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Opened 34 minutes ago
#19465 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508070056 (2025-08-07 00:56:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002029860c0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1058 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1223 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 57)
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{
"uptime" : 7400,
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 1603,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2025-12-02 10:51:06.3181 +0100",
"codeSigningMonitor" : 1,
"incident" : "EDF473E8-9912-404C-876D-D139439F1FAF",
"pid" : 1697,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-02 09:12:11.0086 +0100",
"procStartAbsTime" : 36371676765,
"procExitAbsTime" : 178819269318,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FD0CFA27-A212-50A1-8CF0-62FF1D8A0863","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D93E1587-7AA2-780C-4174-19F7D9E4F252",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "4C9E9285-DFD3-4864-8640-BFF8757E4B21",
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4367433720\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10451c000-104520000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.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":1697},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4367433720\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10451c000-104520000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3603"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6984286208,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3174368,
"uuid" : "1a037942-11e0-3fc8-aad2-20b11e7ae1a4",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6855356416,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21564992,
"uuid" : "860c164c-d04c-30ff-8c6f-e672b74caf11",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.70.52"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6784598016,
"size" : 636280,
"uuid" : "3247e185-ced2-36ff-9e29-47a77c23e004",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6811889664,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14587296,
"uuid" : "b9a92060-f21e-3ecf-9ded-94a65c68a6f4",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3603"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7429861376,
"CFBundleShortVersionString" : "20621",
"CFBundleIdentifier" : "com.apple.WebKit",
"size" : 21306528,
"uuid" : "fb40cbe5-eb40-3ba6-b806-be1abc73a678",
"path" : "\/System\/Library\/Frameworks\/WebKit.framework\/Versions\/A\/WebKit",
"name" : "WebKit",
"CFBundleVersion" : "20621.3.11.11.3"
}
],
"sharedCache" : {
"base" : 6783762432,
"size" : 5040898048,
"uuid" : "4c1223e5-cace-3982-a003-6110a7a8a25c"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.5G written=2104K(0%) resident=2104K(0%) swapped_out=0K(0%) unallocated=3.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 960K 38 \nColorSync 624K 33 \nCoreAnimation 2768K 133 \nCoreGraphics 48K 3 \nCoreServices 1248K 5 \nCoreUI image data 5408K 39 \nFoundation 64K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.9G 119 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 256K 3 \nPROTECTED_MEMORY 16K 1 \nSTACK GUARD 624K 39 \nStack 200.8M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 275.2M 245 \nVM_ALLOCATE (reserved) 192.0M 2 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 33.5M 1069 \n__DATA_CONST 53.5M 1088 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.5M 139 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1097 \n__TEXT (graphics) 9424K 11 \n__TPRO_CONST 128K 2 \ndyld private memory 1840K 17 \nmapped file 592.7M 88 \npage table in kernel 2104K 1 \nshared memory 3680K 24 \n=========== ======= ======= \nTOTAL 6.3G 6251 \nTOTAL, minus reserved VM space 6.1G 6251 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "d30782e577659b2cbc5e15433d07d485ac058d88",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
