ILE 144 N Notch.pdb #2/B LEU 140 O Notch.pdb #2/B ILE 144 HN 3.050 2.042
Notch.pdb #2/B ASN 145 N Notch.pdb #2/B GLU 141 O Notch.pdb #2/B ASN 145 HN 2.779 1.821
Notch.pdb #2/B SER 146 N Notch.pdb #2/B ASP 142 O Notch.pdb #2/B SER 146 HN 3.031 2.215
Notch.pdb #2/B SER 146 N Notch.pdb #2/B LEU 143 O Notch.pdb #2/B SER 146 HN 3.140 2.424
Notch.pdb #2/B HIS 147 N Notch.pdb #2/B ILE 144 O Notch.pdb #2/B HIS 147 HN 3.015 2.081
Notch.pdb #2/B ALA 148 N Notch.pdb #2/B LEU 143 O Notch.pdb #2/B ALA 148 HN 2.995 2.004
Notch.pdb #2/B ASP 149 N Notch.pdb #2/B ASP 118 OD1 Notch.pdb #2/B ASP 149 HN 2.810 1.804
Notch.pdb #2/B ASN 151 N Notch.pdb #2/B ASP 149 OD1 Notch.pdb #2/B ASN 151 HN 2.964 2.039
Notch.pdb #2/B ASN 151 ND2 Notch.pdb #2/B GLY 180 O Notch.pdb #2/B ASN 151 2HD2 3.423 2.518
Notch.pdb #2/B ALA 152 N Notch.pdb #2/B ASP 149 O Notch.pdb #2/B ALA 152 HN 3.397 2.389
Notch.pdb #2/B ASP 154 N Notch.pdb #2/B LYS 158 O Notch.pdb #2/B ASP 154 HN 2.922 1.924
Notch.pdb #2/B ASP 155 N Notch.pdb #2/B ASP 123 O Notch.pdb #2/B ASP 155 HN 2.970 1.978
Notch.pdb #2/B LEU 156 N Notch.pdb #2/B ASP 154 OD1 Notch.pdb #2/B LEU 156 HN 2.947 2.165
Notch.pdb #2/B GLY 157 N Notch.pdb #2/B ASP 154 O Notch.pdb #2/B GLY 157 HN 2.888 1.930
Notch.pdb #2/B LYS 158 N Notch.pdb #2/B ASP 154 OD1 Notch.pdb #2/B LYS 158 HN 3.023 2.094
Notch.pdb #2/B HIS 162 N Notch.pdb #2/B SER 159 OG Notch.pdb #2/B HIS 162 HN 3.168 2.181
Notch.pdb #2/B HIS 162 ND1 Notch.pdb #2/B SER 159 OG Notch.pdb #2/B HIS 162 HD1 2.956 2.093
Notch.pdb #2/B HIS 162 NE2 Notch.pdb #2/B GLU 191 O Notch.pdb #2/B HIS 162 HE2 2.882 1.997
Notch.pdb #2/B TRP 163 N Notch.pdb #2/B SER 159 O Notch.pdb #2/B TRP 163 HN 3.183 2.189
Notch.pdb #2/B TRP 163 NE1 Notch.pdb #2/B ASP 154 OD2 Notch.pdb #2/B TRP 163 HE1 2.893 1.902
Notch.pdb #2/B ALA 164 N Notch.pdb #2/B ALA 160 O Notch.pdb #2/B ALA 164 HN 2.839 1.858
Notch.pdb #2/B ALA 165 N Notch.pdb #2/B LEU 161 O Notch.pdb #2/B ALA 165 HN 2.993 2.025
Notch.pdb #2/B ALA 166 N Notch.pdb #2/B HIS 162 O Notch.pdb #2/B ALA 166 HN 2.946 1.945
Notch.pdb #2/B VAL 167 N Notch.pdb #2/B TRP 163 O Notch.pdb #2/B VAL 167 HN 3.032 2.064
Notch.pdb #2/B ASN 168 N Notch.pdb #2/B ALA 165 O Notch.pdb #2/B ASN 168 HN 3.328 2.374
Notch.pdb #2/B ASN 168 ND2 Notch.pdb #2/B GLU 204 OE1 Notch.pdb #2/B ASN 168 1HD2 2.867 1.930
Notch.pdb #2/B ASN 169 N Notch.pdb #2/B ALA 164 O Notch.pdb #2/B ASN 169 HN 2.807 1.892
Notch.pdb #2/B ASN 169 ND2 Notch.pdb #2/B ALA 132 O Notch.pdb #2/B ASN 169 1HD2 2.810 1.790
Notch.pdb #2/B ALA 172 N Notch.pdb #2/B ASN 169 OD1 Notch.pdb #2/B ALA 172 HN 3.174 2.213
Notch.pdb #2/B ALA 173 N Notch.pdb #2/B ASN 169 O Notch.pdb #2/B ALA 173 HN 3.079 2.113
