![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 weeks ago
Closed 8 weeks ago
#18791 closed defect (duplicate)
Crash adding/removing screen
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000206ede0c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 58)
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{
"uptime" : 290000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 20777,
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"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2025-09-15 16:25:58.4168 +0200",
"codeSigningMonitor" : 1,
"incident" : "D8877FFD-4296-4FBA-BD64-95006A1EB105",
"pid" : 70773,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-15 11:14:03.7551 +0200",
"procStartAbsTime" : 6704722841860,
"procExitAbsTime" : 7064666746523,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D44B6B49-C8F1-50A4-92F9-95517B6FFFA5",
"appleIntelligenceStatus" : {"reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"],"state":"unavailable"},
"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" : "5A388A98-9F64-4059-8DE6-4EFB88EF0C3D",
"wakeTime" : 28,
"sleepWakeUUID" : "264931FD-25BC-4C11-8BD2-DC7EA08B4B6E",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000a98c76d39ef8","rawCodes":[1,186420754095864],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a98c76d39ef8 -> 0x0000298c76d39ef8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":70773},
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"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" : 6857310208,
"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" : 6861115392,
"size" : 51784,
"uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 8584040448,
"CFBundleShortVersionString" : "6.5.4",
"CFBundleIdentifier" : "com.apple.SwiftUICore",
"size" : 12329376,
"uuid" : "84fe33b3-a5db-3ca3-90cc-4d258172e788",
"path" : "\/System\/Library\/Frameworks\/SwiftUICore.framework\/Versions\/A\/SwiftUICore",
"name" : "SwiftUICore",
"CFBundleVersion" : "6.5.4"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6860169216,
"size" : 577528,
"uuid" : "643ed232-ce19-3f63-8015-0aee768c002f",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 6856474624,
"size" : 5040898048,
"uuid" : "4c1223e5-cace-3982-a003-6110a7a8a25c"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=12.8G written=98.1M(1%) resident=7164K(0%) swapped_out=91.1M(1%) unallocated=12.7G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1360K 37 \nColorSync 704K 38 \nCoreAnimation 2576K 151 \nCoreGraphics 80K 5 \nCoreImage 48K 3 \nCoreUI image data 3456K 45 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 12.1G 137 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 624K 39 \nStack 155.9M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 386.7M 369 \nVM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)\n__AUTH 6047K 724 \n__AUTH_CONST 80.4M 977 \n__CTF 824 1 \n__DATA 36.6M 1120 \n__DATA_CONST 37.4M 1137 \n__DATA_DIRTY 2788K 347 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.6M 155 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1158 \n__TPRO_CONST 128K 2 \ndyld private memory 672K 8 \nmapped file 585.6M 105 \npage table in kernel 7164K 1 \nshared memory 3184K 28 \n=========== ======= ======= \nTOTAL 15.6G 6665 \nTOTAL, minus reserved VM space 15.5G 6665 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain"
}
},
"logWritingSignature" : "5027e4406429dba99af58d513784b238a2352082",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67648e5334a82511f4acf879",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000083
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/leahoffmann/Desktop/MsbA/maps/reference/map
Current working directory is:
/Users/leahoffmann/Desktop/MsbA/maps/reference/map
> open *.mrc
Opened A18_wide.mrc as #1.1, grid size 96,88,113, pixel 1.33,1.33,1.33, shown
at level 0.164, step 1, values float32
Opened A18_wider.mrc as #1.2, grid size 103,95,109, pixel 1.33,1.33,1.33,
shown at level 0.132, step 1, values float32
Opened A835_narrow.mrc as #1.3, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.0969, step 1, values float32
Opened A835_wide.mrc as #1.4, grid size 96,88,113, pixel 1.33,1.33,1.33, shown
at level 0.0851, step 1, values float32
Opened A835_wider.mrc as #1.5, grid size 103,95,109, pixel 1.33,1.33,1.33,
shown at level 0.0942, step 1, values float32
Opened DDM.mrc as #1.6, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at
level 0.319, step 1, values float32
Opened GDN_narrow.mrc as #1.7, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.147, step 1, values float32
Opened GDN_wide.mrc as #1.8, grid size 96,88,113, pixel 1.33,1.33,1.33, shown
at level 0.16, step 1, values float32
Opened LMNG_narrow.mrc as #1.9, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.137, step 1, values float32
Opened LMNG_wide.mrc as #1.10, grid size 96,88,113, pixel 1.33,1.33,1.33,
shown at level 0.156, step 1, values float32
Opened MSP1D1-PC.mrc as #1.11, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.139, step 1, values float32
Opened MSP1D1.mrc as #1.12, grid size 83,78,110, pixel 1.33,1.33,1.33, shown
at level 0.128, step 1, values float32
Opened MSP1E3D1.mrc as #1.13, grid size 83,78,110, pixel 1.33,1.33,1.33, shown
at level 0.194, step 1, values float32
Opened MSP2N2_narrow.mrc as #1.14, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.138, step 1, values float32
Opened MSP2N2_wide.mrc as #1.15, grid size 96,88,113, pixel 1.33,1.33,1.33,
shown at level 0.106, step 1, values float32
Opened Triton_wide.mrc as #1.16, grid size 96,88,113, pixel 1.33,1.33,1.33,
shown at level 0.107, step 1, values float32
Opened Triton_wider.mrc as #1.17, grid size 103,95,109, pixel 1.33,1.33,1.33,
shown at level 0.106, step 1, values float32
Opened UDM_narrow.mrc as #1.18, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.217, step 1, values float32
Opened UDM_wide.mrc as #1.19, grid size 96,88,113, pixel 1.33,1.33,1.33, shown
