![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Last modified 7 months ago
#17169 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| 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-15.3.2-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: Bus error
Current thread 0x0000000206d50840 (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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, lxml._elementpath, lxml.etree, lxml.builder, chimerax.mlp._mlp (total: 63)
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"codeSigningMonitor" : 1,
"incident" : "786F4164-DAA0-4EED-81F5-7362492B5B9F",
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"translated" : false,
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"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-17 14:28:26.4067 +0100",
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"procExitAbsTime" : 5190642747818,
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"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"wakeTime" : 14206,
"sleepWakeUUID" : "84A3E910-69C2-4F82-803A-D590AE5188E9",
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"termination" : {"flags":1024,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":9167},
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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/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
> format pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9262
REMARK PDBinfo-LABEL: 1 64.61408909627788
Ignored bad PDB record found on line 9263
REMARK PDBinfo-LABEL: 2 83.22959617224114
Ignored bad PDB record found on line 9264
REMARK PDBinfo-LABEL: 3 87.68443933186607
Ignored bad PDB record found on line 9265
REMARK PDBinfo-LABEL: 4 82.43727171195131
Ignored bad PDB record found on line 9266
REMARK PDBinfo-LABEL: 5 87.56903352758921
597 messages similar to the above omitted
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> split
Split output_1021_dldesign_0_cycle1_af2pred.pdb (#1) into 2 models
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb B #1.2
---
Chain | Description
B | No description available
> color #1.1 #d773ceff
> color #1.1 #d778d5ff
> view ligand
No objects specified.
> view ligand
No objects specified.
> label ligand
> view ligand
No objects specified.
> view interaction
Expected an objects specifier or a view name or a keyword
> style ball
Changed 9250 atom styles
> style still
Expected a keyword
> hide atoms
> show atoms
> hide atoms
> show cartoons
> hide cartoons
> show cartoons
> show surfaces
> hide surfaces
> select ligand
Nothing selected
> select backbone
3601 atoms, 3599 bonds, 597 residues, 2 models selected
> select clear
> select add #1.1
1640 atoms, 1649 bonds, 101 residues, 1 model selected
> select subtract #1.1
1 model selected
> select add #1.1
1640 atoms, 1649 bonds, 101 residues, 1 model selected
> select ligand
Nothing selected
> select add #1.1
1640 atoms, 1649 bonds, 101 residues, 1 model selected
> select add #1.2
9250 atoms, 9333 bonds, 597 residues, 3 models selected
> select ligand
Nothing selected
> select add #1.2
7610 atoms, 7684 bonds, 496 residues, 1 model selected
> select add #1.1
9250 atoms, 9333 bonds, 597 residues, 3 models selected
> view ligand
No objects specified.
> label ligand
> select clear
> show target ab
> hide target a
> surface
> surface hidePatches
> label #1 atoms attribute element
> label #1 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> ~label #1 residues
> label #1 text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> undo
> redo
> ~label #1 residues
> alphafold contacts /A toAtoms /B
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> combine #1,2 modelId 3
> hide #!1.2 models
> hide #!1.1 models
> hide #!1 models
> hide #3 models
> show #3 models
> alphafold contacts /A toAtoms /B
Interface PAE pseudobonds can only be computed for a single structure, got 3.
> select add #3
9250 atoms, 9333 bonds, 597 residues, 1 model selected
> select subtract #3
Nothing selected
> open
> /Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9262
REMARK PDBinfo-LABEL: 1 64.61408909627788
Ignored bad PDB record found on line 9263
REMARK PDBinfo-LABEL: 2 83.22959617224114
Ignored bad PDB record found on line 9264
REMARK PDBinfo-LABEL: 3 87.68443933186607
Ignored bad PDB record found on line 9265
REMARK PDBinfo-LABEL: 4 82.43727171195131
Ignored bad PDB record found on line 9266
REMARK PDBinfo-LABEL: 5 87.56903352758921
597 messages similar to the above omitted
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #2 models
> show #2 models
> hide #3 models
> hide #2 models
> show #2 models
> hide #3 target m
> hide #2 models
> show #2 models
> close #3
> hide #2 models
> show #2 models
> close #2
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> hide #!1 models
> show #!1 models
> save "/Users/dantebangafoe/Downloads/viewing 1021_1.cxs"
> open
> /Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9262
REMARK PDBinfo-LABEL: 1 64.61408909627788
Ignored bad PDB record found on line 9263
REMARK PDBinfo-LABEL: 2 83.22959617224114
Ignored bad PDB record found on line 9264
REMARK PDBinfo-LABEL: 3 87.68443933186607
Ignored bad PDB record found on line 9265
REMARK PDBinfo-LABEL: 4 82.43727171195131
Ignored bad PDB record found on line 9266
REMARK PDBinfo-LABEL: 5 87.56903352758921
597 messages similar to the above omitted
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #2 models
> close
> open
> /Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9262
REMARK PDBinfo-LABEL: 1 64.61408909627788
Ignored bad PDB record found on line 9263
REMARK PDBinfo-LABEL: 2 83.22959617224114
Ignored bad PDB record found on line 9264
REMARK PDBinfo-LABEL: 3 87.68443933186607
Ignored bad PDB record found on line 9265
REMARK PDBinfo-LABEL: 4 82.43727171195131
Ignored bad PDB record found on line 9266
REMARK PDBinfo-LABEL: 5 87.56903352758921
597 messages similar to the above omitted
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> alphafold contacts /A toAtoms /B
Structure output_1021_dldesign_0_cycle1_af2pred.pdb #1 does not have PAE data
opened
> contacts #1 #2 5.0
Expected a keyword
> split
Split output_1021_dldesign_0_cycle1_af2pred.pdb (#1) into 2 models
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb B #1.2
---
Chain | Description
B | No description available
> color #1.1 #a5d77dff
> contacts #1 #2 5.0
Expected a keyword
> contacts #A #B 5.0
Expected a keyword
> contacts #1.1 #1.2 5.0
Expected a keyword
> findclash #1.1 test #1.2 overlap -0.4 hb 0.4 reveal true
Unknown command: findclash #1.1 test #1.2 overlap -0.4 hb 0.4 reveal true
> contacts #1.1 #1.2 5.0
Expected a keyword
> findcontacts #1.1 #1.2 dist 5.0
Unknown command: findcontacts #1.1 #1.2 dist 5.0
> surface #1.1
> surface hidePatches
> style ball
Changed 9250 atom styles
> select add #1.1
1640 atoms, 1649 bonds, 101 residues, 1 model selected
> style sel ball
Changed 1640 atom styles
> select subtract #1.1
1 model selected
> style sphere
Changed 9250 atom styles
> show atoms
> style stick
Changed 9250 atom styles
> style sphere
Changed 9250 atom styles
> style ball
Changed 9250 atom styles
> style stick
Changed 9250 atom styles
> hide cartoons
> show cartoons
> hide atoms
> show cartoons
> hide cartoons
> show cartoons
> show atoms
> hide cartoons
> show cartoons
> hide cartoons
> style ball
Changed 9250 atom styles
> style stick
Changed 9250 atom styles
> hide atoms
> show cartoons
> show #1/A:1-36 atoms
> show #1/A:1-101 atoms
> show #1/A:1-102 atoms
> show #1/A:1-20 atoms
> cartoon hide
> cartoon
> hide target a
> show #1/A:1-20 atoms
> hide target a
> show #1/B:1-20 atoms
> show #1/B:102-200 atoms
> hide target a
> show #1/B:310-597 atoms
> hide target a
> show #1/B:400-500 atoms
> hide target a
> hide #1/B:400-500 atoms
> show #1/B:400-500 atoms
> hide #1/B:400-500 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A
Alignment identifier is 1.1/A
> select #1.1/A:41
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.1/A:41-58
287 atoms, 287 bonds, 18 residues, 1 model selected
> select #1.1/A:101
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.1/A:81-101
338 atoms, 337 bonds, 21 residues, 1 model selected
> select #1.1/A:1-2
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1.1/A:1-29
470 atoms, 474 bonds, 29 residues, 1 model selected
> select #1.1/A:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:61-80
330 atoms, 331 bonds, 20 residues, 1 model selected
> select #1.1/A:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:41-80
643 atoms, 646 bonds, 40 residues, 1 model selected
> select #1.1/A:30
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.1/A:30-80
832 atoms, 836 bonds, 51 residues, 1 model selected
> select #1.1/A:19-20
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.1/A:19-80
1007 atoms, 1013 bonds, 62 residues, 1 model selected
> hide sel cartoons
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2/B
Alignment identifier is 1.2/B
> select #1.2/B:226
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:226-270
732 atoms, 740 bonds, 45 residues, 1 model selected
> select #1.2/B:597
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.2/B:582-597
218 atoms, 218 bonds, 16 residues, 1 model selected
> select #1.2/B:542
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:542-546
92 atoms, 92 bonds, 5 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:382
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:382-581
3181 atoms, 3212 bonds, 200 residues, 1 model selected
> select #1.2/B:142-183
514 atoms, 517 bonds, 42 residues, 1 model selected
> select #1.2/B:142-361
3340 atoms, 3368 bonds, 220 residues, 1 model selected
> select #1.2/B:102
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:102-141
569 atoms, 576 bonds, 40 residues, 1 model selected
> select #1.2/B:102
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:102-181
1058 atoms, 1069 bonds, 80 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:182
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:182-261
1286 atoms, 1293 bonds, 80 residues, 1 model selected
> select #1.2/B:262
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #1.2/B:262-313
823 atoms, 830 bonds, 52 residues, 1 model selected
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-367
384 atoms, 390 bonds, 26 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:262
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #1.2/B:262-264
60 atoms, 61 bonds, 3 residues, 1 model selected
> select #1.2/B:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:302-305
39 atoms, 38 bonds, 4 residues, 1 model selected
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-346
69 atoms, 70 bonds, 5 residues, 1 model selected
> select #1.2/B:382
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:382-387
93 atoms, 94 bonds, 6 residues, 1 model selected
> select #1.2/B:336-378
654 atoms, 663 bonds, 43 residues, 1 model selected
> select #1.2/B:336-379
670 atoms, 679 bonds, 44 residues, 1 model selected
> select #1.2/B:379
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:341-379
588 atoms, 597 bonds, 39 residues, 1 model selected
> select #1.2/B:378
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.2/B:378-381
68 atoms, 67 bonds, 4 residues, 1 model selected
> select #1.2/B:597
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.2/B:477-597
1947 atoms, 1968 bonds, 121 residues, 1 model selected
> select #1.2/B:597
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.2/B:582-597
218 atoms, 218 bonds, 16 residues, 1 model selected
> select #1.2/B:542
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:542-548
121 atoms, 121 bonds, 7 residues, 1 model selected
> select #1.2/B:542-543
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/B:542-581
655 atoms, 660 bonds, 40 residues, 1 model selected
> select #1.2/B:542
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:542-570
474 atoms, 477 bonds, 29 residues, 1 model selected
> select #1.2/B:542-543
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/B:542-575
553 atoms, 556 bonds, 34 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:502-503
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/B:502-513
193 atoms, 195 bonds, 12 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-504
47 atoms, 46 bonds, 3 residues, 1 model selected
> select #1.2/B:502-503
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/B:502-513
193 atoms, 195 bonds, 12 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-508
121 atoms, 123 bonds, 7 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-509
138 atoms, 140 bonds, 8 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-507
100 atoms, 101 bonds, 6 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-509
138 atoms, 140 bonds, 8 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-507
100 atoms, 101 bonds, 6 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-507
