![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8054 closed defect (can't reproduce)
Crash processing geometry change
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000104bd000 (most recent call first):
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010d052600 (most recent call first):
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Users/apple/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2022-11-19 23:17:06.00 +0800","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.3.1 (21E258)","incident_id":"FAB48011-49EE-4D30-8A4F-3EF0AA789CB0","name":"ChimeraX"}
{
"uptime" : 110000,
"procLaunch" : "2022-11-19 20:25:36.2706 +0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir8,2",
"procStartAbsTime" : 111640804578324,
"coalitionID" : 938,
"osVersion" : {
"train" : "macOS 12.3.1",
"build" : "21E258",
"releaseType" : "User"
},
"captureTime" : "2022-11-19 23:17:01.6899 +0800",
"incident" : "FAB48011-49EE-4D30-8A4F-3EF0AA789CB0",
"bug_type" : "309",
"pid" : 25254,
"procExitAbsTime" : 118604329432724,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/Desktop\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C44A2AF7-0F89-560D-B020-174C46A0F82A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "58ECDFA6-D0A5-F9A8-7FF4-2530AF36979E",
"wakeTime" : 876,
"bridgeVersion" : {"build":"19P4243","train":"6.4"},
"sleepWakeUUID" : "3448718A-E619-4945-8A7F-6FCA986E186E",
"sip" : "enabled",
"vmRegionInfo" : "0x6b is not in any region. Bytes before following region: 4356333461\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103a86000-103a87000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x000000000000006b","rawCodes":[1,107],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000006b"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x6b is not in any region. Bytes before following region: 4356333461\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103a86000-103a87000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A.cxs
Log from Fri Nov 18 14:52:35 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A.cxs
Log from Sat Oct 22 22:02:45 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/apple/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/3a9f022abd64618525fcee138c1ecd2b/Message/MessageTemp/094693486b34f3ef278c4d795ea8dccd/File/6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
> coot-9.pdb"
Summary of feedback from opening
/Users/apple/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
Support/com.tencent.xinWeChat/2.0b4.0.9/3a9f022abd64618525fcee138c1ecd2b/Message/MessageTemp/094693486b34f3ef278c4d795ea8dccd/File/6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (467 )
Cannot find LINK/SSBOND residue CYS (822 )
Chain information for
6nb6_initial_model_real_space_refined_012_relax1_0088_noH-coot-9.pdb #1
---
Chain | Description
A | No description available
H | No description available
L | No description available
> set bgColor white
> open
> "/Users/apple/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/3a9f022abd64618525fcee138c1ecd2b/Message/MessageTemp/094693486b34f3ef278c4d795ea8dccd/File/6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
> coot-9.pdb"
Summary of feedback from opening
/Users/apple/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
Support/com.tencent.xinWeChat/2.0b4.0.9/3a9f022abd64618525fcee138c1ecd2b/Message/MessageTemp/094693486b34f3ef278c4d795ea8dccd/File/6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (467 )
Cannot find LINK/SSBOND residue CYS (822 )
Chain information for
6nb6_initial_model_real_space_refined_012_relax1_0088_noH-coot-9.pdb #2
---
Chain | Description
A | No description available
H | No description available
L | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:273
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:273
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:375
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:375
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:306
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:306-482
1372 atoms, 1414 bonds, 1 pseudobond, 171 residues, 2 models selected
> select #1/A:527
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:306-527
1722 atoms, 1774 bonds, 1 pseudobond, 216 residues, 2 models selected
> select #1/A:528
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:528-1127
4372 atoms, 4464 bonds, 3 pseudobonds, 571 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/A:305
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:305
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:305
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:18-305
1945 atoms, 1996 bonds, 6 pseudobonds, 241 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 82 residues
> select up
1306 atoms, 1342 bonds, 158 residues, 2 models selected
> select up
9929 atoms, 10187 bonds, 1256 residues, 2 models selected
> select down
1306 atoms, 1342 bonds, 158 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:393
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:393
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:301
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:301
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:305
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:305-390
687 atoms, 708 bonds, 86 residues, 1 model selected
> select #2/A:302-304
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #2/A:18-304
1934 atoms, 1984 bonds, 6 pseudobonds, 240 residues, 2 models selected
> select #2/A:302-305
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #2/A:18-305
1945 atoms, 1996 bonds, 6 pseudobonds, 241 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A:473
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:473
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:495
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:495
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:496
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:496
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:542
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:542
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:537
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:537
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:527
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:527
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:528
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:528-1127
4372 atoms, 4464 bonds, 3 pseudobonds, 571 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
Drag select of 112 atoms, 112 bonds
> delete atoms sel
> delete bonds sel
> hide #!1 models
> show #!1 models
> color #1 #d6d6d6 transparency 0
> color #1 silver transparency 0
> color #1 darkgrey transparency 0
[Repeated 1 time(s)]
> color #1 #b3b3b3 transparency 0
> color #2 #b3b3b3 transparency 0
Drag select of 248 residues
> select up
2858 atoms, 2934 bonds, 370 residues, 2 models selected
> select up
3330 atoms, 3422 bonds, 432 residues, 2 models selected
> select down
2858 atoms, 2934 bonds, 370 residues, 2 models selected
> select up
3330 atoms, 3422 bonds, 432 residues, 2 models selected
> color sel forest green
> select clear
> hide #!1 models
> show #!1 models
> lighting simple
> lighting soft
> graphics silhouettes true
Drag select of 4 atoms, 8 bonds
> select up
10 atoms, 8 bonds, 2 residues, 2 models selected
> select up
28 atoms, 28 bonds, 2 residues, 2 models selected
> select up
3500 atoms, 3608 bonds, 436 residues, 2 models selected
> select down
28 atoms, 28 bonds, 2 residues, 2 models selected
Drag select of 16 atoms, 16 bonds
> select up
46 atoms, 44 bonds, 4 residues, 2 models selected
> select up
56 atoms, 58 bonds, 4 residues, 2 models selected
> color sel byhetero
> select clear
> select #2/A:326-329,337-339,352-355,371-376,391-396,404-408,489-491
244 atoms, 242 bonds, 31 residues, 1 model selected
> select #1/A:313
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:313
7 atoms, 6 bonds, 1 residue, 1 model selected
> select
> #1/A:306,312-314,341-345,363-366,382-390,419-424,439-441,478-480,493-501,524-527
396 atoms, 397 bonds, 47 residues, 1 model selected
> select #1/A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:327,330
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:327,330
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:327,330
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:306-327,330
177 atoms, 180 bonds, 23 residues, 1 model selected
> select #1/A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:326,330
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/A:324,326,330
19 atoms, 17 bonds, 3 residues, 1 model selected
> select #1/A:324,326,330
19 atoms, 17 bonds, 3 residues, 1 model selected
> select #1/A:324,326-327,330
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/A:324,326-328,330
35 atoms, 33 bonds, 5 residues, 1 model selected
> select #1/A:324,326-328,330,343
44 atoms, 41 bonds, 6 residues, 1 model selected
> select #1/A:324,326-328,330,343-344
53 atoms, 50 bonds, 7 residues, 1 model selected
> select #1/A:324,326-328,330,332,343-344
60 atoms, 56 bonds, 8 residues, 1 model selected
> select #1/A:324,326-328,330-332,343-344
65 atoms, 62 bonds, 9 residues, 1 model selected
> color sel orange red
> hide #!1 models
> show #!1 models
> hide #!2 models
> show sel atoms
> select #1/A:324,326-328,330-332,343-344,433
72 atoms, 68 bonds, 10 residues, 1 model selected
> select #1/A:324,326-328,330-332,343-344,433
72 atoms, 68 bonds, 10 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,433
81 atoms, 77 bonds, 11 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,433,437
89 atoms, 84 bonds, 12 residues, 1 model selected
> select #1/A:431
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:431
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:343-344,431
25 atoms, 23 bonds, 3 residues, 1 model selected
> select #1/A:324,343-344,431
32 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/A:324,326-328,343-344,431
52 atoms, 49 bonds, 7 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,431
81 atoms, 77 bonds, 11 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,431,437
89 atoms, 84 bonds, 12 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,431,433,437
96 atoms, 90 bonds, 13 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,430-431,433,437
101 atoms, 95 bonds, 14 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,428,430-431,433,437
109 atoms, 102 bonds, 15 residues, 1 model selected