at level 0.12, step 1, values float32
Opened UDM_wider.mrc as #1.20, grid size 103,95,109, pixel 1.33,1.33,1.33,
shown at level 0.108, step 1, values float32
Opened peptidisc_narrow.mrc as #1.21, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.13, step 1, values float32
Opened peptidisc_narrower.mrc as #1.22, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.135, step 1, values float32
> cd /Users/leahoffmann/Desktop/MsbA/maps/reference/model
Current working directory is:
/Users/leahoffmann/Desktop/MsbA/maps/reference/model
> open *.pdb
Chain information for A18_wide.pdb #2
---
Chain | Description
A B | No description available
Chain information for A18_wider.pdb #3
---
Chain | Description
A B | No description available
Chain information for A835_narrow.pdb #4
---
Chain | Description
A B | No description available
Chain information for A835_wide.pdb #5
---
Chain | Description
A B | No description available
Chain information for A835_wider.pdb #6
---
Chain | Description
A B | No description available
Chain information for DDM.pdb #7
---
Chain | Description
A B | No description available
Chain information for GDN_narrow.pdb #8
---
Chain | Description
A B | No description available
Chain information for GDN_wide.pdb #9
---
Chain | Description
A B | No description available
Chain information for LMNG_narrow.pdb #10
---
Chain | Description
A B | No description available
Chain information for LMNG_wide.pdb #11
---
Chain | Description
A B | No description available
Chain information for MSP1D1-PC.pdb #12
---
Chain | Description
A B | No description available
Chain information for MSP1D1.pdb #13
---
Chain | Description
A B | No description available
Chain information for MSP1E3D1.pdb #14
---
Chain | Description
A B | No description available
Chain information for MSP2N2_narrow.pdb #15
---
Chain | Description
A B | No description available
Chain information for MSP2N2_wide.pdb #16
---
Chain | Description
A B | No description available
Chain information for Triton_wide.pdb #17
---
Chain | Description
A B | No description available
Chain information for Triton_wider.pdb #18
---
Chain | Description
A B | No description available
Chain information for UDM_narrow.pdb #19
---
Chain | Description
A B | No description available
Chain information for UDM_wide.pdb #20
---
Chain | Description
A B | No description available
Chain information for UDM_wider.pdb #21
---
Chain | Description
A B | No description available
Chain information for peptidisc_narrow.pdb #22
---
Chain | Description
A B | No description available
Chain information for peptidisc_narrower.pdb #23
---
Chain | Description
A B | No description available
> cd /Users/leahoffmann/Desktop/MsbA/maps/reference/environment/
Current working directory is:
/Users/leahoffmann/Desktop/MsbA/maps/reference/environment
> open *.mrc
Opened A18_wide_disc.mrc as #24.1, grid size 96,88,113, pixel 1.33,1.33,1.33,
shown at level 0.0404, step 1, values float32
Opened A18_wider_disc.mrc as #24.2, grid size 103,95,109, pixel
1.33,1.33,1.33, shown at level 0.039, step 1, values float32
Opened A835_narrow_disc.mrc as #24.3, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0442, step 1, values float32
Opened A835_wide_disc.mrc as #24.4, grid size 96,88,113, pixel 1.33,1.33,1.33,
shown at level 0.0453, step 1, values float32
Opened A835_wider_disc.mrc as #24.5, grid size 103,95,109, pixel
1.33,1.33,1.33, shown at level 0.0423, step 1, values float32
Opened DDM_micelle.mrc as #24.6, grid size 96,88,113, pixel 1.33,1.33,1.33,
shown at level 0.0827, step 1, values float32
Opened GDN_narrow_micelle.mrc as #24.7, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0495, step 1, values float32
Opened GDN_wide_micelle.mrc as #24.8, grid size 96,88,113, pixel
1.33,1.33,1.33, shown at level 0.0466, step 1, values float32
Opened LMNG_narrow_micelle.mrc as #24.9, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0506, step 1, values float32
Opened LMNG_wide_micelle.mrc as #24.10, grid size 96,88,113, pixel
1.33,1.33,1.33, shown at level 0.0501, step 1, values float32
Opened MSP1D1-PC_disc.mrc as #24.11, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0537, step 1, values float32
Opened MSP1D1_disc.mrc as #24.12, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.0541, step 1, values float32
Opened MSP1E3D1_disc.mrc as #24.13, grid size 83,78,110, pixel 1.33,1.33,1.33,
shown at level 0.0536, step 1, values float32
Opened MSP2N2_narrow_disc.mrc as #24.14, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0379, step 1, values float32
Opened MSP2N2_wide_disc.mrc as #24.15, grid size 96,88,113, pixel
1.33,1.33,1.33, shown at level 0.0359, step 1, values float32
Opened Triton_wide_micelle.mrc as #24.16, grid size 96,88,113, pixel
1.33,1.33,1.33, shown at level 0.0367, step 1, values float32
Opened Triton_wider_micelle.mrc as #24.17, grid size 103,95,109, pixel
1.33,1.33,1.33, shown at level 0.0384, step 1, values float32
Opened UDM_narrow_micelle.mrc as #24.18, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0511, step 1, values float32
Opened UDM_wide_micelle.mrc as #24.19, grid size 96,88,113, pixel
1.33,1.33,1.33, shown at level 0.0489, step 1, values float32
Opened UDM_wider_micelle.mrc as #24.20, grid size 103,95,109, pixel
1.33,1.33,1.33, shown at level 0.0488, step 1, values float32
Opened peptidisc_narrow_disc.mrc as #24.21, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0504, step 1, values float32
Opened peptidisc_narrower_disc.mrc as #24.22, grid size 83,78,110, pixel
1.33,1.33,1.33, shown at level 0.0506, step 1, values float32
> dssp
> turn x 260
> turn y 55
> turn z -9
> windowsize 1500 1500
> volume #1 step 1
> select /A:1-340
55943 atoms, 56850 bonds, 7260 residues, 22 models selected
> color sel #8FBC8F
> select /A:341-580
40638 atoms, 41100 bonds, 5210 residues, 22 models selected
> color sel #779B77
> select /B:1-340