Notch.pdb #2/B VAL 174 N Notch.pdb #2/B VAL 170 O Notch.pdb #2/B VAL 174 HN 3.021 2.038
Notch.pdb #2/B VAL 175 N Notch.pdb #2/B ASP 171 O Notch.pdb #2/B VAL 175 HN 3.104 2.092
Notch.pdb #2/B LEU 176 N Notch.pdb #2/B ALA 172 O Notch.pdb #2/B LEU 176 HN 2.872 1.870
Notch.pdb #2/B LEU 177 N Notch.pdb #2/B ALA 173 O Notch.pdb #2/B LEU 177 HN 2.911 1.912
Notch.pdb #2/B LYS 178 N Notch.pdb #2/B VAL 174 O Notch.pdb #2/B LYS 178 HN 3.013 2.034
Notch.pdb #2/B ASN 179 N Notch.pdb #2/B VAL 175 O Notch.pdb #2/B ASN 179 HN 3.099 2.366
Notch.pdb #2/B ASN 179 N Notch.pdb #2/B LEU 176 O Notch.pdb #2/B ASN 179 HN 3.086 2.284
Notch.pdb #2/B ASN 179 ND2 Notch.pdb #2/B VAL 175 O Notch.pdb #2/B ASN 179 2HD2 2.826 1.820
Notch.pdb #2/B GLY 180 N Notch.pdb #2/B LEU 177 O Notch.pdb #2/B GLY 180 HN 3.356 2.361
Notch.pdb #2/B ALA 181 N Notch.pdb #2/B LEU 176 O Notch.pdb #2/B ALA 181 HN 3.013 2.043
Notch.pdb #2/B ASN 182 N Notch.pdb #2/B ASN 151 OD1 Notch.pdb #2/B ASN 182 HN 2.862 1.846
Notch.pdb #2/B LYS 183 NZ Notch.pdb #2/B HIS 212 O Notch.pdb #2/B LYS 183 HZ3 2.759 1.777
Notch.pdb #2/B ASP 184 N Notch.pdb #2/B ASN 182 OD1 Notch.pdb #2/B ASP 184 HN 3.039 2.082
Notch.pdb #2/B MET 185 N Notch.pdb #2/B ASN 182 O Notch.pdb #2/B MET 185 HN 3.323 2.340
Notch.pdb #2/B GLN 186 NE2 Notch.pdb #2/B GLU 190 O Notch.pdb #2/B GLN 186 1HE2 3.056 2.053
Notch.pdb #2/B GLN 186 NE2 Notch.pdb #2/B THR 219 O Notch.pdb #2/B GLN 186 1HE2 3.526 2.911
Notch.pdb #2/B ASN 187 N Notch.pdb #2/B GLU 191 O Notch.pdb #2/B ASN 187 HN 2.947 1.978
Notch.pdb #2/B ASN 187 ND2 Notch.pdb #2/B GLU 191 OE1 Notch.pdb #2/B ASN 187 2HD2 2.860 1.843
Notch.pdb #2/B ASN 188 N Notch.pdb #2/B LEU 156 O Notch.pdb #2/B ASN 188 HN 3.022 2.027
Notch.pdb #2/B ARG 189 NE Notch.pdb #2/B GLU 191 OE2 Notch.pdb #2/B ARG 189 HE 2.877 1.871
Notch.pdb #2/B GLU 190 N Notch.pdb #2/B ASN 187 O Notch.pdb #2/B GLU 190 HN 2.894 1.987
Notch.pdb #2/B GLU 191 N Notch.pdb #2/B ASN 187 OD1 Notch.pdb #2/B GLU 191 HN 2.975 2.022
Notch.pdb #2/B PHE 195 N Notch.pdb #2/B THR 192 OG1 Notch.pdb #2/B PHE 195 HN 3.067 2.098
Notch.pdb #2/B LEU 196 N Notch.pdb #2/B THR 192 O Notch.pdb #2/B LEU 196 HN 3.138 2.168
Notch.pdb #2/B ALA 197 N Notch.pdb #2/B PRO 193 O Notch.pdb #2/B ALA 197 HN 2.897 1.885
Notch.pdb #2/B ALA 198 N Notch.pdb #2/B LEU 194 O Notch.pdb #2/B ALA 198 HN 2.937 1.983
Notch.pdb #2/B ARG 199 N Notch.pdb #2/B PHE 195 O Notch.pdb #2/B ARG 199 HN 2.884 1.894
Notch.pdb #2/B ARG 199 NE Notch.pdb #2/B GLU 200 OE2 Notch.pdb #2/B ARG 199 HE 2.828 1.865
Notch.pdb #2/B GLU 200 N Notch.pdb #2/B LEU 196 O Notch.pdb #2/B GLU 200 HN 2.940 2.019
Notch.pdb #2/B GLY 201 N Notch.pdb #2/B ALA 198 O Notch.pdb #2/B GLY 201 HN 3.473 2.529