> select #1/A:324,326-328,330-333,343-344,428,430-431,433,437
109 atoms, 102 bonds, 15 residues, 1 model selected
> show sel cartoons
> color sel red
> color sel orange
> color sel white
> color sel black
> ui tool show "Color Actions"
> color sel sandy brown
> select clear
> select #1/A:324,326-328,330-333,343-344,428,430-431,433,437
109 atoms, 102 bonds, 15 residues, 1 model selected
> show sel atoms
> color sel #fffffffd
> color sel #ffffffcd
> color sel #ffffffbb
> color sel #ffffffb1
> color sel #ffffffac
> color sel #ffffffa7
> color sel #ffffffa8
> color sel #ffffffb1
> color sel #ffffffb3
> color sel #ffffffb5
> color sel #ffffffb9
> color sel #ffffffbb
> color sel #ffffffb9
> color sel #ffffffb0
> color sel #ffffffae
> color sel #ffffffac
> color sel #ffffffa8
> color sel #ffffffa1
> color sel #ffffff9a
> color sel #ffffff8d
> color sel #ffffff85
> color sel #ffffff79
> color sel #ffffff7a
[Repeated 1 time(s)]
> color sel #ffffff7b
> color sel #ffffff7d
> color sel #ffffff81
> color sel #ffffff85
> color sel #ffffff86
> color sel #ffffff87
> color sel #ffffff8c
> color sel #ffffff90
> color sel #ffffff98
> color sel #ffffff9c
> color sel #ffffffa3
> color sel #ffffffa5
> color sel #ffffffa7
[Repeated 1 time(s)]
> color sel #ffffffaa
> color sel #ffffffd6
> color sel #ffffffff
> ui tool show "Color Actions"
> color sel sandy brown
> select clear
> ui tool show "Show Sequence Viewer"
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:324
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:324
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:324,326-328
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #2/A:324,326-328,330-333
56 atoms, 54 bonds, 8 residues, 1 model selected
> select #2/A:324,326-328,330-333,343-344
74 atoms, 71 bonds, 10 residues, 1 model selected
> select #2/A:324,326-328,330-333,343-344,428
82 atoms, 78 bonds, 11 residues, 1 model selected
> select #2/A:324,326-328,330-333,343-344,428,430-431
94 atoms, 89 bonds, 13 residues, 1 model selected
> select #2/A:324,326-328,330-333,343-344,428,430-431,433
101 atoms, 95 bonds, 14 residues, 1 model selected
> select #2/A:324,326-328,330-333,343-344,428,430-431,433,437
109 atoms, 102 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> hide #!1 models
> show #!2 models
> ui tool show "Color Actions"
> color sel sandy brown
> show sel atoms
> style sel sphere
Changed 109 atom styles
> color sel #ffffffff
> color sel #fffffff5
> color sel #ffffff83
> color sel #ffffff53
[Repeated 2 time(s)]
> color sel #ffffff57
> color sel #ffffff5f
> color sel #ffffff61
> color sel #ffffff63
[Repeated 1 time(s)]
> color sel #ffffff61
> color sel #ffffff5d
> color sel #ffffff51
> color sel #ffffff4f
> color sel #ffffff4d
> color sel #ffffff4b
> color sel #ffffff47
> color sel #ffffff3e
> color sel #ffffff39
> color sel #ffffff32
> color sel #ffffff2f
> color sel #ffffff2c
> color sel #ffffff2b
> color sel #ffffff2c
> color sel #ffffff2d
[Repeated 1 time(s)]
> color sel #ffffff2e
> color sel sandy brown
> show #!1 models
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A_SARS.cxs
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/sars.png
> width 757 height 693 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> select #2/A:324
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:324
7 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #2/A:306,312-314,341-345,363-366,382-390,419-424,439-441,478-480,493-501,524-527
396 atoms, 397 bonds, 47 residues, 1 model selected
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!1 models
> hide #!2 models
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/model_building/20220908discussion/SARS2_6H2/best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb
Chain information for
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb
#3
---
Chain | Description
A | No description available
H | No description available
L | No description available
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/model_building/20220908discussion/SARS2_6H2/best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb
Chain information for
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb
#4
---
Chain | Description
A | No description available
H | No description available
L | No description available
> color #3 #b3b3b3 transparency 0
> color #4 #b3b3b3 transparency 0
Drag select of 206 residues
> select up
3067 atoms, 3138 bonds, 400 residues, 3 models selected
> select up
5106 atoms, 5254 bonds, 654 residues, 3 models selected
> select up
10417 atoms, 10719 bonds, 1318 residues, 3 models selected
> select down
5106 atoms, 5254 bonds, 654 residues, 3 models selected
> color (#3-4 & sel) orange red
> select clear
> hide #3 models
> hide #4 models
> show #4 models
Drag select of 3 atoms, 4 bonds
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel byelement
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:122-123
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/A:122-123,126
25 atoms, 23 bonds, 3 residues, 1 model selected
> select #3/A:122-124,126
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #3/A:25,122-124,126
41 atoms, 38 bonds, 5 residues, 1 model selected
> select #3/A:22,25,122-124,126
50 atoms, 46 bonds, 6 residues, 1 model selected
> select #3/A:22,25,122-124,126
50 atoms, 46 bonds, 6 residues, 1 model selected
> select #3/A:26
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:26
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:22,26
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/A:22,25-26
22 atoms, 20 bonds, 3 residues, 1 model selected
> select #3/A:22,25-26,126
31 atoms, 28 bonds, 4 residues, 1 model selected
> select #3/A:22,25-26,122-124,126
55 atoms, 51 bonds, 7 residues, 1 model selected
> select #3/A:22,25-26,29,122-124,126
66 atoms, 62 bonds, 8 residues, 1 model selected
> select #3/A:22,25-26,29,38,122-124,126
75 atoms, 70 bonds, 9 residues, 1 model selected
> show #3 models
> ui tool show "Color Actions"
> color sel sandy brown
[Repeated 7 time(s)]
> ui tool show "Color Actions"
> color sel sandy brown
> hide #4 models
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:22,25-26
22 atoms, 20 bonds, 3 residues, 1 model selected
> select #4/A:22,25-26,29
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #4/A:22,25-26,29,38
42 atoms, 39 bonds, 5 residues, 1 model selected
> select #4/A:22,25-26,29,38,122-124
66 atoms, 62 bonds, 8 residues, 1 model selected
> select #4/A:22,25-26,29,38,122-124,126
75 atoms, 70 bonds, 9 residues, 1 model selected
> hide #3 models
> show #4 models
> ui tool show "Color Actions"
> color sel sandy brown
> show sel atoms
> style sel sphere
Changed 75 atom styles
> color sel byelement
> color sel #b3b3b3ff
> color sel #b3b3b3de
> color sel #b3b3b3b7
> color sel #b3b3b39f
> color sel #b3b3b38e
> color sel #b3b3b384
> color sel #b3b3b380
> color sel #b3b3b376
> color sel #b3b3b375
> color sel #b3b3b372
> color sel #b3b3b371
> color sel #b3b3b370
> color sel #b3b3b36d
> color sel #b3b3b36a
> color sel #b3b3b368
> color sel #b3b3b367
> color sel #b3b3b366
> color sel #b3b3b365
> color sel #b3b3b361
> color sel #b3b3b360
> color sel #b3b3b35e
[Repeated 1 time(s)]
> color sel #b3b3b35d
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> color sel sandy brown
> show #!2 models
> color sel #b3b3b35c
> color sel #b3b3b35a
> color sel #b3b3b353
> color sel #b3b3b350
> color sel #b3b3b34e
> color sel #b3b3b346
> color sel #b3b3b345
> color sel #b3b3b34b
> color sel #b3b3b34e
> color sel #b3b3b351
> color sel #b3b3b354
> color sel #b3b3b356
> color sel #b3b3b358
> color sel #b3b3b35a
> color sel #b3b3b35c
> color sel #b3b3b35f
> color sel #b3b3b35e
> color sel #b3b3b357
> color sel #b3b3b34f
[Repeated 1 time(s)]
> color sel #b3b3b34e
> color sel #b3b3b349
> color sel #b3b3b347
[Repeated 2 time(s)]
> color sel sandy brown
> select clear
> select #3/A:22,25-26,29,38,122-124,126
75 atoms, 70 bonds, 9 residues, 1 model selected
> select #3/A:22,25-26,29,38,122-124,126
75 atoms, 70 bonds, 9 residues, 1 model selected
> hide #!2 models
> show #3 models
> select #1/A:324,326-328,330-333,343-344,428,430-431,433,437
109 atoms, 102 bonds, 15 residues, 1 model selected
> hide #3 models
> show #3 models
> select #1/A:324,326-328,330-333,343-344,428,430-431,433,437
109 atoms, 102 bonds, 15 residues, 1 model selected
> show #!2 models
> hide #!2 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/sars2.png
> width 757 height 693 supersample 3 transparentBackground true
> hide #3 models
> hide #4 models
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/model_building/6H2_SARS2_NXY/7K90/1564fit/6.published_pdb_refine/402_170_368/402_170_368_PDB_REFINE-
> coot-0.pdb
Chain information for 402_170_368_PDB_REFINE-coot-0.pdb #5
---
Chain | Description
B | No description available
H | No description available
L | No description available
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/model_building/6H2_SARS2_NXY/7K90/1564fit/6.published_pdb_refine/402_170_368/402_170_368_PDB_REFINE-
> coot-0.pdb
Chain information for 402_170_368_PDB_REFINE-coot-0.pdb #6
---
Chain | Description
B | No description available
H | No description available
L | No description available
> hide #!5 models
> show #!5 models
> hide #!5 models
> color #5 #b3b3b3 transparency 0
> show #!5 models
> hide #!6 models
> show #!6 models
> color #6 #b3b3b3 transparency 0
Drag select of 228 residues
> select up
3151 atoms, 3229 bonds, 403 residues, 3 models selected
> select up
8534 atoms, 8786 bonds, 1060 residues, 3 models selected
> select down
3151 atoms, 3229 bonds, 403 residues, 3 models selected
> select up
8534 atoms, 8786 bonds, 1060 residues, 3 models selected
> select clear
Drag select of 212 residues
> select up
2620 atoms, 2688 bonds, 340 residues, 2 models selected
> select up
3356 atoms, 3450 bonds, 436 residues, 2 models selected
> color sel cornflower blue
> select clear
Drag select of 28 atoms, 36 bonds
> select up
38 atoms, 38 bonds, 6 residues, 2 models selected
> select up
150 atoms, 154 bonds, 6 residues, 2 models selected
> color sel byelement
> select clear
> show #!1 models
> show #!2 models
> show #3 models
> show #4 models
> hide #3 models
> hide #4 models
> hide #!1 models
> hide #!2 models
> show #3 models
> show #4 models
> hide #3 models
> hide #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> select #5/B:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/B:112-113
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/B:112-113,117