55961 atoms, 56866 bonds, 7260 residues, 22 models selected
> color sel #A7CCE1
> select /B:341-580
40638 atoms, 41100 bonds, 5210 residues, 22 models selected
> color sel #7994A3
> color #1 #a9a9a91a models
> volume #1.1 level 0.09
> volume #1.2 level 0.08
> volume #1.3 level 0.07
> volume #1.4 level 0.06
> volume #1.5 level 0.08
> volume #1.6 level 0.2
> volume #1.7 level 0.075
> volume #1.8 level 0.1
> volume #1.9 level 0.08
> volume #1.10 level 0.085
> volume #1.11 level 0.09
> volume #1.12 level 0.08
> volume #1.13 level 0.11
> volume #1.14 level 0.075
> volume #1.15 level 0.065
> volume #1.16 level 0.07
> volume #1.17 level 0.08
> volume #1.18 level 0.13
> volume #1.19 level 0.09
> volume #1.20 level 0.09
> volume #1.21 level 0.08
> volume #1.22 level 0.08
> select ::name="3PE"::name="JSG"
1569 atoms, 1591 bonds, 13 residues, 9 models selected
> delete sel
> color zone #1.1 near #2 distance 5
> color zone #1.2 near #3 distance 5
> color zone #1.3 near #4 distance 5
> color zone #1.4 near #5 distance 5
> color zone #1.5 near #6 distance 5
> color zone #1.6 near #7 distance 5
> color zone #1.7 near #8 distance 5
> color zone #1.8 near #9 distance 5
> color zone #1.9 near #10 distance 5
> color zone #1.10 near #11 distance 5
> color zone #1.11 near #12 distance 5
> color zone #1.12 near #13 distance 5
> color zone #1.13 near #14 distance 5
> color zone #1.14 near #15 distance 5
> color zone #1.15 near #16 distance 5
> color zone #1.16 near #17 distance 5
> color zone #1.17 near #18 distance 5
> color zone #1.18 near #19 distance 5
> color zone #1.19 near #20 distance 5
> color zone #1.20 near #21 distance 5
> color zone #1.21 near #22 distance 5
> color zone #1.22 near #23 distance 5
> surface dust #1
> lighting soft shadows true intensity 0.5
> graphics silhouettes true
> select subtract all
Nothing selected
> volume #24.1 level 0.03
> volume #24.2 level 0.02
> volume #24.3 level 0.02
> volume #24.4 level 0.02
> volume #24.5 level 0.025
> volume #24.6 level 0.07
> volume #24.7 level 0.03
> volume #24.8 level 0.04
> volume #24.9 level 0.04
> volume #24.10 level 0.04
> volume #24.11 level 0.03
> volume #24.12 level 0.03
> volume #24.13 level 0.035
> volume #24.14 level 0.022
> volume #24.15 level 0.013
> volume #24.16 level 0.02
> volume #24.17 level 0.02
> volume #24.18 level 0.02
> volume #24.19 level 0.027
> volume #24.20 level 0.03
> volume #24.21 level 0.05
> volume #24.22 level 0.05
> color #24 #ebebeb1a
> surface dust #24
> cd /Users/leahoffmann/Desktop/Dissertation/dozen-environments/
Current working directory is: /Users/leahoffmann/Desktop/Dissertation/dozen-
environments
> view clip false
> hide target m
> show #1.1
> save A18_wide.png width 1500 height 1500 supersample 6 transparentBackground
> true
> hide target m
> show #1.2
> save A18_wider.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.3
> save A835_narrow.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.4
> save A835_wide.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.5
> save A835_wider.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.6
> save DDM.png width 1500 height 1500 supersample 6 transparentBackground true
> hide target m
> show #1.7
> save GDN_narrow.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.8
> save GDN_wide.png width 1500 height 1500 supersample 6 transparentBackground
> true
> hide target m
> show #1.9
> save LMNG_narrow.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.10
> save LMNG_wide.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.11
> save MSP1D1-PC.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.12
> save MSP1D1.png width 1500 height 1500 supersample 6 transparentBackground
> true
> hide target m
> show #1.13
> save MSP1E3D1.png width 1500 height 1500 supersample 6 transparentBackground
> true
> hide target m
> show #1.14
> save MSP2N2_narrow.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.15
> save MSP2N2_wide.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.16
> save Triton_wide.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.17
> save Triton_wider.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.18
> save UDM_narrow.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.19
> save UDM_wide.png width 1500 height 1500 supersample 6 transparentBackground
> true
> hide target m
> show #1.20
> save UDM_wider.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.21
> save peptidisc_narrow.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.22
> save peptidisc_narrower.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.1 #24.1
> save A18_wide_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.2 #24.2
> save A18_wider_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.3 #24.3
> save A835_narrow_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.4 #24.4
> save A835_wide_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.5 #24.5
> save A835_wider_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.6 #24.6
> save DDM_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.7 #24.7
> save GDN_narrow_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.8 #24.8
> save GDN_wide_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.9 #24.9
> save LMNG_narrow_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.10 #24.10
> save LMNG_wide_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.11 #24.11
> save MSP1D1-PC_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.12 #24.12
> save MSP1D1_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.13 #24.13
> save MSP1E3D1_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.14 #24.14
> save MSP2N2_narrow_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.15 #24.15
> save MSP2N2_wide_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.16 #24.16
> save Triton_wide_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.17 #24.17
> save Triton_wider_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.18 #24.18