Notch.pdb #2/B SER 202 N Notch.pdb #2/B ALA 197 O Notch.pdb #2/B SER 202 HN 2.813 1.842
Notch.pdb #2/B SER 202 OG Notch.pdb #2/B ALA 165 O Notch.pdb #2/B SER 202 HG 2.769 1.911
Notch.pdb #2/B SER 202 OG Notch.pdb #2/B ALA 166 O Notch.pdb #2/B SER 202 HG 3.525 3.001
Notch.pdb #2/B GLU 204 N Notch.pdb #2/B GLU 204 OE1 Notch.pdb #2/B GLU 204 HN 2.734 1.847
Notch.pdb #2/B THR 205 N Notch.pdb #2/B ASN 168 OD1 Notch.pdb #2/B THR 205 HN 3.016 2.127
Notch.pdb #2/B THR 205 OG1 Notch.pdb #2/B ASN 168 OD1 Notch.pdb #2/B THR 205 HG1 2.748 1.879
Notch.pdb #2/B ALA 206 N Notch.pdb #2/B SER 202 O Notch.pdb #2/B ALA 206 HN 2.936 1.939
Notch.pdb #2/B LYS 207 N Notch.pdb #2/B TYR 203 O Notch.pdb #2/B LYS 207 HN 2.869 1.890
Notch.pdb #2/B LYS 207 NZ Notch.pdb #2/B ASP 211 OD1 Notch.pdb #2/B LYS 207 HZ3 3.486 2.718
Notch.pdb #2/B VAL 208 N Notch.pdb #2/B GLU 204 O Notch.pdb #2/B VAL 208 HN 3.218 2.229
Notch.pdb #2/B LEU 209 N Notch.pdb #2/B THR 205 O Notch.pdb #2/B LEU 209 HN 3.021 2.036
Notch.pdb #2/B LEU 210 N Notch.pdb #2/B ALA 206 O Notch.pdb #2/B LEU 210 HN 2.968 1.978
Notch.pdb #2/B ASP 211 N Notch.pdb #2/B LYS 207 O Notch.pdb #2/B ASP 211 HN 2.875 1.884
Notch.pdb #2/B HIS 212 N Notch.pdb #2/B VAL 208 O Notch.pdb #2/B HIS 212 HN 2.995 2.209
Notch.pdb #2/B HIS 212 ND1 Notch.pdb #2/B VAL 208 O Notch.pdb #2/B HIS 212 HD1 3.018 2.110
Notch.pdb #2/B PHE 213 N Notch.pdb #2/B LEU 210 O Notch.pdb #2/B PHE 213 HN 2.976 2.081
Notch.pdb #2/B ALA 214 N Notch.pdb #2/B LEU 209 O Notch.pdb #2/B ALA 214 HN 2.922 1.941
Notch.pdb #2/B ASN 215 N Notch.pdb #2/B ASP 184 OD1 Notch.pdb #2/B ASN 215 HN 2.793 1.779
Notch.pdb #2/B ASP 217 N Notch.pdb #2/B ASN 215 OD1 Notch.pdb #2/B ASP 217 HN 2.873 1.914
Notch.pdb #2/B ASP 220 N Notch.pdb #2/B ARG 224 O Notch.pdb #2/B ASP 220 HN 2.993 2.024
Notch.pdb #2/B HIS 221 N Notch.pdb #2/B ARG 189 O Notch.pdb #2/B HIS 221 HN 2.968 2.141
Notch.pdb #2/B MET 222 N Notch.pdb #2/B ASP 220 OD1 Notch.pdb #2/B MET 222 HN 2.879 2.124
Notch.pdb #2/B ASP 223 N Notch.pdb #2/B ASP 220 O Notch.pdb #2/B ASP 223 HN 2.850 1.911
Notch.pdb #2/B ARG 224 N Notch.pdb #2/B ASP 220 OD1 Notch.pdb #2/B ARG 224 HN 2.882 1.884
Notch.pdb #2/B ARG 224 NE Notch.pdb #2/B ASP 220 OD1 Notch.pdb #2/B ARG 224 HE 3.522 2.584
Notch.pdb #2/B LEU 225 N Notch.pdb #2/B ASP 228 OD2 Notch.pdb #2/B LEU 225 HN 2.872 1.854
Notch.pdb #2/B ARG 227 NE Notch.pdb #2/B ASP 243 OD1 Notch.pdb #2/B ARG 227 HE 2.786 1.806
Notch.pdb #2/B ARG 227 NH2 Notch.pdb #2/B ASP 243 OD1 Notch.pdb #2/B ARG 227 1HH2 3.264 2.490
Notch.pdb #2/B ARG 227 NH2 Notch.pdb #2/B ASP 243 OD2 Notch.pdb #2/B ARG 227 1HH2 2.766 1.759
Notch.pdb #2/B ILE 229 N Notch.pdb #2/B LEU 225 O Notch.pdb #2/B ILE 229 HN 3.063 2.066
