![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 hours ago
#20384 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-26.4.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000017ee2f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000317387000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000318a6f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000001f0b598c0 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
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{
"uptime" : 5100,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac17,9",
"coalitionID" : 1579,
"osVersion" : {
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"build" : "25E253",
"releaseType" : "User"
},
"captureTime" : "2026-05-24 11:41:31.4908 +0100",
"codeSigningMonitor" : 2,
"incident" : "03AA6640-3A5F-4BE8-B2E8-31ED8F00323E",
"pid" : 2578,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-05-24 10:25:30.8685 +0100",
"procStartAbsTime" : 14164773944,
"procExitAbsTime" : 123599562030,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F757CBBA-C716-7781-2B0E-A61AE18E0FF4",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn"]},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "E8D09A3F-06A6-4B68-AA72-A306881A1577",
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4296900600
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1001d8000-1001dc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2578},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4296900600
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1001d8000-1001dc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"size" : 528120,
"uuid" : "66ebd321-6899-3863-ba24-5cfc3076a0cb",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6523543552,
"size" : 35060,
"uuid" : "d93ec420-f465-3a3a-916d-a04af9b023eb",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6523777024,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5626976,
"uuid" : "04941709-2330-3bf8-9213-6d33964db448",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "4424.1.402"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6739341312,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3125344,
"uuid" : "bcb81496-c81f-3d3e-a617-ccca047989e0",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
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"CFBundleShortVersionString" : "6.9",
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2685.50.120"
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{
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"base" : 6519472128,
"size" : 679624,
"uuid" : "9f682dcf-340c-3bfa-bcdd-dd702f30313e",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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{
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"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 16654816,
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)
Writable regions: Total=2.2G written=2019K(0%) resident=2019K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 80K 5
ColorSync 96K 6
CoreAnimation 1616K 87
CoreGraphics 112K 7
CoreServices 624K 2
CoreUI image data 4192K 30
Foundation 48K 2
Kernel Alloc Once 96K 2
MALLOC 1.1G 342
MALLOC guard page 3872K 4
Mach message 64K 2
Memory Tag 22 64.0M 1
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 848K 53
Stack 269.8M 54
Stack Guard 56.0M 1
VM_ALLOCATE 337.3M 232
VM_ALLOCATE (reserved) 416.0M 2 reserved VM address space (unallocated)
__AUTH 6138K 646
__AUTH_CONST 91.3M 1043
__CTF 824 1
__DATA 42.7M 1136
__DATA_CONST 61.4M 1185
__DATA_DIRTY 8459K 897
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 605.1M 139
__OBJC_RO 79.1M 1
__OBJC_RW 2597K 1
__TEXT 1.5G 1207
__TPRO_CONST 128K 2
dyld private memory 304K 5
mapped file 656.9M 76
page table in kernel 2019K 1
shared memory 3232K 28
=========== ======= =======
TOTAL 5.2G 7209
TOTAL, minus reserved VM space 4.8G 7209
",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "a05a390aa82a7db582d69a66b4cff51870e02139",
"roots_installed" : 0,
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"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : [
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{
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/Ania/Desktop/files_for_fig/deino.cxs
> view name session-start
opened ChimeraX session
> open /Users/Ania/Desktop/HPI/8cka_vs_DALI.cxs
> view name session-start
opened ChimeraX session
> hide #7 models
> select add #4.2
6832 atoms, 927 residues, 1 model selected
> sequence chain #4/A
Alignment identifier is 4/A
> select clear
> select #4/A:19
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:19-28
63 atoms, 63 bonds, 10 residues, 1 model selected
> select #4/A:19
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:19-28
63 atoms, 63 bonds, 10 residues, 1 model selected
> select clear
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> select #4/A:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:173-174
11 atoms, 10 bonds, 2 residues, 1 model selected
> select
> #4/A:32-35,234-236,310-312,334-336,438-442,451-460,597-599,798-800,842-855,857-860,866-874
463 atoms, 458 bonds, 61 residues, 1 model selected
> select clear
> select #4/A:33
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:30-33
24 atoms, 23 bonds, 4 residues, 1 model selected
> select #4/A:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:32-35
23 atoms, 22 bonds, 4 residues, 1 model selected
> select #4/A:40
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:40-289
1749 atoms, 1774 bonds, 250 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> color sel dark salmon
