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Opened 2 hours ago
#19757 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001f74bac40 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
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"procRole" : "Background",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac16,5",
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"codeSigningMonitor" : 2,
"incident" : "7FB96C26-71E6-4281-BB2D-7AA41F19CD1B",
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"cpuType" : "ARM-64",
"procLaunch" : "2026-01-20 14:19:13.9179 +0100",
"procStartAbsTime" : 2774970005218,
"procExitAbsTime" : 3014816599190,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
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"appleIntelligenceStatus" : {"reasons":["notOptedIn"],"state":"unavailable"},
"developerMode" : 1,
"responsiblePid" : 2804,
"responsibleProc" : "Terminal",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "ACDF9C9C-513D-4183-B177-7D72F7DD0CCF",
"wakeTime" : 28504,
"sleepWakeUUID" : "E5663C8A-9C2A-4B37-A9AB-B9A91D8E0828",
"sip" : "enabled",
"vmRegionInfo" : "0x700001200 is in 0x4ce000000-0x7c8c00000; bytes after start: 9428800000 bytes before end: 3368021503
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 4cd800000-4cdb50000 [ 3392K] rw-\/rwx SM=PRV
GAP OF 0x4b0000 BYTES
---> commpage (reserved) 4ce000000-7c8c00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 7c8c00000-7c9000000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000700001200","rawCodes":[2,30064775680],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000700001200"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":66473},
"vmregioninfo" : "0x700001200 is in 0x4ce000000-0x7c8c00000; bytes after start: 9428800000 bytes before end: 3368021503
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 4cd800000-4cdb50000 [ 3392K] rw-\/rwx SM=PRV
GAP OF 0x4b0000 BYTES
---> commpage (reserved) 4ce000000-7c8c00000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 7c8c00000-7c9000000 [ 4096K] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/transfer_11636725_files_2946497c/BRCA2map.cxs
Opened cryosparc_P26_J759_009_volume_map.mrc as #1, grid size 336,336,336,
pixel 0.745, shown at level 0.0137, step 2, values float32
Opened cryosparc_P26_J780_map_locres.mrc as #2, grid size 336,336,336, pixel
0.745, shown at level 6.08, step 2, values float32
> view name session-start
opened ChimeraX session
> select /A
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> volume #1 step 1
> volume #1 style mesh
> graphics silhouettes false
> select #1/X
Nothing selected
> select #1/X
Nothing selected
> show atoms
> hide atoms
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 360 atom styles
> select #3/E
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> rainbow sel
> select #3/C
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> rainbow sel
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> sequence chain #3/X
Alignment identifier is 3/X
> select #3/O
66 atoms, 69 bonds, 8 residues, 1 model selected
> show sel atoms
> sequence chain #3/O
Alignment identifier is 3/O
> select #3/O
66 atoms, 69 bonds, 8 residues, 1 model selected
> view sel
> select zone sel 4.5 #1/C residues true
No target atoms or surfaces
> select zone sel 4.5 #3/C residues true
Selected 99 atoms
> show sel atoms
> style sel ball
Changed 99 atom styles
> color sel bychain
> color sel byhetero
> hide sel cartoons
> select #3/C
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> hide sel cartoons
> show sel atoms
> style sel ball
Changed 2485 atom styles
> color sel byhetero
> show sel cartoons
> view #3 clip false
> select #3/C
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> color sel bychain
> color sel byhetero
> select #3
15583 atoms, 15863 bonds, 11 pseudobonds, 1971 residues, 3 models selected
> color sel bychain
> select #3/C
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> color sel byhetero
> select #3/D
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> show sel atoms
> style sel ball
Changed 2485 atom styles
> open 1V5W
Summary of feedback from opening 1V5W fetched from pdb
---
note | Fetching compressed mmCIF 1v5w from http://files.rcsb.org/download/1v5w.cif
1v5w title:
Crystal structure of the human Dmc1 protein [more info...]
Chain information for 1v5w #4
---
Chain | Description | UniProt
A B | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 1-340
1v5w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> hide #!3 models
> view #4 clip false
> open /Users/pc126390/Integrative_Modelling/Projet_DMC1/1V5W-assembly1.cif
1V5W-assembly1.cif title:
Crystal structure of the human Dmc1 protein [more info...]
Chain information for 1V5W-assembly1.cif #5
---
Chain | Description
A A-2 A-3 A-4 B B-2 B-3 B-4 | Meiotic recombination protein DMC1/LIM15 homolog
> hide #!4 models
> hide #!5 atoms
> show #!5 cartoons
> open 8QQE
Summary of feedback from opening 8QQE fetched from pdb
---
note | Fetching compressed mmCIF 8qqe from http://files.rcsb.org/download/8qqe.cif
8qqe title:
Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2
[more info...]
Chain information for 8qqe #6
---
Chain | Description | UniProt
A B | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 2-340
C D | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 1398-1417 2398-2417
Non-standard residues in 8qqe #6
---
CL — chloride ion
MG — magnesium ion
8qqe mmCIF Assemblies
---
1| author_defined_assembly
39 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4377 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close #6
> close #5
> close #4
> open /Users/pc126390/Integrative_Modelling/Projet_DMC1/8QQE-assembly1.cif
8QQE-assembly1.cif title:
Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2
[more info...]
