![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Closed 2 months ago
#18751 closed defect (duplicate)
Crash moving window between screens
| 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-15.5-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 0x00000002083d5f00 (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.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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, lxml._elementpath, lxml.etree (total: 63)
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{
"uptime" : 290000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 2695,
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"captureTime" : "2025-09-09 18:29:25.2616 -0700",
"codeSigningMonitor" : 1,
"incident" : "B634F428-99E8-4517-AB54-C43325CE85B0",
"pid" : 63455,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-09 11:22:03.4906 -0700",
"procStartAbsTime" : 6487509979492,
"procExitAbsTime" : 7010846703781,
"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":"292D261C-48B5-505D-96AA-1C3B54C1D842","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3587406A-7241-238D-D039-C9AD257A1AF4",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "6AC9D4D4-4788-4B77-ACB3-EC282A48FAB6",
"wakeTime" : 12034,
"sleepWakeUUID" : "3B1A40F4-B43E-41C1-91DC-33CCA771D5D9",
"sip" : "enabled",
"vmRegionInfo" : "0x4ac69f01be98 is not in any region. Bytes after previous region: 81735895334553 Bytes before following region: 23336184594792\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00004ac69f01be98","rawCodes":[1,82216931671704],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00004ac69f01be98"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":63455},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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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/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> select clear
> hide #3.2 models
> hide #3.3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> info rescolor #3/H:20
#!3/H:20 color #9389c3
> info rescolor #3/G:20
#!3/G:20 color #e3f0ef
> ui tool show "Color Actions"
> color #3/G #cyan
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/G cyan
> color #3/G e3f0ef
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/G #e3f0ef
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!1 models
> show #!3 models
> select add #1.10
1 model selected
No visible atoms selected
No visible residues selected
> select subtract #1.10
Nothing selected
> select add #1.10
1 model selected
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> select clear
> hide #!2 models
> hide #!3 models
> color /A,C,E,F,B,D lightgray
> select :276
72 atoms, 63 bonds, 9 residues, 3 models selected
> select ~sel & ##selected
57765 atoms, 59330 bonds, 43 pseudobonds, 7145 residues, 6 models selected
> select clear
> select :295
75 atoms, 66 bonds, 9 residues, 3 models selected
> select :368
72 atoms, 63 bonds, 9 residues, 3 models selected
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show sel & #!3 atoms
> show #!2 models
> hide #!3 models
> show sel & #!2 atoms
> show #!1 models
> hide #!2 models
> show sel & #!1 atoms
> show #!2 models
> show #!3 models
> ui tool show H-Bonds
> hbonds sel color #000404 interModel false angleSlop 50.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 50 degrees
Models used:
1 92-5F04_Q23_J473_real_space_refined_071.pdb
2 6v8x
3 9d7o
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 N 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H TYR 32 OH no hydrogen 3.361 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/G ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/C ASP 368 OD1 no hydrogen 3.015 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/G ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/C ASP 368 OD1 no hydrogen 2.904 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 3.193 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 2.917 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH1 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD2 no hydrogen 2.899 N/A
