![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16418 closed defect (duplicate)
Crash opening mmCIF
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700007cc8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff84857cdc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513 in collated_open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2075 in _open_dropped_file
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 278 in event
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath (total: 55)
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{
"uptime" : 17000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,3",
"coalitionID" : 934,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-12-04 17:46:20.6126 -0700",
"codeSigningMonitor" : 0,
"incident" : "B75361FA-9B71-47EE-B57B-6BFE27E7E875",
"pid" : 3966,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-04 16:37:06.4659 -0700",
"procStartAbsTime" : 13839648274538,
"procExitAbsTime" : 17993643139291,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"200B0C00-C631-5D3A-8F8D-E421AF1A7F31","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "26D916B7-51D3-8A66-D7D9-788B34CACDCE",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sip" : "enabled",
"vmRegionInfo" : "0x13ff00000 is not in any region. Bytes after previous region: 1 Bytes before following region: 528384\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 13fe2b000-13ff00000 [ 852K] r--\/rwx SM=COW Object_id=395d7f18\n---> GAP OF 0x81000 BYTES\n CoreAnimation 13ff81000-13ff84000 [ 12K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000000013ff00000","rawCodes":[1,5367660544],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000013ff00000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3966},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x13ff00000 is not in any region. Bytes after previous region: 1 Bytes before following region: 528384\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 13fe2b000-13ff00000 [ 852K] r--\/rwx SM=COW Object_id=395d7f18\n---> GAP OF 0x81000 BYTES\n CoreAnimation 13ff81000-13ff84000 [ 12K] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"factorPackIds" : {
"SIRI_UNDERSTANDING_NL_OVERRIDES" : "65a8104b6712a43e7922cab8"
},
"deploymentId" : 240000171
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/stellabrenman/Downloads/ChimeraX/AlphaFold/Q13951_ELOB/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033_CTTNBP2NL/fold_q13033_cttnbp2nl_model_0.cif"
Chain information for fold_q13033_cttnbp2nl_model_0.cif #1
---
Chain | Description
A | .
B | .
> set bgColor white
> select /b
4915 atoms, 4995 bonds, 639 residues, 1 model selected
> select /A
6137 atoms, 6266 bonds, 797 residues, 1 model selected
> color sel hot pink
> select /A:1,797 /B:1,639
31 atoms, 27 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033_CTTNBP2NL/fold_q13033_cttnbp2nl_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 1866 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033-2_CTTNBP2NL/fold_q13033_2_cttnbp2nl_model_0.cif"
Chain information for fold_q13033_2_cttnbp2nl_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5473 atoms, 5593 bonds, 713 residues, 1 model selected
> color sel hot pink
> select /A:1,713 /B:1,639
31 atoms, 27 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033-2_CTTNBP2NL/fold_q13033_2_cttnbp2nl_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 1224 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image3.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033_STRN/fold_q13033_strn_model_0.cif"
Chain information for fold_q13033_strn_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
6137 atoms, 6266 bonds, 797 residues, 1 model selected
> color sel hot pink
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033-2_STRN/fold_q13033_2_strn_model_0.cif"
Chain information for fold_q13033_2_strn_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
6059 atoms, 6178 bonds, 780 residues, 1 model selected
> select /A
5473 atoms, 5593 bonds, 713 residues, 1 model selected
> color sel hot pink
> select /A:1,713 /B:1,780
32 atoms, 28 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13033/Q13033-2_STRN/fold_q13033_2_strn_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 907 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13561/Q13561_CCDC172/fold_q13561_ccdc172_model_0.cif"
Chain information for fold_q13561_ccdc172_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
2173 atoms, 2195 bonds, 258 residues, 1 model selected
> select /A
3104 atoms, 3142 bonds, 401 residues, 1 model selected
> color sel hot pink
> select /A:1,401 /B:1,258
36 atoms, 32 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13561/Q13561_CCDC172/fold_q13561_ccdc172_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 854 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13561/Q13561-3_CCDC172/fold_q13561_3_ccdc172_model_0.cif"
Chain information for fold_q13561_3_ccdc172_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
3121 atoms, 3159 bonds, 403 residues, 1 model selected
> color sel hot pink
> select /A:1,403 /B:1,258
36 atoms, 32 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q13561/Q13561-3_CCDC172/fold_q13561_3_ccdc172_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 814 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978_ARRB1/fold_q14978_p49407_model_0.cif"
Chain information for fold_q14978_p49407_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
3312 atoms, 3379 bonds, 418 residues, 1 model selected
> select /A
5166 atoms, 5245 bonds, 699 residues, 1 model selected
> color sel hot pink
