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Opened 15 hours ago
#19508 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-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001ef576080 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, _pyKVFinder, lxml._elementpath, lxml.etree (total: 60)
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{
"uptime" : 2700,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 1560,
"osVersion" : {
"train" : "macOS 26.1",
"build" : "25B78",
"releaseType" : "User"
},
"captureTime" : "2025-12-10 18:31:40.5348 -0500",
"codeSigningMonitor" : 1,
"incident" : "A0CE9676-B3CC-4EB0-A35B-6298C5AE39A4",
"pid" : 1738,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-10 17:56:17.2410 -0500",
"procStartAbsTime" : 17368542647,
"procExitAbsTime" : 66645465271,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A3CFA39D-7314-5C49-B596-D49992DE191F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "586B2263-797D-7078-24E1-C7075CE20F6F",
"appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"],"state":"unavailable"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "57A1735A-92A6-4A7E-B82A-08FEFAF75617",
"wakeTime" : 4,
"sleepWakeUUID" : "AB3BA570-F622-43AD-AB30-121885863D84",
"sip" : "enabled",
"vmRegionInfo" : "0xc00001d00 is in 0x97e000000-0xc70000000; bytes after start: 10770980096 bytes before end: 1879040767\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_LARGE 52ac00000-52b400000 [ 8192K] rw-\/rwx SM=PRV \n GAP OF 0x452c00000 BYTES\n---> commpage (reserved) 97e000000-c70000000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)\n MALLOC_SMALL c70000000-c70400000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000c00001d00","rawCodes":[2,51539614976],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000c00001d00"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":1738},
"vmregioninfo" : "0xc00001d00 is in 0x97e000000-0xc70000000; bytes after start: 10770980096 bytes before end: 1879040767\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_LARGE 52ac00000-52b400000 [ 8192K] rw-\/rwx SM=PRV \n GAP OF 0x452c00000 BYTES\n---> commpage (reserved) 97e000000-c70000000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)\n MALLOC_SMALL c70000000-c70400000 [ 4096K] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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"rolloutId" : "63f9578e238e7b23a1f3030a",
"factorPackIds" : [
],
"deploymentId" : 240000005
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7rdy format mmcif fromDatabase pdb
7rdy title:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase -
nsp13(2)-RTC - engaged class [more info...]
Chain information for 7rdy #1
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
E F | Helicase | R1AB_SARS2 1-601
P | Product RNA |
T | Template RNA |
Non-standard residues in 7rdy #1
---
1N7 — chapso
(2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium)
ADP — adenosine-5'-diphosphate
AF3 — aluminum fluoride
MG — magnesium ion
ZN — zinc ion
> 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 /A
7597 atoms, 7794 bonds, 13 pseudobonds, 934 residues, 2 models selected
> color sel light slate gray
> select /P
719 atoms, 802 bonds, 34 residues, 1 model selected
> color sel burnt brick
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ui tool show "Color Actions"
> color sel fire brick
> select /T
934 atoms, 1042 bonds, 1 pseudobond, 44 residues, 2 models selected
> color sel sky blue
> select B
Nothing selected
> select /B
1408 atoms, 1427 bonds, 186 residues, 1 model selected
> color sel dark green
> select /D
1415 atoms, 1434 bonds, 185 residues, 1 model selected
> color sel forrest green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel forest green
> select /E
4605 atoms, 4706 bonds, 15 pseudobonds, 596 residues, 2 models selected
> color sel salmon
> select /F
4592 atoms, 4691 bonds, 14 pseudobonds, 596 residues, 2 models selected
> color sel dark salmon
> sel/C
Unknown command: sel/C
> select /C
576 atoms, 579 bonds, 75 residues, 1 model selected
> color sel gold
> hide atoms
> show cartoons
> save "/Users/nathansoper/Google Drive/My Drive/Lab - Tania/6th year
> meetings/Figures/holo-RdRp.cxs"
> open 7d4f
7d4f title:
Structure of COVID-19 RNA-dependent RNA polymerase bound to suramin [more
info...]