6v8x #!2/A ASP 368 N 6v8x #!2/C GLY 54 O no hydrogen 3.323 N/A
6v8x #!2/E ASP 368 N 6v8x #!2/G GLY 54 O no hydrogen 3.323 N/A
6v8x #!2/I ASP 368 N 6v8x #!2/K GLY 54 O no hydrogen 3.323 N/A
9d7o #!3/E ASP 368 N 9d7o #!3/H TYR 33 OH no hydrogen 3.265 N/A
9d7o #!3/H TYR 33 OH 9d7o #!3/E ASP 368 OD1 no hydrogen 2.720 N/A
9d7o #!3/H ARG 97 NE 9d7o #!3/E ASP 368 OD2 no hydrogen 2.784 N/A
9d7o #!3/H ARG 97 NH2 9d7o #!3/E ASP 368 OD2 no hydrogen 2.726 N/A
13 hydrogen bonds found
> select clear
> color #1.2-11#2.2-5#3.2-5#!1-3 byhetero
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!1 models
> select :NAG,NAM,MAN,BMA
3746 atoms, 3861 bonds, 274 residues, 3 models selected
> select :NAG,NAM,MAN,BMA
3746 atoms, 3861 bonds, 274 residues, 3 models selected
> show sel atoms
> select clear
> select :276
72 atoms, 63 bonds, 9 residues, 3 models selected
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!1 models
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> hide #3.3 models
> hide #3.2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #2.3
3 atoms, 3 residues, 3 models selected
> select subtract #2.3
2 atoms, 2 residues, 2 models selected
> select add #2.4
2 atoms, 2 residues, 3 models selected
> color #2.4 hot pink
> select clear
> select add #2.4
1 model selected
> color #2.4 black
> select clear
> select add #1.10
1 model selected
> show #!1 models
> color #1.10 black
> select clear
> select add #3.4
1 model selected
> color #1.2-10#2.2-4#!1-2 black
> show #!3 models
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> color #1.10 #2.4 #3.4 black
> hide #3.3 models
> hide #3.2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> hide #3.4 models
> show #3.4 models
> hide #3.4 models
> show #3.4 models
> color #3/G #e3f0ef
> ui tool show "Color Actions"
> color #3/G lightcyan
> color #3/G skyblue
> color #3/G lightskyblue
> color #3/G lpaleturquoise
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/G paleturquoise
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> color #3/G paleturquoise
> hide #3.2 #3.3
> color #1.10 #2.4 #3.4 black
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> color #2/A lightgray
> show #!1 models
> color #1/A lightgray
> hide #!2 models
> select #1/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byelement
> color (#!1 & sel) byhetero
> color #1/A lightgray
> color (#!1 & sel) byelement
> color #1/A lightgray
> color (#!1 & sel) byhetero
> select clear
> color #1/A :NAG,NAM,BMA,MAN
> select #1/A :NAG,NAM,BMA,MAN
344 atoms, 352 bonds, 25 residues, 1 model selected
> show sel atoms
> select #1/A :978,990
28 atoms, 29 bonds, 2 residues, 1 model selected
> select clear
> select #1/A :NAG,NAM,BMA,MAN
344 atoms, 352 bonds, 25 residues, 1 model selected
> hide sel atoms
> select #1/A :978,990
28 atoms, 29 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> color #3/G paleturquoise
> hide #3.2 #3.3
> color #1.10 #2.4 #3.4 black
> color #1/A lightgray
> color #1 byhetero
> select #1/A :978,99028 atoms
Expected a keyword
> show sel atoms
> hide #!2 models
> hide #!3 models
> color #1 byhetero
> select #1/A :978,990,276
36 atoms, 37 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!1 models
> select #2/A :276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A :NAG,NAM,BMA,MAN
56 atoms, 56 bonds, 4 residues, 1 model selected
> show sel atoms
> select #2 :NAG,NAM,BMA,MAN
1416 atoms, 1470 bonds, 105 residues, 1 model selected
> show sel atoms
> select clear
> select #2 /Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> select #2/A :276 /Q
47 atoms, 49 bonds, 4 residues, 1 model selected
> show #!3 models
> hide #!2 models
> select #3/A :276
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/E :276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3 :NAG,NAM,BMA,MAN
1312 atoms, 1351 bonds, 95 residues, 1 model selected
> show sel atoms
> select clear
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> color #3/G paleturquoise
> hide #3.2 #3.3
> color #1.10 #2.4 #3.4 black
> color #1/A lightgray
> color #1 byhetero
> select #1/A :978,990,276