100 atoms, 101 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-467
66 atoms, 65 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:422
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:422-428
121 atoms, 121 bonds, 7 residues, 1 model selected
> select #1.2/B:422
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:422-425
81 atoms, 81 bonds, 4 residues, 1 model selected
> select #1.2/B:422
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:422-423
40 atoms, 39 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:410-411
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/B:410-416
113 atoms, 112 bonds, 7 residues, 1 model selected
> select #1.2/B:106-147
555 atoms, 562 bonds, 42 residues, 1 model selected
> select #1.2/B:106-194
1210 atoms, 1223 bonds, 89 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:102
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:102-191
1238 atoms, 1251 bonds, 90 residues, 1 model selected
> select #1.2/B:194
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:194-283
1433 atoms, 1444 bonds, 90 residues, 1 model selected
> select #1.2/B:193-194
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/B:193-239
742 atoms, 745 bonds, 47 residues, 1 model selected
> select #1.2/B:182
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:182-230
787 atoms, 791 bonds, 49 residues, 1 model selected
> select #1.2/B:235
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:235-242
132 atoms, 132 bonds, 8 residues, 1 model selected
> select #1.2/B:195-235
634 atoms, 637 bonds, 41 residues, 1 model selected
> select #1.2/B:195-274
1262 atoms, 1271 bonds, 80 residues, 1 model selected
> select #1.2/B:222
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:222-276
904 atoms, 914 bonds, 55 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:349-350
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1.2/B:349-359
166 atoms, 166 bonds, 11 residues, 1 model selected
> select #1.2/B:385
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:385-394
158 atoms, 161 bonds, 10 residues, 1 model selected
> select #1.2/B:382
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:382-387
93 atoms, 94 bonds, 6 residues, 1 model selected
> select
> #1.2/B:178-184,186-192,215-225,235-241,245-249,255-257,269-276,463-465,521-526,572-575
996 atoms, 992 bonds, 61 residues, 1 model selected
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-471
143 atoms, 143 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-347
89 atoms, 91 bonds, 6 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:355
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:355-381
418 atoms, 423 bonds, 27 residues, 1 model selected
> select #1.2/B:352
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:352-362
172 atoms, 173 bonds, 11 residues, 1 model selected
> select #1.1/A:101
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.1/A:81-101
338 atoms, 337 bonds, 21 residues, 1 model selected
> hide sel cartoons
> select #1.1/A:1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:1-13
214 atoms, 215 bonds, 13 residues, 1 model selected
> select #1.1/A:1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.1/A:1-26
428 atoms, 430 bonds, 26 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:222-268
764 atoms, 772 bonds, 47 residues, 1 model selected
> select #1.2/B:222-279
952 atoms, 962 bonds, 58 residues, 1 model selected
> select #1.2/B:354
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:354-408
868 atoms, 879 bonds, 55 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:352-353
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/B:352-362
172 atoms, 173 bonds, 11 residues, 1 model selected
> select #1.2/B:369
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:369-376
118 atoms, 119 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:410
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:410-417
124 atoms, 123 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:450-451
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1.2/B:450-457
104 atoms, 103 bonds, 8 residues, 1 model selected
> select #1.2/B:450-451
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1.2/B:450-454
59 atoms, 58 bonds, 5 residues, 1 model selected
> select #1.2/B:457
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:422-457
540 atoms, 542 bonds, 36 residues, 1 model selected
> select #1.2/B:495-496
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #1.2/B:495-498
66 atoms, 66 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:480-481
46 atoms, 45 bonds, 2 residues, 1 model selected
> select #1.2/B:480-488
162 atoms, 166 bonds, 9 residues, 1 model selected
> select #1.2/B:520
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:520-528
135 atoms, 135 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:560-561
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/B:560-570
191 atoms, 192 bonds, 11 residues, 1 model selected
> select #1.2/B:448
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:448-479
456 atoms, 458 bonds, 32 residues, 1 model selected
> select #1.2/B:395-396
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/B:395-442
746 atoms, 749 bonds, 48 residues, 1 model selected
> select #1.2/B:399
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:399-404
97 atoms, 96 bonds, 6 residues, 1 model selected
> select #1.2/B:394-395
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #1.2/B:394-398
87 atoms, 87 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:391
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:391-437
732 atoms, 735 bonds, 47 residues, 1 model selected
> select #1.2/B:399-440
649 atoms, 651 bonds, 42 residues, 1 model selected
> select #1.2/B:399-445
733 atoms, 736 bonds, 47 residues, 1 model selected
> select #1.2/B:397
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:397-400
71 atoms, 71 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:356
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:356-361
102 atoms, 102 bonds, 6 residues, 1 model selected
> select #1.2/B:397-398
36 atoms, 36 bonds, 2 residues, 1 model selected
> select #1.2/B:397-401
81 atoms, 81 bonds, 5 residues, 1 model selected
> select #1.2/B:435
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:435-447
216 atoms, 216 bonds, 13 residues, 1 model selected
> select #1.2/B:422
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:422-423
40 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/B:422
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:422-440
294 atoms, 295 bonds, 19 residues, 1 model selected
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-474
193 atoms, 194 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-356
214 atoms, 217 bonds, 15 residues, 1 model selected
> select #1.2/B:316
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:316-343
438 atoms, 442 bonds, 28 residues, 1 model selected
> select #1.2/B:552
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:552-562
158 atoms, 159 bonds, 11 residues, 1 model selected
> select #1.2/B:581
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:571-581
181 atoms, 182 bonds, 11 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:142
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.2/B:142-597
7041 atoms, 7107 bonds, 456 residues, 1 model selected
> select #1.2/B:102
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:102-141
569 atoms, 576 bonds, 40 residues, 1 model selected
> select #1.2/B:269-316
770 atoms, 774 bonds, 48 residues, 1 model selected
> select #1.2/B:269-330
993 atoms, 1001 bonds, 62 residues, 1 model selected
> select #1.2/B:534-535
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #1.2/B:534-541
147 atoms, 148 bonds, 8 residues, 1 model selected
> select #1.2/B:530
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:530-535
86 atoms, 86 bonds, 6 residues, 1 model selected
> select #1.2/B:533
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:533-535
49 atoms, 49 bonds, 3 residues, 1 model selected
> select #1.2/B:537
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:537-538
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2/B:537-538
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2/B:537-541
104 atoms, 105 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:521
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:521-526
90 atoms, 90 bonds, 6 residues, 1 model selected
> select #1.2/B:528-529
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/B:528-532
70 atoms, 69 bonds, 5 residues, 1 model selected
> select #1.2/B:536
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:536-541
118 atoms, 119 bonds, 6 residues, 1 model selected
> select #1.2/B:536
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:536-541
118 atoms, 119 bonds, 6 residues, 1 model selected
> select #1.2/B:501
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:498-501
64 atoms, 63 bonds, 4 residues, 1 model selected
> select #1.2/B:501
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:495-501
111 atoms, 111 bonds, 7 residues, 1 model selected
> select #1.2/B:501
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:489-501
212 atoms, 212 bonds, 13 residues, 1 model selected
> select #1.2/B:491-492
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/B:491-501
179 atoms, 179 bonds, 11 residues, 1 model selected
> select #1.2/B:501
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:495-501
111 atoms, 111 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:382
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:382-397
249 atoms, 253 bonds, 16 residues, 1 model selected
> select #1.2/B:269
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:269-279
188 atoms, 189 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:281-282
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #1.2/B:281-286
102 atoms, 102 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:358-359
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #1.2/B:358-370
204 atoms, 207 bonds, 13 residues, 1 model selected
> select #1.2/B:358
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:358-362
81 atoms, 81 bonds, 5 residues, 1 model selected
> select #1.2/B:363-364
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #1.2/B:363-372
148 atoms, 150 bonds, 10 residues, 1 model selected
> select #1.2/B:375-376
34 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:375-381
116 atoms, 117 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:404
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:404-415
203 atoms, 203 bonds, 12 residues, 1 model selected
> select #1.2/B:411
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:411-419
122 atoms, 121 bonds, 9 residues, 1 model selected
> select #1.2/B:408-409
35 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:408-419
181 atoms, 181 bonds, 12 residues, 1 model selected
> select #1.2/B:382-383
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/B:382-421
626 atoms, 631 bonds, 40 residues, 1 model selected
> select #1.2/B:382
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:382-388
104 atoms, 105 bonds, 7 residues, 1 model selected
> select #1.2/B:391
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:391-395
72 atoms, 71 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:431
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:431-435
66 atoms, 66 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:441
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:441-447
115 atoms, 115 bonds, 7 residues, 1 model selected
> select #1.2/B:597
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.2/B:593-597
66 atoms, 65 bonds, 5 residues, 1 model selected
> select #1.2/B:575-576
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #1.2/B:575-581
121 atoms, 122 bonds, 7 residues, 1 model selected
> select #1.2/B:309-310
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1.2/B:309-321
203 atoms, 203 bonds, 13 residues, 1 model selected
> select #1.2/B:349
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:349-403
850 atoms, 861 bonds, 55 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:222
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:222-225
67 atoms, 67 bonds, 4 residues, 1 model selected
> select #1.2/B:269-270
35 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:269-276
140 atoms, 141 bonds, 8 residues, 1 model selected
> select #1.2/B:278
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:278-282
91 atoms, 90 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:558-597
604 atoms, 608 bonds, 40 residues, 1 model selected
> select #1.2/B:272-597
5111 atoms, 5161 bonds, 326 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-505
67 atoms, 67 bonds, 4 residues, 1 model selected
> select #1.2/B:422-463
629 atoms, 631 bonds, 42 residues, 1 model selected
> select #1.2/B:422-465
