![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16659 closed defect (duplicate)
Crash on Mac waking from sleep
| 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-14.3-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001deb95c40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 63)
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{
"uptime" : 590000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 120351,
"osVersion" : {
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"build" : "23D2057",
"releaseType" : "User"
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"captureTime" : "2025-01-21 14:13:54.5987 +0900",
"codeSigningMonitor" : 1,
"incident" : "98681C68-2E5E-4493-A3AE-FA351D01BBC4",
"pid" : 5472,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-19 14:06:40.9948 +0900",
"procStartAbsTime" : 12983736201598,
"procExitAbsTime" : 14182922649392,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"52D8EDB5-6218-5637-94A3-00B8E212F067","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AB1C3982-D522-4FA6-F182-EC3A38D7E8AD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6,
"sleepWakeUUID" : "B545C7C3-1638-42CB-B8AB-D86E0B7126A9",
"sip" : "enabled",
"vmRegionInfo" : "0x38a23b1dd298 is not in any region. Bytes after previous region: 61788391330457 Bytes before following region: 43283688598888\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000038a23b1dd298","rawCodes":[1,62269427667608],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000038a23b1dd298"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5472},
"vmregioninfo" : "0x38a23b1dd298 is not in any region. Bytes after previous region: 61788391330457 Bytes before following region: 43283688598888\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/erikookamoto/Downloads/fold_250117_ifx_fab_tnfa_monomer/fold_250117_ifx_fab_tnfa_monomer_model_0.cif
Chain information for fold_250117_ifx_fab_tnfa_monomer_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select /A:1-157
1226 atoms, 1253 bonds, 157 residues, 1 model selected
> select /A:1-157
1226 atoms, 1253 bonds, 157 residues, 1 model selected
Alignment identifier is 1/A
> color sel yellow
> save "/Users/erikookamoto/OneDrive - keio.jp/IFX Fab_TNFa monomer.cxs"
> save /Users/erikookamoto/Desktop/image1.png supersample 3
> close session
> open
> /Users/erikookamoto/Downloads/fold_250117_ada_fab_tnfa_monomer/fold_250117_ada_fab_tnfa_monomer_model_0.cif
Chain information for fold_250117_ada_fab_tnfa_monomer_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select /A:1-214
1647 atoms, 1681 bonds, 214 residues, 1 model selected
> select /B:1-218
1631 atoms, 1670 bonds, 218 residues, 1 model selected
> select /C:1-157
1226 atoms, 1253 bonds, 157 residues, 1 model selected
> color sel yellow
> ui windowfill toggle
> save /Users/erikookamoto/Desktop/image2.png supersample 3
> open
> /Users/erikookamoto/Downloads/fold_250117_glm_fv_tnfa_monomer/fold_250117_glm_fv_tnfa_monomer_model_0.cif
Chain information for fold_250117_glm_fv_tnfa_monomer_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> undo
> redo
> undo
> select add #2
3143 atoms, 3217 bonds, 405 residues, 1 model selected
> close #2
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /C:156-157
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /C
1226 atoms, 1253 bonds, 157 residues, 1 model selected
> color sel yellow
> save "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/ADA Fab_TNFa
> monomer.cxs"
> close session
> open
> /Users/erikookamoto/Downloads/fold_250117_glm_fv_tnfa_monomer/fold_250117_glm_fv_tnfa_monomer_model_0.cif
Chain information for fold_250117_glm_fv_tnfa_monomer_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A
1226 atoms, 1253 bonds, 157 residues, 1 model selected
> color sel yellow
> save /Users/erikookamoto/Desktop/image3.png supersample 3
Unsupported scale factor (0.000000) detected on Display0
> save "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/GLM Fv_TNFa
> monomer.cxs"
> select
> /B:6-10,13-15,21-28,37-42,48-54,61-63,71-76,81-86,95-102,105-107,110-112,116-119,123-127