},
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{
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202508070056 (2025-08-07)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/till/Desktop/titinasingTwcK/molecularReplacement/test/CCP4_DATABASE/tmp/2/2_TitTwcKDtoEAMPPNPE4X3setHeF_warpNtrace.pdb
Chain information for 2_TitTwcKDtoEAMPPNPE4X3setHeF_warpNtrace.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
Q | No description available
Drag select of 8542 atoms, 48 pseudobonds
> show sel cartoons
Computing secondary structure
> hide sel atoms
> select clear
> open /Users/till/Downloads/TTN1_final.pdb
Chain information for TTN1_final.pdb #2
---
Chain | Description
A | No description available
46 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3551 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> close #1
> select clear
> select /A:82
19 atoms, 18 bonds, 1 residue, 1 model selected
> sequence chain #2/A
Alignment identifier is 2/A
> select clear
> hide atoms
> select /A:306
16 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select /A:320
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:312
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> label delete #2
> select clear
> select /A:5
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:5-35
499 atoms, 503 bonds, 31 residues, 1 model selected
> color sel yellow
> ui tool show "Color Actions"
> select /A:293
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:293-370
1037 atoms, 1045 bonds, 2 pseudobonds, 65 residues, 2 models selected
> select /A:367
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:293-367
1003 atoms, 1010 bonds, 2 pseudobonds, 62 residues, 2 models selected
> color sel red
> select /A:368
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:368-463
1440 atoms, 1451 bonds, 96 residues, 1 model selected
> color sel forest green
> set bgColor white
> set bgColor #ffffff00
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select /A:36
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:36-292
4106 atoms, 4151 bonds, 257 residues, 1 model selected
> color sel light gray
> select clear
> lighting simple
> lighting full
> lighting soft
> lighting simple
> select clear
> select /A:293
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:293-306
114 atoms, 114 bonds, 1 pseudobond, 8 residues, 2 models selected
> select
> /A:8-13,32-35,75-87,118-123,131-151,160-162,197-199,202-205,212-228,238-247,255-257,262-269,276-278,282-286,289-292,303-309,338-343,347-349,436-438
2093 atoms, 2098 bonds, 129 residues, 1 model selected
> select /A:307
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:293-307
136 atoms, 136 bonds, 1 pseudobond, 9 residues, 2 models selected
> color (#!2 & sel) #fffeffff
> color (#!2 & sel) #fff2ffff
> color (#!2 & sel) #ffc8ffff
> color (#!2 & sel) #ff80ffff
> color (#!2 & sel) #ff48ffff
> color (#!2 & sel) #ff17ffff
> color (#!2 & sel) #ff00ffff
> color (#!2 & sel) #ff00feff
> color (#!2 & sel) #ff00edff
> color (#!2 & sel) #ff00c8ff
> color (#!2 & sel) #ff009dff
> color (#!2 & sel) #ff0070ff
> color (#!2 & sel) #ff0041ff
> color (#!2 & sel) #ff001cff
> color (#!2 & sel) #ff000aff
> color (#!2 & sel) #ff0004ff
> color (#!2 & sel) #ff0001ff