Chain information for 7d4f #2
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B G | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
Non-standard residues in 7d4f #2
---
H3U — 8-(3-(3-aminobenzamido)-4-methylbenzamido)naphthalene-1,3,5-trisulfonic
acid
ZN — zinc ion
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7rdy, chain A (#1) with 7d4f, chain A (#2), sequence alignment
score = 4588.5
RMSD between 872 pruned atom pairs is 0.542 angstroms; (across all 898 pairs:
1.022)
> select #2
9534 atoms, 9750 bonds, 11 pseudobonds, 1185 residues, 4 models selected
> ~select #2:H3U
9450 atoms, 9660 bonds, 11 pseudobonds, 1183 residues, 4 models selected
> delete sel
> select H3U
Expected an objects specifier or a keyword
> select #2
84 atoms, 90 bonds, 2 residues, 1 model selected
> 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 2.3.5 which is incompatible.
scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.3.5 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> kvfinder #1
159 cavities found for 7rdy #1
7rdy Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.9 | | 2626.56 | 1705.07 | 12160 | 15.3 | 3.59
1.4.94 | | 1259.06 | 1138.87 | 5829 | 21.75 | 8.01
1.4.151 | | 1024.06 | 626.78 | 4741 | 5.47 | 1.55
1.4.116 | | 881.5 | 606.73 | 4081 | 7 | 2.49
1.4.24 | | 555.34 | 535.81 | 2571 | 14.26 | 4.74
1.4.125 | | 551.23 | 390.15 | 2552 | 5.13 | 1.35
1.4.132 | | 444.96 | 306.07 | 2060 | 6.84 | 1.94
1.4.100 | | 443.45 | 414.84 | 2053 | 0 | 0
1.4.57 | | 428.98 | 471.54 | 1986 | 9.84 | 2.6
1.4.81 | | 392.47 | 357.18 | 1817 | 4.8 | 1.46
1.4.149 | | 369.79 | 357.15 | 1712 | 13.2 | 4.19
1.4.84 | | 246.02 | 248.59 | 1139 | 8.14 | 3.09
1.4.102 | | 245.81 | 240.17 | 1138 | 7.25 | 2.38
1.4.32 | | 243 | 228.71 | 1125 | 8.07 | 3.36
1.4.108 | | 240.41 | 243.38 | 1113 | 5.91 | 1.49
1.4.12 | | 232.85 | 268.9 | 1078 | 0 | 0
1.4.127 | | 228.31 | 173.22 | 1057 | 4.24 | 1.44
1.4.96 | | 223.78 | 255.74 | 1036 | 4.69 | 1.56
1.4.95 | | 223.56 | 230.6 | 1035 | 6.71 | 2.9
1.4.117 | | 216.65 | 238.64 | 1003 | 9.66 | 2.58
1.4.62 | | 207.14 | 248.87 | 959 | 9.56 | 3.51
1.4.52 | | 193.32 | 194.01 | 895 | 6.71 | 3.09
1.4.42 | | 178.2 | 197.45 | 825 | 7.78 | 2.42
1.4.99 | | 153.14 | 196.52 | 709 | 4.87 | 1.48
1.4.51 | | 149.04 | 100.32 | 690 | 3.29 | 0.9
1.4.122 | | 146.23 | 150.69 | 677 | 0 | 0
1.4.126 | | 141.91 | 118.99 | 657 | 3.23 | 0.87
1.4.17 | | 134.78 | 127.21 | 624 | 2.62 | 0.73
1.4.78 | | 132.19 | 177.34 | 612 | 7.68 | 2.63
1.4.154 | | 123.12 | 122.54 | 570 | 3.06 | 1
1.4.73 | | 115.78 | 121.71 | 536 | 4.87 | 1.53
1.4.64 | | 111.89 | 161.25 | 518 | 4.72 | 1.33