> save UDM_narrow_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.19 #24.19
> save UDM_wide_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.20 #24.20
> save UDM_wider_micelle.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.21 #24.21
> save peptidisc_narrow_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #1.22 #24.22
> save peptidisc_narrower_disc.png width 1500 height 1500 supersample 6
> transparentBackground true
> close session
> cd /Users/leahoffmann/Desktop/MsbA/maps/reference/model
Current working directory is:
/Users/leahoffmann/Desktop/MsbA/maps/reference/model
> open *.pdb
Chain information for A18_wide.pdb #1
---
Chain | Description
A B | No description available
Chain information for A18_wider.pdb #2
---
Chain | Description
A B | No description available
Chain information for A835_narrow.pdb #3
---
Chain | Description
A B | No description available
Chain information for A835_wide.pdb #4
---
Chain | Description
A B | No description available
Chain information for A835_wider.pdb #5
---
Chain | Description
A B | No description available
Chain information for DDM.pdb #6
---
Chain | Description
A B | No description available
Chain information for GDN_narrow.pdb #7
---
Chain | Description
A B | No description available
Chain information for GDN_wide.pdb #8
---
Chain | Description
A B | No description available
Chain information for LMNG_narrow.pdb #9
---
Chain | Description
A B | No description available
Chain information for LMNG_wide.pdb #10
---
Chain | Description
A B | No description available
Chain information for MSP1D1-PC.pdb #11
---
Chain | Description
A B | No description available
Chain information for MSP1D1.pdb #12
---
Chain | Description
A B | No description available
Chain information for MSP1E3D1.pdb #13
---
Chain | Description
A B | No description available
Chain information for MSP2N2_narrow.pdb #14
---
Chain | Description
A B | No description available
Chain information for MSP2N2_wide.pdb #15
---
Chain | Description
A B | No description available
Chain information for Triton_wide.pdb #16
---
Chain | Description
A B | No description available
Chain information for Triton_wider.pdb #17
---
Chain | Description
A B | No description available
Chain information for UDM_narrow.pdb #18
---
Chain | Description
A B | No description available
Chain information for UDM_wide.pdb #19
---
Chain | Description
A B | No description available
Chain information for UDM_wider.pdb #20
---
Chain | Description
A B | No description available
Chain information for peptidisc_narrow.pdb #21
---
Chain | Description
A B | No description available
Chain information for peptidisc_narrower.pdb #22
---
Chain | Description
A B | No description available
> dssp
> turn x 180
> turn y -5
> turn z -40
> windowsize 1500 1500
> select /A:1-340
55943 atoms, 56850 bonds, 7260 residues, 22 models selected
> color sel #8FBC8F
> select /A:341-580
40638 atoms, 41100 bonds, 5210 residues, 22 models selected
> color sel #779B77
> select /B:1-340
55961 atoms, 56866 bonds, 7260 residues, 22 models selected
> color sel #A7CCE1
> select /B:341-580
40638 atoms, 41100 bonds, 5210 residues, 22 models selected
> color sel #7994A3
> select subtract all
Nothing selected
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix default arrows false xsection round width
> 1.5 thickness 1.5
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides tube/slab shape ellipsoid
> graphics silhouettes true
> hide atoms
> distance #1/A: 506@CA #1/B: 506@CA
Distance between A18_wide.pdb #1/A GLU 506 CA and /B GLU 506 CA: 64.610Å
> distance #1/A: 512@CA #1/B: 512@CA
Distance between A18_wide.pdb #1/A ASP 512 CA and /B ASP 512 CA: 71.958Å
> distance #2/A: 506@CA #2/B: 506@CA
Distance between A18_wider.pdb #2/A GLU 506 CA and /B GLU 506 CA: 73.959Å
> distance #2/A: 512@CA #2/B: 512@CA
Distance between A18_wider.pdb #2/A ASP 512 CA and /B ASP 512 CA: 79.069Å
> distance #3/A: 506@CA #3/B: 506@CA
Distance between A835_narrow.pdb #3/A ARG 506 CA and /B ARG 506 CA: 58.889Å
> distance #3/A: 512@CA #3/B: 512@CA
Distance between A835_narrow.pdb #3/A LEU 512 CA and /B LEU 512 CA: 57.428Å
> distance #4/A: 506@CA #4/B: 506@CA
Distance between A835_wide.pdb #4/A GLU 506 CA and /B GLU 506 CA: 60.854Å
> distance #4/A: 512@CA #4/B: 512@CA
Distance between A835_wide.pdb #4/A ASP 512 CA and /B ASP 512 CA: 71.524Å
> distance #5/A: 506@CA #5/B: 506@CA
Distance between A835_wider.pdb #5/A GLU 506 CA and /B GLU 506 CA: 70.439Å
> distance #5/A: 512@CA #5/B: 512@CA
Distance between A835_wider.pdb #5/A ASP 512 CA and /B ASP 512 CA: 80.011Å
> distance #6/A: 506@CA #6/B: 506@CA
Distance between DDM.pdb #6/A GLU 506 CA and /B GLU 506 CA: 60.799Å
> distance #6/A: 512@CA #6/B: 512@CA
Distance between DDM.pdb #6/A ASP 512 CA and /B ASP 512 CA: 70.212Å
> distance #7/A: 506@CA #7/B: 506@CA
Distance between GDN_narrow.pdb #7/A GLU 506 CA and /B GLU 506 CA: 31.450Å
> distance #7/A: 512@CA #7/B: 512@CA
Distance between GDN_narrow.pdb #7/A ASP 512 CA and /B ASP 512 CA: 40.831Å
> distance #8/A: 506@CA #8/B: 506@CA
Distance between GDN_wide.pdb #8/A GLU 506 CA and /B GLU 506 CA: 57.758Å
> distance #8/A: 512@CA #8/B: 512@CA
Distance between GDN_wide.pdb #8/A ASP 512 CA and /B ASP 512 CA: 67.945Å
> distance #9/A: 506@CA #9/B: 506@CA
Distance between LMNG_narrow.pdb #9/A GLU 506 CA and /B GLU 506 CA: 35.303Å
> distance #9/A: 512@CA #9/B: 512@CA
Distance between LMNG_narrow.pdb #9/A ASP 512 CA and /B ASP 512 CA: 50.077Å
> distance #10/A: 506@CA #10/B: 506@CA
Distance between LMNG_wide.pdb #10/A GLU 506 CA and /B GLU 506 CA: 60.541Å
> distance #10/A: 512@CA #10/B: 512@CA
Distance between LMNG_wide.pdb #10/A ASP 512 CA and /B ASP 512 CA: 68.493Å
> distance #11/A: 506@CA #11/B: 506@CA
Distance between MSP1D1-PC.pdb #11/A GLU 506 CA and /B GLU 506 CA: 23.109Å
> distance #11/A: 512@CA #11/B: 512@CA
Distance between MSP1D1-PC.pdb #11/A ASP 512 CA and /B ASP 512 CA: 34.754Å