> color (#!2 & sel) #ff0000ff
> color (#!2 & sel) #ff0100ff
> color (#!2 & sel) #ff0300ff
> color (#!2 & sel) #ff0600ff
> color (#!2 & sel) #ff0800ff
> color (#!2 & sel) #ff0900ff
> color (#!2 & sel) #ff0a00ff
> color (#!2 & sel) #ff0e00ff
> color (#!2 & sel) #ff0f00ff
> color (#!2 & sel) #ff1000ff
> color (#!2 & sel) #ff1200ff
> color (#!2 & sel) #ff1400ff
> color (#!2 & sel) #ff1700ff
> color (#!2 & sel) #ff1a00ff
> color (#!2 & sel) #ff1d00ff
> color (#!2 & sel) #ff1f00ff
> color (#!2 & sel) #ff2000ff
> color (#!2 & sel) #ff2200ff
> color (#!2 & sel) #ff2500ff
> color (#!2 & sel) #ff2600ff
> color (#!2 & sel) #ff2700ff
> color (#!2 & sel) #ff2800ff
> color (#!2 & sel) #ff2a00ff
> color (#!2 & sel) #ff2b00ff
> color (#!2 & sel) #ff2c00ff
> color (#!2 & sel) #ff2d00ff
> color (#!2 & sel) #ff2e00ff
> color (#!2 & sel) #ff3000ff
> color (#!2 & sel) #ff3200ff
> color (#!2 & sel) #ff3300ff
> color (#!2 & sel) #ff3400ff
> color (#!2 & sel) #ff3600ff
> color (#!2 & sel) #ff3800ff
> color (#!2 & sel) #ff3900ff
> color (#!2 & sel) #ff3a00ff
> color (#!2 & sel) #ff3800ff
> color (#!2 & sel) #fc3800ff
> color (#!2 & sel) #fa3800ff
> color (#!2 & sel) #f83800ff
> color (#!2 & sel) #f63800ff
> color (#!2 & sel) #f53800ff
> color (#!2 & sel) #f23800ff
> color (#!2 & sel) #f03800ff
> color (#!2 & sel) #ef3800ff
> color (#!2 & sel) #eb3800ff
> color (#!2 & sel) #e93800ff
> color (#!2 & sel) #e83800ff
> color (#!2 & sel) #e63800ff
> color (#!2 & sel) #e33800ff
> color (#!2 & sel) #e23800ff
> color (#!2 & sel) #e13800ff
> color (#!2 & sel) #e03800ff
> color (#!2 & sel) #de3800ff
> color (#!2 & sel) #dc3800ff
> color (#!2 & sel) #db3800ff
> color (#!2 & sel) #d83800ff
> color (#!2 & sel) #d63800ff
> color (#!2 & sel) #d73800ff
> color (#!2 & sel) #d73802ff
> color (#!2 & sel) #d73804ff
> color (#!2 & sel) #d73806ff
> color (#!2 & sel) #d73807ff
> color (#!2 & sel) #d73809ff
> color (#!2 & sel) #d7380aff
> color (#!2 & sel) #d7380dff
> color (#!2 & sel) #d73810ff
> color (#!2 & sel) #d73812ff
> color (#!2 & sel) #d73813ff
> color (#!2 & sel) #d73814ff
> color (#!2 & sel) #d73816ff
> color (#!2 & sel) #d73818ff
> color (#!2 & sel) #d7381cff
> color (#!2 & sel) #d7381dff
> color (#!2 & sel) #d7381fff
> color (#!2 & sel) #d73821ff
> color (#!2 & sel) #d73824ff
> color (#!2 & sel) #d73825ff
> color (#!2 & sel) #d7382aff
> color (#!2 & sel) #d7382cff
> color (#!2 & sel) #d7392cff
> color (#!2 & sel) #d73a2cff
> color (#!2 & sel) #d73e2cff
> color (#!2 & sel) #d7432cff
> color (#!2 & sel) #d7442cff
> color (#!2 & sel) #d7452cff
> color (#!2 & sel) #d7462cff
> color (#!2 & sel) #d7482cff
> color (#!2 & sel) #d74b2cff
> color (#!2 & sel) #d74b28ff
> color (#!2 & sel) #d74b22ff
> color (#!2 & sel) #d74b20ff
> color (#!2 & sel) #d74b1cff
> color (#!2 & sel) #d74b18ff
> color (#!2 & sel) #d74b15ff
> color (#!2 & sel) #d74b14ff
> color (#!2 & sel) #d74b13ff
> color (#!2 & sel) #d74b11ff
> color (#!2 & sel) #d74b10ff
> color (#!2 & sel) #d74b0fff
> color (#!2 & sel) #d74b0eff
> color (#!2 & sel) #d74b0dff
> color (#!2 & sel) #d74b0bff
> color (#!2 & sel) #d74b0aff
> color (#!2 & sel) #d74b05ff
> color (#!2 & sel) #d74b00ff
> color (#!2 & sel) #d74b04ff
> color (#!2 & sel) #d74b11ff
> color (#!2 & sel) #d74b17ff
> color (#!2 & sel) #d74b19ff
> color (#!2 & sel) #d74b1aff
> color (#!2 & sel) #d74b1eff
> color (#!2 & sel) #d74b22ff
> color (#!2 & sel) #d74b25ff
> color (#!2 & sel) #d74b26ff
> color (#!2 & sel) #d74b28ff
> color (#!2 & sel) #d74b2cff
> color (#!2 & sel) #d74b37ff
> color (#!2 & sel) #d74b3dff
> color (#!2 & sel) #d74b3eff
> color (#!2 & sel) #d74b40ff
> color (#!2 & sel) #d74b42ff