1.4.50 | | 108.86 | 120.71 | 504 | 4.24 | 1.25
1.4.77 | | 92.23 | 63.75 | 427 | 1.47 | 0.35
1.4.115 | | 92.23 | 98.69 | 427 | 4.28 | 1.23
1.4.88 | | 91.58 | 116.03 | 424 | 0 | 0
1.4.20 | | 87.26 | 101.76 | 404 | 0 | 0
1.4.113 | | 86.83 | 96.4 | 402 | 3.84 | 1.48
1.4.114 | | 80.78 | 84.32 | 374 | 2.47 | 0.68
1.4.18 | | 73.66 | 97.24 | 341 | 0 | 0
1.4.105 | | 71.28 | 65.91 | 330 | 1.9 | 0.39
1.4.134 | | 70.85 | 104.36 | 328 | 2.55 | 0.71
1.4.118 | | 70.63 | 83.24 | 327 | 2.62 | 0.85
1.4.136 | | 63.29 | 66.02 | 293 | 3 | 1.12
1.4.8 | | 59.83 | 82.91 | 277 | 2.94 | 0.95
1.4.45 | | 57.89 | 71.97 | 268 | 4.02 | 1.4
1.4.3 | | 57.46 | 78.9 | 266 | 0 | 0
1.4.130 | | 57.24 | 82.91 | 265 | 5.2 | 2.43
1.4.157 | | 54.86 | 67.85 | 254 | 3.23 | 1.22
1.4.69 | | 51.41 | 70.74 | 238 | 0 | 0
1.4.22 | | 49.03 | 52.23 | 227 | 2.47 | 0.88
1.4.46 | | 49.03 | 46.68 | 227 | 2.4 | 0.69
1.4.38 | | 48.17 | 84.06 | 223 | 0 | 0
1.4.139 | | 48.17 | 68.42 | 223 | 4.02 | 1.74
1.4.140 | | 48.17 | 54.4 | 223 | 3 | 0.88
1.4.145 | | 45.79 | 70.16 | 212 | 1.8 | 0.68
1.4.44 | | 44.71 | 54.41 | 207 | 1.7 | 0.59
1.4.30 | | 42.77 | 50.41 | 198 | 1.9 | 0.67
1.4.72 | | 42.55 | 57.97 | 197 | 3.29 | 1.21
1.4.14 | | 42.34 | 66.92 | 196 | 0 | 0
1.4.23 | | 41.26 | 73.64 | 191 | 0 | 0
1.4.107 | | 40.61 | 54.09 | 188 | 3.65 | 1.13
1.4.138 | | 40.61 | 60.75 | 188 | 5.2 | 2.29
1.4.131 | | 39.31 | 51.21 | 182 | 3.65 | 1.41
1.4.29 | | 37.15 | 58.6 | 172 | 2.47 | 0.74
1.4.156 | | 36.07 | 47.27 | 167 | 2.47 | 0.94
1.4.53 | | 34.78 | 51.76 | 161 | 1.2 | 0.24
1.4.85 | | 34.34 | 45.34 | 159 | 3.23 | 1.38
1.4.159 | | 34.13 | 43.97 | 158 | 1.9 | 0.63
1.4.25 | | 33.48 | 43.28 | 155 | 1.34 | 0.4
1.4.65 | | 32.4 | 47.59 | 150 | 3 | 0.83
1.4.83 | | 32.4 | 54.44 | 150 | 0 | 0
1.4.13 | | 32.18 | 51.64 | 149 | 0 | 0
1.4.26 | | 32.18 | 44.02 | 149 | 1.2 | 0.29
1.4.90 | | 30.89 | 43.49 | 143 | 1.8 | 0.59
1.4.103 | | 30.89 | 47.51 | 143 | 1.7 | 0.5
1.4.37 | | 30.46 | 46.79 | 141 | 1.7 | 0.53
1.4.48 | | 30.02 | 59.94 | 139 | 3.7 | 1.41
1.4.68 | | 30.02 | 45.23 | 139 | 1.34 | 0.39
1.4.106 | | 29.81 | 50.49 | 138 | 3.84 | 1.92
1.4.11 | | 29.16 | 46.36 | 135 | 2.47 | 0.71
1.4.19 | | 29.16 | 41.75 | 135 | 1.7 | 0.34
1.4.89 | | 29.16 | 52.8 | 135 | 0 | 0
1.4.133 | | 29.16 | 43.63 | 135 | 1.34 | 0.43
1.4.49 | | 28.3 | 55.43 | 131 | 0 | 0
1.4.91 | | 28.3 | 46.14 | 131 | 0 | 0
1.4.36 | | 27.65 | 41.39 | 128 | 1.8 | 0.46
1.4.59 | | 27.43 | 53.74 | 127 | 0 | 0
1.4.5 | | 26.57 | 41.47 | 123 | 2.94 | 1.6
1.4.31 | | 26.57 | 36.9 | 123 | 1.34 | 0.34
1.4.21 | | 26.14 | 43.12 | 121 | 3.23 | 1.55
1.4.35 | | 26.14 | 46.24 | 121 | 0 | 0