> color sel salmon
> select clear
> graphics silhouettes false
> graphics silhouettes true
> save /Users/Ania/Desktop/files_for_fig/Fig1/Dradio_lipobox.png width 3000
> height 2202 supersample 3 transparentBackground true
> save /Users/Ania/Desktop/files_for_fig/Fig1/Dradio_lipobox.cxs
> close session
> open /Users/Ania/Desktop/DALI_SSDRAW/caulo.cxs format session
> view name session-start
opened ChimeraX session
> close #1,3,7-10,20-21,39-41
> close #46
> close #48-52,54-58
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI1_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain1.pdb
Chain information for E1H18_RS02850__565_subdomain1.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI1_taxlabels_ids_pdbs/J7528_RS10205__3930_subdomain1.pdb
Chain information for J7528_RS10205__3930_subdomain1.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI2_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain8.pdb
Chain information for E1H18_RS02850__565_subdomain8.pdb #3
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI2_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain4.pdb
Chain information for E1H18_RS02850__565_subdomain4.pdb #4
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI4_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain2.pdb
Chain information for E1H18_RS02850__565_subdomain2.pdb #5
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI4_taxlabels_ids_pdbs/J7528_RS10205__3930_subdomain2.pdb
Chain information for J7528_RS10205__3930_subdomain2.pdb #6
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI6_taxlabels_ids_pdbs/J7528_RS10205__3930_subdomain4.pdb
Chain information for J7528_RS10205__3930_subdomain4.pdb #7
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI6_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain6.pdb
Chain information for E1H18_RS02850__565_subdomain6.pdb #8
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI5_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain3.pdb
Chain information for E1H18_RS02850__565_subdomain3.pdb #9
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI5_taxlabels_ids_pdbs/J7528_RS10205__3930_subdomain3.pdb
Chain information for J7528_RS10205__3930_subdomain3.pdb #10
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI7_taxlabels_ids_pdbs/J7528_RS10205__3930_subdomain5.pdb
Chain information for J7528_RS10205__3930_subdomain5.pdb #11
---
Chain | Description
A | No description available
> open
> /Users/Ania/Desktop/DALI_SSDRAW/RsaA_Caulobacteriaceae/DALI7_taxlabels_ids_pdbs/E1H18_RS02850__565_subdomain9.pdb
Chain information for E1H18_RS02850__565_subdomain9.pdb #12
---
Chain | Description
A | No description available
Computing secondary structure
> mmaker #1,3,4,5,8,9,12 to #44
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
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain1.pdb, chain A (#1), sequence
alignment score = 1240.6
RMSD between 245 pruned atom pairs is 0.000 angstroms; (across all 245 pairs:
0.000)
Matchmaker
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain8.pdb, chain A (#3), sequence
alignment score = 508.2
RMSD between 103 pruned atom pairs is 0.000 angstroms; (across all 103 pairs:
0.000)
Matchmaker
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain4.pdb, chain A (#4), sequence
alignment score = 577.6
RMSD between 118 pruned atom pairs is 0.000 angstroms; (across all 118 pairs:
0.000)
Matchmaker
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain2.pdb, chain A (#5), sequence
alignment score = 589.2
RMSD between 121 pruned atom pairs is 0.000 angstroms; (across all 121 pairs:
0.000)
Matchmaker
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain6.pdb, chain A (#8), sequence
alignment score = 1268.7
RMSD between 268 pruned atom pairs is 0.000 angstroms; (across all 268 pairs:
0.000)
Matchmaker
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain3.pdb, chain A (#9), sequence
alignment score = 787
RMSD between 166 pruned atom pairs is 0.000 angstroms; (across all 166 pairs:
0.000)
Matchmaker
E1H18_RS02850__565___WP_172263482.1_hypothetical_protein__GCF_013181195.1____Caulobacter_sp_RHG1__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#44) with E1H18_RS02850__565_subdomain9.pdb, chain A (#12), sequence
alignment score = 1433.2
RMSD between 295 pruned atom pairs is 0.000 angstroms; (across all 295 pairs:
0.000)
> mmaker #2,6,7,10,11 to #47
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
J7528_RS10205__3930___WP_291873613.1_calcium_binding_protein__GCF_017744445.1____Caulobacter_sp__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#47) with J7528_RS10205__3930_subdomain1.pdb, chain A (#2), sequence
alignment score = 1231
RMSD between 244 pruned atom pairs is 0.000 angstroms; (across all 244 pairs:
0.000)
Matchmaker
J7528_RS10205__3930___WP_291873613.1_calcium_binding_protein__GCF_017744445.1____Caulobacter_sp__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#47) with J7528_RS10205__3930_subdomain2.pdb, chain A (#6), sequence
alignment score = 576.2
RMSD between 119 pruned atom pairs is 0.000 angstroms; (across all 119 pairs:
0.000)
Matchmaker
J7528_RS10205__3930___WP_291873613.1_calcium_binding_protein__GCF_017744445.1____Caulobacter_sp__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#47) with J7528_RS10205__3930_subdomain4.pdb, chain A (#7), sequence
alignment score = 1194.3
RMSD between 250 pruned atom pairs is 0.000 angstroms; (across all 250 pairs:
0.000)
Matchmaker
J7528_RS10205__3930___WP_291873613.1_calcium_binding_protein__GCF_017744445.1____Caulobacter_sp__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#47) with J7528_RS10205__3930_subdomain3.pdb, chain A (#10), sequence