554 atoms, 556 bonds, 67 residues, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
> open
> /Users/erikookamoto/Downloads/fold_trastuzumab_her2_extracellular/fold_trastuzumab_her2_extracellular_model_0.cif
Chain information for fold_trastuzumab_her2_extracellular_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> undo
> select add #2
8139 atoms, 8335 bonds, 1064 residues, 1 model selected
> close #2
> close session
> open
> /Users/erikookamoto/Downloads/fold_trastuzumab_her2_extracellular/fold_trastuzumab_her2_extracellular_model_0.cif
Chain information for fold_trastuzumab_her2_extracellular_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A
4839 atoms, 4956 bonds, 630 residues, 1 model selected
> color sel yellow
> save "/Users/erikookamoto/Library/CloudStorage/OneDrive-
> keio.jp/Trastuzumab_HER2 extracellular.cxs"
> save /Users/erikookamoto/Desktop/image4.png supersample 3
> close session
> open
> /Users/erikookamoto/Downloads/fold_250120_rtx_fab_cd20_extracellular/fold_250120_rtx_fab_cd20_extracellular_model_0.cif
Chain information for fold_250120_rtx_fab_cd20_extracellular_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /C:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:15-47
265 atoms, 273 bonds, 33 residues, 1 model selected
> select /C
384 atoms, 395 bonds, 47 residues, 1 model selected
> color sel yellow
> save "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX
> Fab_CD20.cxs"
> save /Users/erikookamoto/Desktop/image5.png supersample 3
> close session
> open
> /Users/erikookamoto/Downloads/fold_250120_tcz_fab_il6/fold_250120_tcz_fab_il6_model_0.cif
Chain information for fold_250120_tcz_fab_il6_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /A:346
8 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:5-346
2681 atoms, 2758 bonds, 342 residues, 1 model selected
> color sel yellow
> save /Users/erikookamoto/Desktop/image6.png supersample 3
> save /Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/TCZ_IL-6.cxs
Unsupported scale factor (0.000000) detected on Display0
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX
> Fab_CD20.cxs"
opened ChimeraX session
Could not find virtual screen for QCocoaScreen(0x600003cfb230, "Apple TV
(AirPlay)", QRect(0,0 1920x1080), dpr=1, displayId=75, ) with displayId 75
Unsupported scale factor (0.000000) detected on Display0
> ui tool show Distances
> select sel @ show sel target ab
> style sel ball
Changed 437 atom styles
> label sel attribute label_one_letter_code
> ui tool show "Selection Inspector"
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select /A:106@CH2
1 atom, 1 residue, 1 model selected
> select add /C:30@CB
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:106@CH2 /C:30@CB
Distance between /A TRP 106 CH2 and /C ASN 30 CB: 4.352Å
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/IFX Fab_TNFa
> monomer.cxs"
opened ChimeraX session
> toolshed show
> ui tool show "Modeller Comparative"
> ui tool show Matchmaker
> open 4g3y fromDatabase pdb format mmcif
Summary of feedback from opening 4g3y fetched from pdb
---
note | Fetching compressed mmCIF 4g3y from http://files.rcsb.org/download/4g3y.cif
4g3y title:
Crystal structure of TNF-alpha in complex with Infliximab Fab fragment [more
info...]
Chain information for 4g3y #2
---
Chain | Description | UniProt
C | Tumor necrosis factor | TNFA_HUMAN 1-157
H | infliximab Fab H |
L | infliximab Fab L |
4g3y mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain B (#1) with
4g3y, chain H (#2), sequence alignment score = 1113.8
RMSD between 216 pruned atom pairs is 0.564 angstroms; (across all 220 pairs:
0.775)
> save /Users/erikookamoto/Desktop/image7.png supersample 3
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/ADA Fab_TNFa
> monomer.cxs"
opened ChimeraX session
> open 3wd5 fromDatabase pdb format mmcif
Summary of feedback from opening 3wd5 fetched from pdb
---
note | Fetching compressed mmCIF 3wd5 from http://files.rcsb.org/download/3wd5.cif
3wd5 title:
Crystal structure of TNFalpha in complex with Adalimumab Fab fragment [more
info...]