1.4.111 | | 26.14 | 46.8 | 121 | 0 | 0
1.4.86 | | 25.27 | 43.38 | 117 | 0 | 0
1.4.120 | | 25.06 | 35.43 | 116 | 1.34 | 0.32
1.4.121 | | 24.62 | 38.5 | 114 | 2.62 | 1.45
1.4.143 | | 24.62 | 57.97 | 114 | 0 | 0
1.4.82 | | 24.19 | 33.83 | 112 | 2.08 | 0.75
1.4.158 | | 22.9 | 39.53 | 106 | 0.85 | 0.2
1.4.28 | | 22.68 | 35.36 | 105 | 2.24 | 0.88
1.4.75 | | 22.68 | 32.14 | 105 | 1.8 | 0.5
1.4.60 | | 22.25 | 36.32 | 103 | 1.2 | 0.24
1.4.4 | | 21.6 | 35.38 | 100 | 1.34 | 0.42
1.4.43 | | 20.74 | 41.19 | 96 | 0 | 0
1.4.141 | | 20.74 | 33.96 | 96 | 2.16 | 0.87
1.4.7 | | 20.52 | 36.4 | 95 | 0.85 | 0.19
1.4.16 | | 18.79 | 27.92 | 87 | 1.8 | 0.51
1.4.104 | | 18.79 | 20.06 | 87 | 0.85 | 0.23
1.4.137 | | 18.36 | 23.56 | 85 | 1.34 | 0.5
1.4.34 | | 17.5 | 25.82 | 81 | 1.8 | 0.5
1.4.41 | | 17.5 | 30.46 | 81 | 1.7 | 0.65
1.4.61 | | 17.28 | 25.41 | 80 | 1.2 | 0.32
1.4.80 | | 17.28 | 36.68 | 80 | 0 | 0
1.4.93 | | 17.28 | 36.68 | 80 | 0 | 0
1.4.97 | | 17.28 | 36.68 | 80 | 0 | 0
1.4.128 | | 17.28 | 21.6 | 80 | 0.85 | 0.26
1.4.2 | | 17.06 | 35.72 | 79 | 2.75 | 1.55
1.4.15 | | 16.85 | 32.3 | 78 | 0 | 0
1.4.39 | | 16.85 | 32.3 | 78 | 0 | 0
1.4.110 | | 14.69 | 21.77 | 68 | 1.2 | 0.3
1.4.152 | | 14.69 | 23 | 68 | 0.85 | 0.22
1.4.56 | | 14.26 | 25.14 | 66 | 1.99 | 0.85
1.4.70 | | 13.18 | 19.03 | 61 | 1.34 | 0.39
1.4.6 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.33 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.54 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.76 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.79 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.98 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.112 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.123 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.129 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.135 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.144 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.147 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.155 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.109 | | 12.1 | 17.87 | 56 | 1.34 | 0.46
1.4.58 | | 11.66 | 22.28 | 54 | 1.47 | 0.59
1.4.148 | | 11.66 | 21.35 | 54 | 0.6 | 0.18
1.4.153 | | 11.45 | 20.68 | 53 | 1.34 | 0.52
1.4.92 | | 11.02 | 20.98 | 51 | 0.85 | 0.34
1.4.124 | | 10.58 | 19.41 | 49 | 0.85 | 0.21
1.4.71 | | 9.72 | 18 | 45 | 1.34 | 0.54
1.4.27 | | 9.29 | 15.54 | 43 | 0.6 | 0.11
1.4.47 | | 8.86 | 18.26 | 41 | 1.34 | 0.46
1.4.40 | | 8.42 | 19.26 | 39 | 1.2 | 0.48
1.4.142 | | 7.78 | 14.22 | 36 | 0.6 | 0.2
1.4.87 | | 7.34 | 13.01 | 34 | 1.2 | 0.32
1.4.146 | | 7.34 | 15.4 | 34 | 0.85 | 0.28