> distance #12/A: 506@CA #12/B: 506@CA
Distance between MSP1D1.pdb #12/A GLU 506 CA and /B GLU 506 CA: 29.126Å
> distance #12/A: 512@CA #12/B: 512@CA
Distance between MSP1D1.pdb #12/A ASP 512 CA and /B ASP 512 CA: 40.395Å
> distance #13/A: 506@CA #13/B: 506@CA
Distance between MSP1E3D1.pdb #13/A GLU 506 CA and /B GLU 506 CA: 23.800Å
> distance #13/A: 512@CA #13/B: 512@CA
Distance between MSP1E3D1.pdb #13/A ASP 512 CA and /B ASP 512 CA: 37.784Å
> distance #14/A: 506@CA #14/B: 506@CA
Distance between MSP2N2_narrow.pdb #14/A GLU 506 CA and /B GLU 506 CA: 23.800Å
> distance #14/A: 512@CA #14/B: 512@CA
Distance between MSP2N2_narrow.pdb #14/A ASP 512 CA and /B ASP 512 CA: 37.784Å
> distance #15/A: 506@CA #15/B: 506@CA
Distance between MSP2N2_wide.pdb #15/A GLU 506 CA and /B GLU 506 CA: 57.758Å
> distance #15/A: 512@CA #15/B: 512@CA
Distance between MSP2N2_wide.pdb #15/A ASP 512 CA and /B ASP 512 CA: 67.945Å
> distance #16/A: 506@CA #16/B: 506@CA
Distance between Triton_wide.pdb #16/A GLU 506 CA and /B GLU 506 CA: 58.295Å
> distance #16/A: 512@CA #16/B: 512@CA
Distance between Triton_wide.pdb #16/A ASP 512 CA and /B ASP 512 CA: 66.921Å
> distance #17/A: 506@CA #17/B: 506@CA
Distance between Triton_wider.pdb #17/A GLU 506 CA and /B GLU 506 CA: 68.420Å
> distance #17/A: 512@CA #17/B: 512@CA
Distance between Triton_wider.pdb #17/A ASP 512 CA and /B ASP 512 CA: 77.844Å
> distance #18/A: 506@CA #18/B: 506@CA
Distance between UDM_narrow.pdb #18/A ARG 506 CA and /B ARG 506 CA: 53.126Å
> distance #18/A: 512@CA #18/B: 512@CA
Distance between UDM_narrow.pdb #18/A LEU 512 CA and /B LEU 512 CA: 52.744Å
> distance #19/A: 506@CA #19/B: 506@CA
Distance between UDM_wide.pdb #19/A GLU 506 CA and /B GLU 506 CA: 57.902Å
> distance #19/A: 512@CA #19/B: 512@CA
Distance between UDM_wide.pdb #19/A ASP 512 CA and /B ASP 512 CA: 68.515Å
> distance #20/A: 506@CA #20/B: 506@CA
Distance between UDM_wider.pdb #20/A GLU 506 CA and /B GLU 506 CA: 67.918Å
> distance #20/A: 512@CA #20/B: 512@CA
Distance between UDM_wider.pdb #20/A ASP 512 CA and /B ASP 512 CA: 78.702Å
> distance #21/A: 506@CA #21/B: 506@CA
Distance between peptidisc_narrow.pdb #21/A GLU 506 CA and /B GLU 506 CA:
35.794Å
> distance #21/A: 512@CA #21/B: 512@CA
Distance between peptidisc_narrow.pdb #21/A ASP 512 CA and /B ASP 512 CA:
49.480Å
> distance #22/A: 506@CA #22/B: 506@CA
Distance between peptidisc_narrower.pdb #22/A GLU 506 CA and /B GLU 506 CA:
22.487Å
> distance #22/A: 512@CA #22/B: 512@CA
Distance between peptidisc_narrower.pdb #22/A ASP 512 CA and /B ASP 512 CA:
31.765Å
> select :506
404 atoms, 360 bonds, 22 pseudobonds, 44 residues, 23 models selected
> color sel #941751ff
> show sel & #1-22 atoms
> style sel & #1-22 sphere
Changed 404 atom styles
> select :512
352 atoms, 308 bonds, 22 pseudobonds, 44 residues, 23 models selected
> color sel orange
> show sel & #1-22 atoms
> style sel & #1-22 sphere
Changed 352 atom styles
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> hide #23.1
> distance style color black
> distance style color black
> distance style radius 0.25
> distance style radius 0.25
> cd /Users/leahoffmann/Desktop/Dissertation/dozen-environments/
Current working directory is: /Users/leahoffmann/Desktop/Dissertation/dozen-
environments
> view clip false
> set bgColor white
> set bgColor #ffffff00
> ui tool show "Side View"
> select subtract all
Nothing selected
> ui tool show "Side View"
> hide target m
> show #1 models
> show #!23 models
> save A18_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #2 models
> show #!23 models
> save A18_wider_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #3 models
> show #!23 models
> save A835_narrow_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #4 models
> show #!23 models
> save A835_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #5 models
> show #!23 models
> save A835_wider_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #6 models
> show #!23 models
> save DDM_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #7 models
> show #!23 models
> save GDN_narrow_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #8 models
> show #!23 models
> save GDN_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #9 models
> show #!23 models
> save LMNG_narrow_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #10 models
> show #!23 models
> save LMNG_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #11 models
> show #!23 models
> save MSP1D1-PC_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #12 models
> show #!23 models
> save MSP1D1_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #13 models
> show #!23 models
> save MSP1E3D1_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #14 models
> show #!23 models
> save MSP2N2_narrow_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #15 models
> show #!23 models
> save MSP2N2_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #16 models
> show #!23 models
> save Triton_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #17 models
> show #!23 models
> save Triton_wider_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #18 models
> show #!23 models
> save UDM_narrow_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #19 models
> show #!23 models
> save UDM_wide_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #20 models
> show #!23 models
> save UDM_wider_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #21 models
> show #!23 models
> save peptidisc_narrow_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> hide target m
> show #22 models
> show #!23 models
> save peptidisc_narrower_distance.png width 1500 height 1500 supersample 6
> transparentBackground true
> show #19 models
> hide #19 models
> open /Users/leahoffmann/Downloads/step3_packing.pdb
Summary of feedback from opening
/Users/leahoffmann/Downloads/step3_packing.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08.