Chain information for 3wd5 #2
---
Chain | Description | UniProt
A | Tumor necrosis factor | TNFA_HUMAN 1-157
H | Adalimumab Heavy Chain |
L | Adalimumab Light Chain |
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250117_ada_fab_tnfa_monomer_model_0.cif, chain B (#1) with
3wd5, chain H (#2), sequence alignment score = 1066.4
RMSD between 212 pruned atom pairs is 0.854 angstroms; (across all 213 pairs:
0.892)
> view
> save /Users/erikookamoto/Desktop/image8.png supersample 3
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/GLM Fv_TNFa
> monomer.cxs"
opened ChimeraX session
> open 5yoy fromDatabase pdb format mmcif
Summary of feedback from opening 5yoy fetched from pdb
---
note | Fetching compressed mmCIF 5yoy from http://files.rcsb.org/download/5yoy.cif
5yoy title:
Crystal structure of the human tumor necrosis factor in complex with golimumab
Fv [more info...]
Chain information for 5yoy #2
---
Chain | Description | UniProt
A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157
D E F M N O | Golimumab light chain variable region |
G H I P Q R | Golimumab heavy chain variable region |
5yoy mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open 5y0y fromDatabase pdb format mmcif
Summary of feedback from opening 5y0y fetched from pdb
---
notes | Fetching compressed mmCIF 5y0y from http://files.rcsb.org/download/5y0y.cif
Fetching CCD AU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/AU/AU.cif
5y0y title:
RVFV GN-Au [more info...]
Chain information for 5y0y #3
---
Chain | Description | UniProt
A | NSmGnGc | H9BSP3_RVFV 1-316
Non-standard residues in 5y0y #3
---
AU — gold ion
> open 5YOY fromDatabase pdb format mmcif
5yoy title:
Crystal structure of the human tumor necrosis factor in complex with golimumab
Fv [more info...]
Chain information for 5yoy #4
---
Chain | Description | UniProt
A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157
D E F M N O | Golimumab light chain variable region |
G H I P Q R | Golimumab heavy chain variable region |
5yoy mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open 5yoy fromDatabase pdb format mmcif
5yoy title:
Crystal structure of the human tumor necrosis factor in complex with golimumab
Fv [more info...]
Chain information for 5yoy #5
---
Chain | Description | UniProt
A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157
D E F M N O | Golimumab light chain variable region |
G H I P Q R | Golimumab heavy chain variable region |
5yoy mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> ui tool show "Color Actions"
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 fold_250117_glm_fv_tnfa_monomer_model_0.cif, chain A (#1) with
5yoy, chain A (#2), sequence alignment score = 784.8
RMSD between 145 pruned atom pairs is 0.761 angstroms; (across all 152 pairs:
1.296)
> color sel byhetero
> color sel bychain
> color sel bypolymer
> surface hidePatches sel
> select
> #1/B:6-10,13-15,21-28,37-42,48-54,61-63,71-76,81-86,95-102,105-107,110-112,116-119,123-127
554 atoms, 556 bonds, 67 residues, 1 model selected
> style sel sphere
Changed 554 atom styles
> style sel sphere
Changed 554 atom styles
> color sel bypolymer
> surface hidePatches sel
No Surface models open
> cartoon sel
> view
> hide #5 models
> close #5
> close #4
> close #3
> close #2
> color sel bynucleotide
> view
> select /A:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:76-118
339 atoms, 347 bonds, 43 residues, 1 model selected
> select /A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A
1226 atoms, 1253 bonds, 157 residues, 1 model selected
> select
> /B:6-10,13-15,21-28,37-42,48-54,61-63,71-76,81-86,95-102,105-107,110-112,116-119,123-127
554 atoms, 556 bonds, 67 residues, 1 model selected
> select /C:7-10,13-16,22-28,36-41,48-51,65-70,73-78,88-93,107-110
372 atoms, 370 bonds, 47 residues, 1 model selected
> open 5yoy fromDatabase pdb format mmcif
5yoy title:
Crystal structure of the human tumor necrosis factor in complex with golimumab
Fv [more info...]