1.4.150 | | 7.34 | 17.59 | 34 | 1.2 | 0.41
1.4.10 | | 6.91 | 12.61 | 32 | 0.85 | 0.25
1.4.119 | | 6.91 | 13.51 | 32 | 0.85 | 0.18
1.4.74 | | 6.05 | 9.31 | 28 | 0.6 | 0.15
1.4.66 | | 5.83 | 12.01 | 27 | 0.85 | 0.33
1.4.1 | | 5.62 | 11.34 | 26 | 0.6 | 0.18
1.4.67 | | 5.62 | 11.34 | 26 | 0.6 | 0.18
1.4.55 | | 5.18 | 7.82 | 24 | 0.6 | 0.1
1.4.63 | | 5.18 | 11.37 | 24 | 0.85 | 0.24
1.4.101 | | 5.18 | 12.01 | 24 | 0.6 | 0.12
Populating font family aliases took 116 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> view #1.4.9 @ zoom 0.75
moved plane near -65.08717597850756 [ 0.86425838 -0.25540003 -0.4333916 ]
moved plane far -65.08717597850756 [ 0.86425838 -0.25540003 -0.4333916 ]
> surface #1.4.1-159 transparency 50
> ~surface #1.4
> surface #1.4.9
> show
> #!1/F:114,120,123-124,131-132,134-135,138-139,142-143,145-147,149,165,167,173-181,200-203,206-209,227-236,309-312,335,337-340,342,359-362,378-383,385-386,389-390,405-410,417,421-423,484,486,488,490,514-517,519-521,523-524,530-537,560
> view #!1.4.94 @ zoom 0.75
moved plane near -59.30354653828738 [ 0.86425838 -0.25540003 -0.4333916 ]
moved plane far -59.30354653828738 [ 0.86425838 -0.25540003 -0.4333916 ]
> ~surface #1.4
> surface #!1.4.94
> show
> #!1/E:114,120,123-124,131,134-135,138-139,142-143,145-146,149,173-175,177-181,197-199,212-214,227-228,230,309-311,334-335,337-340,342,360-361,378-383,407-411,417,421-423,484-485/T:7-11
> view #1
> undo
Undo failed, probably because structures have been modified.
> select #1/A
7597 atoms, 7794 bonds, 13 pseudobonds, 934 residues, 2 models selected
> ui tool show "Find Cavities"
> kvfinder #1
159 cavities found for 7rdy #1
7rdy Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.4.9 | | 2626.56 | 1705.07 | 12160 | 15.3 | 3.59
1.4.94 | | 1259.06 | 1138.87 | 5829 | 21.75 | 8.01
1.4.151 | | 1024.06 | 626.78 | 4741 | 5.47 | 1.55
1.4.116 | | 881.5 | 606.73 | 4081 | 7 | 2.49
1.4.24 | | 555.34 | 535.81 | 2571 | 14.26 | 4.74
1.4.125 | | 551.23 | 390.15 | 2552 | 5.13 | 1.35
1.4.132 | | 444.96 | 306.07 | 2060 | 6.84 | 1.94
1.4.100 | | 443.45 | 414.84 | 2053 | 0 | 0
1.4.57 | | 428.98 | 471.54 | 1986 | 9.84 | 2.6
1.4.81 | | 392.47 | 357.18 | 1817 | 4.8 | 1.46
1.4.149 | | 369.79 | 357.15 | 1712 | 13.2 | 4.19
1.4.84 | | 246.02 | 248.59 | 1139 | 8.14 | 3.09
1.4.102 | | 245.81 | 240.17 | 1138 | 7.25 | 2.38
1.4.32 | | 243 | 228.71 | 1125 | 8.07 | 3.36
1.4.108 | | 240.41 | 243.38 | 1113 | 5.91 | 1.49
1.4.12 | | 232.85 | 268.9 | 1078 | 0 | 0
1.4.127 | | 228.31 | 173.22 | 1057 | 4.24 | 1.44
1.4.96 | | 223.78 | 255.74 | 1036 | 4.69 | 1.56
1.4.95 | | 223.56 | 230.6 | 1035 | 6.71 | 2.9
