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Opened 7 hours ago
#19195 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-15.0.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003122bf000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001ef5f3240 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 830 in delete
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/delete.py", line 50 in delete_atoms
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221 in run
File "/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1465 in
File "/Applications/ChimeraX-1.10.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.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.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, 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, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 55)
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{
"uptime" : 1400000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 12461,
"osVersion" : {
"train" : "macOS 15.0.1",
"build" : "24A348",
"releaseType" : "User"
},
"captureTime" : "2025-10-21 11:10:26.4408 +0800",
"codeSigningMonitor" : 1,
"incident" : "E301E820-CF9D-4607-ACE7-5C32A3C6D4AC",
"pid" : 63402,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-21 11:09:58.2092 +0800",
"procStartAbsTime" : 33947113485309,
"procExitAbsTime" : 33947790822432,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8AA5D8BE-0809-5F6A-A36B-399C1752C459","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA153C55-5783-7511-A83D-38C3B6202F68",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "F54C5805-71AF-4696-A166-B5E0CD25B251",
"wakeTime" : 8528,
"sleepWakeUUID" : "E610B075-5C8D-4518-B34B-092D91D52564",
"sip" : "enabled",
"vmRegionInfo" : "0x10 is not in any region. Bytes before following region: 4369596400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10472c000-104730000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000010","rawCodes":[1,16],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000010"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":63402},
"vmregioninfo" : "0x10 is not in any region. Bytes before following region: 4369596400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10472c000-104730000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2hf0_cavity_KVFinder.cxs
Populating font family aliases took 200 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
Log from Fri Aug 1 14:06:38 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
Log from Fri Aug 1 09:32:20 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
Log from Thu Jul 31 17:28:37 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> select /A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> hide sel atoms
> ~label (#!1 & sel) residues
> ~label (#!1 & sel) atoms
> label (#!1 & sel) atoms attribute bfactor
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2x1d_forcomp.pdb
> format pdb
2x1d_forcomp.pdb title:
The crystal structure of mature acyl coenzyme A:isopenicillin N
acyltransferase from penicillium chrysogenum [more info...]
Chain information for 2x1d_forcomp.pdb #2
---
Chain | Description
B | acyl-coenzyme
Non-standard residues in 2x1d_forcomp.pdb #2
---
CSD — (CSD)
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide atoms
> ui tool show Matchmaker
> matchmaker #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 8sv7A.pdb, chain A (#1) with 2x1d_forcomp.pdb, chain B (#2),
sequence alignment score = 95.7
RMSD between 38 pruned atom pairs is 1.061 angstroms; (across all 226 pairs:
6.657)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select
> #1/A:3-8,18-29,34-40,46-51,62-65,69-75,119-125,133-138,146-147,151-155,230-231,234-245,249-257,265-273
768 atoms, 773 bonds, 94 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> ~label #1-2 residues
> label delete pseudobonds
> select #1/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> ui tool show "Color Actions"
> color sel gray
> ui tool show "Color Actions"
> color sel light gray
> select #2/B
2257 atoms, 2041 bonds, 514 residues, 1 model selected
> color sel light green
[Repeated 1 time(s)]
> color sel pale green
> color sel light green
> select #1/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> select #1/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> ui tool show "Modeller Comparative"
Populating font family aliases took 203 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/B
Alignment identifier is 2/B
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 2/B:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: COBSH51IVJMNC5Z0
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 2/B:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: 36S2GIWY4QPCD7RA
Webservices job finished: COBSH51IVJMNC5Z0
Modeller job (ID COBSH51IVJMNC5Z0) finished
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1433.1
RMSD between 272 pruned atom pairs is 0.155 angstroms; (across all 272 pairs:
0.155)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1424.1
RMSD between 272 pruned atom pairs is 0.148 angstroms; (across all 272 pairs:
0.148)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1426.5
RMSD between 272 pruned atom pairs is 0.148 angstroms; (across all 272 pairs:
0.148)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1422.3
RMSD between 272 pruned atom pairs is 0.144 angstroms; (across all 272 pairs:
0.144)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1433.7
RMSD between 272 pruned atom pairs is 0.166 angstroms; (across all 272 pairs:
0.166)
Associated target chain A to chain A with 0 mismatches
[Repeated 4 time(s)] Chain information for target
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A | No description available
Webservices job finished: 36S2GIWY4QPCD7RA
Modeller job (ID 36S2GIWY4QPCD7RA) finished
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1433.1
RMSD between 272 pruned atom pairs is 0.155 angstroms; (across all 272 pairs:
0.155)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1424.1
RMSD between 272 pruned atom pairs is 0.148 angstroms; (across all 272 pairs:
0.148)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1426.5
RMSD between 272 pruned atom pairs is 0.148 angstroms; (across all 272 pairs:
0.148)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1422.3
RMSD between 272 pruned atom pairs is 0.144 angstroms; (across all 272 pairs:
0.144)
Parameters
---
Chain pairing | ss
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 8sv7A.pdb, chain A (#1) with target, chain A (#), sequence
alignment score = 1433.7
RMSD between 272 pruned atom pairs is 0.166 angstroms; (across all 272 pairs:
0.166)
Associated target chain A to chain A with 0 mismatches
[Repeated 4 time(s)] Chain information for target
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A | No description available
> select #2/B:120
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/B:120
14 atoms, 15 bonds, 1 residue, 1 model selected
> select
> #2/B:104-108,115-123,130-135,143-148,155-158,163-167,211-216,221-227,230-234,241-244,311-320,325-330,338-343
647 atoms, 649 bonds, 79 residues, 1 model selected
> select #2/B:120
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/B:120
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:122-123
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #2/B:120,122-123
36 atoms, 38 bonds, 3 residues, 1 model selected
> select #2/B:120,122-123,166
48 atoms, 50 bonds, 4 residues, 1 model selected
> show sel atoms
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 2
> label height 1.5
> label height 1.2
[Repeated 1 time(s)]
> select #3.1/A#3.2/A#3.3/A#3.4/A#3.5/A#4.1/A#4.2/A#4.3/A#4.4/A#4.5/A
21780 atoms, 22270 bonds, 2760 residues, 10 models selected
> delete atoms sel
> delete bonds sel
> select #2/B:120
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/B:120
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/B:120,122
25 atoms, 26 bonds, 2 residues, 1 model selected
> select #2/B:120,122-123
36 atoms, 38 bonds, 3 residues, 1 model selected
> select #2/B:120,122-123,166
48 atoms, 50 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel byhetero
> color sel byelement
> color sel byhetero
[Repeated 1 time(s)]
> undo
[Repeated 3 time(s)]
> color sel byhetero
> select #1/A:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:26,28
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/A:26,28-29
31 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A:26,28-29,47
39 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:26,28-29,47
39 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:26,28-29,47
39 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:26,28-29,47
39 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:26,28-29,47
39 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:26,28-29,47
39 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:26,28-29,47,73
47 atoms, 44 bonds, 5 residues, 1 model selected
> select #1/A:26,28-29,47,73
47 atoms, 44 bonds, 5 residues, 1 model selected
> select #1/A:26,28-29,47,73
47 atoms, 44 bonds, 5 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:26,28
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/A:26,28-29
31 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A:26,28-29,73
39 atoms, 37 bonds, 4 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1.2
[Repeated 2 time(s)]
> color sel red target l
> select clear
> label height 1
[Repeated 1 time(s)]
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_2x1d_bindingsites_compX.cxs
> cartoon style width 1.2 thickness 0.2
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #2/B:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> cofr sel
> view sel
[Repeated 1 time(s)]
> ui tool show "Selection Inspector"
> ui tool show "Side View"
> select clear
> view
[Repeated 1 time(s)]
> label height 1
> label height 0.5
> label height 0.6
[Repeated 1 time(s)]
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_2x1d_bindingsites_compX.cxs
[Repeated 2 time(s)]
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2hf0_forcomp.pdb
2hf0_forcomp.pdb title:
Bifidobacterium longum bile salt hydrolase [more info...]