36 atoms, 37 bonds, 3 residues, 1 model selected
> show sel atoms
> color #2 byhetero
> select #2/A :276 /Q
47 atoms, 49 bonds, 4 residues, 1 model selected
> show sel atoms
> color #3 byhetero
> select #3/E :276 /j
36 atoms, 37 bonds, 3 residues, 1 model selected
> show sel atoms
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> color #3/G paleturquoise
> hide #3.2 #3.3
> color #1.10 #2.4 #3.4 black
> color #1/A lightgray
> color #1 byhetero
> select #1/A :978,990,276
36 atoms, 37 bonds, 3 residues, 1 model selected
> show sel atoms
> color #2 byhetero
> select #2/A :276 /Q
47 atoms, 49 bonds, 4 residues, 1 model selected
> color sel lightgray
> show sel atoms
> color #3 byhetero
> select #3/E :276 /j
36 atoms, 37 bonds, 3 residues, 1 model selected
> color set lightgray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> show sel atoms
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> close session
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/RealSpaceRefine_71/92-5F04_Q23_J473_real_space_refined_071.pdb
Chain information for 92-5F04_Q23_J473_real_space_refined_071.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G H | No description available
I L | No description available
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 18366 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 1 item
> set bgColor #ffffff00
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> surface /A,C,E,B,D,F
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
17 contacting residues
> color sel #b0e694 surfaces
> name frozen li_contacts sel
> interfaces select /A,C,E contacting /H,G bothSides true areaCutoff 0
110 contacting residues
> color sel #9cecc7 surfaces
> name frozen hg_contacts sel
> select li_contacts & hg_contacts
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel darkgreen
> hide surfaces
> open 6V8X fromDatabase pdb format mmcif
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #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)
> mmaker #2/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
6v8x, chain A (#2), sequence alignment score = 1782.7
RMSD between 371 pruned atom pairs is 1.148 angstroms; (across all 428 pairs:
1.616)
> color #2/C hotpink target c
> color #2/D lightpink target c
> color #2/A lightgray
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> select #1/A,H,L #2/A,C,D
12478 atoms, 12810 bonds, 7 pseudobonds, 1574 residues, 4 models selected
> select ~sel
30713 atoms, 31536 bonds, 21 pseudobonds, 3795 residues, 4 models selected
> hide sel cartoons
> hide #2/A cartoons
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 43191 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 2 items
> set bgColor #ffffff00
> delete atoms #2/C:111-216
> delete atoms #2/D:107-216
> define centroid #1/A name centroid_ach_5fo4
Centroid 'centroid_ach_5fo4' placed at [193.0331926 170.24173 157.87076935]
> define centroid #2/A name centroid_ach_vrco1
Centroid 'centroid_ach_vrco1' placed at [215.56612197 179.65271473
205.15865745]
> define centroid #2/C,D name centroid_fab_vrco1
Centroid 'centroid_fab_vrco1' placed at [183.3499279 165.48208441
202.42807093]
> define centroid #1/H,L name centroid_5fo4
Centroid 'centroid_5fo4' placed at [193.29210349 200.74479579 147.82209242]
> select #1.8 #1.9
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_5f04
Axis '92-5F04_Q23_J473_real_space_refined_071.pdb #!1/axis_5f04' centered at
[193.16264804 185.4932629 152.84643088] with direction [ 0.00806158 0.94975829
-0.31288049], radius 1, and length 32.1167
> select #2.2 #2.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_vrco1
Axis '6v8x #!2/axis_vrco1' centered at [185.72843727 183.40070153
149.26124612] with direction [-0.41851807 0.73671435 -0.53112578], radius 1,
and length 35.3008
> select #1/A,H,L #2/A,C,D
10859 atoms, 11151 bonds, 7 pseudobonds, 1358 residues, 4 models selected
> select ~sel
30717 atoms, 31536 bonds, 21 pseudobonds, 3799 residues, 10 models selected
> hide sel cartoons
> open 9D7o fromDatabase pdb format mmcif
9d7o title:
Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound [more info...]