24 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/B:112-113,116-117
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #5/B:112-113,116-117,120
41 atoms, 38 bonds, 5 residues, 1 model selected
> select #5/B:15,112-113,116-117,120
49 atoms, 45 bonds, 6 residues, 1 model selected
> select #5/B:15,17,112-113,116-117,120
56 atoms, 51 bonds, 7 residues, 1 model selected
> select #5/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:11,15
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/B:11,15,17
23 atoms, 20 bonds, 3 residues, 1 model selected
> select #5/B:11,15,17,112-113
40 atoms, 36 bonds, 5 residues, 1 model selected
> select #5/B:11,15,17,112-113,116-117
56 atoms, 51 bonds, 7 residues, 1 model selected
> select #5/B:11,15,17,112-113,116-117,120
64 atoms, 58 bonds, 8 residues, 1 model selected
> select #5/B:11,15-17,112-113,116-117,120
69 atoms, 64 bonds, 9 residues, 1 model selected
> select #5/B:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/B:18-19
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #5/B:18-19
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #5/B:11,18-19
30 atoms, 29 bonds, 3 residues, 1 model selected
> select #5/B:11,15-19
50 atoms, 49 bonds, 6 residues, 1 model selected
> select #5/B:11,15-19
50 atoms, 49 bonds, 6 residues, 1 model selected
> select #5/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/B:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/B:15-18
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #5/B:11,15-18
39 atoms, 37 bonds, 5 residues, 1 model selected
> select #5/B:11,15-18,112-113
56 atoms, 53 bonds, 7 residues, 1 model selected
> select #5/B:11,15-18,112-113,116-117
72 atoms, 68 bonds, 9 residues, 1 model selected
> select #5/B:11,15-18,112-113,116-117,120
80 atoms, 75 bonds, 10 residues, 1 model selected
> select #5/B:11,15-18,28,112-113,116-117,120
89 atoms, 83 bonds, 11 residues, 1 model selected
> select #5/B:11-12,15-18,28,112-113,116-117,120
98 atoms, 92 bonds, 12 residues, 1 model selected
> select #5/B:9,11-12,15-18,28,112-113,116-117,120
105 atoms, 99 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sandy brown
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #6/B
Alignment identifier is 6/B
> select #6/B:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:64,112-113
28 atoms, 27 bonds, 3 residues, 1 model selected
> select #6/B:83
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/B:83-84
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/B:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/B:112-113
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/B:112-113,116-117
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #6/B:112-113,116-117,120
41 atoms, 38 bonds, 5 residues, 1 model selected
> select #6/B:17
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/B:17
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/B:17,112-113
24 atoms, 22 bonds, 3 residues, 1 model selected
> select #6/B:17,112-113,116-117
40 atoms, 37 bonds, 5 residues, 1 model selected
> select #6/B:17,112-113,116-117,120
48 atoms, 44 bonds, 6 residues, 1 model selected
> select #6/B:14,17,112-113,116-117,120
59 atoms, 55 bonds, 7 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> select #6/B:14,17,112-113,116-117,120
59 atoms, 55 bonds, 7 residues, 1 model selected
> select #6/B:14-15,17,112-113,116-117,120
67 atoms, 63 bonds, 8 residues, 1 model selected
> select #6/B:14
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:14
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:14-15
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #6/B:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:15,17
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/B:15,17,112-113
32 atoms, 29 bonds, 4 residues, 1 model selected
> select #6/B:15,17,112-113,116-117
48 atoms, 44 bonds, 6 residues, 1 model selected
> select #6/B:15,17,112-113,116-117,120
56 atoms, 51 bonds, 7 residues, 1 model selected
> select #6/B:11,15,17,112-113,116-117,120
64 atoms, 58 bonds, 8 residues, 1 model selected
> select #6/B:11,15-17,112-113,116-117,120
69 atoms, 64 bonds, 9 residues, 1 model selected
> select #6/B:11,15-18,112-113,116-117,120
80 atoms, 75 bonds, 10 residues, 1 model selected
> select #6/B:11-12,15-18,112-113,116-117,120
89 atoms, 84 bonds, 11 residues, 1 model selected
> select #6/B:9,11-12,15-18,112-113,116-117,120
96 atoms, 91 bonds, 12 residues, 1 model selected
> select #6/B:9,11-12,15-18,28,112-113,116-117,120
105 atoms, 99 bonds, 13 residues, 1 model selected
> hide #!5 models
> show #!6 models
> show sel atoms
> style sel sphere
Changed 105 atom styles
> color sel #b3b3b3ff
> color sel #b3b3b3fd
> color sel #b3b3b3f8
> color sel #b3b3b3da
> color sel #b3b3b3bd
> color sel #b3b3b3b0
> color sel #b3b3b3a3
> color sel #b3b3b399
> color sel #b3b3b391
> color sel #b3b3b38c
> color sel #b3b3b383
[Repeated 1 time(s)]
> color sel #b3b3b37c
> color sel #b3b3b35c
> color sel #b3b3b355
> color sel #b3b3b34f
> color sel #b3b3b34a
> color sel #b3b3b343
> color sel #b3b3b33b
> color sel #b3b3b33a
> color sel #b3b3b337
> color sel #b3b3b336
[Repeated 1 time(s)]
> color sel #b3b3b332
[Repeated 1 time(s)]
> color sel #b3b3b331
> color sel #b3b3b330
> color sel #b3b3b32e
> color sel #b3b3b32d
> color sel #b3b3b32c
> color sel #b3b3b32a
> color sel #b3b3b329
> color sel #b3b3b326
> color sel #b3b3b329
> color sel #b3b3b32a
> color sel #b3b3b329
> color sel #b3b3b328
> color sel #b3b3b326
> color sel #b3b3b323
> color sel sandy brown
[Repeated 1 time(s)]
> show #3 models
> show #4 models
> hide #3 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #4 models
> color sel #b3b3b323
> color sel #b3b3b326
> color sel #b3b3b32d
> color sel #b3b3b339
> color sel #b3b3b33a
[Repeated 1 time(s)]
> color sel #b3b3b33c
> color sel #b3b3b33e
> color sel #b3b3b340
> color sel #b3b3b342
> color sel #b3b3b343
> color sel #b3b3b348
> color sel #b3b3b349
> color sel #b3b3b34d
> color sel #b3b3b34f
[Repeated 1 time(s)]
> color sel sandy brown
> select clear
> hide #!2 models
> show #3 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #4 models
> hide #4 models
> show #!5 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/OMI.png
> width 757 height 664 supersample 3 transparentBackground true
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #6/B
Alignment identifier is 6/B
> select #6/B:112-113
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/B:112-113
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/B:113-114
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #6/B:113-131
164 atoms, 167 bonds, 19 residues, 1 model selected
> select clear
> select #6/B:202-203
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/B:202-203
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/B:14
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:14-15
19 atoms, 19 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:1
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:1-6
50 atoms, 50 bonds, 6 residues, 1 model selected
> hide #!5 models
> hide #!6 models
> show #3 models
> show #4 models
> select #6/B:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/B:16-101
693 atoms, 712 bonds, 86 residues, 1 model selected
> select #6/B:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:17
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/B:17
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/B
Destroying pre-existing alignment with identifier 6/B
Alignment identifier is 6/B
> select #6/B:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:10-12,38-43,59-61,76-81,89-93,111-114
223 atoms, 220 bonds, 27 residues, 1 model selected
> select #6/B:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:9,11
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/B:9,11-12
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #6/B:9,11-12,15
32 atoms, 30 bonds, 4 residues, 1 model selected
> select #6/B:9,11-12,15,17
39 atoms, 36 bonds, 5 residues, 1 model selected
> select #6/B:9,11-12,15-17
44 atoms, 42 bonds, 6 residues, 1 model selected
> select #6/B:9,11-12,15-18
55 atoms, 53 bonds, 7 residues, 1 model selected
> select #6/B:9,11-12,15-18,28
64 atoms, 61 bonds, 8 residues, 1 model selected
> select #6/B:9,11-12,15-18,28,112-113
81 atoms, 77 bonds, 10 residues, 1 model selected
> select #6/B:9,11-12,15-18,28,112-113,116-117
97 atoms, 92 bonds, 12 residues, 1 model selected
> select #6/B:9,11-12,15-18,28,112-113,116-117,120
105 atoms, 99 bonds, 13 residues, 1 model selected
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A_SARS.cxs
——— End of log from Sat Oct 22 22:02:45 2022 ———
opened ChimeraX session
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> show #4 models
> hide #!2 models
> hide #!1 models
> show #3 models
> hide #3 models
> show #3 models
> show #!2 models
> show #!1 models
> show #!5 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb, chain A (#1) with
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#3), sequence alignment score = 763.4
RMSD between 178 pruned atom pairs is 0.982 angstroms; (across all 215 pairs:
2.852)
> hide #!5 models
> hide #!6 models
> ui tool show Matchmaker
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb, chain A (#1) with
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#3), sequence alignment score = 763.4
RMSD between 178 pruned atom pairs is 0.982 angstroms; (across all 215 pairs:
2.852)
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb, chain A (#1) with
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#3), sequence alignment score = 763.4
RMSD between 178 pruned atom pairs is 0.982 angstroms; (across all 215 pairs:
2.852)
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb, chain A (#1) with
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#3), sequence alignment score = 763.4
RMSD between 178 pruned atom pairs is 0.982 angstroms; (across all 215 pairs:
2.852)
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb, chain A (#1) with
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#3), sequence alignment score = 763.4
RMSD between 178 pruned atom pairs is 0.982 angstroms; (across all 215 pairs:
2.852)
> hide #4 models
> show #4 models
> hide #4 models
> hide #!1 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> ui tool show Matchmaker
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#3) with
best_model_rbd_fab_addglycan_real_space_refined_021_coot_03_real_space_refined_028-coot-24_real_space_refined_034.pdb,
chain A (#4), sequence alignment score = 1133.9