Chain information for 2hf0_forcomp.pdb #1
---
Chain | Description | UniProt
B | bile salt hydrolase | Q9KK62_BIFLO 1-316
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #2
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #2
---
SO4 — sulfate ion
> label delete pseudobonds
> cartoon style width 1.2 thickness 0.2
> hide atoms
> select #2/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light gray target l
[Repeated 1 time(s)]
> color sel light gray
> color sel gray
> color sel light gray
> select #1/B
2594 atoms, 2528 bonds, 447 residues, 1 model selected
> color sel cyan
> select #2/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> color sel gray
> select clear
> select #2/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> color (#!2 & sel) light gray
> select clear
> select #2/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> color (#!2 & sel) gray
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select #1/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select clear
> ui tool show "Show Sequence Viewer"
> select #1/B:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:17,20
19 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/B:17,20,81
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/B:17,20,81,172
35 atoms, 31 bonds, 4 residues, 1 model selected
> select #1/B:17,20,81,172,225
46 atoms, 41 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero target l
[Repeated 1 time(s)]
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:26-27
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/A:26-27,75
27 atoms, 25 bonds, 3 residues, 1 model selected
> select #2/A:26-27,75,157
35 atoms, 32 bonds, 4 residues, 1 model selected
> select #2/A:26-27,75,157,166
44 atoms, 40 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> label height 0.5
> select clear
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_2hf0_bindingsites_compX.cxs
> ui tool show "Side View"
[Repeated 1 time(s)]
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_2hf0_bindingsites_compX.cxs
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> cartoon style width 1.2 thickness 0.2
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/5u7z_forcomp.pdb
Summary of feedback from opening
/Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/5u7z_forcomp.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (31 )
Cannot find LINK/SSBOND residue CYS (31 )
Cannot find LINK/SSBOND residue CYS (388 )
Cannot find LINK/SSBOND residue NAG (1 )
Cannot find LINK/SSBOND residue NAG (404 )
9 messages similar to the above omitted
5u7z_forcomp.pdb title:
Human acid ceramidase (ASAH1, acdase) self-activated [more info...]
Chain information for 5u7z_forcomp.pdb #2
---
Chain | Description | UniProt
B | acid ceramidase | A8K0B6_HUMAN 141-395
> ui tool show Matchmaker
> matchmaker #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 8sv7A.pdb, chain A (#1) with 5u7z_forcomp.pdb, chain B (#2),
sequence alignment score = 90.9
RMSD between 56 pruned atom pairs is 1.179 angstroms; (across all 214 pairs:
7.586)
> cartoon style width 1.2 thickness 0.2
> label delete pseudobonds
> hide atoms
> select #1/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> ui tool show "Color Actions"
> color sel gray target l
[Repeated 3 time(s)]
> color sel gray
> select #2/B
4071 atoms, 4107 bonds, 266 residues, 1 model selected
> ui tool show "Color Actions"
> color sel brown
> color sel light salmon
> color sel salmon
> select clear
> select #2/B
4071 atoms, 4107 bonds, 266 residues, 1 model selected
> color sel light salmon
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:231
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:231-240
157 atoms, 159 bonds, 10 residues, 1 model selected
> select #2/B:163
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/B:163
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/B:163,165
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #2/B:163,165-166
56 atoms, 56 bonds, 3 residues, 1 model selected
> select #2/B:163,165-166,227
76 atoms, 76 bonds, 4 residues, 1 model selected
> select #2/B:163,165-166,227,328
96 atoms, 96 bonds, 5 residues, 1 model selected
> select #2/B:163,165-166,227,328,367
115 atoms, 114 bonds, 6 residues, 1 model selected
> select #2/B:163,165-166,227,328,367,395
139 atoms, 139 bonds, 7 residues, 1 model selected
> show sel atoms
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui tool show "Color Actions"
> color sel byhetero
> color sel byelement
> color sel byhetero
[Repeated 1 time(s)]
> undo
[Repeated 2 time(s)]
> select H
2017 atoms, 253 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/B:143
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:143
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> ui tool show "Color Actions"
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #1/A:28
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:28
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:28,78
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:28,78,235
22 atoms, 19 bonds, 3 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #1/A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero target l
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #1/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #1/A:76
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero target l
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:210
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:214
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:215
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:213
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:210
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:209
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color sel yellow
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select clear
> ui tool show "Side View"
> select #1/A:78
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:78
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ~label sel residues
> select clear
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_5u7z_bindingsites_compX.cxs
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/6dxx_forcomp.pdb
Summary of feedback from opening
/Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/6dxx_forcomp.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue ASN (37 )
Cannot find LINK/SSBOND residue ASN (107 )
4 messages similar to the above omitted
6dxx_forcomp.pdb title:
Human N-acylethanolamine-hydrolyzing acid amidase (naaa) In complex with non-
covalent benzothiazole-piperazine inhibitor ARN19702, In presence of triton
X-100 [more info...]
Chain information for 6dxx_forcomp.pdb #2
---
Chain | Description | UniProt
B | N-acylethanolamine-hydrolyzing acid amidase subunit β | NAAA_HUMAN 126-359
Non-standard residues in 6dxx_forcomp.pdb #2
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
WTF —
[2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone
> hide atoms
> label delete pseudobonds
> cartoon style width 1.2 thickness 0.2
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:200
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/B:200-202
72 atoms, 77 bonds, 3 residues, 1 model selected
> show sel atoms
> select #2/B
3780 atoms, 3773 bonds, 296 residues, 1 model selected
> select H
1836 atoms, 233 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A
2401 atoms, 2178 bonds, 1 pseudobond, 543 residues, 2 models selected
> ui tool show "Color Actions"
> color sel gray target l
> color sel gray
> select #2/B
1944 atoms, 1937 bonds, 296 residues, 1 model selected
> color sel yellow
> color sel gold
> select clear
> select #2/B:202-203
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #2/B:200-203
51 atoms, 56 bonds, 4 residues, 1 model selected
> select #2/B:202
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/B:200-202
42 atoms, 47 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #1/A:79-80
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:79-84
51 atoms, 53 bonds, 6 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #1/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red target l
> select #2/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> label height 0.5
> label height 1
> label height 0.6
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
> ui tool show "Side View"
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
——— End of log from Thu Jul 31 17:28:37 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Side View"
> label height 0.6
[Repeated 1 time(s)]
> label height 0.7
[Repeated 1 time(s)]
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Figures/Tango2_6dxx_comp_closeup.tif
> width 2500 height 1149 supersample 3
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
——— End of log from Fri Aug 1 09:32:20 2025 ———
> view name session-start
opened ChimeraX session
> label height 0.8
[Repeated 1 time(s)]
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Figures/Tango2_6dxx_comp_closeup.tif
> width 3000 height 1379 supersample 3
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_6dxx_bindingsites_compX.cxs
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2x1d_forcomp.pdb
> format pdb
2x1d_forcomp.pdb title:
The crystal structure of mature acyl coenzyme A:isopenicillin N
acyltransferase from penicillium chrysogenum [more info...]