648 atoms, 650 bonds, 44 residues, 1 model selected
> select #1.2/B:422
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:422-425
81 atoms, 81 bonds, 4 residues, 1 model selected
> ui tool show "Selection Inspector"
> select down
81 atoms, 81 bonds, 4 residues, 1 model selected
> select
> #1.2/B:261-263,278-281,286-289,293-295,299-302,306-310,318-320,335-338,340-343,352-354,358-361,364-366,373-375,379-382,385-387,393-395,400-404,407-409,415-417,420-424,427-429,435-437,441-444,447-449,473-475,485-487,490-492,495-498,510-513,515-519,532-534,537-546,550-554,560-570
2357 atoms, 2347 bonds, 137 residues, 1 model selected
> select #1.2/B:397-398
36 atoms, 36 bonds, 2 residues, 1 model selected
> select #1.2/B:397-443
730 atoms, 733 bonds, 47 residues, 1 model selected
> select #1.2/B:357
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:357-359
52 atoms, 51 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:352
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:352-354
49 atoms, 49 bonds, 3 residues, 1 model selected
> select #1.2/B:262
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #1.2/B:262-266
81 atoms, 83 bonds, 5 residues, 1 model selected
> select #1.2/B:269
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:269-271
50 atoms, 50 bonds, 3 residues, 1 model selected
> select #1.2/B:273
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:273-276
80 atoms, 80 bonds, 4 residues, 1 model selected
> select #1.2/B:277-278
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #1.2/B:277-282
101 atoms, 100 bonds, 6 residues, 1 model selected
> select #1.2/B:284-285
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #1.2/B:284-287
66 atoms, 66 bonds, 4 residues, 1 model selected
> select #1.2/B:290
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:290-293
68 atoms, 67 bonds, 4 residues, 1 model selected
> select #1.2/B:295-296
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #1.2/B:295-297
57 atoms, 56 bonds, 3 residues, 1 model selected
> select #1.2/B:286-287
43 atoms, 43 bonds, 2 residues, 1 model selected
> select #1.2/B:286-291
117 atoms, 117 bonds, 6 residues, 1 model selected
> select #1.2/B:286
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:286-301
285 atoms, 286 bonds, 16 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-345
55 atoms, 56 bonds, 4 residues, 1 model selected
> select #1.2/B:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:302-311
126 atoms, 125 bonds, 10 residues, 1 model selected
> select #1.2/B:313
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:313-320
132 atoms, 132 bonds, 8 residues, 1 model selected
> select #1.2/B:313
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:313-324
193 atoms, 193 bonds, 12 residues, 1 model selected
> select #1.2/B:313
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:313-331
297 atoms, 300 bonds, 19 residues, 1 model selected
> select #1.2/B:313-314
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #1.2/B:313-336
365 atoms, 368 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:336
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:336-341
106 atoms, 105 bonds, 6 residues, 1 model selected
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-349
107 atoms, 109 bonds, 8 residues, 1 model selected
> select #1.2/B:342-343
34 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/B:342-349
107 atoms, 109 bonds, 8 residues, 1 model selected
> select #1.2/B:352
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:352-358
110 atoms, 110 bonds, 7 residues, 1 model selected
> select #1.2/B:351
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:351-360
164 atoms, 164 bonds, 10 residues, 1 model selected
> select #1.2/B:348
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:348-362
220 atoms, 221 bonds, 15 residues, 1 model selected
> select #1.2/B:344-345
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1.2/B:344-356
180 atoms, 182 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:384-385
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1.2/B:384-393
153 atoms, 156 bonds, 10 residues, 1 model selected
> select #1.2/B:359
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:328-359
473 atoms, 476 bonds, 32 residues, 1 model selected
> select #1.2/B:371
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:371-377
104 atoms, 105 bonds, 7 residues, 1 model selected
> select #1.2/B:408-409
35 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:408-415
129 atoms, 129 bonds, 8 residues, 1 model selected
> select #1.2/B:403-404
41 atoms, 40 bonds, 2 residues, 1 model selected
> select #1.2/B:403-411
163 atoms, 163 bonds, 9 residues, 1 model selected
> select #1.2/B:382
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:382-421
626 atoms, 631 bonds, 40 residues, 1 model selected
> select #1.2/B:415
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:415-421
96 atoms, 95 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:454-455
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:454-461
124 atoms, 123 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:493
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:493-501
146 atoms, 146 bonds, 9 residues, 1 model selected
> select #1.2/B:485
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:485-492
134 atoms, 135 bonds, 8 residues, 1 model selected
> select #1.2/B:484
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:484-491
134 atoms, 136 bonds, 8 residues, 1 model selected
> select #1.2/B:482
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:482-486
84 atoms, 87 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:482-483
34 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:482-490
149 atoms, 153 bonds, 9 residues, 1 model selected
> select #1.2/B:521
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:521-528
120 atoms, 120 bonds, 8 residues, 1 model selected
> select #1.2/B:562
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:562-567
104 atoms, 104 bonds, 6 residues, 1 model selected
> select #1.2/B:542
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:542-554
232 atoms, 233 bonds, 13 residues, 1 model selected
> select #1.2/B:542
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:542-581
655 atoms, 660 bonds, 40 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-541
661 atoms, 668 bonds, 40 residues, 1 model selected
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-501
632 atoms, 640 bonds, 40 residues, 1 model selected
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-472
157 atoms, 157 bonds, 11 residues, 1 model selected
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-480
282 atoms, 284 bonds, 19 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:481
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:481-495
250 atoms, 254 bonds, 15 residues, 1 model selected
> select #1.2/B:481-482
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #1.2/B:481-487
121 atoms, 124 bonds, 7 residues, 1 model selected
> select #1.2/B:513
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:513-520
136 atoms, 136 bonds, 8 residues, 1 model selected
> select #1.2/B:514
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1.2/B:514-522
154 atoms, 155 bonds, 9 residues, 1 model selected
> select
> #1.2/B:178-184,186-192,215-225,235-241,245-249,255-257,269-276,463-465,521-526,572-575
996 atoms, 992 bonds, 61 residues, 1 model selected
> select #1.2/B:527-528
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #1.2/B:491-527
603 atoms, 608 bonds, 37 residues, 1 model selected
> select #1.2/B:527-528
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #1.2/B:527-531
70 atoms, 69 bonds, 5 residues, 1 model selected
> select #1.2/B:533
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:533-537
80 atoms, 80 bonds, 5 residues, 1 model selected
> select #1.2/B:530
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:526-530
85 atoms, 84 bonds, 5 residues, 1 model selected
> select #1.2/B:339
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:339-341
54 atoms, 53 bonds, 3 residues, 1 model selected
> select #1.2/B:342
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:342-347
89 atoms, 91 bonds, 6 residues, 1 model selected
> select #1.2/B:343
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:343-353
156 atoms, 158 bonds, 11 residues, 1 model selected
> select #1.2/B:362
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:362-374
186 atoms, 188 bonds, 13 residues, 1 model selected
> select #1.2/B:447-448
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/B:447-459
182 atoms, 181 bonds, 13 residues, 1 model selected
> select #1.2/B:533
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:533-541
167 atoms, 169 bonds, 9 residues, 1 model selected
> select #1.2/B:292
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:292-574
4427 atoms, 4471 bonds, 283 residues, 1 model selected
> select
> #1.2/B:178-184,186-192,215-225,235-241,245-249,255-257,269-276,463-465,521-526,572-575
996 atoms, 992 bonds, 61 residues, 1 model selected
> select #1.2/B:302-303
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1.2/B:302-349
702 atoms, 708 bonds, 48 residues, 1 model selected
> select #1.2/B:344-345
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1.2/B:344-394
770 atoms, 782 bonds, 51 residues, 1 model selected
> select #1.2/B:392-393
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #1.2/B:392-444
826 atoms, 829 bonds, 53 residues, 1 model selected
> select #1.2/B:405-406
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/B:405-413
155 atoms, 155 bonds, 9 residues, 1 model selected
> select #1.2/B:367
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:367-372
80 atoms, 80 bonds, 6 residues, 1 model selected
> select #1.2/B:327
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2/B:327-331
63 atoms, 63 bonds, 5 residues, 1 model selected
> select #1.2/B:329
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:329-336
110 atoms, 109 bonds, 8 residues, 1 model selected
> select #1.2/B:373-374
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/B:365-374
152 atoms, 154 bonds, 10 residues, 1 model selected
> select #1.2/B:372
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:362-372
155 atoms, 157 bonds, 11 residues, 1 model selected
> select #1.2/B:406
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:393-406
233 atoms, 233 bonds, 14 residues, 1 model selected
> select #1.2/B:393-394
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #1.2/B:392-394
39 atoms, 38 bonds, 3 residues, 1 model selected
> select #1.2/B:389
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:389-392
64 atoms, 65 bonds, 4 residues, 1 model selected
> select #1.2/B:391
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:391-393
45 atoms, 44 bonds, 3 residues, 1 model selected
> select #1.2/B:396-397
38 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2/B:396-400
95 atoms, 95 bonds, 5 residues, 1 model selected
> select #1.2/B:364-368
79 atoms, 81 bonds, 5 residues, 1 model selected
> select #1.2/B:364-368
79 atoms, 81 bonds, 5 residues, 1 model selected
> select #1.2/B:405-412
136 atoms, 136 bonds, 8 residues, 1 model selected
> select #1.2/B:405-412
136 atoms, 136 bonds, 8 residues, 1 model selected
> select #1.2/B:445
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1.2/B:445-448
64 atoms, 64 bonds, 4 residues, 1 model selected
> select #1.2/B:447
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:442-447
105 atoms, 105 bonds, 6 residues, 1 model selected
> select #1.2/B:442
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:439-442
53 atoms, 52 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:435
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:432-435
55 atoms, 55 bonds, 4 residues, 1 model selected
> select #1.2/B:430-431
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #1.2/B:428-431
44 atoms, 43 bonds, 4 residues, 1 model selected
> select #1.2/B:388
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:388-393
91 atoms, 92 bonds, 6 residues, 1 model selected
> select #1.2/B:396-397
38 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2/B:396-399
71 atoms, 71 bonds, 4 residues, 1 model selected
> select #1.2/B:400
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:400-402
45 atoms, 44 bonds, 3 residues, 1 model selected
> select #1.2/B:404
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:403-404
41 atoms, 40 bonds, 2 residues, 1 model selected
> select #1.2/B:401-404
62 atoms, 61 bonds, 4 residues, 1 model selected
> select #1.2/B:399-400
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #1.2/B:397-400
71 atoms, 71 bonds, 4 residues, 1 model selected
> select #1.2/B:397-398
36 atoms, 36 bonds, 2 residues, 1 model selected
> select #1.2/B:397-400
71 atoms, 71 bonds, 4 residues, 1 model selected
> select #1.2/B:400-401
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1.2/B:400-402