1.4.117 | | 216.65 | 238.64 | 1003 | 9.66 | 2.58
1.4.62 | | 207.14 | 248.87 | 959 | 9.56 | 3.51
1.4.52 | | 193.32 | 194.01 | 895 | 6.71 | 3.09
1.4.42 | | 178.2 | 197.45 | 825 | 7.78 | 2.42
1.4.99 | | 153.14 | 196.52 | 709 | 4.87 | 1.48
1.4.51 | | 149.04 | 100.32 | 690 | 3.29 | 0.9
1.4.122 | | 146.23 | 150.69 | 677 | 0 | 0
1.4.126 | | 141.91 | 118.99 | 657 | 3.23 | 0.87
1.4.17 | | 134.78 | 127.21 | 624 | 2.62 | 0.73
1.4.78 | | 132.19 | 177.34 | 612 | 7.68 | 2.63
1.4.154 | | 123.12 | 122.54 | 570 | 3.06 | 1
1.4.73 | | 115.78 | 121.71 | 536 | 4.87 | 1.53
1.4.64 | | 111.89 | 161.25 | 518 | 4.72 | 1.33
1.4.50 | | 108.86 | 120.71 | 504 | 4.24 | 1.25
1.4.77 | | 92.23 | 63.75 | 427 | 1.47 | 0.35
1.4.115 | | 92.23 | 98.69 | 427 | 4.28 | 1.23
1.4.88 | | 91.58 | 116.03 | 424 | 0 | 0
1.4.20 | | 87.26 | 101.76 | 404 | 0 | 0
1.4.113 | | 86.83 | 96.4 | 402 | 3.84 | 1.48
1.4.114 | | 80.78 | 84.32 | 374 | 2.47 | 0.68
1.4.18 | | 73.66 | 97.24 | 341 | 0 | 0
1.4.105 | | 71.28 | 65.91 | 330 | 1.9 | 0.39
1.4.134 | | 70.85 | 104.36 | 328 | 2.55 | 0.71
1.4.118 | | 70.63 | 83.24 | 327 | 2.62 | 0.85
1.4.136 | | 63.29 | 66.02 | 293 | 3 | 1.12
1.4.8 | | 59.83 | 82.91 | 277 | 2.94 | 0.95
1.4.45 | | 57.89 | 71.97 | 268 | 4.02 | 1.4
1.4.3 | | 57.46 | 78.9 | 266 | 0 | 0
1.4.130 | | 57.24 | 82.91 | 265 | 5.2 | 2.43
1.4.157 | | 54.86 | 67.85 | 254 | 3.23 | 1.22
1.4.69 | | 51.41 | 70.74 | 238 | 0 | 0
1.4.22 | | 49.03 | 52.23 | 227 | 2.47 | 0.88
1.4.46 | | 49.03 | 46.68 | 227 | 2.4 | 0.69
1.4.38 | | 48.17 | 84.06 | 223 | 0 | 0
1.4.139 | | 48.17 | 68.42 | 223 | 4.02 | 1.74
1.4.140 | | 48.17 | 54.4 | 223 | 3 | 0.88
1.4.145 | | 45.79 | 70.16 | 212 | 1.8 | 0.68
1.4.44 | | 44.71 | 54.41 | 207 | 1.7 | 0.59
1.4.30 | | 42.77 | 50.41 | 198 | 1.9 | 0.67
1.4.72 | | 42.55 | 57.97 | 197 | 3.29 | 1.21
1.4.14 | | 42.34 | 66.92 | 196 | 0 | 0
1.4.23 | | 41.26 | 73.64 | 191 | 0 | 0
1.4.107 | | 40.61 | 54.09 | 188 | 3.65 | 1.13
1.4.138 | | 40.61 | 60.75 | 188 | 5.2 | 2.29
1.4.131 | | 39.31 | 51.21 | 182 | 3.65 | 1.41
1.4.29 | | 37.15 | 58.6 | 172 | 2.47 | 0.74
1.4.156 | | 36.07 | 47.27 | 167 | 2.47 | 0.94
1.4.53 | | 34.78 | 51.76 | 161 | 1.2 | 0.24
1.4.85 | | 34.34 | 45.34 | 159 | 3.23 | 1.38
1.4.159 | | 34.13 | 43.97 | 158 | 1.9 | 0.63
1.4.25 | | 33.48 | 43.28 | 155 | 1.34 | 0.4
1.4.65 | | 32.4 | 47.59 | 150 | 3 | 0.83
1.4.83 | | 32.4 | 54.44 | 150 | 0 | 0
1.4.13 | | 32.18 | 51.64 | 149 | 0 | 0
1.4.26 | | 32.18 | 44.02 | 149 | 1.2 | 0.29
1.4.90 | | 30.89 | 43.49 | 143 | 1.8 | 0.59
1.4.103 | | 30.89 | 47.51 | 143 | 1.7 | 0.5
1.4.37 | | 30.46 | 46.79 | 141 | 1.7 | 0.53
1.4.48 | | 30.02 | 59.94 | 139 | 3.7 | 1.41