Chain information for 2x1d_forcomp.pdb #1
---
Chain | Description
B | acyl-coenzyme
Non-standard residues in 2x1d_forcomp.pdb #1
---
CSD — (CSD)
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Find Cavities"
> kvfinder
11 cavities found for 2x1d_forcomp.pdb #1
2x1d_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.3 | | 180.36 | 150.86 | 835 | 4.02 | 1.19
1.1.8 | | 50.76 | 64.27 | 235 | 4.37 | 2.06
1.1.7 | | 38.45 | 59.28 | 178 | 1.2 | 0.36
1.1.6 | | 32.18 | 49.97 | 149 | 3.06 | 1.04
1.1.10 | | 29.16 | 43.1 | 135 | 1.7 | 0.5
1.1.1 | | 28.94 | 52.49 | 134 | 0 | 0
1.1.9 | | 28.08 | 38.06 | 130 | 1.9 | 0.8
1.1.2 | | 25.7 | 37.43 | 119 | 2.16 | 0.62
1.1.4 | | 8.86 | 17.04 | 41 | 1.34 | 0.47
1.1.11 | | 8.42 | 16.5 | 39 | 0.6 | 0.15
1.1.5 | | 6.91 | 16.05 | 32 | 1.2 | 0.41
Populating font family aliases took 198 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> kvfinder
11 cavities found for 2x1d_forcomp.pdb #1
2x1d_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.3 | | 180.36 | 150.86 | 835 | 4.02 | 1.19
1.1.8 | | 50.76 | 64.27 | 235 | 4.37 | 2.06
1.1.7 | | 38.45 | 59.28 | 178 | 1.2 | 0.36
1.1.6 | | 32.18 | 49.97 | 149 | 3.06 | 1.04
1.1.10 | | 29.16 | 43.1 | 135 | 1.7 | 0.5
1.1.1 | | 28.94 | 52.49 | 134 | 0 | 0
1.1.9 | | 28.08 | 38.06 | 130 | 1.9 | 0.8
1.1.2 | | 25.7 | 37.43 | 119 | 2.16 | 0.62
1.1.4 | | 8.86 | 17.04 | 41 | 1.34 | 0.47
1.1.11 | | 8.42 | 16.5 | 39 | 0.6 | 0.15
1.1.5 | | 6.91 | 16.05 | 32 | 1.2 | 0.41
> color byattribute a:kvfinder_depth #1.1.2-11
1893 atoms, 10 residues, atom kvfinder_depth range 0 to 4.37
> view #1.1.3 @ zoom 0.75
moved plane near -42.45807919011678 [ 0.94629453 -0.02589495 -0.32226715]
moved plane far -42.45807919011678 [ 0.94629453 -0.02589495 -0.32226715]
> surface #1.1.1-11 transparency 50
> color #1.1.1-11 fromatoms transparency 50
> ~surface #1.1
> surface #1.1.3
> view #!1.1.8 @ zoom 0.75
moved plane near -27.56513770867785 [0.89256955 0.25878313 0.36925723]
moved plane far -27.56513770867785 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.8
> view #!1.1.7 @ zoom 0.75
moved plane near -32.03756358433146 [0.89256955 0.25878313 0.36925723]
moved plane far -32.03756358433146 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.7
> view #!1.1.6 @ zoom 0.75
moved plane near -23.916081462921742 [0.89256955 0.25878313 0.36925723]
moved plane far -23.916081462921742 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.6
> view #!1.1.10 @ zoom 0.75
moved plane near -30.07313029072019 [0.89256955 0.25878313 0.36925723]
moved plane far -30.07313029072019 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.10
> view #!1.1.1 @ zoom 0.75
moved plane near -16.12116160744664 [0.89256955 0.25878313 0.36925723]
moved plane far -16.12116160744664 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.1
> view #!1.1.9 @ zoom 0.75
moved plane near -26.497108456846878 [0.89256955 0.25878313 0.36925723]
moved plane far -26.497108456846878 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.9
> view #!1.1.2 @ zoom 0.75
moved plane near -22.815032955737227 [0.89256955 0.25878313 0.36925723]
moved plane far -22.815032955737227 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.2
> view #!1.1.3 @ zoom 0.75
moved plane near -39.23877516315216 [0.89256955 0.25878313 0.36925723]
moved plane far -39.23877516315216 [0.89256955 0.25878313 0.36925723]
> ~surface #1.1
> surface #!1.1.3
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> cartoon style width 1.2 thickness 0.2
> label delete pseudobonds
> hide atoms
> ui tool show "Find Cavities"
> kvfinder
14 cavities found for 8sv7A.pdb #1
8sv7A.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.10 | | 956.45 | 698.59 | 4428 | 15.34 | 4.44
1.2.13 | | 103.03 | 120.16 | 477 | 4.57 | 1.68
1.2.5 | | 47.95 | 72.39 | 222 | 0 | 0
1.2.11 | | 35.64 | 53.06 | 165 | 0 | 0
1.2.4 | | 29.81 | 41.18 | 138 | 2.16 | 0.58
1.2.1 | | 27.43 | 55.27 | 127 | 0 | 0
1.2.6 | | 25.49 | 40.78 | 118 | 0 | 0
1.2.9 | | 15.34 | 31.68 | 71 | 0.85 | 0.19
1.2.3 | | 14.04 | 19.78 | 65 | 1.04 | 0.26
1.2.12 | | 14.04 | 21.78 | 65 | 1.34 | 0.37
1.2.8 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.14 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.2 | | 11.88 | 24.03 | 55 | 0.6 | 0.17
1.2.7 | | 11.02 | 19.4 | 51 | 1.2 | 0.32
> view #1.2.10 @ zoom 0.75
moved plane near -37.24658241073715 [-0. -0. -1.]
moved plane far -37.24658241073715 [-0. -0. -1.]