RMSD between 222 pruned atom pairs is 0.000 angstroms; (across all 222 pairs:
0.000)
> show #4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #3 models
> hide #4 models
> matchmaker #5/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nb6_initial_model_real_space_refined_012_relax1_0088_noH-
coot-9.pdb, chain A (#1) with 402_170_368_PDB_REFINE-coot-0.pdb, chain B (#5),
sequence alignment score = 728.6
RMSD between 169 pruned atom pairs is 0.735 angstroms; (across all 195 pairs:
1.943)
> show #!5 models
> show #!6 models
> hide #!6 models
> matchmaker #!6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 402_170_368_PDB_REFINE-coot-0.pdb, chain B (#5) with
402_170_368_PDB_REFINE-coot-0.pdb, chain B (#6), sequence alignment score =
1033
RMSD between 198 pruned atom pairs is 0.000 angstroms; (across all 198 pairs:
0.000)
> hide #!1 models
> hide #!5 models
> show #3 models
> show #4 models
Drag select of 100 residues
> select up
1614 atoms, 1648 bonds, 214 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #ff9300ff
> color sel #ffd479ff
> color sel #ff9300ff
> select clear
Drag select of 78 residues
> select up
1338 atoms, 1364 bonds, 178 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tomato
> select clear
Drag select of 26 residues
> select up
740 atoms, 752 bonds, 98 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel orange red
> color sel #ff9300fe
> color sel #ff9300f0
> color sel #ff9300a3
> color sel #ff9300ff
> color sel #ff2600ff
> color sel orange red
> color sel #ff2600ff
> color sel #ff2600fd
> color sel #ff2600f1
> color sel #ff2600dc
> color sel #ff2600b1
> color sel #ff2600ac
> color sel #ff260095
[Repeated 1 time(s)]
> color sel #ff260092
> color sel #ff26008a
> color sel #ff260070
> color sel #ff26006d
> color sel #ff260067
> color sel #ff26005d
> color sel #ff26004f
> color sel #ff260047
> color sel #ff260048
> color sel #ff260049
> color sel #ff26006a
> color sel #ff260070
> select clear
> color #3-4 #ff260070
> undo
Drag select of 18 residues
> select up
466 atoms, 470 bonds, 64 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel orange red
> color sel #ff260070
> color sel #ff26006d
> color sel #ff260064
> color sel #ff26005f
> color sel #ff2600c9
> color sel #ff2600fb
> color sel #ff2600ff
> color sel #ff2600f4
> color sel #ff2600e8
> color sel #ff2600d9
> color sel #ff2600a2
> color sel #ff26009f
> color sel #ff26009c
> color sel #ff260095
> color sel #ff26008f
> color sel #ff26008c
> color sel #ff26008a
> color sel #ff260085
> color sel #ff260074
> color sel #ff260070
> color sel #ff26006a
> color sel #ff26005f
> color sel #ff26005e
> color sel #ff26005d
> color sel #ff26005c
> color sel #ff26005b
> select clear
> color #3-4 #ff260059
> undo
Drag select of 50 residues
> select up
850 atoms, 868 bonds, 112 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #ff260059
> color sel #ff260055
> color sel #ff260030
> color sel #ff260028
> color sel #ff260029
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel byelement
> color sel byhetero
> color sel cornflower blue
> select clear
> select ::name="NAG"
388 atoms, 392 bonds, 16 residues, 6 models selected
> color (#3-4 & sel) cornflower blue
> color (#3-4 & sel) byelement
> color (#3-4 & sel) byhetero
> ui tool show "Color Actions"
> color sel byelement
> color sel byhetero
[Repeated 3 time(s)]
> color sel bynucleotide
[Repeated 2 time(s)]
> color sel dark orange
> color sel bynucleotide
> color sel byelement
[Repeated 1 time(s)]
> color sel byhetero
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> show #4 models
> select clear
> show #3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> show #3 models
> hide #4 models
> show #4 models
> color sel #0096ffff
[Repeated 1 time(s)]
> color sel #0096fffb
> color sel #0096ffeb
> color sel #0096ff74
> color sel #0096ff6e
> color sel #0096ff6d
> color sel #0096ff69
> color sel #0096ff37
[Repeated 1 time(s)]
> color sel #0096ff36
> color sel #0096ff34
> color sel #0096ff2e
> color sel #0096ff39
[Repeated 1 time(s)]
> color sel #0096ff41
> color sel #0096ff48
> color sel #0096ff4b
> color sel #0096ff4c
> color sel #0096ff52
[Repeated 2 time(s)]
> select clear
> hide #3 models
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel white
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #3 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> show #4 models
> color sel #b3b3b3ff
> color sel #b3b3b3f1
> color sel #b3b3b372
> color sel #b3b3b360
> color sel #b3b3b361
> color sel #b3b3b364
> color sel #b3b3b36e
> color sel #b3b3b371
> color sel #b3b3b377
> color sel #b3b3b37a
> color sel #b3b3b37d
> color sel #b3b3b381
> color sel #b3b3b3a9
> color sel #b3b3b3b6
> color sel #b3b3b3c2
> color sel #b3b3b3ca
> color sel #b3b3b3dd
> color sel #b3b3b3e9
> color sel #b3b3b3f3
> color sel #b3b3b3f9
> color sel #b3b3b3ff
> select clear
> hide #3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel #0433ffff
> select clear
> show #3 models
> hide #4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel byelement
> color sel #0433ffff
> color sel #0433fff7
> color sel #0433ffb3
> color sel #0433ff9d
> color sel #0433ff9b
> color sel #0433ff99
> color sel #0433ff95
> color sel #0433ff90
> color sel #0433ff8c
> color sel #0433ff6e
> color sel #0433ff5c
> color sel #0433ff4b
> color sel #0433ff44
> color sel #0433ff3f
> color sel #0433ff22
> color sel #0433ff1e
> color sel #0433ff1d
> color sel #0433ff2c
> color sel #0433ff95
> color sel #0433ffff
> show #4 models
> hide #4 models
> hide #3 models
> show #4 models
> show #3 models
> hide #4 models
> color sel byelement
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel #0433ffff
> color sel #0433fffb
> color sel #0433ff68
[Repeated 1 time(s)]
> color sel #0433ff65
> color sel #0433ff5d
> color sel #0433ff58
> color sel #0433ff59
> color sel #0433ff5c
> color sel #0433ff5f
> color sel #0433ff61
> color sel #0433ff67
> color sel #0433ff69
> color sel #0433ff70
> color sel #0433ff73
> color sel #0433ff74
> color sel #0433ff75
> color sel #0433ff79
> color sel #0433ff7d
> color sel #0433ff7e
> color sel #0433ff7d
> color sel byelement
> show #4 models
> hide #3 models
> show #3 models
> select clear
> hide #3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel #0433ff7d
> color sel #0433ff82
> color sel #0433ffa2
> color sel #0433ffbc
> color sel #0433ffc5
> color sel #0433ffc9
> color sel #0433ffe2
> color sel #0433fffc
> color sel #0433ffff
> show #3 models
> select clear
> color #3 #b3b3b3 transparency 0
> undo
[Repeated 3 time(s)]
> redo
> undo
[Repeated 4 time(s)]
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel #b3b3b3fb
> color sel #b3b3b3c4
> color sel #b3b3b389
> color sel #b3b3b381
> color sel #b3b3b37c
> color sel #b3b3b37a
> color sel #b3b3b376
> color sel #b3b3b371
> color sel #b3b3b36d
> color sel #b3b3b36e
> color sel #b3b3b370
> color sel #b3b3b380
> color sel #b3b3b376
> color sel #b3b3b372
> color sel #b3b3b371
> color sel #b3b3b36e
> color sel #b3b3b369
> color sel #b3b3b365
> color sel #b3b3b363
> color sel #b3b3b361
> color sel #b3b3b35f
> color sel #b3b3b35b
> color sel #b3b3b359
[Repeated 1 time(s)]
> color sel byelement
> show #4 models
> select clear
> show #!1 models
> show #!2 models
> hide #3 models
> hide #4 models
Drag select of 56 residues
> select up
646 atoms, 648 bonds, 86 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #b3b3b35a
> color sel #b3b3b361
> color sel #b3b3b395
> color sel #008f00ff
> color sel #008f00fe
> color sel #008f00f6
> color sel #008f0096
> color sel #008f0090
> color sel #008f0089
> color sel #008f0086
> color sel #008f0075
> color sel #008f0067
> color sel #008f0062
> color sel #008f005e
> color sel #008f0059
> color sel #008f0052
> color sel #008f0050
> color sel #008f004f
> color sel #008f004e
> color sel #008f004c
> color sel #008f004a
> color sel #008f0049
> color sel #008f004a
> select clear
Drag select of 38 residues
> select up
498 atoms, 498 bonds, 68 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #008f0049
> color sel #008f0040
> color sel #008f0025
[Repeated 2 time(s)]
> color sel #008f0023
> color sel #008f0021
> color sel #008f0020
[Repeated 2 time(s)]
> color sel #008f0021
[Repeated 1 time(s)]
> color sel #008f0022
> color sel #008f0023
[Repeated 1 time(s)]
> color sel #008f0025
> color sel #008f0027
> color sel #008f0028
> color sel #008f002a
> color sel #008f002b
[Repeated 1 time(s)]
> color sel #008f002d
> color sel #008f002e
> select clear
> color #1-2 #008f002e
> undo
> show #3 models
> hide #3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #3 models
> show #4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> hide #4 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
Drag select of 78 residues
> select up
742 atoms, 746 bonds, 102 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #008f002e
> color sel #008f002c
> color sel #008f002a
> color sel #008f0028
> color sel #008f0027
[Repeated 1 time(s)]
> color sel #008f0026
[Repeated 1 time(s)]
> select clear
> hide #!1 models
> hide #!2 models
> show #!5 models
> show #!6 models
Drag select of 44 residues
> select up
600 atoms, 602 bonds, 80 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #0096ffff
> color sel #0433ffff
> color sel #0096ffff
[Repeated 1 time(s)]
> color sel #0096ffea
> color sel #0096ffad
> color sel #0096ff5a
> color sel #0096ff58
> color sel #0096ff57
> color sel #0096ff56
[Repeated 1 time(s)]
> color sel #0096ff55
> color sel #0096ff50
> color sel #0096ff4a
[Repeated 1 time(s)]
> color sel cornflower blue
> color sel #0096ff4a
> color sel #0096ff44
> color sel #0096ff31
> color sel #0096ff30
[Repeated 1 time(s)]
> color sel #0096ff2f
> color sel #0096ff2d
> color sel #0096ff2c
> color sel #0096ff2a
[Repeated 1 time(s)]
> color sel #0096ff28
> color sel #0096ff22
> color sel #0096ff24
[Repeated 1 time(s)]
> color sel cornflower blue
> select clear
> hide #!5 models
> hide #!6 models
> show #4 models
> show #3 models
> show #!1 models
> show #!2 models
> hide #3 models
> hide #4 models
> hide #!1 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3 models
> hide #!5 models
> show #!5 models
> hide #3 models
> hide #!5 models
> show #3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #3 models
> show #!1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #4 models
> show #!1 models
> show #!2 models
> hide #3 models
> hide #4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