1.4.68 | | 30.02 | 45.23 | 139 | 1.34 | 0.39
1.4.106 | | 29.81 | 50.49 | 138 | 3.84 | 1.92
1.4.11 | | 29.16 | 46.36 | 135 | 2.47 | 0.71
1.4.19 | | 29.16 | 41.75 | 135 | 1.7 | 0.34
1.4.89 | | 29.16 | 52.8 | 135 | 0 | 0
1.4.133 | | 29.16 | 43.63 | 135 | 1.34 | 0.43
1.4.49 | | 28.3 | 55.43 | 131 | 0 | 0
1.4.91 | | 28.3 | 46.14 | 131 | 0 | 0
1.4.36 | | 27.65 | 41.39 | 128 | 1.8 | 0.46
1.4.59 | | 27.43 | 53.74 | 127 | 0 | 0
1.4.5 | | 26.57 | 41.47 | 123 | 2.94 | 1.6
1.4.31 | | 26.57 | 36.9 | 123 | 1.34 | 0.34
1.4.21 | | 26.14 | 43.12 | 121 | 3.23 | 1.55
1.4.35 | | 26.14 | 46.24 | 121 | 0 | 0
1.4.111 | | 26.14 | 46.8 | 121 | 0 | 0
1.4.86 | | 25.27 | 43.38 | 117 | 0 | 0
1.4.120 | | 25.06 | 35.43 | 116 | 1.34 | 0.32
1.4.121 | | 24.62 | 38.5 | 114 | 2.62 | 1.45
1.4.143 | | 24.62 | 57.97 | 114 | 0 | 0
1.4.82 | | 24.19 | 33.83 | 112 | 2.08 | 0.75
1.4.158 | | 22.9 | 39.53 | 106 | 0.85 | 0.2
1.4.28 | | 22.68 | 35.36 | 105 | 2.24 | 0.88
1.4.75 | | 22.68 | 32.14 | 105 | 1.8 | 0.5
1.4.60 | | 22.25 | 36.32 | 103 | 1.2 | 0.24
1.4.4 | | 21.6 | 35.38 | 100 | 1.34 | 0.42
1.4.43 | | 20.74 | 41.19 | 96 | 0 | 0
1.4.141 | | 20.74 | 33.96 | 96 | 2.16 | 0.87
1.4.7 | | 20.52 | 36.4 | 95 | 0.85 | 0.19
1.4.16 | | 18.79 | 27.92 | 87 | 1.8 | 0.51
1.4.104 | | 18.79 | 20.06 | 87 | 0.85 | 0.23
1.4.137 | | 18.36 | 23.56 | 85 | 1.34 | 0.5
1.4.34 | | 17.5 | 25.82 | 81 | 1.8 | 0.5
1.4.41 | | 17.5 | 30.46 | 81 | 1.7 | 0.65
1.4.61 | | 17.28 | 25.41 | 80 | 1.2 | 0.32
1.4.80 | | 17.28 | 36.68 | 80 | 0 | 0
1.4.93 | | 17.28 | 36.68 | 80 | 0 | 0
1.4.97 | | 17.28 | 36.68 | 80 | 0 | 0
1.4.128 | | 17.28 | 21.6 | 80 | 0.85 | 0.26
1.4.2 | | 17.06 | 35.72 | 79 | 2.75 | 1.55
1.4.15 | | 16.85 | 32.3 | 78 | 0 | 0
1.4.39 | | 16.85 | 32.3 | 78 | 0 | 0
1.4.110 | | 14.69 | 21.77 | 68 | 1.2 | 0.3
1.4.152 | | 14.69 | 23 | 68 | 0.85 | 0.22
1.4.56 | | 14.26 | 25.14 | 66 | 1.99 | 0.85
1.4.70 | | 13.18 | 19.03 | 61 | 1.34 | 0.39
1.4.6 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.33 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.54 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.76 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.79 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.98 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.112 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.123 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.129 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.135 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.144 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.147 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.155 | | 12.31 | 29.54 | 57 | 0 | 0