Chain information for 9d7o #3
---
Chain | Description | UniProt
A C E | Surface protein gp120 | Q2N0S5_9HIV1 8-504
B D F | Transmembrane protein gp41 | Q2N0S5_9HIV1 503-664
G | CH103 Fab light chain |
H | CH103 Fab heavy chain |
Non-standard residues in 9d7o #3
---
BMA — beta-D-mannopyranose (beta-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)
> mmaker #3/E to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
9d7o, chain E (#3), sequence alignment score = 1832.3
RMSD between 401 pruned atom pairs is 0.933 angstroms; (across all 425 pairs:
1.395)
> lighting soft
> hide atoms
> show cartoons
> style stick
Changed 58739 atom styles
> graphics silhouettes true width 1.5
> camera ortho
> setattr g display false
Assigning display attribute to 3 items
> cartoon style protein modeHelix default arrows false xsection oval width .6
> thickness .6
> define centroid #3/E name centroid_ech_9d7o
Centroid 'centroid_ech_9d7o' placed at [183.45592569 198.68844702
156.64264453]
> delete atoms #3/H:111-216
> delete atoms #3/G:107-216
> define centroid #3/G,H name centroid_ch103_9d7o
Centroid 'centroid_ch103_9d7o' placed at [185.1498031 223.08081981
180.26864021]
> select #3.2 #3.3
2 atoms, 2 residues, 2 models selected
> define axis sel name axis_ch103
Axis '9d7o #!3/axis_ch103' centered at [193.60557416 185.36448577 149.8010254
] with direction [-0.00335612 0.86371163 -0.50397516], radius 1, and length
34.0007
> hide #1 & ~/A,H,L cartoons
> hide #2 & ~/A,C,D cartoons
> hide #3 & ~/E,H,G cartoons
> color #3/E lightgray
> color #3/G #b0e694
> color #3/H #9389c3
> color #3/G paleturquoise
> hide #3.2 #3.3
> color #1.10 #2.4 #3.4 black
> color #1/A lightgray
> color #1 byhetero
> select #1/A :978,990,276
36 atoms, 37 bonds, 3 residues, 1 model selected
> show sel atoms
> select #2/A :276 /Q
47 atoms, 49 bonds, 4 residues, 1 model selected
> color sel lightgray
> color #2 byhetero
> show sel atoms
> select #3/E :276 /j
36 atoms, 37 bonds, 3 residues, 1 model selected
> color sel lightgray
> color #3 byhetero
> show sel atoms
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"
> save view
Cannot determine format for 'view'
> view name front
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_front.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> show #!2 models
> hide #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_Vrc01_front.png"
> width 894 height 648 supersample 3
> show #!3 models
> hide #!2 models
> hide models
> show #!1 models
> show #!2 models
> show #!3 models
> close session
> open "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"
> format session
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_front.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> show #!2 models
> hide #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01_front.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> show #!3 models
> hide #!2 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103_front.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> buried-area #1/H withAtoms2 #1/A
Unknown command: measure buried-area #1/H withAtoms2 #1/A
> measure buriedarea #2/H withAtoms2 #2/B & ~:NAG,NAM,MAN,BMA
Buried area between #2/H and #2/B & ~:NAG,NAM,MAN,BMA = 0
area #2/H = 12380, area #2/B & ~:NAG,NAM,MAN,BMA = 10725, area both = 23104
> measure buriedarea #2/H withAtoms2 #2/A & ~:NAG,NAM,MAN,BMA
Buried area between #2/H and #2/A & ~:NAG,NAM,MAN,BMA = 3.638e-12
area #2/H = 12380, area #2/A & ~:NAG,NAM,MAN,BMA = 23865, area both = 36244
> measure buriedarea #2/H withAtoms2 #2/A
Buried area between #2/H and #2/A = 0
area #2/H = 12380, area #2/A = 24506, area both = 36886
> measure buriedarea #1/H withAtoms2 #1/A
Buried area between #1/H and #1/A = 1306.8
area #1/H = 6633.3, area #1/A = 25476, area both = 29496
> measure buriedarea #1/H withAtoms2 #1/A
Buried area between #1/H and #1/A = 1306.8
area #1/H = 6633.3, area #1/A = 25476, area both = 29496
> measure buriedarea #1/H withAtoms2 #1/A
Buried area between #1/H and #1/A = 1306.8
area #1/H = 6633.3, area #1/A = 25476, area both = 29496
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> measure buriedarea #1/H withAtoms2 #1/A