> color (#!2 & sel) #d74b44ff
> color (#!2 & sel) #d74b47ff
> color (#!2 & sel) #d74b50ff
> color (#!2 & sel) #d74b54ff
> color (#!2 & sel) #d74b55ff
> color (#!2 & sel) #d74b56ff
> color (#!2 & sel) #d74b5aff
> color (#!2 & sel) #d74b5fff
> color (#!2 & sel) #d74b68ff
> color (#!2 & sel) #d74b6cff
> color (#!2 & sel) #d74b75ff
> color (#!2 & sel) #d74b7bff
> color (#!2 & sel) #d74b80ff
> color (#!2 & sel) #d74b8aff
> color (#!2 & sel) #d74b8cff
> color (#!2 & sel) #d74b93ff
> color (#!2 & sel) #d74b9dff
> color (#!2 & sel) #d74ba1ff
> color (#!2 & sel) #d74ba7ff
> color (#!2 & sel) #d74ba9ff
> color (#!2 & sel) #d74ba8ff
> color (#!2 & sel) #d74b9eff
> color (#!2 & sel) #d74b8bff
> color (#!2 & sel) #d74b7aff
> color (#!2 & sel) #d74b66ff
> color (#!2 & sel) #d74b51ff
> color (#!2 & sel) #d74b43ff
> color (#!2 & sel) #d74b40ff
> color (#!2 & sel) #d74b39ff
> color (#!2 & sel) #d74b38ff
> color (#!2 & sel) #d74b36ff
> color (#!2 & sel) #d74b32ff
> color (#!2 & sel) #d74b2eff
> color (#!2 & sel) #d74b2dff
> color (#!2 & sel) #d74b28ff
> color (#!2 & sel) #d74b25ff
> color (#!2 & sel) #d74b22ff
> color (#!2 & sel) #d74b1dff
> color (#!2 & sel) #d74b1aff
> color (#!2 & sel) #d74b14ff
> color (#!2 & sel) #d74b11ff
> color (#!2 & sel) #d74b0eff
> color (#!2 & sel) #d74b0bff
> color (#!2 & sel) #d74b08ff
> color (#!2 & sel) #d74b05ff
> color (#!2 & sel) #d74b00ff
> color (#!2 & sel) #d94b00ff
> color (#!2 & sel) #ff4b00ff
> color (#!2 & sel) #ff4b02ff
> color (#!2 & sel) #ff4b03ff
> color (#!2 & sel) #ff4b06ff
> color (#!2 & sel) #ff4b08ff
> color (#!2 & sel) #ff4b0aff
> color (#!2 & sel) #ff4b0bff
> color (#!2 & sel) #ff4b0cff
> color (#!2 & sel) #ff4b0dff
> color (#!2 & sel) #ff4b10ff
> color (#!2 & sel) #ff4b12ff
> color (#!2 & sel) #ff4b16ff
> color (#!2 & sel) #ff4b19ff
> color (#!2 & sel) #ff4b1aff
> color (#!2 & sel) #ff4b1dff
> color (#!2 & sel) #ff4b1eff
> color (#!2 & sel) #ff4b1fff
> color (#!2 & sel) #ff4c1fff
> color (#!2 & sel) #ff531fff
> color (#!2 & sel) #ff581fff
> color (#!2 & sel) #ff5a1fff
> color (#!2 & sel) #ff5c1fff
> color (#!2 & sel) #ff5f1fff
> color (#!2 & sel) #ff601fff
> color (#!2 & sel) #ff611fff
> color (#!2 & sel) #ff631fff
> color (#!2 & sel) #ff651fff
> color (#!2 & sel) #ff661fff
> color (#!2 & sel) #ff671fff
> color (#!2 & sel) #ff691fff
> color (#!2 & sel) #ff6b1fff
> color (#!2 & sel) #ff6c1fff
> color (#!2 & sel) #ff6d1fff
> color (#!2 & sel) #ff6e1fff
> color (#!2 & sel) #ff6f1fff
> color (#!2 & sel) #ff701fff
> color (#!2 & sel) #ff711fff
> color (#!2 & sel) #ff721fff
> color (#!2 & sel) #ff731fff
> color (#!2 & sel) #ff741fff
> color (#!2 & sel) #ff751fff
> color (#!2 & sel) #ff761fff
> color (#!2 & sel) #ff771fff
> color (#!2 & sel) #ff781fff
> color (#!2 & sel) #ff791fff
> select clear
> turn 0,180,0 40
> turn 0,180,0 -40
> turn 0,180,0 40
> turn 0,180,0 90
> turn 0,180,0 -90
> turn 0,180,0 90
> turn 0,180,0 -90
> save /Users/till/Desktop/TTN-1/Figures/fullView-TTN1.cxs
> save /Users/till/Desktop/TTN-1/Figures/fullViewFront.jpg width 2000 height
> 1712 supersample 3
> turn 0,180,0 90
> save /Users/till/Desktop/TTN-1/Figures/fullViewSide.jpg width 2000 height
> 1712 supersample 3
> turn 0,180,0 -90
> open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb
Chain information for TTN1_final.pdb #1
---
Chain | Description
A | No description available
46 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3551 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> hide #!1 models
> show #!1 models
> hide #!2 models
> label delete #1
> open 6ygn
6ygn title:
Titin kinase and its flanking domains [more info...]