Chain information for 5yoy #2
---
Chain | Description | UniProt
A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157
D E F M N O | Golimumab light chain variable region |
G H I P Q R | Golimumab heavy chain variable region |
5yoy mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 fold_250117_glm_fv_tnfa_monomer_model_0.cif, chain A (#1) with
5yoy, chain A (#2), sequence alignment score = 784.8
RMSD between 145 pruned atom pairs is 0.761 angstroms; (across all 152 pairs:
1.296)
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/ADA Fab_TNFa
> monomer.cxs"
opened ChimeraX session
> view
> ui tool show H-Bonds
> hbonds saltOnly true reveal true
34 hydrogen bonds found
Unsupported scale factor (0.000000) detected on Display0
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX
> Fab_CD20.cxs" format session
opened ChimeraX session
> ui tool show Distances
> select /C:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
3674 atoms, 3768 bonds, 484 residues, 1 model selected
> select sel @ show sel target ab
> style sel ball
Changed 3674 atom styles
> label sel attribute label_one_letter_code
> label sel attribute label_specifier
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/IFX Fab_TNFa
> monomer.cxs"
opened ChimeraX session
> open 3g4y fromDatabase pdb format mmcif
Summary of feedback from opening 3g4y fetched from pdb
---
notes | Fetching compressed mmCIF 3g4y from http://files.rcsb.org/download/3g4y.cif
Fetching CCD 9CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/9CL/9CL.cif
Fetching CCD CMO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CMO/CMO.cif
Fetching CCD HEM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif
3g4y title:
Ligand migration and cavities within scapharca dimeric hemoglobin: wild type
with co bound to heme and chloromethyl benzene bound to the XE4 cavity [more
info...]
Chain information for 3g4y #2
---
Chain | Description | UniProt
A B | GLOBIN-1 | GLB1_SCAIN 1-146
Non-standard residues in 3g4y #2
---
9CL — (chloromethyl)benzene
CMO — carbon monoxide
HEM — protoporphyrin IX containing Fe (HEME)
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A (#1) with
3g4y, chain A (#2), sequence alignment score = 1.9
Fewer than 3 residues aligned; cannot match
fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A with 3g4y, chain A
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A (#1) with
3g4y, chain A (#2), sequence alignment score = 1.9
Fewer than 3 residues aligned; cannot match
fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A with 3g4y, chain A
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/IFX Fab_TNFa
> monomer.cxs"
opened ChimeraX session
> open 4g3y fromDatabase pdb format mmcif
4g3y title:
Crystal structure of TNF-alpha in complex with Infliximab Fab fragment [more
info...]
Chain information for 4g3y #2
---
Chain | Description | UniProt
C | Tumor necrosis factor | TNFA_HUMAN 1-157
H | infliximab Fab H |
L | infliximab Fab L |
4g3y mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain B (#1) with
4g3y, chain H (#2), sequence alignment score = 1113.8
RMSD between 216 pruned atom pairs is 0.564 angstroms; (across all 220 pairs:
0.775)
> show sel target ab
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
9052 atoms, 9265 bonds, 1179 residues, 2 models selected
> hide #* target a
> show sel target ab
> style sel stick
Changed 9052 atom styles
> style sel ball
Changed 9052 atom styles
> label sel attribute label_one_letter_code
> label sel attribute label_specifier
> hide sel target a
> label sel attribute label_one_letter_code
> label sel attribute label_specifier
> label sel attribute label_one_letter_code
> select #1/A:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
9052 atoms, 9265 bonds, 1179 residues, 2 models selected
> style sel stick
Changed 9052 atom styles
> select #1/A:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/L:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/C:91
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show Matchmaker
> ui tool show Distances
> style sel ball
Changed 12 atom styles
> select
9186 atoms, 9265 bonds, 1313 residues, 4 models selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
9052 atoms, 9265 bonds, 1179 residues, 2 models selected
> style sel ball
Changed 9052 atom styles
> show sel target ab
> select #1/A:73@CD2
1 atom, 1 residue, 1 model selected
> select add #1/C:50@CB
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/A:73@CD2 #1/C:50@CB
Distance between fold_250117_ifx_fab_tnfa_monomer_model_0.cif #1/A HIS 73 CD2
and /C TYR 50 CB: 3.990Å
Unsupported scale factor (0.000000) detected on Display0
> hide sel target a
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
9052 atoms, 9265 bonds, 1 pseudobond, 1179 residues, 3 models selected
> hide (#!1-2 & sel) target a
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
9052 atoms, 9265 bonds, 1 pseudobond, 1179 residues, 3 models selected
> show (#!1-2 & sel) target ab
> select #1/A:104@CD
1 atom, 1 residue, 1 model selected
> select add #1/C:49@CE
2 atoms, 2 residues, 1 model selected
> distance #1/A:104@CD #1/C:49@CE
Distance between fold_250117_ifx_fab_tnfa_monomer_model_0.cif #1/A GLU 104 CD
and /C LYS 49 CE: 4.776Å
> close session
> open
> /Users/erikookamoto/Downloads/fold_250121_certolizumab_fab_tnfa_monomer/fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif
Chain information for fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select /A:1-214
1648 atoms, 1685 bonds, 214 residues, 1 model selected
> select /B:1-229
1713 atoms, 1756 bonds, 229 residues, 1 model selected
> select /C:1-157
1226 atoms, 1253 bonds, 157 residues, 1 model selected
> color sel yellow
> open 4g3y fromDatabase pdb format mmcif
4g3y title:
Crystal structure of TNF-alpha in complex with Infliximab Fab fragment [more
info...]