Buried area between #1/H and #1/A = 1306.8
area #1/H = 6633.3, area #1/A = 25476, area both = 29496
> measure buriedarea #1/L withAtoms2 #1/A
Buried area between #1/L and #1/A = 183.36
area #1/L = 5984.2, area #1/A = 25476, area both = 31094
> measure buriedarea #2/C withAtoms2 #2/A
Buried area between #2/C and #2/A = 876.62
area #2/C = 6814.1, area #2/A = 24506, area both = 29567
> measure buriedarea #2/D withAtoms2 #2/A
Buried area between #2/D and #2/A = 202.75
area #2/D = 5617.7, area #2/A = 24506, area both = 29718
> measure buriedarea #3/H withAtoms2 #3/E
Buried area between #3/H and #3/E = 838.66
area #3/H = 6548.2, area #3/E = 23696, area both = 28566
> measure buriedarea #3/G withAtoms2 #3/E
Buried area between #3/G and #3/E = 284.47
area #3/G = 5811.3, area #3/E = 23696, area both = 28938
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"
> hide #1.10 models
> measure buriedarea #1/H withAtoms2 #1/A
Buried area between #1/H and #1/A = 1306.8
area #1/H = 6633.3, area #1/A = 25476, area both = 29496
> measure buriedarea #1/L withAtoms2 #1/A
Buried area between #1/L and #1/A = 183.36
area #1/L = 5984.2, area #1/A = 25476, area both = 31094
> measure buriedarea #2/C withAtoms2 #2/A
Buried area between #2/C and #2/A = 876.62
area #2/C = 6814.1, area #2/A = 24506, area both = 29567
> measure buriedarea #2/D withAtoms2 #2/A
Buried area between #2/D and #2/A = 202.75
area #2/D = 5617.7, area #2/A = 24506, area both = 29718
> measure buriedarea #3/H withAtoms2 #3/E
Buried area between #3/H and #3/E = 838.66
area #3/H = 6548.2, area #3/E = 23696, area both = 28566
> measure buriedarea #3/G withAtoms2 #3/E
Buried area between #3/G and #3/E = 284.47
area #3/G = 5811.3, area #3/E = 23696, area both = 28938
> close session
> open "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"
> format session
opened ChimeraX session
> measure buriedarea #1/H withAtoms2 #1/A
Buried area between #1/H and #1/A = 1306.8
area #1/H = 6633.3, area #1/A = 25476, area both = 29496
> measure buriedarea #1/L withAtoms2 #1/A
Buried area between #1/L and #1/A = 183.36
area #1/L = 5984.2, area #1/A = 25476, area both = 31094
> measure buriedarea #2/C withAtoms2 #2/A
Buried area between #2/C and #2/A = 876.62
area #2/C = 6814.1, area #2/A = 24506, area both = 29567
> measure buriedarea #2/D withAtoms2 #2/A
Buried area between #2/D and #2/A = 202.75
area #2/D = 5617.7, area #2/A = 24506, area both = 29718
> measure buriedarea #3/H withAtoms2 #3/E
Buried area between #3/H and #3/E = 838.66
area #3/H = 6548.2, area #3/E = 23696, area both = 28566
> measure buriedarea #3/G withAtoms2 #3/E
Buried area between #3/G and #3/E = 284.47
area #3/G = 5811.3, area #3/E = 23696, area both = 28938
> select #1/A:368
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #1/A:368, #2/A:368, #3/E:368
Expected an objects specifier or a keyword
> select #1/A:368 #2/A:368 #3/E:368
24 atoms, 21 bonds, 3 residues, 3 models selected
> show #!2 models
> show #!1 models
> show sel atoms
> hide #!3 models
> hide #!2 models
> hide #1.10 models
> show #!2 models
> show #!3 models
> ui tool show H-Bonds
> hbonds sel color #000404 interModel false angleSlop 50.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 50 degrees
Models used:
1 92-5F04_Q23_J473_real_space_refined_071.pdb
2 6v8x
3 9d7o
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 N 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H TYR 32 OH no hydrogen 3.361 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 3.193 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 2.917 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH1 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD2 no hydrogen 2.899 N/A
6v8x #!2/A ASP 368 N 6v8x #!2/C GLY 54 O no hydrogen 3.323 N/A
9d7o #!3/E ASP 368 N 9d7o #!3/H TYR 33 OH no hydrogen 3.265 N/A
9d7o #!3/H TYR 33 OH 9d7o #!3/E ASP 368 OD1 no hydrogen 2.720 N/A
9d7o #!3/H ARG 97 NE 9d7o #!3/E ASP 368 OD2 no hydrogen 2.784 N/A
9d7o #!3/H ARG 97 NH2 9d7o #!3/E ASP 368 OD2 no hydrogen 2.726 N/A
9 hydrogen bonds found
> select clear
