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Opened 4 years ago
Last modified 4 years ago
#5459 accepted defect
MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| 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: 1.2.dev202103170256 (2021-03-17 02:56:09 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.dev202103170256 (2021-03-17)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/zhaixiuwen/Desktop/文章图/fig3/构象-1.cxs format session
Opened Terip_PTH1R_Gs_j139_j184_combined.mrc as #1, grid size 224,224,224,
pixel 1.01, shown at level 0.278, step 1, values float32
Opened Aba_PTH1R_Gs_j056_j103_combined.mrc as #3, grid size 224,224,224, pixel
1.01, shown at level 0.278, step 1, values float32
Log from Fri Sep 17 21:16:27 2021UCSF ChimeraX version: 1.2.dev202103170256
(2021-03-17)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/zhaixiuwen/Desktop/文章图/fig1/cartoons.cxs format session
Opened Terip_PTH1R_Gs_j139_j184_combined.mrc as #1, grid size 224,224,224,
pixel 1.01, shown at level 0.278, step 1, values float32
Opened Aba_PTH1R_Gs_j056_j103_combined.mrc as #3, grid size 224,224,224, pixel
1.01, shown at level 0.278, step 1, values float32
Log from Fri Sep 17 14:01:39 2021UCSF ChimeraX version: 1.2.dev202103170256
(2021-03-17)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/zhaixiuwen/Desktop/结构分析图/fig1/ter-map.cxs format session
Opened Terip_PTH1R_Gs_j139_j184_combined.mrc as #1, grid size 224,224,224,
pixel 1.01, shown at level 0.278, step 1, values float32
Log from Wed Jun 30 18:23:37 2021UCSF ChimeraX version: 1.2.dev202103170256
(2021-03-17)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/zhaixiuwen/Desktop/PTH1R-structure/Terip_PTH1R_Gs_j139_j184_combined.mrc
> /Users/zhaixiuwen/Desktop/PTH1R-structure/Terip_PTH1R_Gs-
> coot-17_real_space_refined.pdb
Summary of feedback from opening
/Users/zhaixiuwen/Desktop/PTH1R-structure/Terip_PTH1R_Gs-
coot-17_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 3193
TER
Ignored bad PDB record found on line 3482
TER
Ignored bad PDB record found on line 5341
TER
Ignored bad PDB record found on line 7943
TER
Ignored bad PDB record found on line 8389
TER
2 messages similar to the above omitted
Opened Terip_PTH1R_Gs_j139_j184_combined.mrc as #1, grid size 224,224,224,
pixel 1.01, shown at level 0.0319, step 1, values float32
Chain information for Terip_PTH1R_Gs-coot-17_real_space_refined.pdb #2
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> set bgColor white
> hide #!1 models
> style stick
Changed 9218 atom styles
> show cartoons
> hide cartoons
> show cartoons
> hide atoms
> select /R:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
278 atoms, 288 bonds, 33 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select down
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #004f72ff
> select /A:36
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
228 atoms, 228 bonds, 26 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #ebb128ff
> color sel #2afdeeff
> color sel #2afdeeff
> color sel #2afdedff
> color sel #27fde5ff
> color sel #27fde3ff
> color sel #26fde0ff
> color sel #26fde0ff
> color sel #26fde0ff
> color sel #26fddfff
> color sel #26fddfff
> color sel #25fddcff
> color sel #25fddaff
> color sel #22fbd2ff
> color sel #21fbcdff
> color sel #1ffac6ff
> color sel #1ff8bfff
> color sel #1ff7beff
> color sel #1ff7beff
> color sel #1ff7bdff
> color sel #1bf6b2ff
> color sel #1bf4aeff
> color sel #18f2a5ff
> color sel #16f09cff
> color sel #15f097ff
> color sel #15ef96ff
> color sel #15ef96ff
> color sel #16ee97ff
> color sel #16ed97ff
> color sel #16eb96ff
> color sel #17ea99ff
> color sel #18e798ff
> color sel #1ae5a0ff
> color sel #1ce4a5ff
> color sel #1ce1a7ff
> color sel #20dfadff
> color sel #20ddb2ff
> color sel #23dcbbff
> color sel #23dabaff
> color sel #25d9bdff
> color sel #24d8bdff
> color sel #25d7bfff
> color sel #24d6bfff
> color sel #24d5beff
> color sel #25d3beff
> color sel #24d0baff
> color sel #24cab5ff
> color sel #25c3b1ff
> color sel #25bcafff
> color sel #25a8a5ff
> color sel #25a2a1ff
> color sel #259ea0ff
> color sel #249d9eff
> color sel #259a9eff
> color sel #25999eff
> color sel #25969dff
> color sel #258d9cff
> color sel #25809aff
> color sel #267199ff
> color sel #275b98ff
> color sel #274c98ff
> color sel #274499ff
> color sel #274099ff
> color sel #273c99ff
> color sel #273798ff
> color sel #27369aff
> color sel #28379aff
> color sel #28399cff
> color sel #283a9fff
> color sel #293aa6ff
> color sel #2c42b4ff
> color sel #2e50c9ff
> color sel #315dddff
> color sel #336df0ff
> color sel #3479f8ff
> color sel #3479faff
> color sel #3478fbff
> color sel #347bfaff