Chain information for 6ygn #3
---
Chain | Description | UniProt
A B | Titin | TITIN_HUMAN 5-553
Non-standard residues in 6ygn #3
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
6ygn mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
8852 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open 3uto
3uto title:
Twitchin kinase region from C.elegans (Fn31-NL-kin-CRD-Ig26) [more info...]
Chain information for 3uto #4
---
Chain | Description | UniProt
A B | Twitchin | UNC22_CAEEL 1-570
Non-standard residues in 3uto #4
---
FLC — citrate anion
GOL — glycerol (glycerin; propane-1,2,3-triol)
P33 — 3,6,9,12,15,18-hexaoxaicosane-1,20-diol (heptaethylene glycol; PEG330)
PEG — di(hydroxyethyl)ether
3uto mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
8784 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #3#!2,4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TTN1_final.pdb, chain A (#1) with 6ygn, chain A (#3), sequence
alignment score = 978
RMSD between 214 pruned atom pairs is 0.865 angstroms; (across all 427 pairs:
10.485)
Matchmaker TTN1_final.pdb, chain A (#1) with TTN1_final.pdb, chain A (#2),
sequence alignment score = 2363.7
RMSD between 446 pruned atom pairs is 0.000 angstroms; (across all 446 pairs:
0.000)
Matchmaker TTN1_final.pdb, chain A (#1) with 3uto, chain A (#4), sequence
alignment score = 1132.3
RMSD between 247 pruned atom pairs is 0.874 angstroms; (across all 425 pairs:
12.959)
> select #3/B:512
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 6 residues, 1 model selected
> select up
4426 atoms, 4512 bonds, 549 residues, 1 model selected
> select up
4586 atoms, 4534 bonds, 687 residues, 1 model selected
> select up
9213 atoms, 9068 bonds, 1415 residues, 1 model selected
> select down
4586 atoms, 4534 bonds, 687 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/B:430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
106 atoms, 107 bonds, 12 residues, 1 model selected
> select up
4545 atoms, 4661 bonds, 566 residues, 1 model selected
> select up
4781 atoms, 4682 bonds, 781 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> label delete #4
> select #1/A:339
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
Drag select of 1 residues
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:124
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:5-124
882 atoms, 904 bonds, 1 pseudobond, 113 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select ::name="EDO"::name="FLC"::name="GOL"::name="HOH"::name="PEG"
1217 atoms, 45 bonds, 1172 residues, 4 models selected
> hide sel & #3#!1,4 atoms
> select #3/A:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:97
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:5-97
727 atoms, 743 bonds, 93 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 1348 residues, 2 pseudobonds, 112 atoms, 101 bonds
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> select #3/A:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:98-553
3699 atoms, 3768 bonds, 456 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #3/A:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:98-454
2895 atoms, 2946 bonds, 357 residues, 1 model selected
> color sel cornflower blue
> color sel #ff791fff
> color sel #6495edff
> color sel #6195edff
> color sel #6095edff
> color sel #5e95edff
> color sel #5c95edff
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> color sel #5795edff
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> color sel #5295edff
> color sel #4f95edff
> color sel #4e95edff
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> color sel #4b95edff
> color sel #4b95ecff
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> color sel #4b95deff
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> color sel #4b95d9ff
> color sel #4b95d8ff
> color sel #4b95d7ff
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> color sel #4b95d5ff
> color sel #4b95d4ff
> color sel #4b95d2ff
> color sel #4b95ceff
> color sel #4b95cbff
> color sel #4b95caff
> color sel #4b95c8ff
> color sel #4b95c7ff
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> color sel #4b95cdff
> color sel #4b95ceff
> color sel #4b95cdff
> color sel #4b92cdff
> color sel #4b8fcdff
> color sel #4b8ecdff
> color sel #4b8dcdff
> color sel #4b8ccdff
> color sel #4b8bcdff
> color sel #4b8ccdff
> color sel #4b90cdff
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> color sel #4ba3cdff
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> color sel #4ba9cdff
> color sel #4babcdff
> color sel #4baccdff
> color sel #4baecdff
> color sel #4bb0cdff
> color sel #4bafcdff
> color sel #4aafcdff
> color sel #47afcdff
> color sel #45afcdff
> color sel #42afcdff
> color sel #41afcdff
> color sel #3fafcdff
> color sel #3eafcdff
> color sel #3dafcdff
> color sel #3cafcdff
> color sel #3bafcdff