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> hide #3.4 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> hide #2.4 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #1/C:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:59
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right select
> select #!2/C:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!2/C:55
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #!2/C:54
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #!2/C:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/C:71
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #!2/C:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 6 residues, 1 model selected
> select up
948 atoms, 975 bonds, 118 residues, 1 model selected
> hide sel atoms
> select #2/C:71
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> open 3Jwd fromDatabase pdb format mmcif
Summary of feedback from opening 3Jwd fetched from pdb
---
notes | Fetching compressed mmCIF 3jwd from http://files.rcsb.org/download/3jwd.cif
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif
Fetching CCD YCM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/YCM/YCM.cif
3jwd title:
Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture
and Basis of Conformational Mobility [more info...]
Chain information for 3jwd #4
---
Chain | Description | UniProt
A B | HIV-1 GP120 ENVELOPE GLYCOPROTEIN |
C D | T-cell surface glycoprotein CD4 | CD4_HUMAN 1001-1183
H P | FAB 48D HEAVY CHAIN |
L O | FAB 48D LIGHT CHAIN |
Non-standard residues in 3jwd #4
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
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)
3jwd mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> hide #!4 atoms
> show #!4 cartoons
> mmaker #4 to #1
Specify a single 'to' model only
Drag select of 487 residues, 1 pseudobonds
> select up
4574 atoms, 4657 bonds, 1 pseudobond, 587 residues, 2 models selected
> select up
7574 atoms, 7757 bonds, 1 pseudobond, 977 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> mmaker #4/A to #1/A
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 92-5F04_Q23_J473_real_space_refined_071.pdb, chain A (#1) with
3jwd, chain A (#4), sequence alignment score = 1293.4
RMSD between 260 pruned atom pairs is 0.898 angstroms; (across all 351 pairs:
5.931)
> show #!1 models
> hide #!1 models
> show #!1 models
> select #4/L:195
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
46 atoms, 46 bonds, 6 residues, 1 model selected
> select up
1635 atoms, 1672 bonds, 213 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/H:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 11 residues, 1 model selected
> select up
1654 atoms, 1697 bonds, 220 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/A:368
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> hide #!1 models
> select #4/C:71
Nothing selected
> select #4/C:1058
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> show #!3 models
> hide #!3 models
> ui tool show "Side View"
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> select #!2/C:71@NE
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> color #2/C hotpink target a
> color sel byhetero
> select clear
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!4 models
> hide #!1 models
> show #!3 models
> hide #!4 models
> cartoon style #3.2-3,5#!3 xsection oval modeHelix default
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!1 models
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> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #1 models
> hide #!1 models
> show #!1 models
> hide #1.10 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> show #!2 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> show #!3 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> show #!4 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!1 models
> show #!2 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!3 models
> show #!4 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!4 models
> show #!4 models
> color #4/A lightgray
> color #4 byhetero
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!1 models