> color sel #3482f8ff
> color sel #3485f9ff
> color sel #3388f8ff
> color sel #338bf7ff
> color sel #3399f9ff
> color sel #32aef8ff
> color sel #30d5f8ff
> color sel #2df8f6ff
> color sel #2af8e7ff
> color sel #21f7c6ff
> color sel #19f8aaff
> color sel #12f794ff
> color sel #07f782ff
> color sel #00f96cff
> color sel #00f960ff
> color sel #00f94fff
> color sel #00fb44ff
> color sel #00fc3cff
> color sel #00fb33ff
> color sel #00fc2eff
> color sel #00fc2cff
> color sel #00fd2bff
> color sel #00fd2aff
> color sel #00fd2aff
> color sel #00fd2aff
> color sel #00fc29ff
> color sel #00fd29ff
> color sel #27fc29ff
> color sel #4efa29ff
> color sel #aaf42bff
> color sel #c2f22bff
> color sel #cfef2bff
> color sel #d3ef2cff
> color sel #dbec2cff
> color sel #e6e72bff
> color sel #e2de2aff
> color sel #dcc828ff
> color sel #d8b125ff
> color sel #d4a724ff
> color sel #d1a123ff
> color sel #cf9f22ff
> color sel #cf9e22ff
> color sel #ce9d22ff
> color sel #c89922ff
> color sel #bf9222ff
> color sel #b48a22ff
> color sel #a58020ff
> color sel #997a20ff
> color sel #8f791fff
> color sel #8a771fff
> color sel #877820ff
> color sel #867920ff
> color sel #847820ff
> color sel #857a20ff
> color sel #887c20ff
> color sel #908221ff
> color sel #978922ff
> color sel #9f9022ff
> color sel #a79924ff
> color sel #b1a024ff
> color sel #b8a825ff
> color sel #beac25ff
> color sel #c3b026ff
> color sel #c7b526ff
> color sel #ccb926ff
> color sel #cfbc27ff
> color sel #d1bf27ff
> color sel #d5c127ff
> color sel #d6c227ff
> color sel #d8c428ff
> color sel #d8c729ff
> color sel #d7c728ff
> color sel #d9c829ff
> color sel #d9c929ff
> color sel #dacb29ff
> color sel #dccc29ff
> color sel #ddce29ff
> color sel #ded029ff
> color sel #dfd029ff
> color sel #dfcf29ff
> color sel #dfcf29ff
> color sel #e0cb28ff
> color sel #dfc328ff
> color sel #e0be26ff
> color sel #e2b124ff
> color sel #e2ac24ff
> color sel #e3ac24ff
> color sel #e3ab24ff
> color sel #e3a723ff
> color sel #e4a523ff
> color sel #e6a723ff
> color sel #e8a723ff
> color sel #eaa021ff
> color sel #eb9f21ff
> color sel #ed9b20ff
> color sel #ee9b21ff
> color sel #ef9b21ff
> color sel #ef9b21ff
> color sel #ffc85fff
> color sel #f2ad23ff
> color sel #f2ad23ff
> color sel #f2ad23ff
> color sel #f2b424ff
> color sel #f1b424ff
> color sel #f1b324ff
> color sel #ffd479ff
> color sel #f4c726ff
> color sel #f4c726ff
> color sel #f4c926ff
> color sel #f5ca26ff
> color sel #f5d428ff
> color sel #f5d528ff
> color sel #f4de29ff
> color sel #f5de29ff
> color sel #f5e32aff
> color sel #f4e32aff
> color sel #f4e32aff
> color sel #f4e32aff
> color sel #f4e32aff
> color sel #f3e22aff
> color sel #f4de29ff
> color sel #f4d428ff
> color sel #f4d228ff
> color sel #f4ce27ff
> color sel #f4ce27ff
> color sel #f4ce27ff
> color sel #f4cc27ff
> color sel #f4c826ff
> color sel #f4c826ff
> color sel #f4c726ff
> color sel #f4c726ff
> color sel #f4be25ff
> color sel #f4bb25ff
> color sel #f4b624ff
> color sel #f4b023ff
> color sel #f4ae23ff
> color sel #f4a621ff
> color sel #f4a621ff
> color sel #f4a521ff
> color sel #f49e20ff
> color sel #f49e20ff
> color sel #f59f20ff
> color sel #f59f20ff
> color sel #ffce64ff
> color sel #f7a046ff
> select /N:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #98cabfff
> select clear
> select /B:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
43 atoms, 44 bonds, 5 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #eeb528ff
> select /G:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #e8e0afff
> select clear
> select /B:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
43 atoms, 44 bonds, 5 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #bf5e1aff
> select clear
> select /P:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #b1ccc2ff
> select clear
> select clear
Drag select of 1153 residues, 10 pseudobonds
> transparency sel 30 cartoons
> select clear
> show #!1 models
> ui tool show "Fit in Map"
Fit molecule Terip_PTH1R_Gs-coot-17_real_space_refined.pdb (#2) to map
Terip_PTH1R_Gs_j139_j184_combined.mrc (#1) using 9218 atoms
average map value = 0.4651, steps = 40
shifted from previous position = 0.0205
rotated from previous position = 0.0285 degrees
atoms outside contour = 582, contour level = 0.031863
Position of Terip_PTH1R_Gs-coot-17_real_space_refined.pdb (#2) relative to
Terip_PTH1R_Gs_j139_j184_combined.mrc (#1) coordinates:
Matrix rotation and translation
0.99999990 -0.00018575 0.00040398 -0.03236053
0.00018566 0.99999996 0.00022269 -0.04731326
-0.00040402 -0.00022261 0.99999989 0.09539565
Axis -0.44775164 0.81243964 0.37344384
Axis point 225.30823905 0.00000000 67.21980783
Rotation angle (degrees) 0.02849111