1.4.109 | | 12.1 | 17.87 | 56 | 1.34 | 0.46
1.4.58 | | 11.66 | 22.28 | 54 | 1.47 | 0.59
1.4.148 | | 11.66 | 21.35 | 54 | 0.6 | 0.18
1.4.153 | | 11.45 | 20.68 | 53 | 1.34 | 0.52
1.4.92 | | 11.02 | 20.98 | 51 | 0.85 | 0.34
1.4.124 | | 10.58 | 19.41 | 49 | 0.85 | 0.21
1.4.71 | | 9.72 | 18 | 45 | 1.34 | 0.54
1.4.27 | | 9.29 | 15.54 | 43 | 0.6 | 0.11
1.4.47 | | 8.86 | 18.26 | 41 | 1.34 | 0.46
1.4.40 | | 8.42 | 19.26 | 39 | 1.2 | 0.48
1.4.142 | | 7.78 | 14.22 | 36 | 0.6 | 0.2
1.4.87 | | 7.34 | 13.01 | 34 | 1.2 | 0.32
1.4.146 | | 7.34 | 15.4 | 34 | 0.85 | 0.28
1.4.150 | | 7.34 | 17.59 | 34 | 1.2 | 0.41
1.4.10 | | 6.91 | 12.61 | 32 | 0.85 | 0.25
1.4.119 | | 6.91 | 13.51 | 32 | 0.85 | 0.18
1.4.74 | | 6.05 | 9.31 | 28 | 0.6 | 0.15
1.4.66 | | 5.83 | 12.01 | 27 | 0.85 | 0.33
1.4.1 | | 5.62 | 11.34 | 26 | 0.6 | 0.18
1.4.67 | | 5.62 | 11.34 | 26 | 0.6 | 0.18
1.4.55 | | 5.18 | 7.82 | 24 | 0.6 | 0.1
1.4.63 | | 5.18 | 11.37 | 24 | 0.85 | 0.24
1.4.101 | | 5.18 | 12.01 | 24 | 0.6 | 0.12
> close session
> open "/Users/nathansoper/Google Drive/My Drive/Lab - Tania/6th year
> meetings/Figures/holo-RdRp.cxs" format session
> view name session-start
opened ChimeraX session
> select /P:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /P:35
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Volume Viewer"
> toolshed show
> ui tool show "Find Cavities"
> surface #2.1 /T @ select /P:34
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /P:35
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add /P:33
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add /P:32
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add /P:31
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add /P:30
129 atoms, 139 bonds, 6 residues, 1 model selected
> select add /P:29
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add /P:28
174 atoms, 188 bonds, 8 residues, 1 model selected
> surface #2.1 /sel@ surface #2.1 sel @
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 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: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 53 minutes, 16 seconds
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
P24q-30:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL E2423H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 2.13.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.3.5
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.4
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.3
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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