> color sel #38afcdff
> color sel #37afcdff
> color sel #36afcdff
> color sel #34afcdff
> color sel #33afcdff
> color sel #c1d4f9ff
> color sel #c1d4f7ff
> select #3/A:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:98-442
2811 atoms, 2862 bonds, 345 residues, 1 model selected
> select #3/A:510
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 6 residues, 1 model selected
> select up
4426 atoms, 4512 bonds, 549 residues, 1 model selected
> color sel #c1d3f7ff
> color sel #c1ccf7ff
> color sel #c1bdf7ff
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> color sel #c1bff7ff
> color sel #c1c7f7ff
> color sel #c1cef7ff
> color sel #c1d4f7ff
> color sel #b1caf6ff
> select clear
> select #3/A:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:5
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:5-9
39 atoms, 41 bonds, 5 residues, 1 model selected
> select clear
> select #1/A:380
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
59 atoms, 58 bonds, 4 residues, 1 model selected
> select up
2235 atoms, 2253 bonds, 144 residues, 1 model selected
> select up
2268 atoms, 2286 bonds, 147 residues, 1 model selected
> select up
2422 atoms, 2441 bonds, 156 residues, 1 model selected
> select down
2268 atoms, 2286 bonds, 147 residues, 1 model selected
> select up
2422 atoms, 2441 bonds, 156 residues, 1 model selected
> select #4/A:20-21
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/A:20-23
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #4/A:558
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
18 atoms, 18 bonds, 2 residues, 1 model selected
> select up
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> select up
3746 atoms, 3839 bonds, 465 residues, 1 model selected
> select up
4482 atoms, 4597 bonds, 559 residues, 1 model selected
> select down
3746 atoms, 3839 bonds, 465 residues, 1 model selected
> color sel #81c487ff
> color sel #81c787ff
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> select clear
> color #1,3-4 #c0e3c1ff
> undo
> select #4/A:108-110
27 atoms, 27 bonds, 3 residues, 1 model selected
> select #4/A:108-111
35 atoms, 35 bonds, 4 residues, 1 model selected
> select #4/A:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
61 atoms, 61 bonds, 7 residues, 1 model selected
> select up
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> select up
3746 atoms, 3839 bonds, 465 residues, 1 model selected
> select down
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> select clear
> select #4/A:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
61 atoms, 61 bonds, 7 residues, 1 model selected
> select up
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> color sel #c0e3c2ff
> color sel #c0e3c1ff
> select clear
> select #4/A:460
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
61 atoms, 61 bonds, 7 residues, 1 model selected
> select up
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> color sel #b3ddb1ff
> color sel #b3ddb5ff
> select clear
> select #1/A:373
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
71 atoms, 70 bonds, 4 residues, 1 model selected
> select up
2235 atoms, 2253 bonds, 144 residues, 1 model selected
> select up
2268 atoms, 2286 bonds, 147 residues, 1 model selected
> select up
2422 atoms, 2441 bonds, 156 residues, 1 model selected
> select up
2443 atoms, 2462 bonds, 158 residues, 1 model selected
> select up
7048 atoms, 7118 bonds, 446 residues, 1 model selected
> color sel coral
> select clear
> lighting simple
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> ui tool show "Side View"
> select #1/A:373
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
71 atoms, 70 bonds, 4 residues, 1 model selected
> select up
2235 atoms, 2253 bonds, 144 residues, 1 model selected
> select up
2268 atoms, 2286 bonds, 147 residues, 1 model selected
> select up
2422 atoms, 2441 bonds, 156 residues, 1 model selected
> select up
2443 atoms, 2462 bonds, 158 residues, 1 model selected
> select up
7048 atoms, 7118 bonds, 446 residues, 1 model selected
> color sel #ff7f50ff
> select clear
> save /Users/till/Desktop/TTN-1/Figures/fullView-TTN1-compTK-TwcK.cxs
> turn 0,180,0 -90
> turn 0,180,0 90
> undo
> select #1/A:370
14 atoms, 14 bonds, 1 residue, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:368
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:368-463
1440 atoms, 1451 bonds, 96 residues, 1 model selected
> hide sel cartoons
> select #3/A:454
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:453
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:453-553
816 atoms, 833 bonds, 101 residues, 1 model selected
> hide sel cartoons
> select #4/A:479
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:479-480
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/A:479-570
744 atoms, 760 bonds, 92 residues, 1 model selected
> hide sel cartoons