45 atoms, 44 bonds, 3 residues, 1 model selected
> select #1.2/B:400
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:400-405
108 atoms, 107 bonds, 6 residues, 1 model selected
> select #1.2/B:404-405
44 atoms, 43 bonds, 2 residues, 1 model selected
> select #1.2/B:400-405
108 atoms, 107 bonds, 6 residues, 1 model selected
> select #1.2/B:400-401
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1.2/B:400-405
108 atoms, 107 bonds, 6 residues, 1 model selected
> select #1.2/B:400-401
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1.2/B:400-403
64 atoms, 63 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:357
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:357-362
95 atoms, 95 bonds, 6 residues, 1 model selected
> select #1.2/B:364
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:364-366
52 atoms, 53 bonds, 3 residues, 1 model selected
> select #1.2/B:366
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:366-371
90 atoms, 91 bonds, 6 residues, 1 model selected
> select #1.2/B:372
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:372-374
42 atoms, 41 bonds, 3 residues, 1 model selected
> select #1.2/B:375
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:375-376
34 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:377
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:377-378
26 atoms, 25 bonds, 2 residues, 1 model selected
> select #1.2/B:379
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:379-380
40 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/B:383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:383-384
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1.2/B:385-386
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/B:385-386
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/B:388
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:388-389
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #1.2/B:391
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:391-392
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #1.2/B:394-395
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #1.2/B:394-397
65 atoms, 65 bonds, 4 residues, 1 model selected
> select #1.2/B:398-399
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1.2/B:398-400
57 atoms, 56 bonds, 3 residues, 1 model selected
> select #1.2/B:402
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:402-404
52 atoms, 51 bonds, 3 residues, 1 model selected
> select #1.2/B:407
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:407-408
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #1.2/B:409-410
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2/B:409-410
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2/B:423
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:423-425
57 atoms, 57 bonds, 3 residues, 1 model selected
> select #1.2/B:429
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:429-431
34 atoms, 33 bonds, 3 residues, 1 model selected
> select #1.2/B:433
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:433-436
67 atoms, 67 bonds, 4 residues, 1 model selected
> select #1.2/B:433
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:433-437
83 atoms, 83 bonds, 5 residues, 1 model selected
> select #1.2/B:433
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:433-439
116 atoms, 116 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:433-434
31 atoms, 31 bonds, 2 residues, 1 model selected
> select #1.2/B:433-437
83 atoms, 83 bonds, 5 residues, 1 model selected
> select #1.2/B:440
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:440-442
42 atoms, 41 bonds, 3 residues, 1 model selected
> select #1.2/B:443-444
41 atoms, 40 bonds, 2 residues, 1 model selected
> select #1.2/B:443-447
89 atoms, 89 bonds, 5 residues, 1 model selected
> select #1.2/B:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:449-453
58 atoms, 57 bonds, 5 residues, 1 model selected
> select #1.2/B:455
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:417-455
577 atoms, 579 bonds, 39 residues, 1 model selected
> select #1.2/B:456
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:456-458
38 atoms, 37 bonds, 3 residues, 1 model selected
> select #1.2/B:459
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/B:459-460
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #1.2/B:461
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:461
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:462-463
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #1.2/B:464
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.2/B:464-465
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #1.2/B:467
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:467-468
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #1.2/B:469
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:469-470
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #1.2/B:471
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:471-473
55 atoms, 54 bonds, 3 residues, 1 model selected
> select #1.2/B:473
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:473-476
62 atoms, 62 bonds, 4 residues, 1 model selected
> select #1.2/B:477
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:477-480
63 atoms, 63 bonds, 4 residues, 1 model selected
> select #1.2/B:481
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/B:444-481
572 atoms, 575 bonds, 38 residues, 1 model selected
> select #1.2/B:479
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:479-481
57 atoms, 56 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:482
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/B:482-484
48 atoms, 50 bonds, 3 residues, 1 model selected
> select #1.2/B:485
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/B:485-486
36 atoms, 36 bonds, 2 residues, 1 model selected
> select #1.2/B:489
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:489-491
52 atoms, 51 bonds, 3 residues, 1 model selected
> select #1.2/B:492
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:492-495
60 atoms, 59 bonds, 4 residues, 1 model selected
> select #1.2/B:495
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:495-497
47 atoms, 47 bonds, 3 residues, 1 model selected
> select #1.2/B:499
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:499-500
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1.2/B:502
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2/B:502-504
47 atoms, 46 bonds, 3 residues, 1 model selected
> select #1.2/B:505
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2/B:505-507
53 atoms, 54 bonds, 3 residues, 1 model selected
> select #1.2/B:510-511
25 atoms, 24 bonds, 2 residues, 1 model selected
> select #1.2/B:510-512
44 atoms, 43 bonds, 3 residues, 1 model selected
> select #1.2/B:513
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:513-516
64 atoms, 64 bonds, 4 residues, 1 model selected
> select #1.2/B:519
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:519-520
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1.2/B:517
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.2/B:517-522
101 atoms, 101 bonds, 6 residues, 1 model selected
> select #1.2/B:514
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1.2/B:514-519
110 atoms, 110 bonds, 6 residues, 1 model selected
> select #1.2/B:515
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/B:515-518
74 atoms, 73 bonds, 4 residues, 1 model selected
> select #1.2/B:517-518
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #1.2/B:517-520
72 atoms, 71 bonds, 4 residues, 1 model selected
> select #1.2/B:516-517
41 atoms, 40 bonds, 2 residues, 1 model selected
> select #1.2/B:516-527
200 atoms, 200 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select #1.2/B:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:302-307
64 atoms, 63 bonds, 6 residues, 1 model selected
> select #1.2/B:302
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2/B:302-317
217 atoms, 216 bonds, 16 residues, 1 model selected
> hide sel cartoons
> style sel ball
Changed 217 atom styles
> select #1.2/B:558
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:558-584
426 atoms, 429 bonds, 27 residues, 1 model selected
> select #1.2/B:558-585
440 atoms, 443 bonds, 28 residues, 1 model selected
> select #1.2/B:597
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.2/B:142-597
7041 atoms, 7107 bonds, 456 residues, 1 model selected
> show sel target ab
> select clear
> hide H
> hide atoms
> show atoms
> hide cartoons
> show cartoons
> hide cartoons
> show cartoons
> hide cartoons
> show atoms
> hide atoms
> show atoms
> show cartoons
> hide atoms
> undo
> hide target a
> save /Users/dantebangafoe/Desktop/image1.png supersample 3
> save "/Users/dantebangafoe/Downloads/viewing interaction 2.cxs"
> style ball
Changed 9250 atom styles
> style stick
Changed 9250 atom styles
> style sphere
Changed 9250 atom styles
> style ball
Changed 9250 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> show surfaces
> hide surfaces
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#1.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#1.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> show surfaces
> coulombic
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#1.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#1.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor
9250 atoms, 597 residues, 2 surfaces, atom bfactor range 0 to 0
> hide surfaces
> undo
> interfaces ~solvent
1 buried areas: #1.2/B #1.1/A 1732
> show cartoons
> hide cartoons
> undo
> show atoms
> hide H
> hide atoms
> hide #* target a
> show target ab
> hide atoms
> style stick
Changed 9250 atom styles
> hide (protein|nucleic) target a
> cartoon hide
> show backbone target ab
> undo
> redo
> undo
> show #1/A:27-80 atoms
> show #1/B:195-221 atoms
> show #1/B:337-343 atoms
> show #1/B:360-368 atoms
> show #1/B:382-390 atoms
> show #1/B:404-409 atoms
> show #1/B:424-430 atoms
> show #1/B:443-453 atoms
> show #1/B:487-494 atoms
> show #1/B:508-515 atoms
> show #1/B:529-536 atoms
> show #1/B:576-597 atoms
> hide H
> hide #!1.1 models
> show #!1.1 models
> select add #1.1
1640 atoms, 1649 bonds, 101 residues, 1 model selected
> select subtract #1.1
1 model selected
> select add #1.1
1640 atoms, 1649 bonds, 101 residues, 1 model selected
> color bfactor sel
1640 atoms, 101 residues, 1 surfaces, atom bfactor range 0 to 0
> color sel bynucleotide
> color bfactor sel
1640 atoms, 101 residues, 1 surfaces, atom bfactor range 0 to 0
> select subtract #1.1
1 model selected
> ~hbonds
> hbonds reveal true
398 hydrogen bonds found
> ~hbonds
> undo
> redo
> undo
> hide atoms
> show #1/A:27-80 atoms
> show #1/B:195-221 atoms
> show #1/B:337-343 atoms
> show #1/B:360-368 atoms
> show #1/B:382-390 atoms
> show #1/B:404-409 atoms
> show #1/B:424-430 atoms
> show #1/B:443-453 atoms
> show #1/B:487-494 atoms
> show #1/B:508-515 atoms
> show #1/B:529-536 atoms
> show #1/B:576-597 atoms
> Hide H
Unknown command: Hide H
> hide H
> save "/Users/dantebangafoe/Downloads/view 3.cxs"
> style ball
Changed 9250 atom styles
> findcontacts
Unknown command: findcontacts
> findcontacts 1/A 1/B
Unknown command: findcontacts 1/A 1/B
> contacts #1.1 #1.2
5298 contacts
> ~contacts
> contacts
5298 contacts
> ~contacts
> clashes
48 clashes
> contacts
5298 contacts
> ~contacts
> ~clashes
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> interfaces
1 buried areas: #1.2/B #1.1/A 1732
> crystalcontacts
No unit cell parameters for output_1021_dldesign_0_cycle1_af2pred.pdb A
> viewdockx
No suitable models found for ViewDockX
> ui tool show "Find Cavities"
> color bynucleotide
> coulombic
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#1.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#1.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> mlp
Map values for surface "output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES
surface": minimum -28.77, mean -4.399, maximum 25.13
Map values for surface "output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES
surface": minimum -22.57, mean -2.381, maximum 23.22
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> color bynucleotide
> color bfactor
9250 atoms, 597 residues, 2 surfaces, atom bfactor range 0 to 0
> undo
> overlap
Unknown command: overlap
> contacts
5298 contacts
> color bychain
> undo
> color byhetero
> help help:user/tools/toolbar.html
> color byhetero
> save "/Users/dantebangafoe/Downloads/view 4.cxs"
> open
> /Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
> format pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9262
REMARK PDBinfo-LABEL: 1 64.61408909627788
Ignored bad PDB record found on line 9263
REMARK PDBinfo-LABEL: 2 83.22959617224114
Ignored bad PDB record found on line 9264
REMARK PDBinfo-LABEL: 3 87.68443933186607
Ignored bad PDB record found on line 9265
REMARK PDBinfo-LABEL: 4 82.43727171195131
Ignored bad PDB record found on line 9266