1750 atoms, 1804 bonds, 218 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> color sel #0096ff23
> color sel #0096ff20
> color sel #0096ff16
> color sel #0096ff17
> color sel #0096ff19
[Repeated 1 time(s)]
> color sel #0096ff26
> color sel #0096ff2a
> color sel #0096ff2c
> color sel #0096ff30
> color sel #0096ff35
[Repeated 1 time(s)]
> color sel #0096ff3a
> color sel #0096ff3c
> color sel #0096ff40
> color sel #0096ff3b
> color sel #0096ff38
> color sel #0096ff36
[Repeated 1 time(s)]
> color sel #0096ff35
> color sel #0096ff34
> color sel #0096ff3a
> color sel #0096ff4f
> color sel #0096ff52
> color sel #0096ff36
> color sel #0096ff2a
> color sel #0096ff25
[Repeated 2 time(s)]
> color sel #0096ff23
[Repeated 1 time(s)]
> color sel #0096ff22
> color sel #0096ff21
> color sel byhetero
> color sel byelement
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select add #2/A:1316@C4
29 atoms, 30 bonds, 3 residues, 2 models selected
> select up
31 atoms, 30 bonds, 4 residues, 2 models selected
> select up
56 atoms, 58 bonds, 4 residues, 2 models selected
> show #!1 models
> hide #!1 models
> color (#!2 & sel) blue
> show #!1 models
> hide #!2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel #0096ff21
> color sel #0096ff36
> color sel #0096ff5a
[Repeated 1 time(s)]
> color sel #0096ff5b
> color sel #0096ff5c
> color sel byhetero
> show #!2 models
> hide #!1 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> color sel #0096ff5b
> color sel #0096ff56
> color sel #0096ff44
> color sel #0096ff3e
> color sel #0096ff3d
> color sel #0096ff39
> color sel #0096ff37
[Repeated 1 time(s)]
> color sel #0096ff36
> color sel #0096ff58
> color sel #0096ff6c
> color sel #0096ff6e
> color sel #0096ff70
> color sel #0096ff73
> color sel #0433ffff
[Repeated 1 time(s)]
> color sel #0433fff7
> color sel #0433ffda
> color sel #0433ff70
[Repeated 1 time(s)]
> color sel #0433ff6c
> color sel #0433ff64
> color sel #0433ff61
[Repeated 1 time(s)]
> color sel #0433ff63
> color sel #0433ff65
> color sel #0433ff69
> color sel #0433ff6d
> color sel #0433ff80
> color sel #0433ff99
> color sel #0433ffa0
> color sel #0433ffa1
> color sel #0433ffa5
> color sel #0433ffa8
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel #0433ffff
> color sel #0433fffe
> color sel #0433fff9
> color sel #0433ff9e
> color sel #0433ff71
> color sel #0433ff6b
> color sel #0433ff62
> color sel #0433ff5b
> color sel #0433ff5f
> color sel #0433ff67
> color sel #0433ff6f
> color sel #0433ff70
[Repeated 1 time(s)]
> color sel byhetero
> show #!2 models
> select up
16 atoms, 16 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> color sel gray
> color sel #d6d6d6ff
> hide #!2 models
> show #!2 models
> hide #!2 models
> color sel #0433ffff
[Repeated 1 time(s)]
> color sel #0433fffb
> color sel #0433ffea
> color sel #0433ffcf
> color sel #0433ffc3
> color sel #0433ffc0
> color sel #0433ffbe
> color sel #0433ffbd
> color sel #0433ffbb
> color sel #0433ffb5
> color sel #0433ffb0
> color sel #0433ffae
> color sel #0433ffad
> color sel byhetero
> select clear
> show #!2 models
> hide #!1 models
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> color sel light gray
> color sel dark gray
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color sel #a9a9a9ff
[Repeated 1 time(s)]
> color sel #a9a9a9fd
> color sel #a9a9a9e6
> color sel #a9a9a979
> color sel #a9a9a971
> color sel #a9a9a95e
> color sel #a9a9a959
> color sel #a9a9a953
> color sel #a9a9a94f
> color sel #a9a9a94c
> color sel #a9a9a94a
> color sel #a9a9a936
> color sel #a9a9a931
> color sel #a9a9a91a
> color sel #a9a9a915
> color sel #a9a9a914
> color sel #a9a9a905
> color sel #a9a9a900
> select clear
> show #3 models
> show #4 models
> hide #!2 models
> hide #!1 models
> hide #4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel #0433ffff
> color sel #0433fffe
> color sel #0433fff0
> color sel #0433ffad
> color sel #0433ffae
> color sel #0433ffb8
> color sel #0433ffb9
> color sel #0433ffbb
> color sel #0433ffbc
> color sel #0433ffc1
> color sel #0433ffc5
> color sel #0433ffca
> color sel #0433ffcb
> color sel #0433ffce
> color sel #0433ffcf
> color sel byhetero
> select clear
> hide #3 models
> show #4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel #c0c0c0ff
[Repeated 1 time(s)]
> color sel #c0c0c0d7
> color sel #c0c0c07b
> color sel #c0c0c000
> show #3 models
> show #!5 models
> show #!6 models
> hide #4 models
> hide #3 models
> select add #5/B:46@CE2
29 atoms, 28 bonds, 2 residues, 2 models selected
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
75 atoms, 77 bonds, 3 residues, 1 model selected
> color sel #0433ffff
> hide #!5 models
> hide #!6 models
> show #4 models
> show #3 models
> show #!2 models
> show #!1 models
> hide #3 models
> hide #4 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> show #!6 models
> select #5
3392 atoms, 3491 bonds, 1 pseudobond, 421 residues, 2 models selected
> ~select #5
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!6 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> select up
1714 atoms, 1766 bonds, 203 residues, 1 model selected
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
75 atoms, 77 bonds, 3 residues, 1 model selected
> color sel byhetero
> select clear
> hide #!5 models
> show #!6 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #6/B:205@C5
3 atoms, 4 bonds, 1 residue, 1 model selected
> select add #6/B:46@CE1
4 atoms, 4 bonds, 2 residues, 1 model selected
> select up
8 atoms, 7 bonds, 2 residues, 1 model selected
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
75 atoms, 77 bonds, 3 residues, 1 model selected
> color sel #ebebebff
> color sel #ebebebfe
> color sel #ebebebe8
> color sel #ebebeb00
> show #!5 models
> show #!1 models
> show #!2 models
> show #3 models
> show #4 models
> hide #!5 models
> hide #!6 models
> hide #4 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!1 models
> show #!2 models
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 804 height 693 supersample 3 transparentBackground true
> hide #!1 models
> hide #!2 models
> show #3 models
> show #4 models
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars2.png
> width 804 height 693 supersample 3 transparentBackground true
> hide #4 models
> hide #3 models
> show #!5 models
> show #!6 models
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/OMI.png
> width 804 height 693 supersample 3 transparentBackground true
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A.cxs
> hide #!5 models
> hide #!6 models
> show #!1 models
> show #!2 models
Drag select of 88 residues
> select up
1327 atoms, 1363 bonds, 167 residues, 3 models selected
> select up
3426 atoms, 3524 bonds, 425 residues, 3 models selected
> color (#!1-2 & sel) #009051ff
[Repeated 1 time(s)]
> color (#!1-2 & sel) #009051d1
> color (#!1-2 & sel) #00905192
> color (#!1-2 & sel) #00905185
> color (#!1-2 & sel) #0090517c
> color (#!1-2 & sel) #00905168
> color (#!1-2 & sel) #00905162
[Repeated 1 time(s)]
> color (#!1-2 & sel) #0090515f
> color (#!1-2 & sel) #009051ff
[Repeated 1 time(s)]
> color (#!1-2 & sel) #009051cc
> color (#!1-2 & sel) #00905181
> color (#!1-2 & sel) #00905177
> color (#!1-2 & sel) #00905164
> color (#!1-2 & sel) #0090514b
> color (#!1-2 & sel) #00905147
> color (#!1-2 & sel) #00905144
> color (#!1-2 & sel) #0090513d
[Repeated 1 time(s)]
> color (#!1-2 & sel) #00905139
[Repeated 1 time(s)]
> color (#!1-2 & sel) #00905156
[Repeated 1 time(s)]
> color (#!1-2 & sel) #00905165
> color (#!1-2 & sel) #0090516c
> color (#!1-2 & sel) #00905179
[Repeated 1 time(s)]
> color (#!1-2 & sel) #0090517a
> select clear
Drag select of 38 residues
> select up
488 atoms, 492 bonds, 68 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel forest green
> select ~sel
18904 atoms, 19458 bonds, 6 pseudobonds, 2372 residues, 10 models selected
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 804 height 693 supersample 3 transparentBackground true
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 804 height 693 supersample 3
> hide #!2 models
> show #!2 models
Drag select of 30 residues
> select up
466 atoms, 468 bonds, 64 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #0090517a
> color sel #00905173
> color sel #00905165
> color sel #00905162
> color sel #0090515d
> color sel #0090514f
> color sel #0090514e
> color sel #0090514c
> color sel #0090514d
> color sel forest green
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 804 height 693 supersample 3 transparentBackground true
Drag select of 46 residues
> select up
728 atoms, 738 bonds, 102 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #0090514d
> color sel #0090515d
> color sel #0090517c
> color sel #00905184
> color sel #00905185
> color sel #00905188
> color sel #0090518b
> color sel #0090518c
> color sel #0090518b
> color sel #00905189
> color sel #00905187
[Repeated 1 time(s)]
> color sel forest green
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 804 height 693 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> hide #!1 models
> hide #!2 models
> show #3 models
> show #4 models
Drag select of 32 residues
> select up
1066 atoms, 1084 bonds, 146 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #00905188
> color sel #00905189
> color sel #009051a0
> color sel #009051aa
> color sel #009051ac
[Repeated 1 time(s)]
> color sel #009051ae
> color sel #009051b2
> color sel #009051b6
> color sel #009051b7
[Repeated 1 time(s)]
> color sel #009051b5
> color sel #009051b1
> color sel #009051aa
> color sel #009051ac
> color sel #009051ad
> color sel orange red
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars2.png
> width 804 height 693 supersample 3 transparentBackground true
Drag select of 16 residues
> select up
974 atoms, 988 bonds, 134 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #009051ad
> color sel #009051a2
> color sel #00905190
> color sel #00905193
[Repeated 1 time(s)]
> color sel #00905195
> color sel #00905199
> color sel #0090519b
> color sel #0090519c
> color sel orange red
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars2.png
> width 804 height 693 supersample 3 transparentBackground true
> hide #4 models
> hide #3 models
> show #!5 models
> show #!6 models
Drag select of 56 residues
> select up
1368 atoms, 1406 bonds, 176 residues, 2 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 2 models selected
> color sel #0090519b
> color sel #00905195
> color sel #0090518a
> color sel #00905199
> color sel #0090519b
> color sel #0090518c
> color sel #00905187