> select #4/A:438
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
106 atoms, 107 bonds, 12 residues, 1 model selected
> select up
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> color sel #b3ddb5ff
> color sel #d9eedaff
> select clear
> select #4/A:458
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
61 atoms, 61 bonds, 7 residues, 1 model selected
> select up
3731 atoms, 3824 bonds, 463 residues, 1 model selected
> color sel #cce8cdff
> select clear
> save /Users/till/Desktop/TTN-1/Figures/fullView-TTN1-compTK-TwcK.cxs
> select #4/A:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:412-478
549 atoms, 566 bonds, 67 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:301-446
2187 atoms, 2205 bonds, 1 pseudobond, 139 residues, 2 models selected
> hide sel cartoons
> select #3/A:435
8 atoms, 7 bonds, 1 residue, 1 model selected
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:392
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:392-553
1295 atoms, 1316 bonds, 162 residues, 1 model selected
> hide sel cartoons
> select clear
> save /Users/till/Desktop/TTN-1/Figures/KinaseOnly-TTN1-compTK-TwcK.cxs
> save /Users/till/Desktop/TTN-1/Figures/KinaseDomainComp.jpg width 2000
> height 2201 supersample 3
> hide #3 models
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> select #1/A:65
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:65
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:177
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:177-179
39 atoms, 39 bonds, 3 residues, 1 model selected
> show sel atoms
> select #1/A:81
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:161
15 atoms, 14 bonds, 1 residue, 1 model selected
> select H
6996 atoms, 884 residues, 3 models selected
> hide sel & #!1 atoms
> select up
14034 atoms, 14166 bonds, 884 residues, 3 models selected
> select add #1/A:177@CG
1 atom, 2 bonds, 1 residue, 1 model selected
> select add #1/A:178@CB
2 atoms, 2 bonds, 2 residues, 1 model selected
> select up
8 atoms, 3 bonds, 5 residues, 1 model selected
> select up
81 atoms, 78 bonds, 5 residues, 1 model selected
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> select #1/A:65@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 4 bonds, 5 residues, 1 model selected
> select up
81 atoms, 78 bonds, 5 residues, 1 model selected
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> select add #1/A:177@OD1
1 atom, 1 bond, 1 residue, 1 model selected
> select add #1/A:81@CD
2 atoms, 2 bonds, 2 residues, 1 model selected
> select up
8 atoms, 3 bonds, 5 residues, 1 model selected
> select up
81 atoms, 78 bonds, 5 residues, 1 model selected
> color sel byhetero target a
> select #1/A:44
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:43
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:43-48
74 atoms, 74 bonds, 6 residues, 1 model selected
> select clear
> select #1/A:65@NZ
1 atom, 1 residue, 1 model selected
> select add #1/A:81@OE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/A:65@NZ #1/A:81@OE2
Distance between TTN1_final.pdb #1/A LYS 65 NZ and GLU 81 OE2: 3.121Å
> select #1/A:81@OE1
1 atom, 1 residue, 1 model selected
> select add #1/A:65@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/A:81@OE1 #1/A:65@NZ
Distance between TTN1_final.pdb #1/A GLU 81 OE1 and LYS 65 NZ: 3.119Å
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> select
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2093 atoms, 2098 bonds, 129 residues, 1 model selected
> select #1/A:43
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:43-48
74 atoms, 74 bonds, 6 residues, 1 model selected
> distance style color #ffba48
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> distance style color #a81414
> distance style color #9c1414
> distance style color #891414
> distance style color #7e1414
> distance style color #761414
> distance style color #5c1414
> distance style color #4b1414
> distance style color #3b1414
> distance style color #3a1414
> distance style color #391414
> distance style color #381414
> distance style color #361414
> distance style color #2e1414
> distance style color #2b1414
> distance style color #291414
> distance style color #281414
> distance style color #261414
> distance style color #251414
> distance style color #241414
> distance style color #221414
> distance style color #211414
> distance style color #1f1414
> distance style color #1e1414
> distance style color #1d1414
> distance style color #1c1414
> distance style color #1b1414
> distance style color #1a1414
> distance style color #191414
> distance style color #181414
> distance style color #171414
> distance style color #161414
> distance style color #141414
> distance style color #131414
> distance style color #121414
> distance style color #111414
> distance style color #121414