REMARK PDBinfo-LABEL: 5 87.56903352758921
597 messages similar to the above omitted
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb #3
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #!1 models
> contacts
121437 contacts
> hide #3 models
> hide #2 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> ui tool show "Side View"
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> view
> view orient
> view
Drag select of 2 residues
> select clear
Drag select of 307 atoms, 83 residues, 258 bonds
> select clear
> select #1.2/B:207@OE1
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 44 atoms, 12 residues, 37 bonds
> select clear
Drag select of 54 atoms, 15 residues, 41 bonds
> hide
> undo
> select clear
Drag select of 55 atoms, 16 residues, 44 bonds
> hide select
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide select clear
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide select of 55 atoms, 16 residues, 44 bonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select clear
Drag select of 45 atoms, 11 residues, 36 bonds
Drag select of 55 atoms, 18 residues, 43 bonds
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel cartoons
Drag select of 40 atoms, 9 residues, 31 bonds
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 738 atoms, 147 residues, 625 bonds
> select clear
Drag select of 747 atoms, 149 residues, 632 bonds
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
> ~hbonds
> hbonds sel reveal true
388 hydrogen bonds found
> ~hbonds
> select clear
> undo
> select clear
> ~hbonds
> hbonds #!1.1-2 reveal true
1200 hydrogen bonds found
> ~hbonds
> undo
> redo
> undo
> redo
> select clear
> ~hbonds
> select clear
Drag select of 797 atoms, 1 residues, 773 bonds
> hide sel atoms
> select clear
> hide #!1.1-2 atoms
Drag select of 120 residues
> select clear
Drag select of 40 residues
> select clear
Drag select of 43 residues
> select clear
Drag select of 31 residues
> select clear
Drag select of 74 residues
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> ~hbonds
> style sel ball
Changed 1144 atom styles
> style sel stick
Changed 1144 atom styles
> style sel sphere
Changed 1144 atom styles
> style sel ball
Changed 1144 atom styles
> style sel stick
Changed 1144 atom styles
> style sel ball
Changed 1144 atom styles
> color sel byhetero
> color sel bychain
> color sel byhetero
> color sel bypolymer
> color sel byhetero
> coulombic sel
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#1.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#1.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> coulombic sel
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#1.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#1.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> style sel stick
Changed 1144 atom styles
> style sel ball
Changed 1144 atom styles
> color bfactor sel
1144 atoms, 74 residues, 2 surfaces, atom bfactor range 0 to 0
> color bfactor sel
1144 atoms, 74 residues, 2 surfaces, atom bfactor range 0 to 0
> ~colordef bfactor sel
> color delete bfactor sel
Expected fewer arguments
> ~colordef
> color delete
Missing or invalid "name" argument: Expected 'custom' or a text string
> ~colordef bfactor
Unknown color 'bfactor'
> undo
> color sel byhetero
> color sel bypolymer
> color sel bynucleotide
> hide sel surfaces
> color sel byhetero
> select clear
Drag select of 768 atoms, 149 residues, 713 bonds
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> ~hbonds
> style sel stick
Changed 2347 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 2347 atom styles
> style sel stick
Changed 2347 atom styles
> style sel ball
Changed 2347 atom styles
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> hide H
> save "/Users/dantebangafoe/Downloads/view 5.cxs"
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> show #2 models
> show #3 models
> hide #3 models
> show #3 models
> select add #2
121437 pseudobonds, 1 model selected
> select add #3
9250 atoms, 9333 bonds, 121437 pseudobonds, 597 residues, 2 models selected
> close #2
> select subtract #3
Nothing selected
> hide #3 models
> show #3 models
> close #3
> open
> /Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9277
REMARK PDBinfo-LABEL: 1 77.90870171732783
Ignored bad PDB record found on line 9278
REMARK PDBinfo-LABEL: 2 78.58208652123538
Ignored bad PDB record found on line 9279
REMARK PDBinfo-LABEL: 3 83.79474718719153
Ignored bad PDB record found on line 9280
REMARK PDBinfo-LABEL: 4 84.48686134704904
Ignored bad PDB record found on line 9281
REMARK PDBinfo-LABEL: 5 84.17748292791156
589 messages similar to the above omitted
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> split
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Split output_1125_dldesign_0_cycle1_af2pred.pdb (#2) into 2 models
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb B #2.2
---
Chain | Description
B | No description available
> color #2.1 #ec7a99ff
> select clear
Drag select of 243 residues
> hide sel cartoons
Drag select of 81 residues
> select clear
Drag select of 95 residues
> hide sel atoms
> hide sel cartoons
Drag select of 26 residues
> hide sel cartoons
Drag select of 13 residues
> hide sel cartoons
Drag select of 23 residues
> hide sel cartoons
Drag select of 22 residues
> hide sel cartoons
> select clear
Drag select of 6 residues
> hide sel cartoons
Drag select of 11 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 7 residues
> select clear
Drag select of 14 residues
> hide sel cartoons
Drag select of 22 residues
> select clear
Drag select of 3 residues
> select clear
Drag select of 21 residues
> select clear
Drag select of 5 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel atoms
> hide sel cartoons
Drag select of 6 residues
> hide sel cartoons
Drag select of 6 residues
> hide sel atoms
> hide sel cartoons
Drag select of 114 residues
> show sel atoms
> hide sel cartoons
> show sel cartoons
> style sel ball
Changed 1864 atom styles
> ~hbonds
> hide H
> color sel byhetero
> select clear
Drag select of 80 atoms, 31 residues, 65 bonds
> select clear
Drag select of 45 atoms, 18 residues, 41 bonds
> select clear
> interfaces #2.1-2 & ~solvent
1 buried areas: #2.2/B #2.1/A 1631
> color #2.1-2 bynucleotide
> show residues
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
18515 atoms, 18679 bonds, 1186 residues, 4 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> color sel & #2.1-2 bynucleotide
> select clear
> coulombic #2.1-2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> select #2.2/B:500@OH
1 atom, 1 residue, 1 model selected
> select clear
> show (#2 & sidechain) target ab
> undo
Destroying pre-existing alignment with identifier 1.1/A
Alignment identifier is 1.1/A
Alignment identifier is 1
Alignment identifier is 2.1/A
> label #2 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> select clear
Drag select of 581 atoms, 114 residues, 492 bonds
Drag select of 582 atoms, 114 residues, 492 bonds
> select clear
Drag select of 583 atoms, 114 residues, 493 bonds
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select clear
> select #2.1/A:9@CD1
1 atom, 1 residue, 1 model selected
> select #2.1/A:9@CE2
1 atom, 1 residue, 1 model selected
> select clear
> color byattribute charge
18515 atoms, 1186 residues, 4 surfaces, atom charge range -0.941 to 0.885
> select clear
Drag select of 583 atoms, 114 residues, 493 bonds
> ~label (#!2.1-2 & sel) residues
> label (#!2.1-2 & sel) atoms attribute name
> ~label (#!2.1-2 & sel) atoms
> label (#!2.1-2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> coulombic sel
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color sel byhetero
> color sel bychain
> color sel byhetero
> undo
> mlp sel
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES
surface": minimum -22.53, mean -1.52, maximum 23.94
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES
surface": minimum -26.6, mean -4.285, maximum 27.8
To also show corresponding color key, enter the above mlp command and add key
true
> help help:user/tools/toolbar.html
> help help:quickstart
> hide sel surfaces
> mlp sel
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES
surface": minimum -22.53, mean -1.52, maximum 23.94
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES
surface": minimum -26.6, mean -4.285, maximum 27.8
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
Drag select of 1280 atoms, 114 residues, 1190 bonds
> ~label (#!2.1-2 & sel) residues
> select clear
> hide H
> select #2.1/A:28
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2.1/A:28
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
Drag select of 583 atoms, 114 residues, 493 bonds
> hide sel cartoons
> select clear
Drag select of 931 atoms, 937 bonds
> show sel cartoons
> select clear
Drag select of 565 atoms, 111 residues, 476 bonds
> color sel byhetero
> color sel bychain
> select clear
> select #2.1/A:29@OG
1 atom, 1 residue, 1 model selected
> select #2.1/A:25@CE
1 atom, 1 residue, 1 model selected
> select #2.1/A:29@CB
1 atom, 1 residue, 1 model selected
> select #2.1/A:29@OG
1 atom, 1 residue, 1 model selected
> select #2.1/A:29@CB
1 atom, 1 residue, 1 model selected
> select #2.1/A:25@CE
1 atom, 1 residue, 1 model selected
> select #2.1/A:25@CE
1 atom, 1 residue, 1 model selected
> select #2.1/A:32@NZ
1 atom, 1 residue, 1 model selected
> select #2.1/A:32@CE
1 atom, 1 residue, 1 model selected
> select #2.1/A:17@CD1
1 atom, 1 residue, 1 model selected
> select #2.1/A:26@CG
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #2.1/A:26@OD1
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #2.1/A:29@CB
1 atom, 1 residue, 1 model selected
> select #2.1/A:29@OG
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:29@CB
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:25@CE
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:9@CZ
1 atom, 1 residue, 1 model selected
> select #2.1/A:9@CE2
1 atom, 1 residue, 1 model selected
> select #2.1/A:9@CE1
1 atom, 1 residue, 1 model selected
> select #2.1/A:9@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:9@CE2
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label (#!2.1 & sel) atoms attribute element
> ~label (#!2.1 & sel) atoms
> select #2.1/A:13@CD
1 atom, 1 residue, 1 model selected
> select #2.1/A:13@CZ
1 atom, 1 residue, 1 model selected
> select #2.1/A:13@NH2
1 atom, 1 residue, 1 model selected
> select #2.1/A:13@NH1
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:13@CZ
1 atom, 1 residue, 1 model selected
> select #2.1/A:13@NH2
1 atom, 1 residue, 1 model selected
> select #2.1/A:13@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:16@CB
1 atom, 1 residue, 1 model selected
> select #2.1/A:16@CG
1 atom, 1 residue, 1 model selected
> select #2.1/A:16@CD
1 atom, 1 residue, 1 model selected
> select clear
> select #2.1/A:16@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #2.1/A:16@CD
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:20@CD
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:24@CD
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:39@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:43@CD
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:6@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:2@CG
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:13@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:16
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2.1/A:24@CD
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:40@CG1
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:44@CG
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.1/A:6@CZ
1 atom, 1 residue, 1 model selected
> select clear
> select #2.1/A:12@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> select #2.2/B:356@CB
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:377@CB
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:399@CG
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:419@CG1
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:439@CE
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:482@CG2
1 atom, 1 residue, 1 model selected
> select #2.2/B:482@CD1
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:503@CG
1 atom, 1 residue, 1 model selected
> select #2.2/B:503@CG
1 atom, 1 residue, 1 model selected
> select #2.2/B:503@ND2
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:525@CG
1 atom, 1 residue, 1 model selected
> select #2.2/B:525@CZ
1 atom, 1 residue, 1 model selected
> select #2.2/B:525@CB
1 atom, 1 residue, 1 model selected
> select #2.2/B:525@CB
1 atom, 1 residue, 1 model selected
> select #2.2/B:525@CG
1 atom, 1 residue, 1 model selected
> select #2.2/B:525@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:527@CE
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:505@OG
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:484@CB
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:441@CB