Chain information for 4g3y #2
---
Chain | Description | UniProt
C | Tumor necrosis factor | TNFA_HUMAN 1-157
H | infliximab Fab H |
L | infliximab Fab L |
4g3y mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> close #2
> redo
> open 5wux fromDatabase pdb format mmcif
Summary of feedback from opening 5wux fetched from pdb
---
note | Fetching compressed mmCIF 5wux from http://files.rcsb.org/download/5wux.cif
5wux title:
TNFalpha-certolizumab Fab [more info...]
Chain information for 5wux #2
---
Chain | Description | UniProt
A C H | heavy |
B D L | light |
E F G | Tumor necrosis factor alpha | C1K3N5_HUMAN 1-157
5wux mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> hide #1 models
> show #1 models
> select add #2
14019 atoms, 14360 bonds, 9 pseudobonds, 1825 residues, 3 models selected
> select add #1
17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 3 models selected
> select subtract #1
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected
> cartoon hide (#!2 & sel)
> surface hidePatches (#!2 & sel)
> style sel sphere
Changed 12793 atom styles
> style sel sphere
Changed 12793 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 12793 atom styles
> select subtract #2
Nothing selected
> hide atoms
> show atoms
> color bynucleotide
> select add #2
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel sphere
Changed 12793 atom styles
> style sel ball
Changed 12793 atom styles
> select add #1
17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif, chain B (#1)
with 5wux, chain H (#2), sequence alignment score = 1098
RMSD between 199 pruned atom pairs is 1.071 angstroms; (across all 212 pairs:
1.348)
> select subtract #1
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected
> close #2
> open /Users/erikookamoto/Downloads/5wux-sf.cif
Summary of feedback from opening /Users/erikookamoto/Downloads/5wux-sf.cif
---
warning | No mmCIF models found.
> open /Users/erikookamoto/Downloads/5wux-sf.cif
Summary of feedback from opening /Users/erikookamoto/Downloads/5wux-sf.cif
---
warning | No mmCIF models found.
> open 5wux fromDatabase pdb format mmcif
5wux title:
TNFalpha-certolizumab Fab [more info...]
Chain information for 5wux #2
---
Chain | Description | UniProt
A C H | heavy |
B D L | light |
E F G | Tumor necrosis factor alpha | C1K3N5_HUMAN 1-157
5wux mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> select add #2
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected
> hide (#!2 & sel) target a
> style (#!2 & sel) sphere
Changed 12793 atom styles
> hide #* target a
> show (#!2 & sel) target ab
> view
> hide (#!2 & sel) target a
> hide (#!2 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2 & sel-residues)
> show (#!2 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> undo
> surface (#!2 & sel)
> surface hidePatches (#!2 & sel)
> select add #1
17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 12 models selected
> select subtract #2
4587 atoms, 4694 bonds, 600 residues, 10 models selected
> select add #2
17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 3 models selected
> select subtract #1
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 11 models selected
> rainbow sel
> color sel byhetero
> color sel bychain
> style sel sphere
Changed 12793 atom styles
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> color (#!2 & sel) light sea green
> color (#!2 & sel) cyan
> select subtract #2
9 models selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif, chain B (#1)
with 5wux, chain H (#2), sequence alignment score = 1098
RMSD between 199 pruned atom pairs is 1.071 angstroms; (across all 212 pairs:
1.348)
> view
> save /Users/erikookamoto/Desktop/image9.png supersample 3
> save "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/CZP_TNFa
> monomer.cxs"
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX
> Fab_CD20.cxs"
opened ChimeraX session
> open 6vja fromDatabase pdb format mmcif
Summary of feedback from opening 6vja fetched from pdb
---
notes | Fetching compressed mmCIF 6vja from http://files.rcsb.org/download/6vja.cif
Fetching CCD Y01 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/Y01/Y01.cif
6vja title:
Structure of CD20 in complex with rituximab Fab [more info...]