> distance style color #131414
> distance style color #141414
> distance style color #151414
> distance style color #141414
> select #1/A:44
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> distance style color #141416
> distance style color #141419
> distance style color #141425
> distance style color #14142c
> distance style color #14142f
> distance style color #141430
> distance style color #141433
> distance style color #141434
> distance style color #141435
> distance style color #141437
> distance style color #14143b
> distance style color #141440
> distance style color #141441
> distance style color #141442
> distance style color #141443
> distance style color #141445
> distance style color #141447
> distance style color #141449
> ui tool show "Color Actions"
> color sel byhetero target acsp
> color sel #14144aff target acsp
> color sel #141453ff target acsp
> color sel #141460ff target acsp
> color sel #141461ff target acsp
> color sel #141462ff target acsp
> color sel #141464ff target acsp
> color sel #141467ff target acsp
> color sel #14146eff target acsp
> color sel #141471ff target acsp
> color sel #141472ff target acsp
> color sel #141471ff target acsp
> color sel #141470ff target acsp
> color sel #14146fff target acsp
> color sel #14146cff target acsp
> color sel #141465ff target acsp
> color sel #141460ff target acsp
> color sel #14145fff target acsp
> color sel #14145bff target acsp
> undo
> color sel #ff7f50ff target acsp
> hide sel atoms
> select #1/A:43
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:43-48
74 atoms, 74 bonds, 6 residues, 1 model selected
> color sel #ffba48ff target acsp
> select clear
> save /Users/till/Desktop/TTN-1/Figures/TTN1-activeSite.jpg width 2000 height
> 2061 supersample 3
> hide #!5 models
Drag select of 30 atoms, 280 residues, 26 bonds
> color sel #ff7f50ff target acsp
> hide sel atoms
> undo
> show #!5 models
> select clear
> save /Users/till/Desktop/TTN-1/Figures/TTN1-ActiveSite.cxs
Drag select of 30 atoms, 290 residues, 26 bonds, 2 pseudobonds
> hide sel atoms
> color (#!1 & sel) #ff7f50ff target acsp
> color (#!1 & sel) #ff7f61ff target acsp
> color (#!1 & sel) #ff7f6dff target acsp
> color (#!1 & sel) #ff7f64ff target acsp
> color (#!1 & sel) #ff7f5dff target acsp
> color (#!1 & sel) #ff7f5bff target acsp
> color (#!1 & sel) #ff7f50ff target acsp
> select clear
> close #3#2,4-5
> open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb
Chain information for TTN1_final.pdb #2
---
Chain | Description
A | No description available
46 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3551 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb
Chain information for TTN1_final.pdb #3
---
Chain | Description
A | No description available
46 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3551 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> rename #2 C-spine
> rename #3 R-spine
> open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb
Chain information for TTN1_final.pdb #4
---
Chain | Description
A | No description available
46 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3551 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202508070056 (2025-08-07)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
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: 6.9.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000EQD/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 2 hours, 4 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: G4FQX9PD4K
Display Firmware Version: Version 17.0 (Build 21A329)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.4
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.10
ChimeraX-AtomicLibrary: 14.1.21
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: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508070056
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: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.0
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
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: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.4
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
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: 1.48
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.2.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.10.2
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.2
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 5.0.0
lxml: 5.3.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.2
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.1
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
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: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.5
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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