2025. JOB
Ignored bad PDB record found on line 2
REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE
Ignored bad PDB record found on line 3
REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui
Chain information for step3_packing.pdb #24
---
Chain | Description
? | No description available
> close #1-23
> hide #!24 models
> show #!24 models
> view clip false
> select ::name="ADDM"
300 atoms, 300 residues, 1 model selected
> molmap ::name="ADDM"
Missing or invalid "resolution" argument: Expected a number
> molmap ::name="ADDM" 8
Opened step3_packing.pdb map 8 as #1, grid size 49,49,32, pixel 2.67, shown at
level 0.00567, step 1, values float32
> molmap ::name="ADDM" 10
Opened step3_packing.pdb map 10 as #1, grid size 43,43,29, pixel 3.33, shown
at level 0.00446, step 1, values float32
> hide #!1 models
> show #!1 models
> color #1 #941751ff models
> color #1 #941100ff models
> color #1 #945200ff models
> color #1 #ff2600ff models
> color #1 #9437ffff models
> color #1 #942193ff models
> color #1 #941751ff models
> color #1 #531b93ff models
> color #1 #011993ff models
> color #1 #941751ff models
> color #1 #771242ff models
> color #1 #801447ff models
> color #1 #802d52ff models
> color #1 #80435eff models
> color #1 #803044ff models
> color #1 #803354ff models
> color #1 #803650ff models
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #2
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #2
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> hide #!24 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!24 models
> show #2 models
> hide #!1 models
> select add #2
9224 atoms, 9050 bonds, 1440 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #24,1,0,0,-1.9936,0,1,0,-1.2847,0,0,1,-19.876,#2,1,0,0,-1.9936,0,1,0,-1.2847,0,0,1,-19.876
> select add #24
27538 atoms, 27498 bonds, 1 pseudobond, 2604 residues, 3 models selected
> select subtract #24
8924 atoms, 9050 bonds, 1140 residues, 1 model selected
> view matrix models #2,1,0,0,-120.47,0,1,0,3.4772,0,0,1,-209.38
> view matrix models #2,1,0,0,-185.23,0,1,0,-105.88,0,0,1,-175.33
> view matrix models #2,1,0,0,-140.29,0,1,0,-120.24,0,0,1,-174.46
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> mmaker #2 to #24
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 step3_packing.pdb, chain (blank) (#24) with 9fuq, chain A (#2),
sequence alignment score = 2812.6
RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs:
0.000)
> show #!1 models
> hide #!1 models
> close #24
> open /Users/leahoffmann/Downloads/step3_packing.pdb
Summary of feedback from opening
/Users/leahoffmann/Downloads/step3_packing.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08.
2025. JOB
Ignored bad PDB record found on line 2
REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE
Ignored bad PDB record found on line 3
REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui
Chain information for step3_packing.pdb #3
---
Chain | Description
? | No description available
> mmaker #2 to #3
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 step3_packing.pdb, chain (blank) (#3) with 9fuq, chain A (#2),
sequence alignment score = 2812.6
RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs:
0.000)
> show #!1 models
> close #3
> select /A: 1-340
2535 atoms, 2576 bonds, 329 residues, 1 model selected
> color sel #8FBC8F
> select /A:341-580
1876 atoms, 1898 bonds, 240 residues, 1 model selected
> color sel #779B77
> select /B: 1-340
2535 atoms, 2576 bonds, 329 residues, 1 model selected
> color sel #A7CCE1
> select /B:341-580
1876 atoms, 1898 bonds, 240 residues, 1 model selected
> color sel #7994A3
> hide #2 models
> show #2 models
> surface resolution 10
2 Gaussian surfaces, threshold level 0.049 - 0.051
> color #1 #cc6689ff models
> color #1 #e9749cff models
> color #1 #bd5e7fff models
> color #1 #b05877ff models
> color #1 #b05d73ff models
> hide #2.1 models
> hide #2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> select add #2
8924 atoms, 9050 bonds, 1140 residues, 3 models selected
> select subtract #2
Nothing selected
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #3
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #3
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #4
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #4
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #5
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #5
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> select add #3
8924 atoms, 9050 bonds, 1140 residues, 1 model selected
> select add #4
17848 atoms, 18100 bonds, 2280 residues, 2 models selected
> select add #5
26772 atoms, 27150 bonds, 3420 residues, 3 models selected
> view matrix models
> #3,1,0,0,-109.27,0,1,0,17.656,0,0,1,-167.28,#4,1,0,0,-109.27,0,1,0,17.656,0,0,1,-167.28,#5,1,0,0,-109.27,0,1,0,17.656,0,0,1,-167.28
> view matrix models
> #3,1,0,0,-186.34,0,1,0,-102.3,0,0,1,-140.03,#4,1,0,0,-186.34,0,1,0,-102.3,0,0,1,-140.03,#5,1,0,0,-186.34,0,1,0,-102.3,0,0,1,-140.03
> view matrix models
> #3,1,0,0,-152.69,0,1,0,-135.8,0,0,1,-153.07,#4,1,0,0,-152.69,0,1,0,-135.8,0,0,1,-153.07,#5,1,0,0,-152.69,0,1,0,-135.8,0,0,1,-153.07
> view matrix models
> #3,1,0,0,-149.77,0,1,0,-135.88,0,0,1,-145.63,#4,1,0,0,-149.77,0,1,0,-135.88,0,0,1,-145.63,#5,1,0,0,-149.77,0,1,0,-135.88,0,0,1,-145.63
> mmaker #3 to #2
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 9fuq, chain A (#2) with 9fuq, chain A (#3), sequence alignment
score = 2869.3
RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs:
0.000)
> mmaker #4 to #2
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 9fuq, chain A (#2) with 9fuq, chain A (#4), sequence alignment
score = 2869.3
RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs:
0.000)
> mmaker #5 to #2
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 9fuq, chain A (#2) with 9fuq, chain A (#5), sequence alignment
score = 2869.3
RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs:
0.000)
> close #2.2
> close #2.1
> select #2:341-580
3752 atoms, 3796 bonds, 480 residues, 1 model selected
> delete sel
> select #2/B: 1-340
2535 atoms, 2576 bonds, 329 residues, 1 model selected
> delete sel
> color #2 #8FBC8F
> select #3:1-340
5070 atoms, 5152 bonds, 658 residues, 1 model selected
> delete sel
> select #3/B:341-580
1876 atoms, 1898 bonds, 240 residues, 1 model selected
> delete sel
> color #3 #779B77
> select #4:341-580
3752 atoms, 3796 bonds, 480 residues, 1 model selected
> delete sel
> select #4/A: 1-340
2535 atoms, 2576 bonds, 329 residues, 1 model selected
> delete sel
> color #4 #A7CCE1
> select #5:1-340
5070 atoms, 5152 bonds, 658 residues, 1 model selected
> delete sel
> select #5/A:341-580
1876 atoms, 1898 bonds, 240 residues, 1 model selected
> delete sel
> color #5 #7994A3
> surface resolution 10
4 Gaussian surfaces, threshold level 0.049 - 0.052
> view clp false
Expected an objects specifier or a view name or a keyword
> view clip false
> color #1 #4541bfff models
> color #1 #7c64bfff models
> color #1 #866bceff models
> color #1 #a296ceff models
> color #1 #9587ceff models
> color #1 #a296ceff models
> color #1 #968bbfff models
> open /Users/leahoffmann/Downloads/step3_packing.pdb
Summary of feedback from opening
/Users/leahoffmann/Downloads/step3_packing.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08.