> color sel #00905183
> color sel #00905184
> color sel #0090518c
> color sel #00905192
> color sel #00905194
[Repeated 1 time(s)]
> color sel #00905195
> color sel #00905196
[Repeated 2 time(s)]
> color sel cornflower blue
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/OMI.png
> width 804 height 693 supersample 3 transparentBackground true
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A.cxs
——— End of log from Fri Nov 18 14:52:35 2022 ———
opened ChimeraX session
> show #!1 models
> hide #1.1 models
> show #1.1 models
> show #!2 models
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> hide #!2 models
> hide #1.1 models
> hide #!1 models
> hide #!5 models
> hide #!6 models
> show #!1 models
Drag select of 134 residues
> select up
1497 atoms, 1537 bonds, 194 residues, 1 model selected
> select up
1665 atoms, 1711 bonds, 216 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select add #1/A:383
1677 atoms, 1723 bonds, 217 residues, 1 model selected
> select up
1737 atoms, 1784 bonds, 225 residues, 1 model selected
> select up
3415 atoms, 3515 bonds, 434 residues, 1 model selected
> surface sel
> undo
> hide #1.3 models
> hide #1.4 models
> color #1.2 silver transparency 0
> color #1.2 #b3b3b3 transparency 0
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:516-517
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:516-517
13 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show Log
> hide #1.2 models
> show #1.2 models
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime
> color sel lawn green
> color sel chartreuse
> color sel green yellow
> color sel medium spring green
> color sel lime green
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,1316,330,326,324,327,343,344,328,343,332,330,1316,331,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,1316,330,326,324,327,343,344,328,343,332,330,1316,331
79 atoms, 77 bonds, 10 residues, 1 model selected
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,1316,330,326,324,327,343,344,328,343,332,330,1316,331,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,330,326,324,327,343,344,328,343,332,330,1316,331
79 atoms, 77 bonds, 10 residues, 1 model selected
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,330,326,324,327,343,344,328,343,332,330,1316,331
79 atoms, 77 bonds, 10 residues, 1 model selected
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,330,326,324,327,343,344,328,343,332,330,1316,331
79 atoms, 77 bonds, 10 residues, 1 model selected
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,330,326,324,327,343,344,328,343,332,330,331
65 atoms, 62 bonds, 9 residues, 1 model selected
> color (#!1 & sel) forest green
> select clear
> hide #1.2 models
Drag select of 24 residues
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show #1.2 models
> select
> #1/A:1045,1071,1072,1136,1137,1138,1139,330,326,324,327,343,344,328,343,332,330,331
65 atoms, 62 bonds, 9 residues, 1 model selected
> color (#!1 & sel) forest green
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime green
> select clear
> save
> /Users/apple/OneDrive/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars_footprint.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #1.2 models
> hide #!1 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> select #1
3226 atoms, 3323 bonds, 2 pseudobonds, 410 residues, 2 models selected
> show sel cartoons
> show #!2 models
> select clear
Drag select of 22 residues
> select up
546 atoms, 550 bonds, 74 residues, 3 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 3 models selected
> ui tool show "Color Actions"
> color sel chartreuse
> color sel lime
> color sel lawn green
> select clear
Drag select of 36 residues
> select up
546 atoms, 550 bonds, 74 residues, 3 models selected
> select up
1712 atoms, 1758 bonds, 222 residues, 3 models selected
> ui tool show "Color Actions"
> color sel lawn green
> color sel chartreuse
> color sel lime
> select clear
> hide #!1 models
> hide #1.1 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #!2 models
> show #4 models
> hide #4 models
Drag select of 66 residues
> select up
1357 atoms, 1383 bonds, 180 residues, 1 model selected
> select up
1678 atoms, 1725 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 17 residues
> delete atoms sel
> delete bonds sel
Drag select of 3 residues, 1 pseudobonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
Drag select of 6 residues
> select up
539 atoms, 556 bonds, 1 pseudobond, 66 residues, 2 models selected
> select up
1664 atoms, 1716 bonds, 1 pseudobond, 204 residues, 2 models selected
> surface (#!3 & sel)
> color #3.2 #b3b3b3 transparency 0
> color #3.2 #ebebeb transparency 0
> color #3.2 darkgrey transparency 0
> color #3.2 #ebebeb transparency 0
> color #3.2 #929292 transparency 0
> color #3.2 #ebebeb transparency 0
> color #3.2 #5e5e5e transparency 0
> color #3.2 #797979 transparency 0
> color #3.2 #919191 transparency 0
> color #3.2 #797979 transparency 0
> select #3/A:1180,433,1183,333,437,1184,431,1185,430,428,431
Nothing selected
> hide #!3 models
> show #!3 models
> hide #3.2 models
> show #!2 models
> hide #!2 models
> show #3.2 models
> select #3/A:389,224,386,122,383,122,382,123,364,126,363,126,124,123,362,126
61 atoms, 59 bonds, 5 residues, 1 model selected
> color (#!3 & sel) orange
> undo
> select add #3/A:53@OG
62 atoms, 55 bonds, 6 residues, 2 models selected
> undo
> select #3/A:389,386,122,383,122,382,123,364,126,363,126,124,123,362,126
33 atoms, 31 bonds, 4 residues, 1 model selected
> color (#!3 & sel) orange
> select #3/A:317,224,316,25,22,315,26,25,253,29,251,29,249,38,22,248,22
70 atoms, 68 bonds, 6 residues, 1 model selected
> select #3/A:317,316,25,22,315,26,25,253,29,251,29,249,38,22,248,22
42 atoms, 39 bonds, 5 residues, 1 model selected
> color (#!3 & sel) orange red
> show #!1 models
> show #1.1 models
> hide #1.1 models
> hide #!1 models
> show #1.2 models
> color #1.2 #d6d6d6 transparency 0
> color #1.2 #ebebeb transparency 0
> hide #!1 models
> select clear
> hide #3.1 models
> hide #!3 models
> hide #3.2 models
> show #4 models
> show #!5 models
> hide #4 models
> hide #!5 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #3.1 models
> hide #3.1 models
> show #!2 models
> hide #!2 models
> show #3.1 models
> hide #3.1 models
> select #3
3342 atoms, 3441 bonds, 1 pseudobond, 422 residues, 2 models selected
> show sel cartoons
> select clear
Drag select of 11 residues
> select up
268 atoms, 274 bonds, 36 residues, 1 model selected
> select up
856 atoms, 879 bonds, 111 residues, 1 model selected
> color sel orange
> select clear
> hide #!3 models
> show #!5 models
Drag select of 41 residues
> select up
848 atoms, 876 bonds, 104 residues, 1 model selected
> select up
1678 atoms, 1725 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 13 residues, 1 pseudobonds
> select up
249 atoms, 253 bonds, 1 pseudobond, 32 residues, 2 models selected
> select down
84 atoms, 1 pseudobond, 13 residues, 2 models selected
> select add #5/B:145
96 atoms, 12 bonds, 1 pseudobond, 14 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select add #5/B:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
48 atoms, 49 bonds, 6 residues, 1 model selected
> select up
1618 atoms, 1668 bonds, 189 residues, 1 model selected
> surface sel
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> show #3.2 models
> hide #3.2 models
> hide #5.2 models
> undo
> hide #!2 models
> hide #!5 models
> hide #5.1 models
> hide #1.2 models
> show #5.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #5.1 models
> hide #5.2 models
> show #!6 models
Drag select of 69 residues
> select up
1257 atoms, 1293 bonds, 160 residues, 1 model selected
> select up
1678 atoms, 1725 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #5.2 models
> show #5.1 models
> show #4 models
> hide #4 models
> hide #5.1 models
> hide #!5 models
> hide #5.2 models
> show #5.2 models
> hide #5.2 models
> hide #!5 models
> show #5.2 models
> hide #5.2 models
> select #5
3296 atoms, 3393 bonds, 1 pseudobond, 407 residues, 2 models selected
> hide #!5 models
> ~select #5
1 model selected
> select #5.1
1 pseudobond, 1 model selected
> hide #6.1 models
> show #6.1 models
> ~select #5.1
Nothing selected
> select add #6/B:104
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
48 atoms, 49 bonds, 6 residues, 1 model selected
> select up
1714 atoms, 1766 bonds, 203 residues, 1 model selected
> surface sel
> color #6.2 darkgrey transparency 0
> hide #!6 models
> show #!6 models
> hide #6.2 models
> select ~sel
18458 atoms, 18999 bonds, 6 pseudobonds, 2333 residues, 10 models selected
> select add #6/B:117@CG1
18459 atoms, 18999 bonds, 6 pseudobonds, 2334 residues, 15 models selected
> select clear
> select add #6/B:112@CE
1 atom, 1 residue, 1 model selected
> select add #6/B:113@CD2
2 atoms, 2 residues, 2 models selected
> select clear
> hide #!6 models
> hide #6.1 models
> show #!5 models
> show #5.1 models
> show #5.2 models
> hide #5.2 models
> hide #5.1 models
> hide #!5 models
> show #!5 models
> show #5.1 models
> show #5.2 models
> hide #5.2 models
> hide #5.1 models
> hide #!5 models
> open /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/model_building/6H2_Omi/20220801Omicron_combine/6.published_pdb_refine/402_170_368/402_170_368_PDB_REFINE-
> coot-0.pdb
Chain information for 402_170_368_PDB_REFINE-coot-0.pdb #7
---
Chain | Description
B | No description available
H | No description available
L | No description available
> show #6.2 models
> hide #6.2 models
> hide #!6 models
> show #5.2 models
> hide #5.2 models
> hide #!7 models
> show #5.1 models
> show #5.2 models
> show #!6 models
> show #6.1 models
> show #6.2 models
> hide #6.2 models
> hide #5.2 models
> select #5
3296 atoms, 3393 bonds, 1 pseudobond, 407 residues, 2 models selected
> show sel cartoons
> select clear
> show #!7 models
> hide #!7 models
> ui tool show Matchmaker
> matchmaker #7/B to #6/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 402_170_368_PDB_REFINE-coot-0.pdb, chain B (#6) with
402_170_368_PDB_REFINE-coot-0.pdb, chain B (#7), sequence alignment score =
1033
RMSD between 198 pruned atom pairs is 0.000 angstroms; (across all 198 pairs:
0.000)
> show #!7 models
> hide #!7 models
> hide #6.1 models
> hide #!6 models
> hide #5.1 models
> hide #!5 models
> show #!7 models
Drag select of 152 residues
> select up
1640 atoms, 1685 bonds, 213 residues, 1 model selected
> select up
1678 atoms, 1725 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 17 atoms, 17 bonds