alignment score = 539.5
RMSD between 114 pruned atom pairs is 0.000 angstroms; (across all 114 pairs:
0.000)
Matchmaker
J7528_RS10205__3930___WP_291873613.1_calcium_binding_protein__GCF_017744445.1____Caulobacter_sp__relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#47) with J7528_RS10205__3930_subdomain5.pdb, chain A (#11), sequence
alignment score = 1632.7
RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 332 pairs:
0.000)
> hide #2 models
> show #2 models
> hide #1 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #8 models
> hide #9 models
> hide #12 models
> hide #44 models
> select add #2
3462 atoms, 3486 bonds, 244 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #47 models
> select add #2
3462 atoms, 3486 bonds, 244 residues, 1 model selected
> color sel dim gray
> select subtract #2
Nothing selected
> select add #6
1581 atoms, 1588 bonds, 119 residues, 1 model selected
> color sel white
> select subtract #6
Nothing selected
> select add #10
1434 atoms, 1433 bonds, 114 residues, 1 model selected
> color sel gray
> color sel dark gray
> color sel gray
> select subtract #10
Nothing selected
> select add #7
3350 atoms, 3359 bonds, 250 residues, 1 model selected
> color sel light gray
> select subtract #7
Nothing selected
> select add #6
1581 atoms, 1588 bonds, 119 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
1581 atoms, 1588 bonds, 119 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #11
4436 atoms, 4450 bonds, 332 residues, 1 model selected
> ui tool show "Color Actions"
> color sel coral
> select subtract #11
Nothing selected
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> save /Users/Ania/Desktop/files_for_fig/Fig2/Caulo_fig2.cxs
> save /Users/Ania/Desktop/files_for_fig/Fig2/Caulo_J7528_fig2.png width 3000
> height 2202 supersample 3 transparentBackground true
> hide #2 models
> hide #6 models
> hide #7 models
> hide #10 models
> hide #11 models
> show #1 models
> show #3 models
> show #4 models
> show #5 models
> show #8 models
> show #9 models
> show #12 models
> show #44 models
> select add #1
3500 atoms, 3526 bonds, 245 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
3500 atoms, 3526 bonds, 245 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #44 models
> show #44 models
> hide #12 models
> hide #9 models
> hide #8 models
> hide #5 models
> hide #4 models
> hide #3 models
> select add #1
3500 atoms, 3526 bonds, 245 residues, 1 model selected
> select add #44
21747 atoms, 21861 bonds, 1581 residues, 2 models selected
> sequence chain #44/A
Alignment identifier is 44/A
> sequence chain #1/A
Alignment identifier is 1/A
> select clear
> select #44/A:246
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #44/A:1-246
3514 atoms, 3540 bonds, 246 residues, 1 model selected
> color sel dim gray
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> select add #5
5175 atoms, 5205 bonds, 367 residues, 2 models selected
> sequence chain #44/A
Destroying pre-existing alignment with identifier 44/A
Alignment identifier is 44/A
> sequence chain #5/A
Alignment identifier is 5/A
> select #44/A:247
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #44/A:247-369
1685 atoms, 1689 bonds, 123 residues, 1 model selected
> color sel white
> hide #5 models
> hide #1 models
> show #8 models
> hide #8 models
> show #9 models
> sequence chain #44/A
Destroying pre-existing alignment with identifier 44/A
Alignment identifier is 44/A
> select add #9
3872 atoms, 3880 bonds, 289 residues, 2 models selected
> sequence chain #44/A
Destroying pre-existing alignment with identifier 44/A
Alignment identifier is 44/A
> sequence chain #9/A
Alignment identifier is 9/A
> select #44/A:370
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #44/A:370-532
2149 atoms, 2153 bonds, 163 residues, 1 model selected
> select #44/A:370-371
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #44/A:370-528
2103 atoms, 2107 bonds, 159 residues, 1 model selected
> color sel gray
> show #3 models
> hide #3 models
> show #4 models
> select add #4
3688 atoms, 3700 bonds, 277 residues, 2 models selected
> sequence chain #44/A
Destroying pre-existing alignment with identifier 44/A
Alignment identifier is 44/A
> sequence chain #4/A
Alignment identifier is 4/A
> select #44/A:529
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #44/A:529-650
1631 atoms, 1639 bonds, 122 residues, 1 model selected
> select #44/A:529-658
1732 atoms, 1740 bonds, 130 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime green
> hide #4 models
> show #5 models
> hide #5 models
> show #8 models
> select add #8
5403 atoms, 5425 bonds, 398 residues, 2 models selected
> sequence chain #44/A
Destroying pre-existing alignment with identifier 44/A
Alignment identifier is 44/A
> sequence chain #8/A
Alignment identifier is 8/A
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac17,9
Model Number: Z1ML0017VB/A
Chip: Apple M5 Pro
Total Number of Cores: 18 (6 Super and 12 Performance)
Memory: 64 GB
System Firmware Version: 18000.101.7
OS Loader Version: 18000.101.7
Software:
System Software Overview:
System Version: macOS 26.4.1 (25E253)
Kernel Version: Darwin 25.4.0
Time since boot: 1 hour, 26 minutes
Graphics/Displays:
Apple M5 Pro:
Chipset Model: Apple M5 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.21.2
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: 2.4.6
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
plotly: 6.7.0
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
pyKVFinder: 0.9.2
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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