> show #!2 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103__CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!3 models
> show #!4 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_CD4BS.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!4 models
> show #!4 models
> info rescolor #4/C:1058
#4/C:1058 color #e0f38d
> show #!3 models
> hide #!4 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/session_090925.cxs"
> hide #1.8-9#!1 atoms
> show #1.8-9#!1 atoms
> hide #1.8-9#!1 atoms
> hide #!1 models
> show #!1 models
> ui tool show "Side View"
> setattr g display false
Assigning display attribute to 7 items
> select add #1
18368 atoms, 18867 bonds, 17 pseudobonds, 2269 residues, 6 models selected
> show sel cartoons
> select clear
> show #!4 models
> hide #!4 models
> select #1 ~/A
Expected a keyword
> select #1 & ~/A
14531 atoms, 14917 bonds, 10 pseudobonds, 1804 residues, 5 models selected
> hide sel cartoons
> show #!2 models
> hide #!1 models
> select #2 & ~/A
19699 atoms, 20229 bonds, 11 pseudobonds, 2445 residues, 5 models selected
> hide sel cartoons
> select clear
> hide #2.2-3#!2 atoms
> show #!3 models
> hide #!2 models
> select #3 & ~/E
12728 atoms, 13061 bonds, 12 pseudobonds, 1557 residues, 5 models selected
> hide sel cartoons
> hide sel atoms
> select clear
> hide #3.2-3#!3 atoms
> show #!4 models
> hide #!3 models
> hide #!4 atoms
> select #4 & ~/A
1759 atoms, 1464 bonds, 501 residues, 1 model selected
> hide sel cartoons
> show #!1 models
> hide #!4 models
> interfaces select /A, contacting /H,L bothSides true areaCutoff 0
Missing required "contacting" argument
> interfaces select #1/A, contacting /H,L bothSides true areaCutoff 0
Missing required "contacting" argument
> interfaces select #1/A, contacting #1/H,L bothSides true areaCutoff 0
Missing required "contacting" argument
> interfaces select /A,C,E contacting /L,I bothSides true areaCutoff 0
1376 contacting residues
> color sel #b0e694 surfaces
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> select clear
> interfaces select /A,C,E contacting /L,H bothSides true areaCutoff 0
1061 contacting residues
> interfaces select /A contacting /L,H bothSides true areaCutoff 0
388 contacting residues
> interfaces select /A contacting /L,H bothSides false areaCutoff 0
193 contacting residues
> surface (#!1 & sel)
> color sel #b0e694 surfaces
> surface #1/A
> color /A,C,E,F,B,D lightgray
> color /L,I #b0e694
> color /H,G #9cecc7
> select up
3045 atoms, 3031 bonds, 397 residues, 5 models selected
> select clear
> interfaces select /A contacting /L,H bothSides false areaCutoff 0
193 contacting residues
> color sel #b0e694 surfaces
> select clear
> show #!2 models
> hide #!1 models
> surface #2/A
> interfaces select #2/A contacting #2/C,D bothSides false areaCutoff 0
25 contacting residues
> show #!1 models
> hide #!1 models
> color sel hotpink
> select clear
> show #!3 models
> hide #!2 models
> surface #3/E
> interfaces select #3/E contacting #3/H,G bothSides false areaCutoff 0
25 contacting residues
> color sel #9389c3
> show #!4 models
> hide #!3 models
> select add #4
4992 atoms, 4486 bonds, 1 pseudobond, 1028 residues, 4 models selected
> show sel & #!4 cartoons
> interfaces select #4/A contacting #3/C bothSides false areaCutoff 0
4 contacting residues
> interfaces select #4/A contacting #4/C bothSides false areaCutoff 0
26 contacting residues
> select clear
> select #4/C:1168
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
78 atoms, 78 bonds, 9 residues, 1 model selected
> select up
1432 atoms, 1454 bonds, 184 residues, 1 model selected
> hide sel cartoons
> interfaces select #4/A contacting #4/C bothSides false areaCutoff 0
26 contacting residues
> surface #4/A
> interfaces select #4/A contacting #4/C bothSides false areaCutoff 0
26 contacting residues
> color sel #e0f38d
> hide #!4 models
> show #!4 models
> select add #4
4834 atoms, 4486 bonds, 1 pseudobond, 1006 residues, 3 models selected
> select clear
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> view name footprint
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_footprint.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!1 models