2025. JOB
Ignored bad PDB record found on line 2
REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE
Ignored bad PDB record found on line 3
REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui
Chain information for step3_packing.pdb #6
---
Chain | Description
? | No description available
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #2.1 models
> hide #!2 models
> hide #!1 models
> select ::name="ADDM"
300 atoms, 300 residues, 1 model selected
> molmap ::name="ADDM" 6
Opened step3_packing.pdb map 6 as #7, grid size 59,59,37, pixel 2, shown at
level 0.0078, step 1, values float32
> molmap ::name="ADDM" 7
Opened step3_packing.pdb map 7 as #7, grid size 53,53,34, pixel 2.33, shown at
level 0.00665, step 1, values float32
> molmap ::name="ADDM" 5
Opened step3_packing.pdb map 5 as #7, grid size 67,67,40, pixel 1.67, shown at
level 0.00976, step 1, values float32
> hide #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #2.1 models
> color #7 #968bbfff models
> set bgColor black
> set bgColor transparent
> open /Users/leahoffmann/Desktop/MsbA/Deposition/DDM/DDM_sharpend_map.mrc
Opened DDM_sharpend_map.mrc as #8, grid size 320,320,320, pixel 0.837, shown
at level 0.078, step 2, values float32
> select add #6
18614 atoms, 18448 bonds, 1 pseudobond, 1464 residues, 2 models selected
> select subtract #6
Nothing selected
> select add #8
2 models selected
> view matrix models #8,1,0,0,-69.899,0,1,0,31.03,0,0,1,-135.76
> view matrix models #8,1,0,0,-154.44,0,1,0,-137.59,0,0,1,-148.43
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.9945,-0.018818,-0.10303,-139.54,0.044029,0.9677,0.24824,-167.53,0.095033,-0.25142,0.9632,-124.37
> view matrix models
> #8,0.94804,-0.31725,-0.023887,-102.47,0.31814,0.94572,0.066328,-182.62,0.0015478,-0.070481,0.99751,-139.04
> view matrix models
> #8,0.94059,-0.32699,-0.091441,-92.503,0.33702,0.93185,0.13445,-191.13,0.041247,-0.15728,0.98669,-131.92
> view matrix models
> #8,0.76168,-0.64794,0.0048864,-35.766,0.64375,0.75757,0.10806,-208.21,-0.073716,-0.079159,0.99413,-126.93
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.76168,-0.64794,0.0048864,-22.034,0.64375,0.75757,0.10806,-207.41,-0.073716,-0.079159,0.99413,-125.77
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 2 maps.
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #2.1 models
> hide #!2 models
> fitmap #8 inMap #7
Fit map DDM_sharpend_map.mrc in map step3_packing.pdb map 5 using 40842 points
correlation = 0.1209, correlation about mean = -0.1382, overlap = 28.57
steps = 128, shift = 5.41, angle = 7.89 degrees
Position of DDM_sharpend_map.mrc (#8) relative to step3_packing.pdb map 5 (#7)
coordinates:
Matrix rotation and translation
0.75031647 -0.64980357 0.12157516 -34.60487664
0.65085976 0.75832925 0.03630890 -194.13565813
-0.11578765 0.05188521 0.99191791 -138.00080275
Axis 0.01178028 0.17951618 0.98368448
Axis point 203.45852639 -128.33202085 0.00000000
Rotation angle (degrees) 41.38520479
Shift along axis -171.00739632
> show #!5 models
> hide #!7 models
> fitmap #5 inMap #8
Fit molecule 9fuq (#5) to map DDM_sharpend_map.mrc (#8) using 1978 atoms
average map value = 0.2004, steps = 128
shifted from previous position = 8.14
rotated from previous position = 13.4 degrees
atoms outside contour = 239, contour level = 0.07797
Position of 9fuq (#5) relative to DDM_sharpend_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.97842157 -0.00579002 -0.20653742 300.24428007
-0.00548330 -0.99852759 0.05396832 257.30895941
-0.20654579 0.05393627 0.97694918 24.36417708
Axis -0.10387115 0.02713334 0.99422058
Axis point 151.38488281 128.33366335 0.00000000
Rotation angle (degrees) 179.99116189
Shift along axis 0.01829874
> undo
> volume #8 step 1
> volume #8 level 0.09733
> close #8
> show #!4 models
> show #!3 models
> show #2.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> hide #4.1 models
> close #4.1
> close #5.1
> close #3.1
> close #1
> close #2.1
> close #5
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #1
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #1
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> select add #7
2 models selected
> select subtract #7
Nothing selected
> select add #1
8924 atoms, 9050 bonds, 1140 residues, 1 model selected
> view matrix models #1,1,0,0,-94.286,0,1,0,39.428,0,0,1,-132.64
> view matrix models #1,1,0,0,-141.83,0,1,0,-122.59,0,0,1,-160.02
> view matrix models #1,1,0,0,-152.6,0,1,0,-133.26,0,0,1,-149.6
> view matrix models #1,1,0,0,-147.66,0,1,0,-140.96,0,0,1,-148.23
> mmaker #1 to #2
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 9fuq, chain A (#2) with 9fuq, chain A (#1), sequence alignment
score = 2514.1
RMSD between 329 pruned atom pairs is 0.000 angstroms; (across all 329 pairs:
0.000)
> select #1: 1-395
5916 atoms, 6014 bonds, 768 residues, 1 model selected
> delete sel
> select #1/A: 396-680
1504 atoms, 1517 bonds, 186 residues, 1 model selected
> delete sel
> color #1 #A7CCE1
> close #1-4#6-7
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #1
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #1
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #2
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #2
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #3
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #3
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> open 9FUQ
9fuq title:
MsbA in DDM inward-facing wide open [more info...]
Chain information for 9fuq #4
---
Chain | Description | UniProt
A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582
Non-standard residues in 9fuq #4
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
> select #1:341-580
3752 atoms, 3796 bonds, 480 residues, 1 model selected
> delete sel
> select #1/B: 1-340
2535 atoms, 2576 bonds, 329 residues, 1 model selected
> delete sel
> color #1 #8FBC8F
> select #2:1-340
5070 atoms, 5152 bonds, 658 residues, 1 model selected
> delete sel
> select #2/B:341-580
1876 atoms, 1898 bonds, 240 residues, 1 model selected
> delete sel
> color #2 #779B77
> select #3:341-580
3752 atoms, 3796 bonds, 480 residues, 1 model selected
> delete sel
> select #3/A: 1-340
2535 atoms, 2576 bonds, 329 residues, 1 model selected
> delete sel
> color #3 #A7CCE1
> select #4:1-340
5070 atoms, 5152 bonds, 658 residues, 1 model selected
> delete sel
> select #4/A:341-580
1876 atoms, 1898 bonds, 240 residues, 1 model selected
> delete sel
> color #4 #7994A3
> surface resolution 10
4 Gaussian surfaces, threshold level 0.049 - 0.052
> select ::name="3PE"
408 atoms, 400 bonds, 8 residues, 4 models selected
> delete sel
> open /Users/leahoffmann/Downloads/step3_packing.pdb
Summary of feedback from opening
/Users/leahoffmann/Downloads/step3_packing.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08.