> surface #1.2.1-14 transparency 50
> ~surface #1.2
> surface #1.2.10
> select #!1.2.10
4428 atoms, 1 residue, 1 model selected
> ~select #!1.2.10
1 model selected
> select #!1 & (#!1.2.10 @ ~select #!1 & (#!1.2.10 @ show
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> hide
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> color byattribute a:kvfinder_depth #!1.2.2-4,7,9-10,12-13
5350 atoms, 8 residues, 8 surfaces, atom kvfinder_depth range 0 to 15.3
> ui tool show "Render/Select by Attribute"
> view #!1.2.13 @ zoom 0.75
moved plane near -21.28794025080688 [-0.90926844 -0.24612183 0.3356411 ]
moved plane far -21.28794025080688 [-0.90926844 -0.24612183 0.3356411 ]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.10 @ zoom 0.75
moved plane near -40.60877178983332 [-0.71692665 0.28784738 -0.63494887]
moved plane far -40.60877178983332 [-0.71692665 0.28784738 -0.63494887]
> ~surface #1.2
> surface #!1.2.10
> ui tool show "Surface Color"
No map chosen for coloring
[Repeated 5 time(s)]
> color single #1.2.10.1
No map chosen for coloring
[Repeated 5 time(s)]
> color #1.2.10 #c00d2b
No map chosen for coloring
[Repeated 4 time(s)]
> color single #1.2.10.1
No map chosen for coloring
[Repeated 3 time(s)]
> select #!1.2.10
4428 atoms, 1 residue, 1 model selected
> ~select #!1.2.10
1 model selected
> show
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> hide
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> show
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> hide
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> select #!1 & (#!1.2.10 @ ~select #!1 & (#!1.2.10 @ select #!1.2.10
4428 atoms, 1 residue, 1 model selected
> ~select #!1.2.10
1 model selected
> view #!1.2.13 @ zoom 0.75
moved plane near -17.278803539624093 [-0.16973462 0.29972305 -0.93880576]
moved plane far -17.278803539624093 [-0.16973462 0.29972305 -0.93880576]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.5 @ zoom 0.75
moved plane near -12.381815063062106 [-0.16973462 0.29972305 -0.93880576]
moved plane far -12.381815063062106 [-0.16973462 0.29972305 -0.93880576]
> ~surface #1.2
> surface #!1.2.5
> view #!1.2.10 @ zoom 0.75
moved plane near -25.645900495557516 [-0.16973462 0.29972305 -0.93880576]
moved plane far -25.645900495557516 [-0.16973462 0.29972305 -0.93880576]
> ~surface #1.2
> surface #!1.2.10
> ui tool show "Surface Color"
> color radial #1.2.2.1 palette #ff0000:#ffffff:#0000ff
> color radial #1.2.10.1 palette 32.53,#ff0000:34.32,#ffffff:36.12,#0000ff
No map chosen for coloring
[Repeated 1 time(s)]
> select #!1 & (#!1.2.10 @ ~select #!1 & (#!1.2.10 @ show
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> hide
> #!1/A:2,4,24-29,32,51,56,59-62,72-83,85-90,117,157,216,220,224,234,238-240
> select #!1 & (#!1.2.10 @ show sel atoms
> surface sel
> ui tool show "Surface Color"
No map chosen for coloring
[Repeated 2 time(s)]
> ui tool show "Surface Color"
> color radial #1.3 palette 32.53,#ff0000:34.32,#ffffff:36.12,#0000ff
> ui tool show "Find Cavities"
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2x1d_forcomp.pdb
> format pdb
2x1d_forcomp.pdb title:
The crystal structure of mature acyl coenzyme A:isopenicillin N
acyltransferase from penicillium chrysogenum [more info...]
Chain information for 2x1d_forcomp.pdb #1
---
Chain | Description
B | acyl-coenzyme
Non-standard residues in 2x1d_forcomp.pdb #1
---
CSD — (CSD)
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Find Cavities"
> kvfinder
11 cavities found for 2x1d_forcomp.pdb #1
2x1d_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.3 | | 180.36 | 150.86 | 835 | 4.02 | 1.19
1.1.8 | | 50.76 | 64.27 | 235 | 4.37 | 2.06
1.1.7 | | 38.45 | 59.28 | 178 | 1.2 | 0.36
1.1.6 | | 32.18 | 49.97 | 149 | 3.06 | 1.04
1.1.10 | | 29.16 | 43.1 | 135 | 1.7 | 0.5
1.1.1 | | 28.94 | 52.49 | 134 | 0 | 0
1.1.9 | | 28.08 | 38.06 | 130 | 1.9 | 0.8
1.1.2 | | 25.7 | 37.43 | 119 | 2.16 | 0.62
1.1.4 | | 8.86 | 17.04 | 41 | 1.34 | 0.47
1.1.11 | | 8.42 | 16.5 | 39 | 0.6 | 0.15
1.1.5 | | 6.91 | 16.05 | 32 | 1.2 | 0.41
> view #1.1.3 @ zoom 0.75
moved plane near -20.27633690049001 [ 0.00258366 0.97721708 -0.21222655]
moved plane far -20.27633690049001 [ 0.00258366 0.97721708 -0.21222655]
> surface #1.1.1-11 transparency 50
> ~surface #1.1
> surface #1.1.3
> select #!1 & (#1.1.3 @ close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2hf0_forcomp.pdb
> format pdb
2hf0_forcomp.pdb title:
Bifidobacterium longum bile salt hydrolase [more info...]
Chain information for 2hf0_forcomp.pdb #1
---
Chain | Description | UniProt
B | bile salt hydrolase | Q9KK62_BIFLO 1-316
> ui tool show "Find Cavities"
> kvfinder
14 cavities found for 2hf0_forcomp.pdb #1
2hf0_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.11 | | 899.21 | 605.61 | 4163 | 9.62 | 2.96
1.1.10 | | 60.7 | 72.68 | 281 | 4.2 | 1.33
1.1.14 | | 56.81 | 79.96 | 263 | 1.8 | 0.45
1.1.9 | | 55.3 | 76.96 | 256 | 2.47 | 0.6
1.1.8 | | 29.59 | 51.3 | 137 | 0 | 0
1.1.7 | | 23.11 | 42.35 | 107 | 0 | 0
1.1.2 | | 18.36 | 33.35 | 85 | 2.16 | 0.79
1.1.5 | | 17.93 | 28.1 | 83 | 1.8 | 0.71
1.1.13 | | 17.28 | 36.68 | 80 | 0 | 0
1.1.3 | | 16.42 | 28.26 | 76 | 1.2 | 0.28
1.1.4 | | 12.96 | 17.76 | 60 | 1.34 | 0.42
1.1.12 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.6 | | 9.94 | 17.92 | 46 | 0.85 | 0.24
1.1.1 | | 9.72 | 19.27 | 45 | 0.6 | 0.11
> view #1.1.11 @ zoom 0.75
moved plane near -33.222142626207955 [-0.91731221 0.33896845 0.20889877]
moved plane far -33.222142626207955 [-0.91731221 0.33896845 0.20889877]
> surface #1.1.1-14 transparency 50
> ~surface #1.1
> surface #1.1.11
> select #!1 & (#1.1.11 @ close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/5u7z_forcomp.pdb
> format pdb
Summary of feedback from opening
/Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/5u7z_forcomp.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (31 )
Cannot find LINK/SSBOND residue CYS (31 )
Cannot find LINK/SSBOND residue CYS (388 )
Cannot find LINK/SSBOND residue NAG (1 )
Cannot find LINK/SSBOND residue NAG (404 )
9 messages similar to the above omitted
5u7z_forcomp.pdb title:
Human acid ceramidase (ASAH1, acdase) self-activated [more info...]