Chain information for 8QQE-assembly1.cif #4
---
Chain | Description
A A-2 A-3 A-4 B B-2 B-3 B-4 | Meiotic recombination protein DMC1/LIM15 homolog
C C-2 C-3 C-4 D D-2 D-3 D-4 | Breast cancer type 2 susceptibility protein
Non-standard residues in 8QQE-assembly1.cif #4
---
CL — chloride ion
MG — magnesium ion
156 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
17508 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #!4 atoms
> show #!4 cartoons
> color #!4 bychain
> mmaker #4/A to #3/C
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 BRCA2L-J759_m1_real_space_refined_001.pdb, chain C (#3) with 8QQE-
assembly1.cif, chain A (#4), sequence alignment score = 1514.3
RMSD between 222 pruned atom pairs is 0.707 angstroms; (across all 296 pairs:
8.936)
> view #3/C
> show #!3 models
> hide #!3 models
> show #!3 models
> view #4/D
> select #4/D
39 atoms, 41 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 39 atom styles
> hide #!3 models
> mmaker #4/B to #3/C
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 BRCA2L-J759_m1_real_space_refined_001.pdb, chain C (#3) with 8QQE-
assembly1.cif, chain B (#4), sequence alignment score = 1453.7
RMSD between 222 pruned atom pairs is 0.703 angstroms; (across all 247 pairs:
2.555)
> show #!3 models
> view #4/B
> hide #!3 models
> show #!3 models
> hide #!4 models
> view #3/C
> select #3/C
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> sequence chain #3/C
Alignment identifier is 3/C
> ui tool show "Selection Inspector"
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_structs.cxs
> show #!1 models
> show #!2 models
> show #!4 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> select #3/A
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> select #3/A
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_A.pdb models #3
> selectedOnly true
> select #3/B
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_B.pdb models #3
> selectedOnly true
> select #3/C
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_C.pdb models #3
> selectedOnly true
> select #3/D
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_D.pdb models #3
> selectedOnly true
> select #3/E
2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_E.pdb models #3
> selectedOnly true
> select #3/F
2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_F.pdb models #3
> selectedOnly true
> select #3/O
66 atoms, 69 bonds, 8 residues, 1 model selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/brca2_O.pdb models #3
> selectedOnly true
> open /Users/pc126390/Integrative_Modelling/Projet_DMC1/brca2_O.pdb
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_A.pdb
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_B.pdb
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_C.pdb
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_D.pdb
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_E.pdb
> /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_F.pdb
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/brca2_O.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
151 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_A.pdb
---
warnings | Start residue of secondary structure not found: HELIX 16 16 ILE B 24 HIS B 30 1 7
Start residue of secondary structure not found: HELIX 17 17 VAL B 34 VAL B 43
1 10
Start residue of secondary structure not found: HELIX 18 18 ILE B 48 MET B 53
1 6
Start residue of secondary structure not found: HELIX 19 19 ARG B 56 ASN B 61
1 6
Start residue of secondary structure not found: HELIX 20 20 GLU B 67 LEU B 80
1 14
125 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
125 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_C.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
125 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_D.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
125 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_E.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
124 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_F.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
126 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Chain information for brca2_O.pdb #5
---
Chain | Description
O | No description available
Chain information for dmc1_A.pdb #6
---
Chain | Description
A | No description available
Chain information for dmc1_B.pdb #7
---
Chain | Description
B | No description available
Chain information for dmc1_C.pdb #8
---
Chain | Description
C | No description available
Chain information for dmc1_D.pdb #9
---
Chain | Description
D | No description available
Chain information for dmc1_E.pdb #10
---
Chain | Description
E | No description available
Chain information for dmc1_F.pdb #11
---
Chain | Description
F | No description available
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #5 models
> show #5 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> select #3/X
360 atoms, 395 bonds, 18 residues, 1 model selected
> save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_X.pdb models #3
> selectedOnly true
> open /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_X.pdb
Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7
Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1
10
Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1
6
Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1
6
Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1
14
151 messages similar to the above omitted
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Cannot find LINK/SSBOND residue ANP (401 )
Chain information for dmc1_X.pdb #12
---
Chain | Description
X | No description available
Computing secondary structure
> hide #5 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #12 models
> show #!11 models
> hide #!11 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> select #3/A:ANP
31 atoms, 33 bonds, 1 residue, 1 model selected
> view sel
No displayed objects specified.
> select #3/A:ANP
31 atoms, 33 bonds, 1 residue, 1 model selected
> view #8/A:ANP
No objects specified.
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #12 models
> hide #12 models
> show #12 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #12 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
Unsupported scale factor (0.000000) detected on Display0
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: fr_FR.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,5
Model Number: Z1FV000H9FN/A
Chip: Apple M4 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 2 jours, 12 heures et 55 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: LY0X41HPJ4
Display Firmware Version: Version 17.0 (Build 21A329)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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