2025. JOB
Ignored bad PDB record found on line 2
REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE
Ignored bad PDB record found on line 3
REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui
Chain information for step3_packing.pdb #5
---
Chain | Description
? | No description available
> select add #5
18614 atoms, 18448 bonds, 1 pseudobond, 1464 residues, 2 models selected
> view matrix models #5,1,0,0,3.2874,0,1,0,-5.1725,0,0,1,150.4
> view matrix models #5,1,0,0,119.99,0,1,0,140.27,0,0,1,145.11
> view matrix models #5,1,0,0,128.35,0,1,0,118.47,0,0,1,151.79
> mmaker #5 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 9fuq, chain A (#1) with step3_packing.pdb, chain (blank) (#5),
sequence alignment score = 2457.4
RMSD between 329 pruned atom pairs is 0.001 angstroms; (across all 329 pairs:
0.001)
> select subtract #5
Nothing selected
> hide #!5 models
> select ::name="ADDM"
300 atoms, 300 residues, 1 model selected
> molmap ::name="ADDM" 5
Opened step3_packing.pdb map 5 as #6, grid size 67,67,40, pixel 1.67, shown at
level 0.00976, step 1, values float32
> color #6 #968bbfff models
> view clip false
> save /Users/leahoffmann/Desktop/Dissertation/Figures/Detergent-DDM300.png
> width 4000 height 4000 supersample 6 transparentBackground true
> open
> /Users/leahoffmann/Desktop/MsbA/Deposition/peptidisc_narrow/peptidisc_narrow_sharpend_map.mrc
Opened peptidisc_narrow_sharpend_map.mrc as #7, grid size 320,320,320, pixel
0.837, shown at level 0.0269, step 2, values float32
> select add #5
18614 atoms, 18448 bonds, 1 pseudobond, 1464 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!6 models
> volume #7 step 1
> volume #7 level 0.0676
> ui mousemode right "pick blobs"
> measure blob #!7.1 triangleNumber 275348 color #0000ccff outline true
Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob:
volume = 68531
area = 68331
size = 118.89 86.668 65.492
> volume #7 level 0.09007
> measure blob #!7.1 triangleNumber 140767 color #c7129fff
Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob:
volume = 269.15
area = 403.39
size = 23.478 9.9367 7.2338
> measure blob #!7.1 triangleNumber 142347 color #c7129fff
Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob:
volume = 268.79
area = 403.39
size = 23.478 9.9267 7.1826
> measure blob #!7.1 triangleNumber 172491 color #c7129fff
Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob:
volume = 214.78
area = 329.65
size = 23.192 9.908 5.0399
> open /Users/leahoffmann/Downloads/7NMN.cif
7NMN.cif title:
Rabbit HCN4 stabilised in amphipol A8-35 [more info...]
Chain information for 7NMN.cif #8
---
Chain | Description | UniProt
A B C D | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4,Rabbit HCN4 | HCN4_RABIT 1-721
> close #8
> open /Users/leahoffmann/Downloads/step3_packing-2.pdb
Summary of feedback from opening
/Users/leahoffmann/Downloads/step3_packing-2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 15.
2025. JOB
Ignored bad PDB record found on line 2
REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE
Ignored bad PDB record found on line 3
REMARK DATE: 9/15/25 8:56: 6 CREATED BY USER: charmm-gui
Chain information for step3_packing-2.pdb #8
---
Chain | Description
? | No description available
> hide #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> mmaker #8 to #5
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 step3_packing.pdb, chain (blank) (#5) with step3_packing-2.pdb,
chain (blank) (#8), sequence alignment score = 5654
RMSD between 1164 pruned atom pairs is 0.001 angstroms; (across all 1164
pairs: 0.001)
> molmap ::name="ADDM" 5
Opened map 5 as #9, grid size 122,123,91, pixel 1.67, shown at level 0.00827,
step 1, values float32
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #9
> close #8
> open /Users/leahoffmann/Downloads/step3_packing-3.pdb
Summary of feedback from opening
/Users/leahoffmann/Downloads/step3_packing-3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 15.
2025. JOB
Ignored bad PDB record found on line 2
REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE
Ignored bad PDB record found on line 3
REMARK DATE: 9/15/25 9:12:51 CREATED BY USER: charmm-gui
Chain information for step3_packing-3.pdb #8
---
Chain | Description
? | No description available
> mmaker #9 to #5
No molecules/chains to match specified
> mmaker #8 to #5
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 step3_packing.pdb, chain (blank) (#5) with step3_packing-3.pdb,
chain (blank) (#8), sequence alignment score = 5661.2
RMSD between 1164 pruned atom pairs is 0.000 angstroms; (across all 1164
pairs: 0.000)
> molmap ::name="ADDM" 5
Opened map 5 as #9, grid size 67,67,40, pixel 1.67, shown at level 0.0205,
step 1, values float32
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!8 models
> hide #!5 models
> color #9 #968bbfff models
> view clip false
> save /Users/leahoffmann/Desktop/Dissertation/Figures/Detergent-DDM350.png
> width 4000 height 4000 supersample 6 transparentBackground true
> select ::name="ADDM"
650 atoms, 650 residues, 2 models selected
> show #!1-4 atoms
> show #!1-4 cartoons
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!9 models
> show #!8 models
> show #!5 models
> close #8
> close #5
> show #!9 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> show #!6 models
> hide #!4 models
> hide #!9 models
> hide #!6 models
> show #!9 models
> hide #!9 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 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
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD82D/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 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: 20 days, 23 hours, 22 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PA278CV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PA278CV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 8 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash adding/removing screen |
comment:2 by , 8 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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