> select /A:1,699 /B:1,418
38 atoms, 34 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978_ARRB1/fold_q14978_p49407_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 111 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978-2_ARRB1/fold_q14978_2_p49407_model_0.cif"
Chain information for fold_q14978_2_p49407_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5247 atoms, 5328 bonds, 709 residues, 1 model selected
> color sel hot pink
> select /A:1,709 /B:1,418
38 atoms, 34 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978-2_ARRB1/fold_q14978_2_p49407_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 87 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978_ARRB2/fold_q14978_p32121_model_0.cif"
Chain information for fold_q14978_p32121_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
3247 atoms, 3322 bonds, 409 residues, 1 model selected
> select /A
5166 atoms, 5245 bonds, 699 residues, 1 model selected
> color sel hot pink
> select /A:1,699 /B:1,409
33 atoms, 29 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978_ARRB2/fold_q14978_p32121_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 136 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978-2_ARRB2/fold_q14978_2_p32121_model_0.cif"
Chain information for fold_q14978_2_p32121_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5247 atoms, 5328 bonds, 709 residues, 1 model selected
> color sel hot pink
> select /A:1,709 /B:1,409
33 atoms, 29 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q14978/Q14978-2_ARRB2/fold_q14978_2_p32121_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 52 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q15366/Q15366_SRSF3/fold_q15366_p84103_model_0.cif"
Chain information for fold_q15366_p84103_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
1360 atoms, 1389 bonds, 164 residues, 1 model selected
> select /A
2695 atoms, 2738 bonds, 365 residues, 1 model selected
> color sel hot pink
> select /A:1,365 /B:1,164
33 atoms, 29 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q15366/Q15366_SRSF3/fold_q15366_p84103_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 206 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q15366/Q15366-J5_SRSF3/fold_q15366_j5_p84103_model_0.cif"
Chain information for fold_q15366_j5_p84103_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
2354 atoms, 2385 bonds, 320 residues, 1 model selected
> color sel hot pink
> select /A:1,320 /B:1,164
33 atoms, 29 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q15366/Q15366-J5_SRSF3/fold_q15366_j5_p84103_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 254 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4_TMOD1/fold_q32mz4_p28289_model_0.cif"
Chain information for fold_q32mz4_p28289_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
2846 atoms, 2889 bonds, 359 residues, 1 model selected
> select /A
6238 atoms, 6307 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,359
31 atoms, 27 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4_TMOD1/fold_q32mz4_p28289_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 422 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-3_TMOD1/fold_q32mz4_3_p28289_model_0.cif"
Chain information for fold_q32mz4_3_p28289_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5781 atoms, 5848 bonds, 752 residues, 1 model selected
> color sel hot pink
> select /A:1,752 /B:1,359
31 atoms, 27 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-3_TMOD1/fold_q32mz4_3_p28289_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 123 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-4_TMOD1/fold_q32mz4_4_p28289_model_0.cif"
Chain information for fold_q32mz4_4_p28289_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5119 atoms, 5168 bonds, 640 residues, 1 model selected
> color sel hot pink
> select /A:1,640 /B:1,359
34 atoms, 30 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-4_TMOD1/fold_q32mz4_4_p28289_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 0 residue or atom pairs within distance 8
> alphafold contacts /A toAtoms /B distance 13
Found 17 residue or atom pairs within distance 13
> save /Users/stellabrenman/Desktop/image3.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4_CEP44/fold_q32mz4_q9c0f1_model_0.cif"
Chain information for fold_q32mz4_q9c0f1_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
3085 atoms, 3129 bonds, 390 residues, 1 model selected
> select /A
6238 atoms, 6307 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,390
32 atoms, 28 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4_CEP44/fold_q32mz4_q9c0f1_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 482 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-3_CEP44/fold_q32mz4_3_q9c0f1_model_0.cif"
Chain information for fold_q32mz4_3_q9c0f1_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5781 atoms, 5848 bonds, 752 residues, 1 model selected
> color sel hot pink
> select /A:1,752 /B:1,390
32 atoms, 28 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-3_CEP44/fold_q32mz4_3_q9c0f1_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 408 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-4_CEP44/fold_q32mz4_4_q9c0f1_model_0.cif"
Chain information for fold_q32mz4_4_q9c0f1_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
5119 atoms, 5168 bonds, 640 residues, 1 model selected
> color sel hot pink
> select /A:1,640 /B:1,390
35 atoms, 31 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q32MZ4/Q32MZ4-4_CEP44/fold_q32mz4_4_q9c0f1_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 678 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image3.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3_MAPRE1/fold_q3kqu3_q15691_model_0.cif"