1 atom, 1 residue, 1 model selected
> select #2.2/B:441@SG
1 atom, 1 residue, 1 model selected
> select #2.2/B:441@CB
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:421@CB
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:401@CD
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:379@CG
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:333@NH1
1 atom, 1 residue, 1 model selected
> select #2.2/B:333@CZ
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2.2/B:358@CG
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> select #2.1/A:32@CE
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> select #2.1/A:36@CB
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> select #2.1/A:17@CD1
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> select #2.1/A:5@CE
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> show #!2.2 models
> select #2.1/A:28@CD
1 atom, 1 residue, 1 model selected
> label (#!2.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #2.2/B:397@NZ
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> save "/Users/dantebangafoe/Downloads/1125 view 1.cxs"
> coulombic sel
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> mlp #!2.1-2
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES
surface": minimum -22.53, mean -1.52, maximum 23.94
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES
surface": minimum -26.6, mean -4.285, maximum 27.8
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1-2 surfaces
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> select #2.2/B:374@NH2
1 atom, 1 residue, 1 model selected
> label (#!2.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> show #!2.1-2 surfaces
> hide #!2.1-2 surfaces
> show #!2.1-2 surfaces
> hide #!2.1-2 surfaces
> show #!2.1-2 surfaces
> hide #!2.1-2 surfaces
> select #2.2/B:219
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2.2/B:219
24 atoms, 23 bonds, 1 residue, 1 model selected
> show #2.2/B:219
> show #1.2/A:72
> select #1.2/A:72
Nothing selected
> show #1.1/A:72
> show #2.1/A:72
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> save "/Users/dantebangafoe/Downloads/1125 view 2.cxs"
> open "/Users/dantebangafoe/Downloads/viewing 1021_1.cxs"
opened ChimeraX session
> open "/Users/dantebangafoe/Downloads/viewing 1021_1.cxs"
opened ChimeraX session
> open "/Users/dantebangafoe/Downloads/1125 view 1.cxs" format session
opened ChimeraX session
> open "/Users/dantebangafoe/Downloads/viewing 1021_1.cxs" format session
opened ChimeraX session
> set bgColor black
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> open "/Users/dantebangafoe/Downloads/viewing 1021_1.cxs" format session
opened ChimeraX session
> open "/Users/dantebangafoe/Downloads/viewing interaction 2.cxs" format
> session
opened ChimeraX session
> open "/Users/dantebangafoe/Downloads/viewing 1021_1.cxs" format session
opened ChimeraX session
> color #1.1 #d694d9ff
> undo
> open "/Users/dantebangafoe/Downloads/viewing interaction 2.cxs" format
> session
opened ChimeraX session
> color #1.1 #e47fe2ff
> color #1.2 #e8c89cff
> color #1.2 #f8d5a6ff
> open
> /Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
> format pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9277
REMARK PDBinfo-LABEL: 1 77.90870171732783
Ignored bad PDB record found on line 9278
REMARK PDBinfo-LABEL: 2 78.58208652123538
Ignored bad PDB record found on line 9279
REMARK PDBinfo-LABEL: 3 83.79474718719153
Ignored bad PDB record found on line 9280
REMARK PDBinfo-LABEL: 4 84.48686134704904
Ignored bad PDB record found on line 9281
REMARK PDBinfo-LABEL: 5 84.17748292791156
589 messages similar to the above omitted
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #!1 models
> hide #!1.1 models
> hide #1.2 models
> open "/Users/dantebangafoe/Downloads/view 5.cxs" format session
opened ChimeraX session
> open
> /Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
> format pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9277
REMARK PDBinfo-LABEL: 1 77.90870171732783
Ignored bad PDB record found on line 9278
REMARK PDBinfo-LABEL: 2 78.58208652123538
Ignored bad PDB record found on line 9279
REMARK PDBinfo-LABEL: 3 83.79474718719153
Ignored bad PDB record found on line 9280
REMARK PDBinfo-LABEL: 4 84.48686134704904
Ignored bad PDB record found on line 9281
REMARK PDBinfo-LABEL: 5 84.17748292791156
589 messages similar to the above omitted
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb #4
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open
> /Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
> format pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9277
REMARK PDBinfo-LABEL: 1 77.90870171732783
Ignored bad PDB record found on line 9278
REMARK PDBinfo-LABEL: 2 78.58208652123538
Ignored bad PDB record found on line 9279
REMARK PDBinfo-LABEL: 3 83.79474718719153
Ignored bad PDB record found on line 9280
REMARK PDBinfo-LABEL: 4 84.48686134704904
Ignored bad PDB record found on line 9281
REMARK PDBinfo-LABEL: 5 84.17748292791156
589 messages similar to the above omitted
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #!1 models
> hide #!1.2 models
> hide #!1.1 models
> hide #5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> split
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Split output_1021_dldesign_0_cycle1_af2pred.pdb (#3) into 2 models
Split output_1125_dldesign_0_cycle1_af2pred.pdb (#4) into 2 models
Split output_1125_dldesign_0_cycle1_af2pred.pdb (#5) into 2 models
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1
---
Chain | Description
A | No description available
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2
---
Chain | Description
B | No description available
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb B #5.2
---
Chain | Description
B | No description available
> hide #!4 models
> hide #4.1 models
> hide #4.2 models
> hide #!5 models
> show #5.1 models
> show #5.2 models
> hide #5.1 models
> show #5.1 models
> color #5.1 #bfd0efff
> color #5.1 #c2d8efff
> color #5.1 #dc73efff
> color #5.1 #ef84e5ff
> color #5.1 #ef83e4ff
> color #5.2 #efc78eff
> color #5.2 #efc98cff
> hide #!5 models
> hide #5.1 models
> hide #5.2 models
> close #5.1
> hide #!3 models
> close #3
> close
> open "/Users/dantebangafoe/Downloads/1125 view 1.cxs" format session
opened ChimeraX session
> color #2.1 #ed82e3ff
> color #2.2 #c9a876ff
Drag select of 577 atoms, 114 residues, 488 bonds
> color sel byhetero
> select clear
> ui tool show "Side View"
> view
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting shadows true
> graphics silhouettes true
> lighting shadows false
> graphics silhouettes false
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> coulombic #!2.1-2
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#2.1.1: minimum, -12.91, mean 1.29, maximum 14.05
Coulombic values for output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#2.2.1: minimum, -16.09, mean 1.06, maximum 29.44
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.1-2 surfaces
> mlp #!2.1-2
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb B_B SES
surface": minimum -26.6, mean -4.285, maximum 27.8
Map values for surface "output_1125_dldesign_0_cycle1_af2pred.pdb A_A SES
surface": minimum -22.53, mean -1.52, maximum 23.94
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!2.1-2 surfaces
> ui mousemode right distance
> select #2.1/A:32@CG
1 atom, 1 residue, 1 model selected
> select #2.2/B:401@CB
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right distance
> ui mousemode right "tape measure"
> ui mousemode right select
> ui mousemode right distance
> ui mousemode right label
> ui mousemode right distance
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> ui mousemode right distance
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> ui mousemode right distance
> select add #2.2/B:380@SG
1 atom, 1 residue, 1 model selected
> select add #2.2/B:402@NH1
2 atoms, 2 residues, 2 models selected
> ui mousemode right distance
> select clear
> select add #2.1/A:32@CG
1 atom, 1 residue, 1 model selected
> select add #2.2/B:401@OE1
2 atoms, 2 residues, 3 models selected
> ui mousemode right distance
> select clear
> ui mousemode right distance
> select add #2.1/A:32@CG
1 atom, 1 residue, 1 model selected
> select add #2.2/B:401@OE1
2 atoms, 2 residues, 3 models selected
> split
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb B, has only one piece
> distance
Missing or invalid "objects" argument: empty atom specifier
> ui mousemode right "tape measure"
> ui mousemode right distance
> ui windowfill toggle
> ui mousemode right distance
> distance #2.1/A:32@CG #2.2/B:401@OE1
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #2.1/A LYS 32 CG
and output_1125_dldesign_0_cycle1_af2pred.pdb B #2.2/B GLU 401 OE1: 6.187Å
> set bgColor black
> set bgColor transparent
> select clear
> ui mousemode right distance
> distance #2.1/A:28@OE2 #2.2/B:333@NH2
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #2.1/A GLU 28 OE2
and output_1125_dldesign_0_cycle1_af2pred.pdb B #2.2/B ARG 333 NH2: 2.724Å
> ui mousemode right distance
> distance #2.1/A:20@OE2 #2.2/B:397@NZ
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #2.1/A GLU 20 OE2
and output_1125_dldesign_0_cycle1_af2pred.pdb B #2.2/B LYS 397 NZ: 2.317Å
> ui mousemode right distance
> distance #2.1/A:20@CB #2.2/B:397@NZ
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #2.1/A GLU 20 CB
and output_1125_dldesign_0_cycle1_af2pred.pdb B #2.2/B LYS 397 NZ: 4.145Å
> distance #2.2/B:397@NZ #2.1/A:20@CB
Distance already exists; modify distance properties with 'distance style'
> ui mousemode right distance
> distance #2.1/A:20@CB #2.2/B:397@NZ
Distance already exists; modify distance properties with 'distance style'
> ~distance #2.1/A:20@CB #2.2/B:397@NZ
Drag select of 3 atoms, 3 bonds
> ui mousemode right swapaa
> style sel stick
Changed 3 atom styles
> style sel ball
Changed 3 atom styles
> style sel stick
Changed 3 atom styles
> style sel ball
Changed 3 atom styles
> select clear
> show B #2.2/B GLU 586
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #!1 models
> hide #!1 models
> swapaa mousemode #2.2/B:353 HIS
> select #2.2/B:353@NE2
1 atom, 1 residue, 1 model selected
> undo
Drag select of 8 atoms, 1 residues, 8 bonds
> style sel ball
Changed 30 atom styles
> ~hbonds
> color sel byhetero
> ~hbonds
Drag select of 44 atoms, 39 bonds, 9 residues
> ~hbonds
> hbonds sel reveal true
23 hydrogen bonds found
> ~hbonds
> color sel byhetero
> undo
> redo
> select clear
Drag select of 8 atoms, 4 bonds
Drag select of 35 atoms, 3 residues, 32 bonds
> select clear
Drag select of 19 atoms, 2 residues, 15 bonds
> select clear
> select #2.2/B:293@C
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
Drag select of 6 atoms, 5 bonds
> hide sel atoms
Drag select of 5 atoms, 4 bonds
> select clear
Drag select of 8 atoms, 6 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select clear
> hide #!2.1-2 atoms
> undo
> select clear
Drag select of 1 atoms
> hide sel atoms
> select clear
> show #!2.1-2 atoms
> undo
> save "/Users/dantebangafoe/Downloads/1125 view 3.cxs"
> show #!2.1-2 atoms
> ~hbonds
> color #!2.1-2 byhetero
> ~hbonds
> hide #!2.1-2 surfaces
> hide #!2.1-2 cartoons
> show #!2.1-2 cartoons
> undo
> show #!2.1-2 cartoons
> undo
> hide #!2 models
> show #!2 models
> hide #!2 models
> open
> /Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1125_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9277
REMARK PDBinfo-LABEL: 1 77.90870171732783
Ignored bad PDB record found on line 9278
REMARK PDBinfo-LABEL: 2 78.58208652123538
Ignored bad PDB record found on line 9279
REMARK PDBinfo-LABEL: 3 83.79474718719153
Ignored bad PDB record found on line 9280
REMARK PDBinfo-LABEL: 4 84.48686134704904
Ignored bad PDB record found on line 9281
REMARK PDBinfo-LABEL: 5 84.17748292791156
589 messages similar to the above omitted
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb #4
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> split
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Split output_1125_dldesign_0_cycle1_af2pred.pdb (#4) into 2 models
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1
---
Chain | Description
A | No description available
Chain information for output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2
---
Chain | Description
B | No description available
> color #4.1 #ec8a9fff
> color #4.2 #ecb37eff
> color #4.2 #ecb57bff
Drag select of 202 residues
> select clear
Drag select of 149 residues
> hide
> hide sel cartoons
Drag select of 25 residues
> hide sel cartoons
Drag select of 156 residues
> select clear
> undo
> redo
> select #4.2/B:586
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel ball
Changed 15 atom styles
> style sel ball
Changed 15 atom styles
> style sel ball
Changed 15 atom styles
> style sel ball
Changed 15 atom styles
> style sel ball
Changed 15 atom styles