Chain information for 6vja #2
---
Chain | Description | UniProt
C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297
H I | Rituximab Fab heavy chain |
L M | Rituximab Fab light chain |
Non-standard residues in 6vja #2
---
Y01 — cholesterol hemisuccinate
> hide sel surfaces
> show sel cartoons
> hide sel surfaces
> select add #2
9726 atoms, 9988 bonds, 1257 residues, 2 models selected
> select add #1
13016 atoms, 13361 bonds, 1694 residues, 2 models selected
> select subtract #1
9342 atoms, 9593 bonds, 1210 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> hide sel surfaces
> hide sel target a
> select add #1
13016 atoms, 13361 bonds, 1694 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 fold_250120_rtx_fab_cd20_extracellular_model_0.cif, chain A (#1)
with 6vja, chain H (#2), sequence alignment score = 1142.9
RMSD between 103 pruned atom pairs is 0.571 angstroms; (across all 224 pairs:
9.363)
> view
> select subtract #2
3674 atoms, 3768 bonds, 484 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
3674 atoms, 3768 bonds, 484 residues, 1 model selected
> select add #2
13016 atoms, 13361 bonds, 1694 residues, 2 models selected
> select subtract #1
9342 atoms, 9593 bonds, 1210 residues, 1 model selected
> color sel cyan
> select subtract #2
Nothing selected
> save /Users/erikookamoto/Desktop/image10.png supersample 3
> open /Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/TCZ_IL-6.cxs
opened ChimeraX session
> open 8j6f fromDatabase pdb format mmcif
Summary of feedback from opening 8j6f fetched from pdb
---
notes | Fetching compressed mmCIF 8j6f from http://files.rcsb.org/download/8j6f.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
8j6f title:
Cryo-EM structure of the Tocilizumab Fab/IL-6R complex [more info...]
Chain information for 8j6f #2
---
Chain | Description | UniProt
B | IL6R-D2 peptide | IL6RA_HUMAN 103-112
H | Heavy chain of Tocilizumab Fab |
I | Interleukin-6 receptor subunit alpha | IL6RA_HUMAN 1-365
L | Light chain of Tocilizumab Fab |
Non-standard residues in 8j6f #2
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select add #2
6551 atoms, 6729 bonds, 4 pseudobonds, 839 residues, 4 models selected
> select add #1
9931 atoms, 10187 bonds, 4 pseudobonds, 1283 residues, 4 models selected
> select subtract #1
3870 atoms, 3971 bonds, 4 pseudobonds, 497 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #1
6061 atoms, 6216 bonds, 786 residues, 1 model selected
> select add #2
9931 atoms, 10187 bonds, 4 pseudobonds, 1283 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250120_tcz_fab_il6_model_0.cif, chain A (#1) with 8j6f, chain
I (#2), sequence alignment score = 1325.1
RMSD between 64 pruned atom pairs is 0.771 angstroms; (across all 66 pairs:
0.850)
> select subtract #1
3870 atoms, 3971 bonds, 4 pseudobonds, 497 residues, 3 models selected
> select subtract #2
Nothing selected
> view
> view orient
> view
> ui tool show "Side View"
> view orient
> view
> save /Users/erikookamoto/Desktop/image11.png supersample 3
> close session
> open
> /Users/erikookamoto/Downloads/fold_250121_certolizumab_fab_tnfa_trimer/fold_250121_certolizumab_fab_tnfa_trimer_model_0.cif
Chain information for fold_250121_certolizumab_fab_tnfa_trimer_model_0.cif #1
---
Chain | Description
A B C | .
D E F | .
G H I | .