Chain information for fold_q3kqu3_q15691_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
2112 atoms, 2154 bonds, 268 residues, 1 model selected
> select /A
6523 atoms, 6667 bonds, 841 residues, 1 model selected
> color sel hot pink
> select /A:1,841 /B:1,268
38 atoms, 35 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3_MAPRE1/fold_q3kqu3_q15691_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 315 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3-4_MAPRE1/fold_q3kqu3_4_q15691_model_0.cif"
Chain information for fold_q3kqu3_4_q15691_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
6287 atoms, 6423 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,268
38 atoms, 35 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3-4_MAPRE1/fold_q3kqu3_4_q15691_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 337 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3_KIF2A/fold_q3kqu3_o00139_model_0.cif"
Chain information for fold_q3kqu3_o00139_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
5608 atoms, 5698 bonds, 706 residues, 1 model selected
> select /A
6523 atoms, 6667 bonds, 841 residues, 1 model selected
> color sel hot pink
> select /A:1,841 /B:1,706
34 atoms, 30 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3_KIF2A/fold_q3kqu3_o00139_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 425 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3-4_KIF2A/fold_q3kqu3_4_o00139_model_0.cif"
Chain information for fold_q3kqu3_4_o00139_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
6287 atoms, 6423 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,706
34 atoms, 30 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q3KQU3/Q3KQU3-4_KIF2A/fold_q3kqu3_4_o00139_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 733 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71_RPS23/fold_q8ne71_p62266_model_0.cif"
Chain information for fold_q8ne71_p62266_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
1113 atoms, 1131 bonds, 143 residues, 1 model selected
> select /A
6287 atoms, 6423 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,143
32 atoms, 28 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71_RPS23/fold_q8ne71_p62266_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 23 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71-J1_RPS23/fold_q8ne71_j1_p62266_model_0.cif"
Chain information for fold_q8ne71_j1_p62266_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
6750 atoms, 6857 bonds, 846 residues, 1 model selected
> color sel hot pink
> select /A:1,846 /B:1,143
33 atoms, 29 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71-J1_RPS23/fold_q8ne71_j1_p62266_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 125 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71_RPL10A/fold_q8ne71_p62906_model_0.cif"
Chain information for fold_q8ne71_p62906_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
1744 atoms, 1772 bonds, 217 residues, 1 model selected
> select /A
6287 atoms, 6423 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,217
38 atoms, 35 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71_RPL10A/fold_q8ne71_p62906_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 33 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71-J1_RPL10A/fold_q8ne71_j1_p62906_model_0.cif"
Chain information for fold_q8ne71_j1_p62906_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A
6750 atoms, 6857 bonds, 846 residues, 1 model selected
> color sel hot pink
> select /A:1,846 /B:1,217
39 atoms, 36 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71-J1_RPL10A/fold_q8ne71_j1_p62906_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 365 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image2.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71_RPL11/fold_q8ne71_p62913_model_0.cif"
Chain information for fold_q8ne71_p62913_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /b
1424 atoms, 1447 bonds, 178 residues, 1 model selected
> select /A
6287 atoms, 6423 bonds, 808 residues, 1 model selected
> color sel hot pink
> select /A:1,808 /B:1,178
35 atoms, 31 bonds, 4 residues, 1 model selected
> label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code}
> label height 3
> alphafold pae #1 file "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71_RPL11/fold_q8ne71_p62913_full_data_0.json"
> alphafold contacts /A toAtoms /B distance 8
Found 171 residue or atom pairs within distance 8
> save /Users/stellabrenman/Desktop/image1.png supersample 3
> close
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q8NE71/Q8NE71-J1_RPL11/fold_q8ne71_j1_p62913_model_0.cif"
Failed opening file /Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
3/Q8NE71/Q8NE71-J1_RPL11/fold_q8ne71_j1_p62913_model_0.cif:
mmCIF parsing error: not enough data values, foundEnd of input on line 10433
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q9NUQ6/Q9NUQ6_IFI16/fold_q9nuq6_q16666_model_0.cif"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold
> 3/Q9NUQ6/Q9NUQ6-2_IFI16/fold_q9nuq6_2_q16666_model_0.cif"
Chain information for fold_q9nuq6_2_q16666_model_0.cif #1
---
Chain | Description
A | .
B | .
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 5 hours
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2415Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 59JJ48BG0V3B
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash opening mmCIF |
comment:2 by , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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