> show sel atoms
> style sel stick
Changed 15 atom styles
> style sel ball
Changed 15 atom styles
> color sel byhetero
> ~hbonds
> hide sel cartoons
> show sel cartoons
> color sel bychain
> color sel byhetero
> hbonds sel reveal true
3 hydrogen bonds found
> ~hbonds
> select clear
> select #4.2/B:586@CA
1 atom, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #4.1/A:5
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 22 atom styles
> color sel byhetero
> ~hbonds
> color sel bychain
> color sel byhetero
> color bfactor sel
22 atoms, 1 residues, atom bfactor range 0 to 0
> color sel byhetero
> color sel bychain
> color sel byhetero
> style sel ball
Changed 22 atom styles
> style sel sphere
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> style sel ball
Changed 22 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> ~hbonds
> color sel byhetero
> color sel bypolymer
> rainbow sel
> color bfactor sel
22 atoms, 1 residues, atom bfactor range 0 to 0
> color sel byhetero
> color sel bychain
> color sel byhetero
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> color sel bynucleotide
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> ui mousemode right distance
> distance #4.1/A:5@CE #4.2/B:586@OE2
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1/A LYS 5 CE
and output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2/B GLU 586 OE2: 5.469Å
> select #4.1/A:8
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4.1/A:12
48 atoms, 46 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 48 atom styles
> color sel byhetero
> ~hbonds
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> ui mousemode right distance
> distance #4.1/A:12@CZ #4.2/B:586@CG
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1/A ARG 12 CZ
and output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2/B GLU 586 CG: 2.972Å
> ui mousemode right distance
> distance #4.1/A:8@CD #4.2/B:586@CG
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1/A ARG 8 CD
and output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2/B GLU 586 CG: 5.593Å
> select #4.1/A:24
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 15 atom styles
> ~hbonds
> color sel bychain
> color sel byhetero
> ~hbonds
> hide H
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #4.2/B:374
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 24 atom styles
> label sel text "{0.name} {0.number}{0.insertion_code}"
> hide H
> ui mousemode right distance
> distance #4.1/A:24@CD #4.2/B:374@CZ
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1/A GLU 24 CD
and output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2/B ARG 374 CZ: 2.522Å
> select #4.1/A:72
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 15 atom styles
> hide H
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #4.2/B:220
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 17 atom styles
> color sel byhetero
> hide H
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #4.2/B:219
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 24 atom styles
> color sel byhetero
> hide H
> label sel text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right distance
> distance #4.1/A:72@CD #4.2/B:219@NH2
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1/A GLU 72 CD
and output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2/B ARG 219 NH2: 6.967Å
> ~distance #4.1/A:72@CD #4.2/B:219@NH2
> ui mousemode right distance
> distance #4.2/B:219@NH1 #4.1/A:72@CD
Distance between output_1125_dldesign_0_cycle1_af2pred.pdb B #4.2/B ARG 219
NH1 and output_1125_dldesign_0_cycle1_af2pred.pdb A #4.1/A GLU 72 CD: 6.349Å
> hide #!4 models
> show #!2 models
> hide #!2 models
> hide #!2.1 models
> show #!2.1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3.1 models
> hide #!3 models
> hide #!2.2 models
> hide #!2.1 models
> hide #!2 models
> show #!4 models
> show #!3 models
> show #3.1 models
> save "/Users/dantebangafoe/Downloads/1125 view4.cxs"
> hide #!3 models
> hide #3.1 models
> hide #!4 models
> hide #!4.1 models
> hide #!4.2 models
> show #!2.1 models
> show #!2.2 models
Drag select of 114 residues
> show sel atoms
> hide H
> style sel ball
Changed 1865 atom styles
> show #!3 models
> show #3.1 models
> color sel byhetero
> select clear
Alignment identifier is 1.1/A
Alignment identifier is 1
Alignment identifier is 2
> select #2.1/A:1 #4.1/A:1
36 atoms, 34 bonds, 2 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A:48-93 #4.1/A:48-93
1670 atoms, 1676 bonds, 92 residues, 2 models selected
2 [ID: 2] region 2 chains [48-93] RMSD: 0.000
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #2.1/A:92-93 #4.1/A:92-93
76 atoms, 74 bonds, 4 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A:41-93 #4.1/A:41-93
1906 atoms, 1914 bonds, 106 residues, 2 models selected
2 [ID: 2] region 2 chains [41-93] RMSD: 0.000
> select #2.1/A:1 #4.1/A:1
36 atoms, 34 bonds, 2 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #1.2/B:597 #2.2/B:589 #4.2/B:589
39 atoms, 36 bonds, 3 residues, 3 models selected
> select #1.2/B:582-597 #2.2/B:574-589 #4.2/B:574-589
654 atoms, 654 bonds, 48 residues, 3 models selected
1 [ID: 1] region 3 chains [481-496] RMSD: 1.941
> select #1.2/B:597 #2.2/B:589 #4.2/B:589
39 atoms, 36 bonds, 3 residues, 3 models selected
> select #1.2/B:342-597 #2.2/B:334-589 #4.2/B:334-589
12010 atoms, 12136 bonds, 768 residues, 3 models selected
1 [ID: 1] region 3 chains [241-496] RMSD: 2.113
> select #2.1/A:1 #4.1/A:1
36 atoms, 34 bonds, 2 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A:81-93 #4.1/A:81-93
486 atoms, 488 bonds, 26 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
2 [ID: 2] region 2 chains [1-93] RMSD: 0.000
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #2.1/A:93 #4.1/A:93
38 atoms, 36 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [93] RMSD: 0.000
> select add #2.1
1674 atoms, 1680 bonds, 94 residues, 4 models selected
> select subtract #2.1
19 atoms, 18 bonds, 1 residue, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> hide #!2 models
> hide #!2.2 models
> hide #!3 models
> hide #3.1 models
> select add #4.1
1655 atoms, 1662 bonds, 93 residues, 2 models selected
> select add #4
9265 atoms, 9346 bonds, 5 pseudobonds, 589 residues, 6 models selected
> select subtract #4.1
7610 atoms, 7684 bonds, 496 residues, 3 models selected
> select add #4
9265 atoms, 9346 bonds, 5 pseudobonds, 589 residues, 6 models selected
> select subtract #4
Nothing selected
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1 models
> open
> /Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
Summary of feedback from opening
/Users/dantebangafoe/Downloads/output_1021_dldesign_0_cycle1_af2pred.pdb
---
warnings | Ignored bad PDB record found on line 9262
REMARK PDBinfo-LABEL: 1 64.61408909627788
Ignored bad PDB record found on line 9263
REMARK PDBinfo-LABEL: 2 83.22959617224114
Ignored bad PDB record found on line 9264
REMARK PDBinfo-LABEL: 3 87.68443933186607
Ignored bad PDB record found on line 9265
REMARK PDBinfo-LABEL: 4 82.43727171195131
Ignored bad PDB record found on line 9266
REMARK PDBinfo-LABEL: 5 87.56903352758921
597 messages similar to the above omitted
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> color #5 #efb583ff
> color #5 #efe2d7ff
> color #5 #90d8efff
> split
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1021_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb A, has only one piece
Did not split output_1125_dldesign_0_cycle1_af2pred.pdb B, has only one piece
Split output_1021_dldesign_0_cycle1_af2pred.pdb (#5) into 2 models
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2
---
Chain | Description
B | No description available
> color #5.1 #f0906aff
> color #5.1 #f09164ff
Drag select of 153 residues
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
Drag select of 16 residues
> select clear
Drag select of 9 residues
> hide sel cartoons
Drag select of 20 residues
> select clear
Drag select of 15 residues
> hide sel cartoons
Drag select of 13 residues
> hide sel surfaces
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 5 residues
> hide sel cartoons
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#5.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> color #5.1#!5.2 bychain
> undo
> coulombic #5.1#!5.2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#5.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#5.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5.1-2 surfaces
Drag select of 236 residues
> select clear
> style #!5.1-2 ball
Changed 9250 atom styles
Drag select of 396 residues
> style sel ball
Changed 6258 atom styles
> style sel ball
Changed 6258 atom styles
> style sel stick
Changed 6258 atom styles
> style sel ball
Changed 6258 atom styles
> color sel byhetero
> show sel atoms
> style sel ball
Changed 6258 atom styles
> ~hbonds
> hide H
> color sel byhetero
> style sel stick
Changed 6258 atom styles
> style sel ball
Changed 6258 atom styles
> style sel stick
Changed 6258 atom styles
> style sel ball
Changed 6258 atom styles
> style sel stick
Changed 6258 atom styles
> select clear
Drag select of 173 atoms, 45 residues, 152 bonds
> select clear
Drag select of 115 atoms, 29 residues, 101 bonds
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
Drag select of 28 atoms, 7 residues, 26 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 331 atoms, 73 residues, 273 bonds
> select clear
Drag select of 41 atoms, 7 residues, 32 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 160 atoms, 38 residues, 131 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 29 atoms, 10 residues, 26 bonds
> select clear
Drag select of 113 atoms, 31 residues, 99 bonds
> select clear
Drag select of 1477 atoms, 303 residues, 1233 bonds
> label (#!5.1-2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
Drag select of 1491 atoms, 303 residues, 1243 bonds
> ~label (#!5.1-2 & sel) residues
> select clear
> hide #!5.2 models
Drag select of 507 atoms, 101 residues, 418 bonds
> label (#!5.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> show #!5.2 models
Drag select of 56 atoms, 12 residues, 50 bonds
> hide sel cartoons
> hide sel atoms
> undo
> hide #!5.1 models
> select clear
Drag select of 321 atoms, 80 residues, 266 bonds
Drag select of 101 atoms, 29 residues, 84 bonds
> select clear
Drag select of 255 atoms, 74 residues, 209 bonds
> select clear
Drag select of 970 atoms, 201 residues, 815 bonds
> label (#!5.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
Drag select of 86 atoms, 24 residues, 67 bonds
> select clear
> show #!5.1 models
> coulombic #!5.1-2
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#5.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#5.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5.1-2 surfaces
> hide #!5.1 models
> ui tool show "Side View"
Drag select of 26 atoms, 7 residues, 21 bonds
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
Drag select of 18 atoms, 19 residues, 13 bonds
> select clear
Drag select of 38 atoms, 6 residues, 34 bonds
> hide sel cartoons
> hide sel atoms
> select clear
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> ~label sel residues
> select clear
Drag select of 1 bonds
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
Drag select of 9 atoms, 2 bonds
Drag select of 6 atoms, 4 bonds
> select clear
Drag select of 13 atoms, 3 residues, 8 bonds
> select clear
Drag select of 27 atoms, 7 residues, 17 bonds
> select clear
Drag select of 13 atoms, 3 residues, 6 bonds
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
Drag select of 886 atoms, 180 residues, 745 bonds
> ~label (#!5.2 & sel) residues
> select clear
Drag select of 879 atoms, 180 residues, 739 bonds
> hide #* target a
> show (#!5.2 & sel) target ab
> undo
> redo
> select clear
> hide H
Drag select of 883 atoms, 180 residues, 742 bonds
> select clear
Drag select of 161 atoms, 41 residues, 128 bonds
> select clear
> select #5.2/B:364
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/B:385
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #5.2/B:365
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #5.2/B:386
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #5.2/B:365
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #5.2/B:386
40 atoms, 40 bonds, 2 residues, 2 models selected
> select add #5.2/B:408
60 atoms, 60 bonds, 3 residues, 2 models selected
> select add #5.2/B:428
70 atoms, 69 bonds, 4 residues, 2 models selected
> select add #5.2/B:448
86 atoms, 84 bonds, 5 residues, 2 models selected
> select add #5.2/B:491
105 atoms, 102 bonds, 6 residues, 2 models selected
> select add #5.2/B:513
116 atoms, 112 bonds, 7 residues, 2 models selected
> select add #5.2/B:533
136 atoms, 132 bonds, 8 residues, 2 models selected
> select add #5.2/B:387@CD2
137 atoms, 133 bonds, 9 residues, 2 models selected
> select add #5.2/B:366@CD2
138 atoms, 133 bonds, 10 residues, 2 models selected