Chain information for 5u7z_forcomp.pdb #1
---
Chain | Description | UniProt
B | acid ceramidase | A8K0B6_HUMAN 141-395
> ui tool show "Find Cavities"
> kvfinder
13 cavities found for 5u7z_forcomp.pdb #1
5u7z_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.5 | | 362.88 | 334.81 | 1680 | 6.18 | 1.73
1.1.13 | | 106.92 | 109.88 | 495 | 3.7 | 1.66
1.1.3 | | 80.35 | 122.76 | 372 | 7.22 | 3.63
1.1.10 | | 74.52 | 99.77 | 345 | 5.16 | 2.56
1.1.1 | | 55.51 | 68.62 | 257 | 3.55 | 1.5
1.1.11 | | 42.98 | 52.99 | 199 | 1.8 | 0.74
1.1.9 | | 36.07 | 59.9 | 167 | 0 | 0
1.1.6 | | 28.08 | 54.76 | 130 | 4.84 | 3
1.1.8 | | 23.11 | 35.28 | 107 | 1.8 | 0.54
1.1.2 | | 18.58 | 27.35 | 86 | 2.4 | 0.85
1.1.7 | | 8.42 | 15.83 | 39 | 1.2 | 0.33
1.1.4 | | 7.34 | 13.6 | 34 | 0.6 | 0.19
1.1.12 | | 7.13 | 14.97 | 33 | 0.6 | 0.2
> view #1.1.5 @ zoom 0.75
moved plane near -26.197777215314204 [-0. -0. -1.]
moved plane far -26.197777215314204 [-0. -0. -1.]
> surface #1.1.1-13 transparency 50
> ~surface #1.1
> surface #1.1.5
> select #!1 & (#1.1.5 @ close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/6dxx_forcomp.pdb
> format pdb
Summary of feedback from opening
/Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/6dxx_forcomp.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue ASN (37 )
Cannot find LINK/SSBOND residue ASN (107 )
4 messages similar to the above omitted
6dxx_forcomp.pdb title:
Human N-acylethanolamine-hydrolyzing acid amidase (naaa) In complex with non-
covalent benzothiazole-piperazine inhibitor ARN19702, In presence of triton
X-100 [more info...]
Chain information for 6dxx_forcomp.pdb #1
---
Chain | Description | UniProt
B | N-acylethanolamine-hydrolyzing acid amidase subunit β | NAAA_HUMAN 126-359
Non-standard residues in 6dxx_forcomp.pdb #1
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
WTF —
[2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone
> hide atoms
> ui tool show "Find Cavities"
> kvfinder
7 cavities found for 6dxx_forcomp.pdb #1
6dxx_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.7 | | 102.82 | 129.21 | 476 | 3.89 | 1.31
1.1.4 | | 47.95 | 63.42 | 222 | 3 | 0.81
1.1.3 | | 27 | 45.07 | 125 | 3.6 | 1.68
1.1.1 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.2 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.5 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.6 | | 9.72 | 16.91 | 45 | 0.85 | 0.17
> view #1.1.7 @ zoom 0.75
moved plane near -26.36102890222392 [-0.84853172 0.50795012 -0.14825856]
moved plane far -26.36102890222392 [-0.84853172 0.50795012 -0.14825856]
> surface #1.1.1-7 transparency 50
> ~surface #1.1
> surface #1.1.7
> select #!1 & (#1.1.7 @ close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> hide atoms
> label delete pseudobonds
> ui tool show "Find Cavities"
> kvfinder
14 cavities found for 8sv7A.pdb #1
8sv7A.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.10 | | 956.45 | 698.59 | 4428 | 15.34 | 4.44
1.2.13 | | 103.03 | 120.16 | 477 | 4.57 | 1.68
1.2.5 | | 47.95 | 72.39 | 222 | 0 | 0
1.2.11 | | 35.64 | 53.06 | 165 | 0 | 0
1.2.4 | | 29.81 | 41.18 | 138 | 2.16 | 0.58
1.2.1 | | 27.43 | 55.27 | 127 | 0 | 0
1.2.6 | | 25.49 | 40.78 | 118 | 0 | 0
1.2.9 | | 15.34 | 31.68 | 71 | 0.85 | 0.19
1.2.3 | | 14.04 | 19.78 | 65 | 1.04 | 0.26
1.2.12 | | 14.04 | 21.78 | 65 | 1.34 | 0.37
1.2.8 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.14 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.2 | | 11.88 | 24.03 | 55 | 0.6 | 0.17
1.2.7 | | 11.02 | 19.4 | 51 | 1.2 | 0.32
> view #1.2.10 @ zoom 0.75
moved plane near -24.658459398507137 [-0. -0. -1.]
moved plane far -24.658459398507137 [-0. -0. -1.]
> surface #1.2.1-14 transparency 50
> ~surface #1.2
> surface #1.2.10
> select #!1 & (#1.2.10 @ ~select #!1 & (#!1.2.10 @ view #!1.2.13 @ zoom 0.75
moved plane near -24.413652383828367 [ 0.01105958 -0.83352862 0.55236557]
moved plane far -24.413652383828367 [ 0.01105958 -0.83352862 0.55236557]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.5 @ zoom 0.75
moved plane near -14.383927998550115 [ 0.59263135 0.39467137 -0.70215568]
moved plane far -14.383927998550115 [ 0.59263135 0.39467137 -0.70215568]
> ~surface #1.2
> surface #!1.2.5
> view #!1.2.13 @ zoom 0.75
moved plane near -24.130028032896337 [ 0.59263135 0.39467137 -0.70215568]
moved plane far -24.130028032896337 [ 0.59263135 0.39467137 -0.70215568]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.10 @ zoom 0.75
moved plane near -36.774467449414566 [ 0.59263135 0.39467137 -0.70215568]
moved plane far -36.774467449414566 [ 0.59263135 0.39467137 -0.70215568]
> ~surface #1.2
> surface #!1.2.10
> view #!1.2.13 @ zoom 0.75
moved plane near -24.166454481449467 [-0.38236314 -0.91645035 -0.1179711 ]
moved plane far -24.166454481449467 [-0.38236314 -0.91645035 -0.1179711 ]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.10 @ zoom 0.75
moved plane near -36.660551896014844 [-0.46607824 -0.59193229 -0.65756159]
moved plane far -36.660551896014844 [-0.46607824 -0.59193229 -0.65756159]
> ~surface #1.2
> surface #!1.2.10
> view #!1.2.13 @ zoom 0.75
moved plane near -24.536082151462534 [-0.46607824 -0.59193229 -0.65756159]
moved plane far -24.536082151462534 [-0.46607824 -0.59193229 -0.65756159]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.5 @ zoom 0.75
moved plane near -13.542036714474131 [-0.46607824 -0.59193229 -0.65756159]
moved plane far -13.542036714474131 [-0.46607824 -0.59193229 -0.65756159]
> ~surface #1.2
> surface #!1.2.5
> view #!1.2.13 @ zoom 0.75
moved plane near -24.536082151462534 [-0.46607824 -0.59193229 -0.65756159]
moved plane far -24.536082151462534 [-0.46607824 -0.59193229 -0.65756159]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.10 @ zoom 0.75
moved plane near -36.660551896014844 [-0.46607824 -0.59193229 -0.65756159]
moved plane far -36.660551896014844 [-0.46607824 -0.59193229 -0.65756159]
> ~surface #1.2
> surface #!1.2.10
> ui tool show "Find Cavities"
> ui windowfill toggle
[Repeated 3 time(s)]
> select #!1.2.10
4428 atoms, 1 residue, 1 model selected
> ~select #!1.2.10
1 model selected
> select #!1 & (#!1.2.10 @ ~select #!1 & (#!1.2.10 @ view #!1.2.13 @ zoom 0.75
moved plane near -23.108837427320186 [ 0.27561638 -0.95107255 0.13963023]
moved plane far -23.108837427320186 [ 0.27561638 -0.95107255 0.13963023]
> ~surface #1.2
> surface #!1.2.13
> view #!1.2.5 @ zoom 0.75
moved plane near -13.262029120079008 [ 0.27561638 -0.95107255 0.13963023]
moved plane far -13.262029120079008 [ 0.27561638 -0.95107255 0.13963023]
> ~surface #1.2
> surface #!1.2.5
> view #!1.2.10 @ zoom 0.75
moved plane near -37.50479614394951 [ 0.27561638 -0.95107255 0.13963023]
moved plane far -37.50479614394951 [ 0.27561638 -0.95107255 0.13963023]
> ~surface #1.2
> surface #!1.2.10
> view #!1.2.14 @ zoom 0.75
moved plane near -15.19837108023883 [ 0.27561638 -0.95107255 0.13963023]
moved plane far -15.19837108023883 [ 0.27561638 -0.95107255 0.13963023]
> ~surface #1.2
> surface #!1.2.14
> showTool true
Unknown command: showTool true
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/8sv7A.pdb format pdb
8sv7A.pdb title:
The 1.53 angstrom structure of human TANGO2 [more info...]