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 2 bonds
> select up
31 atoms, 30 bonds, 2 residues, 1 model selected
> select up
56 atoms, 56 bonds, 2 residues, 1 model selected
> select up
1714 atoms, 1766 bonds, 203 residues, 1 model selected
> select down
56 atoms, 56 bonds, 2 residues, 1 model selected
> hide sel atoms
Drag select of 12 residues
> select up
402 atoms, 407 bonds, 45 residues, 1 model selected
> select up
1714 atoms, 1766 bonds, 203 residues, 1 model selected
> select down
402 atoms, 407 bonds, 45 residues, 1 model selected
> select up
1714 atoms, 1766 bonds, 203 residues, 1 model selected
> surface sel
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
75 atoms, 77 bonds, 3 residues, 1 model selected
> color sel blue
> color sel byelement
> color sel byhetero
> color sel #0433ffff
> color sel byhetero
> select clear
> color #7 silver transparency 0
> color #7 darkgrey transparency 0
> show #3.2 models
> hide #3.2 models
> color #7 silver transparency 0
> color #7 #d6d6d6 transparency 0
> show #3.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> color #7 darkgrey transparency 0
> color #7 silver transparency 0
> color #7 darkgrey transparency 0
> color #3.2 #797979 transparency 0
> color #3.2 #5e5e5e transparency 0
> color #3.2 #797979 transparency 0
> color #3.2 #5e5e5e transparency 0
> color #3.2 #797979 transparency 0
> hide #3.2 models
> hide #!3 models
> hide #!1 models
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
75 atoms, 77 bonds, 3 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
> select
> #3/A:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
43 atoms, 39 bonds, 7 residues, 1 model selected
> select
> #7/B:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
90 atoms, 87 bonds, 7 residues, 1 model selected
> select
> #7/B:372,371,370,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
41 atoms, 38 bonds, 5 residues, 1 model selected
> color (#!7 & sel) magenta
> color (#!7 & sel) hot pink
> select
> #7/B:298,206,297,15,17,11,296,16,17,295,17,234,18,231,28,230,12,9,229,12,205,12
113 atoms, 110 bonds, 10 residues, 1 model selected
> color (#!7 & sel) purple
> color (#!7 & sel) #9437ffff
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
49 atoms, 49 bonds, 2 residues, 1 model selected
> color sel medium blue
> color sel blue
> color sel byhetero
> select clear
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!7 models
> show #6.2 models
> hide #6.2 models
> hide #!6 models
> select
> #7/B:298,206,297,15,17,11,296,16,17,295,17,234,18,231,28,230,12,9,229,12,205,12
113 atoms, 110 bonds, 10 residues, 1 model selected
> color (#!7 & sel) cornflower blue
> color (#!7 & sel) medium blue
> ui tool show "Color Actions"
> color sel dodger blue
> color (#!7 & sel) medium blue
> color (#!7 & sel) #0096ffff
> select
> #3/A:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
43 atoms, 39 bonds, 7 residues, 1 model selected
> select
> #7/B:298,206,297,15,17,11,296,16,17,295,17,234,18,231,28,230,12,9,229,12,205,12
113 atoms, 110 bonds, 10 residues, 1 model selected
> select
> #7/B:372,371,370,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
41 atoms, 38 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!7 & sel) #76d6ffff
> color (#!7 & sel) #73fdffff
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
49 atoms, 49 bonds, 2 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!5 models
Drag select of 14 residues
> select up
307 atoms, 308 bonds, 42 residues, 1 model selected
> select up
856 atoms, 879 bonds, 111 residues, 1 model selected
> color sel #00fdffff
> color sel #73fdffff
> select clear
> hide #!7 models
> show #6.2 models
> show #!7 models
> hide #6.2 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #3.2 models
> hide #!3 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> hide #!3 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> show #1.2 models
> select
> #1/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> color (#!1 & sel) forest green
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lawn green
> select clear
Drag select of 8 residues
> select up
249 atoms, 250 bonds, 34 residues, 2 models selected
> select up
856 atoms, 879 bonds, 111 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lawn green
> select clear
> hide #!1 models
> hide #1.2 models
> show #!3 models
> show #3.1 models
> show #3.2 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> select add #1/A:1316@C3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
1561 atoms, 1612 bonds, 194 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 2 models selected
> color sel blue
> color sel byhetero
> select clear
> show #!3 models
> show #3.1 models
> hide #1.2 models
> hide #1.1 models
> hide #!1 models
> show #3.2 models
> select #3/A:389,224,386,122,383,122,382,123,364,126,363,126,124,123,362,126
61 atoms, 59 bonds, 5 residues, 1 model selected
> color (#!3 & sel) orange
> select #3/A:317,224,316,25,22,315,26,25,253,29,251,29,249,38,22,248,22
70 atoms, 68 bonds, 6 residues, 1 model selected
> color (#!3 & sel) orange red
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> color sel blue
> color sel byhetero
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> show #1.2 models
> hide #!1 models
> show #!1 models
Drag select of 42 residues
> select up
738 atoms, 753 bonds, 92 residues, 4 models selected
> select up
3329 atoms, 3427 bonds, 420 residues, 4 models selected
> hide sel & #!1 cartoons
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #1.2 models
> hide #!1 models
> show #3.2 models
> select clear
Drag select of 36 residues
> select up
825 atoms, 848 bonds, 107 residues, 1 model selected
> select up
1678 atoms, 1725 bonds, 218 residues, 1 model selected
> hide sel cartoons
Drag select of 2 atoms, 1 bonds
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> select up
1664 atoms, 1716 bonds, 204 residues, 1 model selected
> select down
28 atoms, 28 bonds, 1 residue, 2 models selected
> hide sel atoms
> hide #!3 models
> hide #3.2 models
> show #!1 models
> show #1.2 models
> hide #1.2 models
> hide #!1 models
> show #!7 models
> hide #7.1 models
> hide #7.2 models
> hide #!7 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> hide #!1 models
> show #!5 models
> show #5.1 models
> hide #5.1 models
> hide #!5 models
> show #!3 models
> show #3.1 models
> show #3.2 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars2_footprint.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars_footprint.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> show #7.2 models
> show #7.1 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/omi_footprint.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #7.1 models
> hide #7.2 models
> hide #!7 models
> show #!1 models
> show #1.1 models
> show #!2 models
> show #!3 models
> hide #!1 models
> hide #1.1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #6.1 models
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> select
> #5/A:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
Nothing selected
> select
> #5/A:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
Nothing selected
> select
> #5/B:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
90 atoms, 87 bonds, 7 residues, 1 model selected
> color (#!5 & sel) #76d6ffff
> color (#!5 & sel) #73fdffff
> select clear
> select add #5/B:205@C7
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
49 atoms, 49 bonds, 2 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 2 residues, 1 model selected
> select up
56 atoms, 56 bonds, 2 residues, 1 model selected
> hide sel atoms
> select
> #5/B:298,206,297,15,17,11,296,16,17,295,17,234,18,231,28,230,12,9,229,12,205,12
113 atoms, 110 bonds, 10 residues, 1 model selected
> color (#!5 & sel) #0096ffff
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> select add #5/B:206@C2
29 atoms, 28 bonds, 2 residues, 1 model selected
> select up
49 atoms, 49 bonds, 2 residues, 1 model selected
> select up
1618 atoms, 1668 bonds, 189 residues, 1 model selected
> select down
49 atoms, 49 bonds, 2 residues, 2 models selected
> color sel blue
> color sel byhetero
> select clear
Drag select of 20 residues
> select up
480 atoms, 490 bonds, 58 residues, 4 models selected
> select up
3332 atoms, 3434 bonds, 392 residues, 4 models selected
> color (#!5-6 & sel) #a9a9a9ff
> undo
> select clear
> select add #5/B:76
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 6 residues, 2 models selected
> select up
1618 atoms, 1668 bonds, 189 residues, 2 models selected
> color (#!5 & sel) #929292ff
> color (#!5 & sel) #a9a9a9ff
> select clear
> select
> #5/B:298,206,297,15,17,11,296,16,17,295,17,234,18,231,28,230,12,9,229,12,205,12
113 atoms, 110 bonds, 10 residues, 1 model selected
> color (#!5 & sel) #0096ffff
> select
> #5/B:372,205,371,206,370,206,368,112,113,365,117,344,113,343,116,120,342,116,341,116,339,117,116
90 atoms, 87 bonds, 7 residues, 1 model selected
> color (#!5 & sel) #73fdffff
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
75 atoms, 77 bonds, 3 residues, 1 model selected
> color sel blue
> color sel byhetero
> ui tool show "Model Panel"
> hide #!5 models
> hide #!6 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> show #1.3 models
> hide #1.3 models
> show #!2 models
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> select
> #1/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> select clear
Drag select of 9 residues
> select up
80 atoms, 79 bonds, 11 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select clear
> select add #1/A:440
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 3 residues, 2 models selected
> select up
1561 atoms, 1612 bonds, 194 residues, 2 models selected
> color (#!1 & sel) byelement
> color (#!1 & sel) #d6d6d6ff
> select clear
Drag select of 30 residues
> select up
900 atoms, 924 bonds, 108 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select down
900 atoms, 924 bonds, 108 residues, 3 models selected
> select add #1/A:438
912 atoms, 936 bonds, 109 residues, 3 models selected
> select up
1011 atoms, 1037 bonds, 122 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select down
1011 atoms, 1037 bonds, 122 residues, 3 models selected
> select add #1/A:384
1016 atoms, 1041 bonds, 123 residues, 3 models selected
> select up
1083 atoms, 1111 bonds, 131 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select down
1083 atoms, 1111 bonds, 131 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select down