> select add #5.2/B:343@CB
139 atoms, 133 bonds, 11 residues, 2 models selected
> select add #5.2/B:405@CE
140 atoms, 140 bonds, 12 residues, 2 models selected
> select add #5.2/B:594@CA
141 atoms, 142 bonds, 13 residues, 2 models selected
> select add #5.2/B:597@CG
142 atoms, 143 bonds, 14 residues, 2 models selected
> select add #5.2/B:585@CB
143 atoms, 143 bonds, 15 residues, 2 models selected
> select add #5.2/B:588@CD
144 atoms, 143 bonds, 16 residues, 2 models selected
> select add #5.2/B:578@CG
145 atoms, 143 bonds, 17 residues, 2 models selected
> select add #5.2/B:530@CG
146 atoms, 143 bonds, 18 residues, 2 models selected
Drag select of 2 atoms, 4 residues, 1 bonds
> select add #5.2/B:216
226 atoms, 158 bonds, 23 residues, 2 models selected
> select add #5.2/B:384
237 atoms, 172 bonds, 24 residues, 2 models selected
> select add #5.2/B:363
253 atoms, 187 bonds, 25 residues, 2 models selected
> select add #5.2/B:304@OD1
254 atoms, 188 bonds, 26 residues, 2 models selected
> select add #5.2/B:260@CA
255 atoms, 190 bonds, 27 residues, 2 models selected
> label (#!5.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> color #5.2 #f08fa1ff
> color #5.2 #c47583ff
> color #5.2 #c48f5dff
> color #5.2 #c49061ff
> select add #5.2/B:337
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #5.2/B:340
35 atoms, 33 bonds, 2 residues, 2 models selected
> select subtract #5.2/B:340
19 atoms, 18 bonds, 1 residue, 2 models selected
> select add #5.2/B:361@CA
20 atoms, 18 bonds, 2 residues, 2 models selected
> select add #5.2/B:381
36 atoms, 33 bonds, 3 residues, 2 models selected
> select clear
> select #5.2/B:409
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/B:429
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/B:449
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/B:492
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/B:513
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/B:515
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/B:450
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5.2/B:409
15 atoms, 15 bonds, 1 residue, 1 model selected
> select add #5.2/B:429
26 atoms, 25 bonds, 2 residues, 2 models selected
> select add #5.2/B:449
37 atoms, 34 bonds, 3 residues, 2 models selected
> select add #5.2/B:450
44 atoms, 40 bonds, 4 residues, 2 models selected
> select add #5.2/B:492
58 atoms, 53 bonds, 5 residues, 2 models selected
> select add #5.2/B:513
69 atoms, 63 bonds, 6 residues, 2 models selected
> select add #5.2/B:404
91 atoms, 85 bonds, 7 residues, 2 models selected
> select add #5.2/B:490
110 atoms, 103 bonds, 8 residues, 2 models selected
> select add #5.2/B:511
124 atoms, 116 bonds, 9 residues, 2 models selected
> select add #5.2/B:447
141 atoms, 131 bonds, 10 residues, 2 models selected
> select add #5.2/B:427
157 atoms, 146 bonds, 11 residues, 2 models selected
> select add #5.2/B:408
177 atoms, 166 bonds, 12 residues, 2 models selected
> select add #5.2/B:407
196 atoms, 184 bonds, 13 residues, 2 models selected
> select add #5.2/B:448
212 atoms, 199 bonds, 14 residues, 2 models selected
> select add #5.2/B:491
231 atoms, 217 bonds, 15 residues, 2 models selected
> select add #5.2/B:512
250 atoms, 235 bonds, 16 residues, 2 models selected
Drag select of 7 atoms, 4 residues, 8 bonds
> select add #5.2/B:342
324 atoms, 265 bonds, 21 residues, 2 models selected
> select add #5.2/B:341
348 atoms, 288 bonds, 22 residues, 2 models selected
> select add #5.2/B:340
364 atoms, 303 bonds, 23 residues, 2 models selected
> select add #5.2/B:343
378 atoms, 316 bonds, 24 residues, 2 models selected
> select add #5.2/B:510
389 atoms, 326 bonds, 25 residues, 2 models selected
> select add #5.2/B:514@CB
390 atoms, 326 bonds, 26 residues, 2 models selected
> label (#!5.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> select clear
Drag select of 107 atoms, 27 residues, 91 bonds
> label (#!5.2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> show #!5.1 models
> color #5.1 #e97e8eff
> select clear
> coulombic #!5.1-2
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES surface
#5.1.1: minimum, -17.48, mean -3.53, maximum 8.63
Coulombic values for output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES surface
#5.2.1: minimum, -17.04, mean 1.02, maximum 30.55
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
> hide #!5.1-2 surfaces
> style #!5.1-2 stick
Changed 9250 atom styles
Drag select of 273 residues, 823 atoms, 693 bonds
Drag select of 280 residues, 873 atoms, 732 bonds
> style sel ball
Changed 4435 atom styles
> style sel stick
Changed 4435 atom styles
> color sel byhetero
> ~hbonds
> select clear
Drag select of 281 residues, 879 atoms, 739 bonds
> ~label (#!5.1-2 & sel) residues
> select clear
> undo
> redo
Drag select of 280 residues, 869 atoms, 729 bonds
> label (#!5.1-2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
Drag select of 22 residues
> hide sel cartoons
Drag select of 82 residues, 140 atoms, 119 bonds
> select clear
Drag select of 72 residues, 114 atoms, 98 bonds
> select clear
Drag select of 12 residues, 7 atoms, 7 bonds
> select clear
> hide #!5.2 models
> select clear
Drag select of 29 residues
> hide sel cartoons
> select clear
> show #!5.2 models
> hide #!5.1 models
> show #!5.2 cartoons
> undo
> show #!5.1 models
> hide #!5.2 models
Drag select of 50 residues
> show sel atoms
> hide H
> ~hbonds
> color sel byhetero
> style sel stick
Changed 813 atom styles
> select clear
> show #!5.2 models
> ui mousemode right distance
> distance #5.2/B:206@NH2 #5.1/A:65@OE2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206
NH2 and output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 65 OE2: 6.192Å
> ui mousemode right distance
> select #5.2/B:206@NH2
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right distance
> distance #5.2/B:206@CZ #5.1/A:65@OE2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206 CZ
and output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 65 OE2: 7.265Å
> distance #5.1/A:65@OE2 #5.2/B:206@CZ
Distance already exists; modify distance properties with 'distance style'
> show #!3 models
> ui mousemode right distance
> distance #5.2/B:206@NH2 #5.1/A:65@OE2
Distance already exists; modify distance properties with 'distance style'
> ~distance #5.2/B:206@NH2 #5.1/A:65@OE2
> ~distance #5.1/A:65@OE2 #5.2/B:206@CZ
> ui mousemode right distance
> distance #5.1/A:65@OE2 #5.2/B:206@CZ
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 65 OE2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206 CZ: 7.265Å
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right "tape measure"
> ui mousemode right distance
> select add #3
9 pseudobonds, 2 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> ui mousemode right label
> ui mousemode right distance
> distance #5.1/A:62@OE2 #5.1/A:62@CD
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 62 OE2
and CD: 1.252Å
> distance #5.2/B:208@CZ #5.1/A:62@CD
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 208 CZ
and output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 62 CD: 4.383Å
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui tool show "Find Cavities"
> ui tool show Distances
> distance style symbol false
> distance style symbol true
> distance #5.2/B:206@NH2 #5.2/B:206@CZ
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206
NH2 and CZ: 1.325Å
> show #3.1 models
> ~Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 65
> OE2 and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206 CZ:
> 7.265Å
Unknown command: ~Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A
#5.1/A GLU 65 OE2 and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG
206 CZ: 7.265Å
> ~Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 65
> OE2 and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206 C
Unknown command: ~Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A
#5.1/A GLU 65 OE2 and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG
206 C
> ~distance #5.1/A:65@OE2 #5.2/B:206@CZ
> ~distance #5.2/B:206@NH2 #5.2/B:206@CZ
> distance #5.1/A:65@OE2 #5.2/B:206@NH2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 65 OE2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 206 NH2: 6.192Å
> ui tool show "Side View"
> hide #!5.2 models
Drag select of 156 atoms, 39 residues, 127 bonds
> select clear
Drag select of 23 atoms, 10 residues, 16 bonds
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide H
> hide #!5.1 models
> show #!5.1 models
> select clear
> show #!5.1 cartoons
Drag select of 1 atoms, 27 residues
> select clear
Drag select of 27 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 1 pseudobonds, 196 atoms, 67 residues, 162 bonds
Drag select of 1 pseudobonds, 249 atoms, 70 residues, 208 bonds
> select clear
Drag select of 1 pseudobonds, 231 atoms, 63 residues, 191 bonds
> select clear
Drag select of 216 atoms, 66 residues, 184 bonds
> show sel atoms
> color sel byhetero
> hide H
> select clear
> show #!5.2 models
> select clear
> distance #5.1/A:53@OE2 #5.2/B:405@NZ
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 53 OE2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B LYS 405 NZ: 2.322Å
> distance #5.1/A:60@OD2 #5.2/B:341@NH1
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A ASP 60 OD2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 341 NH1: 4.541Å
> distance #5.1/A:62@OE2 #5.2/B:341@NH2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 62 OE2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 341 NH2: 3.981Å
> distance #5.1/A:62@OE2 #5.2/B:579@NE2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 62 OE2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B HIS 579 NE2: 45.307Å
> ~distance #5.1/A:62@OE2 #5.2/B:579@NE2
> distance #5.1/A:32@OE1 #5.2/B:579@NE2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 32 OE1
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B HIS 579 NE2: 3.407Å
> distance #5.2/B:576@NH2 #5.1/A:32@OE1
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B ARG 576
NH2 and output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A GLU 32 OE1: 6.592Å
> distance #5.1/A:41@CD #5.2/B:594@OE1
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A ARG 41 CD
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B GLU 594 OE1: 4.319Å
> distance #5.1/A:38@NE #5.1/A:38@CG
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A ARG 38 NE
and CG: 2.468Å
> ~distance #5.1/A:38@NE #5.1/A:38@CG
> distance #5.1/A:38@NE #5.2/B:594@OE2
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A ARG 38 NE
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B GLU 594 OE2: 5.103Å
> save "/Users/dantebangafoe/Downloads/1021 with atoms and measurements.cxs"
> mlp #!5.1-2
Map values for surface "output_1021_dldesign_0_cycle1_af2pred.pdb B_B SES
surface": minimum -28.77, mean -4.399, maximum 25.13
Map values for surface "output_1021_dldesign_0_cycle1_af2pred.pdb A_A SES
surface": minimum -22.57, mean -2.381, maximum 23.22
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!5.1-2 surfaces
> select clear
> select #5.1/A:26@CG
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 1 atoms, 2 bonds, 2 residues
> show sel atoms
> hide H
> select clear
Drag select of 3 atoms, 1 residues, 4 bonds
> show sel atoms
> color sel byhetero
> hide H
> select clear
> distance #5.1/A:101@CD #5.1/A:26@CD1
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A ARG 101 CD
and LEU 26 CD1: 34.432Å
> select clear
> ui mousemode right distance
> distance #5.2/B:535@SD #5.1/A:26@CG
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B MET 535 SD
and output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A LEU 26 CG: 6.449Å
> ui tool show "Side View"
> view
> distance #5.1/A:28@CZ2 #5.2/B:533@CZ
Distance between output_1021_dldesign_0_cycle1_af2pred.pdb A #5.1/A TRP 28 CZ2
and output_1021_dldesign_0_cycle1_af2pred.pdb B #5.2/B PHE 533 CZ: 4.963Å
> save "/Users/dantebangafoe/Downloads/1021 with atoms and measurements.cxs"
> show #!5.1-2 atoms
> show #!5.1-2 cartoons
> hide #!5.1-2 atoms
Drag select of 597 residues
> ~label (#!5.1-2 & sel) residues
> select clear
> color #!5.1-2 bynucleotide
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1.1/A:101 #5.1/A:101
48 atoms, 46 bonds, 2 residues, 2 models selected
> select #1.1/A #5.1/A
3280 atoms, 3298 bonds, 2 pseudobonds, 202 residues, 3 models selected
1 [ID: 1] region 2 chains [1-101] RMSD: 0.000
> select #2.1/A:92-93 #4.1/A:92-93
76 atoms, 74 bonds, 4 residues, 2 models selected
> select #2.1/A #4.1/A
3310 atoms, 3324 bonds, 186 residues, 2 models selected
3 [ID: 3] region 2 chains [1-93] RMSD: 0.000
===== 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 - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63N/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 9 days, 19 hours, 15 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
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