> show #!2 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/6v8x_vrc01_footprint.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/9d7o_ch103_footprint.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!3 models
> show #!4 models
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/3jwd_cd4_GP120_footprint.png"
> width 2000 height 1450 supersample 4 transparentBackground true
> hide #!4 models
> show #!1 models
> surface hidePatches #1.2-9,12-13#!1
> select #1/H,L
1807 atoms, 1856 bonds, 234 residues, 1 model selected
> show sel cartoons
> select clear
> select #!1/H:96
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #!1/H:100C
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add #!1/H:100B
31 atoms, 29 bonds, 3 residues, 1 model selected
> select add #!1/H:100
37 atoms, 34 bonds, 4 residues, 1 model selected
> select add #!1/H:99
43 atoms, 39 bonds, 5 residues, 1 model selected
> select add #!1/H:98
49 atoms, 44 bonds, 6 residues, 1 model selected
> select add #!1/H:97
53 atoms, 47 bonds, 7 residues, 1 model selected
> select add #!1/H:100A
67 atoms, 62 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #!1/H:100E
78 atoms, 72 bonds, 9 residues, 1 model selected
> select add #!1/H:100D
82 atoms, 75 bonds, 10 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel color #000404 interModel false angleSlop 50.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 50 degrees
Models used:
1 92-5F04_Q23_J473_real_space_refined_071.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASN 195 ND2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H SER 100 O no hydrogen 3.395 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASN 195 ND2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H TRP 100A O no hydrogen 2.913 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASN 425 ND2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H LEU 100C O no hydrogen 2.872 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 3.193 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 96 NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD1 no hydrogen 2.917 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NE 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A GLN 428 OE1 no hydrogen 2.930 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH1 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A ASP 368 OD2 no hydrogen 2.899 N/A
92-5F04_Q23_J473_real_space_refined_071.pdb #!1/H ARG 100E NH2 92-5F04_Q23_J473_real_space_refined_071.pdb #!1/A GLN 428 OE1 no hydrogen 2.894 N/A
8 hydrogen bonds found
> color (#!1 & sel) byhetero
> select clear
> show #1.11 models
> select #1/L
815 atoms, 835 bonds, 108 residues, 1 model selected
> hide sel cartoons
> select #!1/H:98@CB
1 atom, 1 residue, 1 model selected
> select add #!1/H:100@OG
2 atoms, 1 bond, 2 residues, 1 model selected
> hide sel atoms
> select up
5 atoms, 2 bonds, 3 residues, 1 model selected
> hide sel atoms
> select #!1/H:98@OG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!1/H:100@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #!1/H:100B@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> ui tool show "Side View"
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/92-5F04_Q23-SOSIP/analysis/92_5f04_alpha_helix.png"
> width 2000 height 1450 supersample 4 transparentBackground true
===== 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 - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Z1B600163LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 5 days, 4 hours, 10 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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-QScore: 1.2
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 , 2 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel explained what we know about this crash:
"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."
You might try the ChimeraX daily build which uses a newer Qt version 6.9.2 where we have not seen these Mac multi-display crashes.
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Reported by Swastik