Notch.pdb #2/B ALA 230 N Notch.pdb #2/B PRO 226 O Notch.pdb #2/B ALA 230 HN 3.001 2.011
Notch.pdb #2/B GLN 231 N Notch.pdb #2/B ARG 227 O Notch.pdb #2/B GLN 231 HN 3.025 2.047
Notch.pdb #2/B GLU 232 N Notch.pdb #2/B ASP 228 O Notch.pdb #2/B GLU 232 HN 2.897 1.896
Notch.pdb #2/B ARG 233 N Notch.pdb #2/B ILE 229 O Notch.pdb #2/B ARG 233 HN 3.003 2.116
Notch.pdb #2/B MET 234 N Notch.pdb #2/B GLN 231 O Notch.pdb #2/B MET 234 HN 3.163 2.246
Notch.pdb #2/B HIS 235 N Notch.pdb #2/B ALA 230 O Notch.pdb #2/B HIS 235 HN 2.833 1.914
Notch.pdb #2/B HIS 235 NE2 Notch.pdb #2/B ARG 199 O Notch.pdb #2/B HIS 235 HE2 2.886 2.133
Notch.pdb #2/B ILE 238 N Notch.pdb #2/B ASP 237 OD1 (alt loc B, occupancy 0.5) Notch.pdb #2/B ILE 238 HN 3.048 2.228
Notch.pdb #2/B VAL 239 N Notch.pdb #2/B HIS 235 O Notch.pdb #2/B VAL 239 HN 3.161 2.183
Notch.pdb #2/B ARG 240 N Notch.pdb #2/B HIS 236 O Notch.pdb #2/B ARG 240 HN 2.868 1.858
Notch.pdb #2/B LEU 241 N Notch.pdb #2/B ASP 237 O Notch.pdb #2/B LEU 241 HN 2.858 1.862
Notch.pdb #2/B LEU 242 N Notch.pdb #2/B ILE 238 O Notch.pdb #2/B LEU 242 HN 2.828 1.849
Notch.pdb #2/B ASP 243 N Notch.pdb #2/B VAL 239 O Notch.pdb #2/B ASP 243 HN 2.894 1.958
180 hydrogen bonds found
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 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 M5
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: Mac17,2
Model Number: MDE04CH/A
Chip: Apple M5
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 2 days, 13 hours, 16 minutes
Graphics/Displays:
Apple M5:
Chipset Model: Apple M5
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: 4.12.1
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-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: 1.11.1
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-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: 2.7.12
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: 7.13.1
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: 4.26.0
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
msgpack: 1.1.1
multidict: 6.7.0
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: 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
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
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
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
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: 4.1.0
roman-numerals-py: 4.1.0
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: 2.8.3
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: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
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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