1083 atoms, 1111 bonds, 131 residues, 3 models selected
> select add #1/A:424
1091 atoms, 1118 bonds, 132 residues, 3 models selected
> select up
1131 atoms, 1162 bonds, 137 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select down
1131 atoms, 1162 bonds, 137 residues, 3 models selected
> select add #2/A:319
1139 atoms, 1169 bonds, 138 residues, 3 models selected
> select up
1223 atoms, 1257 bonds, 148 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> select down
1223 atoms, 1257 bonds, 148 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #1.3 models
> hide #1.3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
3415 atoms, 3515 bonds, 2 pseudobonds, 434 residues, 2 models selected
> hide #!2 models
> show #!2 models
> select clear
> show #1.3 models
> hide #1.3 models
> show #1.2 models
> hide #1.2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 99 atoms, 155 residues, 88 bonds
> select up
1279 atoms, 1312 bonds, 157 residues, 2 models selected
> select up
1561 atoms, 1612 bonds, 194 residues, 2 models selected
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
Drag select of 20 residues
> select up
756 atoms, 778 bonds, 94 residues, 3 models selected
> select up
3311 atoms, 3416 bonds, 412 residues, 3 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select clear
> show #!2 models
> select
> #3/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
Nothing selected
> select
> #3/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
Nothing selected
> select
> #2/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> hide #!1 models
> hide #!2 models
> show #!2 models
> select clear
Drag select of 12 residues
> select up
275 atoms, 279 bonds, 36 residues, 1 model selected
> select up
1750 atoms, 1804 bonds, 218 residues, 1 model selected
> color sel #ebebebff
> color sel #d6d6d6ff
> select clear
> select
> #2/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> color sel orange red
> color sel #d6d6d6ff
> color sel #d6d6d6bd
> color sel #d6d6d642
> color sel #d6d6d63a
> color sel #d6d6d639
> color sel #d6d6d638
> color sel #d6d6d63a
> color sel #d6d6d63b
> color sel #d6d6d63e
> color sel #d6d6d644
> color sel #d6d6d646
> color sel #d6d6d648
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #ff2600eb
> color sel #ff2600b6
> color sel #ff26006d
> color sel #ff260062
> color sel #ff26005d
> color sel #ff260059
> color sel #ff260054
> color sel #ff26004c
> color sel #ff26004a
> color sel #ff260043
> color sel #ff260041
> color sel #ff26003d
> color sel #ff260038
> color sel #ff260036
> color sel #ff260032
> color sel #ff260030
> color sel #ff26002e
> color sel #ff26002d
> color sel #ff26002c
> color sel #ff26002a
> color sel #ff260020
> color sel #ff26001d
> color sel #ff26001c
> color sel #ff26001a
> color sel #ff26001b
> color sel #ff26001c
> color sel #ff26001d
> color sel #ff26001c
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> select #2/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> color sel #ff7e79ff
> color sel #ff2600ff
> color sel #ff2600fe
> color sel #ff2600dc
> color sel #ff260028
> color sel #ff260027
> color sel #ff260025
> color sel #ff260024
> color sel #ff26001f
> color sel #ff26001d
> color sel #ff26001b
> color sel #ff260017
> color sel #ff260013
> color sel #ff260012
> color sel #ff260013
> color sel #ff260014
> color sel #ff260015
> color sel #ff260016
> color sel #ff260017
> select clear
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> show #!1 models
> ui tool show "Color Actions"
> color sel lawn green
> select
> #1/A:1045,1316,330,326,1071,324,327,343,344,328,1072,343,1136,332,1137,332,1138,332,330,1316,331,1139,1316
79 atoms, 77 bonds, 10 residues, 1 model selected
> color (#!1 & sel) forest green
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel medium blue
> select clear
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_chimerasession/fig3_A.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel blue
> color sel byhetero
> show #!1 models
> hide #!2 models
> show #!2 models
> select clear
> hide #!2 models
> hide #!1 models
> show #7.2 models
> show #7.1 models
> show #6.2 models
> hide #6.2 models
> hide #!7 models
> hide #7.1 models
> hide #7.2 models
> hide #!6 models
> show #!5 models
> show #!6 models
Drag select of 11 atoms, 10 bonds
> select up
13 atoms, 11 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> select up
1714 atoms, 1766 bonds, 203 residues, 1 model selected
> select down
28 atoms, 28 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!6 models
> hide #!5 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #4 models
> show #!3 models
> select #3/A:317,224,316,25,22,315,26,25,253,29,251,29,249,38,22,248,22
70 atoms, 68 bonds, 6 residues, 1 model selected
> select #3/A:389,224,386,122,383,122,382,123,364,126,363,126,124,123,362,126
61 atoms, 59 bonds, 5 residues, 1 model selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
Drag select of 13 residues
> select up
1055 atoms, 1084 bonds, 129 residues, 3 models selected
> select up
3487 atoms, 3593 bonds, 428 residues, 3 models selected
> color (#4 & sel) #919191ff
> color (#4 & sel) #797979ff
> select clear
> select #5/A:389,224,386,122,383,122,382,123,364,126,363,126,124,123,362,126
Nothing selected
> select #4/A:389,224,386,122,383,122,382,123,364,126,363,126,124,123,362,126
61 atoms, 59 bonds, 5 residues, 1 model selected
> color sel #ff2600ff
> color sel #ff2600fe
> color sel #ff2600f3
> color sel #ff2600d5
> color sel #ff2600ca
> color sel #ff2600b4
> color sel #ff2600b0
> color sel #ff2600a8
> color sel #ff2600a2
> color sel #ff26009e
> color sel #ff260099
> color sel #ff26008c
> color sel #ff260088
> color sel #ff260086
> color sel #ff260083
> color sel #ff260081
> color sel #ff26007a
> color sel #ff260079
> color sel #ff260071
> color sel #ff260068
> color sel #ff260065
> color sel #ff260063
> color sel #ff26005d
> color sel #ff260055
> color sel #ff26004a
> color sel #ff26003b
> color sel #ff26002e
> color sel #ff26002b
> color sel #ff260024
> color sel #ff260022
> color sel #ff260023
> color sel #ff260025
> color sel #ff260026
> color sel #ff260027
> color sel #ff260026
> color sel #ff260027
> color sel #ff260028
> color sel #ff26002a
> color sel #ff26002b
> color sel #ff26002d
> color sel #ff26002e
> select clear
> show #!1 models
> show #1.1 models
> hide #1.1 models
> hide #4 models
> show #4 models
> hide #!1 models
> show #!2 models
> hide #4 models
> show #4 models
> select #4/A:389,224,386,122,383,122,382,123,364,126,363,126,124,123,362,126
61 atoms, 59 bonds, 5 residues, 1 model selected
> color sel #ff26002d
> color sel #ff26002b
> color sel #ff260027
> color sel #ff260025
> color sel #ff260024
> color sel #ff260022
> color sel #ff260021
> color sel #ff260020
> color sel #ff26001d
> color sel #ff26001a
> select clear
> hide #!2 models
> select #4/A:317,224,316,25,22,315,26,25,253,29,251,29,249,38,22,248,22
70 atoms, 68 bonds, 6 residues, 1 model selected
> color sel #ff2600ff
> color sel #ff2600fd
> color sel #ff2600b7
> color sel #ff26001e
> color sel #ff26001d
> color sel #ff26001a
> color sel #ff26001b
> color sel #ff26001c
> color sel #ff26001d
> color sel #ff26001c
> color sel #ff26001b
> color sel #ff26001e
> color sel #ff26001f
> select clear
> show #!3 models
Drag select of 15 residues
> select up
233 atoms, 235 bonds, 32 residues, 1 model selected
> select up
856 atoms, 879 bonds, 111 residues, 1 model selected
> color sel orange
> select clear
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #4 models
Drag select of 3 residues
> select up
40 atoms, 39 bonds, 6 residues, 1 model selected
> select up
856 atoms, 879 bonds, 111 residues, 1 model selected
> color sel #ff26001f
> color sel #ff2600b7
> color sel #ff2600ff
> color sel #ff2600f6
> color sel #ff2600ef
> color sel #ff2600e9
> color sel #ff2600e3
> color sel #ff2600ff
> color sel #00f900ff
> ui tool show "Color Actions"
> color sel lawn green
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> show #!6 models
Drag select of 20 residues
> select up
300 atoms, 301 bonds, 40 residues, 1 model selected
> select up
856 atoms, 879 bonds, 111 residues, 1 model selected
> color sel #73fdffff
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #4 models
Drag select of 16 residues
> select up
532 atoms, 541 bonds, 72 residues, 1 model selected
> select up
856 atoms, 879 bonds, 111 residues, 1 model selected
> color sel #73fdffff
> color sel #73fdffb7
> color sel #73fdff6a
> color sel #ffd479ff
> color sel orange
> select clear
> hide #4 models
> hide #!3 models
> show #!1 models
> show #!2 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #!1 models
> hide #!2 models
> show #4 models
> show #!5 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!3 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/sars2.png
> width 802 height 693 supersample 3 transparentBackground true
> hide #!3 models
> hide #4 models
> show #!6 models
> show #!5 models
> save /Users/apple/Library/CloudStorage/OneDrive-
> 个人/SARS1-IgG-2022-张林琦/6H2_manuscript/6H2_figures/6H2_figure_pieces/Fig3/A/OMI.png
> width 802 height 693 supersample 3 transparentBackground true
> show #!1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> show #1.4 models
> hide #!1 models
> hide #1.4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> show #4 models
> hide #4 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #1.2 models
> hide #!1 models
> hide #1.2 models
> hide #!2 models
> show #1.3 models
> hide #1.3 models
> show #1.2 models
> select #1/A:1180,433,1183,333,437,1184,431,1185,430,428,431
44 atoms, 39 bonds, 6 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select #1/A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:328
7 atoms, 6 bonds, 1 residue, 1 model selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.5.8
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir8,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.6 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)
OS Loader Version: 540.100.7~23
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 3 days 47 minutes
Graphics/Displays:
Intel UHD Graphics 617:
Chipset Model: Intel UHD Graphics 617
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x87c0
Revision ID: 0x0002
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash processing geometry change |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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