Chain information for 8sv7A.pdb #1
---
Chain | Description | UniProt
A | transport and golgi organization protein 2 homolog | TNG2_HUMAN 1-276
Non-standard residues in 8sv7A.pdb #1
---
SO4 — sulfate ion
> ui tool show "Find Cavities"
> kvfinder
14 cavities found for 8sv7A.pdb #1
8sv7A.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.10 | | 956.45 | 698.59 | 4428 | 15.34 | 4.44
1.2.13 | | 103.03 | 120.16 | 477 | 4.57 | 1.68
1.2.5 | | 47.95 | 72.39 | 222 | 0 | 0
1.2.11 | | 35.64 | 53.06 | 165 | 0 | 0
1.2.4 | | 29.81 | 41.18 | 138 | 2.16 | 0.58
1.2.1 | | 27.43 | 55.27 | 127 | 0 | 0
1.2.6 | | 25.49 | 40.78 | 118 | 0 | 0
1.2.9 | | 15.34 | 31.68 | 71 | 0.85 | 0.19
1.2.3 | | 14.04 | 19.78 | 65 | 1.04 | 0.26
1.2.12 | | 14.04 | 21.78 | 65 | 1.34 | 0.37
1.2.8 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.14 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.2 | | 11.88 | 24.03 | 55 | 0.6 | 0.17
1.2.7 | | 11.02 | 19.4 | 51 | 1.2 | 0.32
> view #1.2.10 @ zoom 0.75
moved plane near -37.90505864429557 [-0. -0. -1.]
moved plane far -37.90505864429557 [-0. -0. -1.]
> surface #1.2.1-14 transparency 50
> ~surface #1.2
> surface #1.2.10
> showTool true
Unknown command: showTool true
> mlp (#1 & protein) surfaces #1.2.10true
Invalid "surfaces" argument: only initial part "#1.2.10" of atom specifier
valid
> mlp (#1 & protein) surfaces #1.2.10
Map values for surface "cavity 10_cavity SES surface": minimum -25.79, mean
-3.551, maximum 18.13
> hide atoms
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/Tango2_cavity_KVFinder.cxs
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2x1d_forcomp.pdb
> format pdb
2x1d_forcomp.pdb title:
The crystal structure of mature acyl coenzyme A:isopenicillin N
acyltransferase from penicillium chrysogenum [more info...]
Chain information for 2x1d_forcomp.pdb #1
---
Chain | Description
B | acyl-coenzyme
Non-standard residues in 2x1d_forcomp.pdb #1
---
CSD — (CSD)
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Find Cavities"
> kvfinder
11 cavities found for 2x1d_forcomp.pdb #1
2x1d_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.3 | | 180.36 | 150.86 | 835 | 4.02 | 1.19
1.1.8 | | 50.76 | 64.27 | 235 | 4.37 | 2.06
1.1.7 | | 38.45 | 59.28 | 178 | 1.2 | 0.36
1.1.6 | | 32.18 | 49.97 | 149 | 3.06 | 1.04
1.1.10 | | 29.16 | 43.1 | 135 | 1.7 | 0.5
1.1.1 | | 28.94 | 52.49 | 134 | 0 | 0
1.1.9 | | 28.08 | 38.06 | 130 | 1.9 | 0.8
1.1.2 | | 25.7 | 37.43 | 119 | 2.16 | 0.62
1.1.4 | | 8.86 | 17.04 | 41 | 1.34 | 0.47
1.1.11 | | 8.42 | 16.5 | 39 | 0.6 | 0.15
1.1.5 | | 6.91 | 16.05 | 32 | 1.2 | 0.41
> view #1.1.3 @ zoom 0.75
moved plane near -22.60917140871646 [-0. -0. -1.]
moved plane far -22.60917140871646 [-0. -0. -1.]