> hide surfaces
> hide cartoons
> show cartoons
Computing secondary structure
> select add #1
13761 atoms, 14082 bonds, 1800 residues, 1 model selected
> hide sel surfaces
> hide sel target a
> show sel cartoons
> hide sel cartoons
> show sel cartoons
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select /G-I:157
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /G-I
3678 atoms, 3759 bonds, 471 residues, 1 model selected
> color sel yellow
> select /D-F:229
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /D-F
5139 atoms, 5268 bonds, 687 residues, 1 model selected
> color sel dim gray
> color sel light gray
> select /A-C:180
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A-C:142-180
906 atoms, 912 bonds, 117 residues, 1 model selected
> select /A-C:214
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A-C:71-214
3393 atoms, 3468 bonds, 432 residues, 1 model selected
> select /A-C:1-214
4944 atoms, 5055 bonds, 642 residues, 1 model selected
> color sel light gray
> open 5wux fromDatabase pdb format mmcif
5wux title:
TNFalpha-certolizumab Fab [more info...]
Chain information for 5wux #2
---
Chain | Description | UniProt
A C H | heavy |
B D L | light |
E F G | Tumor necrosis factor alpha | C1K3N5_HUMAN 1-157
5wux mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> select add #2
17737 atoms, 18162 bonds, 9 pseudobonds, 2310 residues, 3 models selected
> select add #1
26554 atoms, 27189 bonds, 9 pseudobonds, 3468 residues, 3 models selected
> select subtract #1
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected
> hide sel surfaces
> hide (#!2 & sel) target a
> show sel cartoons
> color (#!2 & sel) cyan
> select add #1
26554 atoms, 27189 bonds, 9 pseudobonds, 3468 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_250121_certolizumab_fab_tnfa_trimer_model_0.cif, chain A (#1)
with 5wux, chain L (#2), sequence alignment score = 1080.8
RMSD between 213 pruned atom pairs is 0.686 angstroms; (across all 213 pairs:
0.686)
> save "/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/CZP_TNFa
> trimer.cxs"
> select subtract #1
12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected
> select subtract #2
Nothing selected
> view
> save /Users/erikookamoto/Desktop/image12.png supersample 3
> close session
> open "/Users/erikookamoto/Library/CloudStorage/OneDrive-
> keio.jp/Trastuzumab_HER2 extracellular.cxs"
opened ChimeraX session
> open 6oge fromDatabase pdb format mmcif
Summary of feedback from opening 6oge fetched from pdb
---
notes | Fetching compressed mmCIF 6oge from http://files.rcsb.org/download/6oge.cif
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
6oge title:
Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab
complex [more info...]
Chain information for 6oge #2
---
Chain | Description | UniProt
A | Receptor tyrosine-protein kinase erbB-2 | ERBB2_HUMAN 23-644
B | Pertuzumab FAB LIGHT CHAIN | IGKC_HUMAN 108-214
C | Pertuzumab FAB HEAVY CHAIN | IGG1_HUMAN 103-216
D | Trastuzumab FAB LIGHT CHAIN | IGKC_HUMAN 108-214
E | Trastuzumab FAB HEAVY CHAIN | Q6GMX6_HUMAN 109-220
Non-standard residues in 6oge #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide sel surfaces
> select add #2
16333 atoms, 16765 bonds, 1 pseudobond, 2128 residues, 3 models selected
> select add #1
19633 atoms, 20144 bonds, 1 pseudobond, 2562 residues, 3 models selected
> select subtract #1
11494 atoms, 11809 bonds, 1 pseudobond, 1498 residues, 2 models selected
> style sel sphere
Changed 11494 atom styles
> style sel sphere
Changed 11494 atom styles
> hide sel surfaces
> show sel cartoons
> hide sel surfaces
> hide (#!2 & sel) target a
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 fold_trastuzumab_her2_extracellular_model_0.cif, chain A (#1) with
6oge, chain A (#2), sequence alignment score = 3032.8
RMSD between 461 pruned atom pairs is 0.964 angstroms; (across all 619 pairs:
3.312)
> select subtract #2
Nothing selected
> select add #2
11494 atoms, 11809 bonds, 1 pseudobond, 1498 residues, 2 models selected
> color (#!2 & sel) cyan
> select subtract #2
Nothing selected
> save /Users/erikookamoto/Desktop/image13.png supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MRXT3J/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D2057)
Kernel Version: Darwin 23.3.0
Time since boot: 36日 28分
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
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-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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