> surface #1.1.1-11 transparency 50
> ~surface #1.1
> surface #1.1.3
> mlp (#1 & protein) surfaces #1.1.3
Map values for surface "cavity 3_cavity SES surface": minimum nan, mean nan,
maximum nan
/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorvol.py:247: RuntimeWarning: invalid value
encountered in cast
rgba8 = (255*rgba).astype(uint8)
> view #!1.1.8 @ zoom 0.75
moved plane near -15.838972615031372 [ 0.99720757 -0.02167071 -0.07146642]
moved plane far -15.838972615031372 [ 0.99720757 -0.02167071 -0.07146642]
> ~surface #1.1
> surface #!1.1.8
> view #!1.1.3 @ zoom 0.75
moved plane near -22.933255211535922 [ 0.99720757 -0.02167071 -0.07146642]
moved plane far -22.933255211535922 [ 0.99720757 -0.02167071 -0.07146642]
> ~surface #1.1
> surface #!1.1.3
> view #!1.1.8 @ zoom 0.75
moved plane near -19.020339581229845 [0.65607322 0.18354291 0.7320382 ]
moved plane far -19.020339581229845 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.8
> view #!1.1.7 @ zoom 0.75
moved plane near -24.78366217962295 [0.65607322 0.18354291 0.7320382 ]
moved plane far -24.78366217962295 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.7
> view #!1.1.6 @ zoom 0.75
moved plane near -18.292201576856502 [0.65607322 0.18354291 0.7320382 ]
moved plane far -18.292201576856502 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.6
> view #!1.1.10 @ zoom 0.75
moved plane near -22.17286704761159 [0.65607322 0.18354291 0.7320382 ]
moved plane far -22.17286704761159 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.10
> view #!1.1.1 @ zoom 0.75
moved plane near -12.285774068538963 [0.65607322 0.18354291 0.7320382 ]
moved plane far -12.285774068538963 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.1
> view #!1.1.9 @ zoom 0.75
moved plane near -18.42599101098824 [0.65607322 0.18354291 0.7320382 ]
moved plane far -18.42599101098824 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.9
> view #!1.1.2 @ zoom 0.75
moved plane near -16.63684445958934 [0.65607322 0.18354291 0.7320382 ]
moved plane far -16.63684445958934 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.2
> view #!1.1.4 @ zoom 0.75
moved plane near -16.414902047717934 [0.65607322 0.18354291 0.7320382 ]
moved plane far -16.414902047717934 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.4
> view #!1.1.11 @ zoom 0.75
moved plane near -18.38642362025197 [0.65607322 0.18354291 0.7320382 ]
moved plane far -18.38642362025197 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.11
> view #!1.1.5 @ zoom 0.75
moved plane near -16.304766172987993 [0.65607322 0.18354291 0.7320382 ]
moved plane far -16.304766172987993 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.5
> view #!1.1.3 @ zoom 0.75
moved plane near -27.598300781751323 [0.65607322 0.18354291 0.7320382 ]
moved plane far -27.598300781751323 [0.65607322 0.18354291 0.7320382 ]
> ~surface #1.1
> surface #!1.1.3
> transparency #1.1.3 30
> transparency #1.1.3 50
> transparency #1.1.3 0
> transparency #1.1.3
Missing or invalid "percent" argument: Expected a number
> transparency #1.1.3 10
> transparency #1.1.3 50
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/6dxx_forcomp.pdb
> format pdb
Summary of feedback from opening
/Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/6dxx_forcomp.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue CYS (103 )
Cannot find LINK/SSBOND residue ASN (37 )
Cannot find LINK/SSBOND residue ASN (107 )
4 messages similar to the above omitted
6dxx_forcomp.pdb title:
Human N-acylethanolamine-hydrolyzing acid amidase (naaa) In complex with non-
covalent benzothiazole-piperazine inhibitor ARN19702, In presence of triton
X-100 [more info...]
Chain information for 6dxx_forcomp.pdb #1
---
Chain | Description | UniProt
B | N-acylethanolamine-hydrolyzing acid amidase subunit β | NAAA_HUMAN 126-359
Non-standard residues in 6dxx_forcomp.pdb #1
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
WTF —
[2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone
> hide atoms
> ui tool show "Find Cavities"
> kvfinder
7 cavities found for 6dxx_forcomp.pdb #1
6dxx_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.7 | | 102.82 | 129.21 | 476 | 3.89 | 1.31
1.1.4 | | 47.95 | 63.42 | 222 | 3 | 0.81
1.1.3 | | 27 | 45.07 | 125 | 3.6 | 1.68
1.1.1 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.2 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.5 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.6 | | 9.72 | 16.91 | 45 | 0.85 | 0.17
> view #1.1.7 @ zoom 0.75
moved plane near -23.138188727315367 [-0. -0. -1.]
moved plane far -23.138188727315367 [-0. -0. -1.]
> surface #1.1.1-7 transparency 50
> ~surface #1.1
> surface #1.1.7
> mlp (#1 & protein) surfaces #1.1.7
Map values for surface "cavity 7_cavity SES surface": minimum -16.88, mean
5.33, maximum 20.92
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/5u7z_forcomp.pdb
> format pdb
Summary of feedback from opening
/Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/5u7z_forcomp.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (31 )
Cannot find LINK/SSBOND residue CYS (31 )
Cannot find LINK/SSBOND residue CYS (388 )
Cannot find LINK/SSBOND residue NAG (1 )
Cannot find LINK/SSBOND residue NAG (404 )
9 messages similar to the above omitted
5u7z_forcomp.pdb title:
Human acid ceramidase (ASAH1, acdase) self-activated [more info...]
Chain information for 5u7z_forcomp.pdb #1
---
Chain | Description | UniProt
B | acid ceramidase | A8K0B6_HUMAN 141-395
> ui tool show "Find Cavities"
> kvfinder
13 cavities found for 5u7z_forcomp.pdb #1
5u7z_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.5 | | 362.88 | 334.81 | 1680 | 6.18 | 1.73
1.1.13 | | 106.92 | 109.88 | 495 | 3.7 | 1.66
1.1.3 | | 80.35 | 122.76 | 372 | 7.22 | 3.63
1.1.10 | | 74.52 | 99.77 | 345 | 5.16 | 2.56
1.1.1 | | 55.51 | 68.62 | 257 | 3.55 | 1.5
1.1.11 | | 42.98 | 52.99 | 199 | 1.8 | 0.74
1.1.9 | | 36.07 | 59.9 | 167 | 0 | 0
1.1.6 | | 28.08 | 54.76 | 130 | 4.84 | 3
1.1.8 | | 23.11 | 35.28 | 107 | 1.8 | 0.54
1.1.2 | | 18.58 | 27.35 | 86 | 2.4 | 0.85
1.1.7 | | 8.42 | 15.83 | 39 | 1.2 | 0.33
1.1.4 | | 7.34 | 13.6 | 34 | 0.6 | 0.19
1.1.12 | | 7.13 | 14.97 | 33 | 0.6 | 0.2
> view #1.1.5 @ zoom 0.75
moved plane near -39.65249553726486 [-0.29191227 0.85451381 -0.42964331]
moved plane far -39.65249553726486 [-0.29191227 0.85451381 -0.42964331]
> surface #1.1.1-13 transparency 50
> ~surface #1.1
> surface #1.1.5
> mlp (#1 & protein) surfaces #1.1.5
Map values for surface "cavity 5_cavity SES surface": minimum -25.61, mean
-1.562, maximum 20.47
> close session
> open /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2hf0_forcomp.pdb
> format pdb
2hf0_forcomp.pdb title:
Bifidobacterium longum bile salt hydrolase [more info...]
Chain information for 2hf0_forcomp.pdb #1
---
Chain | Description | UniProt
B | bile salt hydrolase | Q9KK62_BIFLO 1-316
> ui tool show "Find Cavities"
> kvfinder
14 cavities found for 2hf0_forcomp.pdb #1
2hf0_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.11 | | 899.21 | 605.61 | 4163 | 9.62 | 2.96
1.1.10 | | 60.7 | 72.68 | 281 | 4.2 | 1.33
1.1.14 | | 56.81 | 79.96 | 263 | 1.8 | 0.45
1.1.9 | | 55.3 | 76.96 | 256 | 2.47 | 0.6
1.1.8 | | 29.59 | 51.3 | 137 | 0 | 0
1.1.7 | | 23.11 | 42.35 | 107 | 0 | 0
1.1.2 | | 18.36 | 33.35 | 85 | 2.16 | 0.79
1.1.5 | | 17.93 | 28.1 | 83 | 1.8 | 0.71
1.1.13 | | 17.28 | 36.68 | 80 | 0 | 0
1.1.3 | | 16.42 | 28.26 | 76 | 1.2 | 0.28
1.1.4 | | 12.96 | 17.76 | 60 | 1.34 | 0.42
1.1.12 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.6 | | 9.94 | 17.92 | 46 | 0.85 | 0.24
1.1.1 | | 9.72 | 19.27 | 45 | 0.6 | 0.11
> view #1.1.11 @ zoom 0.75
moved plane near -33.10490310151244 [-0.35798124 0.92803331 0.10297386]
moved plane far -33.10490310151244 [-0.35798124 0.92803331 0.10297386]
> surface #1.1.1-14 transparency 50
> ~surface #1.1
> surface #1.1.11
> mlp (#1 & protein) surfaces #1.1.11
Map values for surface "cavity 11_cavity SES surface": minimum -24.12, mean
0.362, maximum 23.17
> select protein
2463 atoms, 2528 bonds, 316 residues, 1 model selected
> ui tool show "Basic Actions"
> ui tool show "Color Actions"
> color sel bychain
> color coil gray
> color helix orange red
> color strand purple
> ui tool show "Color Actions"
> color helix yellow
> color helix gold
> color helix light yellow
> color helix gold
> color strand turquoise
> select clear
> color strand medium turquoise
> color helix sandy brown
> color #1.1.11 #0b7905
> color #1.1.11 #6d5079
> color #1.1.11 #6e5079
> color #1.1.11 #333b79
> color #1.1.11 #792e2c
> color #1.1.11 #796c33
> color #1.1.11 #6f1279
> color #1.1.11 #256379
> color #1.1.11 #796318
> color #1.1.11 #1c0679
> color #1.1.11 #1b0679
> color #1.1.11 #130a79
> transparency #1.1.11 50
> transparency #1.1.11 30
> ui tool show "Find Cavities"
> kvfinder volumeCutoff 50
4 cavities found for 2hf0_forcomp.pdb #1
2hf0_forcomp.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.3 | | 899.21 | 605.61 | 4163 | 9.62 | 2.96
1.1.2 | | 60.7 | 72.68 | 281 | 4.2 | 1.33
1.1.4 | | 56.81 | 79.96 | 263 | 1.8 | 0.45
1.1.1 | | 55.3 | 76.96 | 256 | 2.47 | 0.6
> view #1.1.3 @ zoom 0.75
moved plane near -36.662915572748936 [-0.5331149 0.76136199 0.36893959]
moved plane far -36.662915572748936 [-0.5331149 0.76136199 0.36893959]
> surface #1.1.1-4 transparency 50
> ~surface #1.1
> surface #1.1.3
> view #!1.1.2 @ zoom 0.75
moved plane near -23.00105657031177 [-0.5331149 0.76136199 0.36893959]
moved plane far -23.00105657031177 [-0.5331149 0.76136199 0.36893959]
> ~surface #1.1
> surface #!1.1.2
> view #!1.1.4 @ zoom 0.75
moved plane near -24.751349236332846 [-0.5331149 0.76136199 0.36893959]
moved plane far -24.751349236332846 [-0.5331149 0.76136199 0.36893959]
> ~surface #1.1
> surface #!1.1.4
> view #!1.1.1 @ zoom 0.75
moved plane near -23.36801995932231 [-0.5331149 0.76136199 0.36893959]
moved plane far -23.36801995932231 [-0.5331149 0.76136199 0.36893959]
> ~surface #1.1
> surface #!1.1.1
> view #!1.1.3 @ zoom 0.75
moved plane near -36.662915572748936 [-0.5331149 0.76136199 0.36893959]
moved plane far -36.662915572748936 [-0.5331149 0.76136199 0.36893959]
> ~surface #1.1
> surface #!1.1.3
> color #1.1.3 #998798
> color #1.1.3 #927a99
> color #1.1.3 #976b99
> ui tool show "Color Actions"
> color deep pink
> color slate blue
> color medium slate blue
> color helix sandy brown
> color strand medium turquoise
> color coil gray
> view
[Repeated 2 time(s)]
> select #!1/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 6 atom styles
> show sel atoms
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label height 1
> label height 1.5
[Repeated 1 time(s)]
> select clear
> view #!1.1.1 @ zoom 0.75
moved plane near -24.499848458712496 [ 0.60863115 0.37890103 -0.69713854]
moved plane far -24.499848458712496 [ 0.60863115 0.37890103 -0.69713854]
> ~surface #1.1
> surface #!1.1.1
> view #!1.1.1,4 @ zoom 0.75
moved plane near -32.78823181406694 [ 0.60863115 0.37890103 -0.69713854]
moved plane far -32.78823181406694 [ 0.60863115 0.37890103 -0.69713854]
> ~surface #1.1
> surface #!1.1.1,4
> view #!1.1.1-2,4 @ zoom 0.75
moved plane near -39.55025183385154 [ 0.60863115 0.37890103 -0.69713854]
moved plane far -39.55025183385154 [ 0.60863115 0.37890103 -0.69713854]
> ~surface #1.1
> surface #!1.1.1-2,4
> view #!1.1.1-4 @ zoom 0.75
moved plane near -49.59804632908499 [ 0.60863115 0.37890103 -0.69713854]
moved plane far -49.59804632908499 [ 0.60863115 0.37890103 -0.69713854]
> ~surface #1.1
> surface #!1.1.1-4
> view #!1.1.3 @ zoom 0.75
moved plane near -35.65181385822235 [ 0.60863115 0.37890103 -0.69713854]
moved plane far -35.65181385822235 [ 0.60863115 0.37890103 -0.69713854]
> ~surface #1.1
> surface #!1.1.3
> view #!1.1.1-4 @ zoom 0.75
moved plane near -49.59804632908499 [ 0.60863115 0.37890103 -0.69713854]
moved plane far -49.59804632908499 [ 0.60863115 0.37890103 -0.69713854]
> ~surface #1.1
> surface #!1.1.1-4
> view #!1.1.3 @ zoom 0.75
moved plane near -35.27795093621785 [ 0.63064904 0.38458439 -0.67407467]
moved plane far -35.27795093621785 [ 0.63064904 0.38458439 -0.67407467]
> ~surface #1.1
> surface #!1.1.3
> save
> /Users/dayongzhou/Documents/TANGO2_PAPER_FIGURES/2hf0_cavity_KVFinder.cxs
——— End of log from Fri Aug 1 14:06:38 2025 ———
> view name session-start
opened ChimeraX session
> cartoon style width 1.3 thickness 0.25
> select H
Nothing selected
> delete atoms
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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 Air
Model Identifier: Mac14,2
Model Number: MN6Y3CH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.1.1
OS Loader Version: 11881.1.1
Software:
System Software Overview:
System Version: macOS 15.0.1 (24A348)
Kernel Version: Darwin 24.0.0
Time since boot: 31 days, 3 hours, 1 minute
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
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: 14.1.18
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-Clipper: 0.25.2
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
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: 1.1.2
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: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
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: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 1.48.0
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: 2.2.6
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: 6.0.1
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
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.1
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: 0.13.2
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
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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