Shift along axis 0.01167523
> volume #1 level 0.2332
> volume #1 level 0.2779
> ui tool show "Color Zone"
> color zone #1 near #2 distance 6.08
> hide #!2 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/zhaixiuwen/Desktop/movie1.mp4
Movie saved to /Users/zhaixiuwen/Desktop/movie1.mp4
> hide #!1 models
> show #!2 models
> save /Users/zhaixiuwen/Desktop/image10.png supersample 3
> select clear
Drag select of 1153 residues, 10 pseudobonds
> transparency sel 30 cartoons
> select clear
> hide #!2 models
> show #!1 models
> save /Users/zhaixiuwen/Desktop/image11.png supersample 3
> show #!2 models
> hide #!1 models
> select /R:195
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
261 atoms, 264 bonds, 33 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #3186a9ff
> select clear
> show #!1 models
> color zone #1 near #2 distance 6.08
> save /Users/zhaixiuwen/Desktop/image12.png supersample 3
> hide #!1 models
> save /Users/zhaixiuwen/Desktop/image13.png supersample 3
> save /Users/zhaixiuwen/Desktop/结构分析图/fig1/ter-map.cxs
——— End of log from Wed Jun 30 18:23:37 2021 ———
opened ChimeraX session
> select /R:440
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
226 atoms, 234 bonds, 26 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select down
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #5766aeff
> select /A:385
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /B:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select down
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #f9f871ff
> select /A:334
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
172 atoms, 175 bonds, 20 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #f276a0ff
> select /N:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> select clear
> select /P:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #b06bb4ff
> color sel #f276a0ff
> select clear
> set bgColor black
> select /N:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #ff9481ff
> select /A:374
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #b06bb4ff
> select clear
> select /R:342
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
122 atoms, 125 bonds, 16 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #4378b7ff
> select /P:19
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /P:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #00d7afff
> color sel #00bccbff
> select clear
> select /G:39
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #95ec89ff
> select clear
> select /A:380
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #f9f871ff
> select /B:71
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #00d7afff
> select /A:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
228 atoms, 228 bonds, 26 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #009bcfff
> select clear
> set bgColor white
> volume #1 transparency 0.3
> show #!1 models
> hide #!2 models
> volume #1 transparency 0.9
> volume #1 transparency 0.5
> volume #1 transparency 0.3
> hide #!1 models
> show #!2 models
> select /R:361
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
246 atoms, 250 bonds, 30 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #cf6db8ff
> select /A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:32
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
228 atoms, 228 bonds, 26 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #fd75a3ff
> select /B:306
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:306
4 atoms, 3 bonds, 1 residue, 1 model selected
> set bgColor black
> select /B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
52 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #ff8b88ff
> select /N:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #ffac6fff
> select clear
> select /G:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #ffd264ff
> select clear
> set bgColor white
> select /A:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
228 atoms, 228 bonds, 26 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #8d78cfff
> select /B:338
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
50 atoms, 52 bonds, 5 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #1a80cdff
> select /N:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #0080b1ff
> select /G:35
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #007986ff
> select /P:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #006e58ff
> select clear
> select /P:20
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #007986ff
> select clear
> select /B:234
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /G:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #006e58ff
> select clear
Drag select of 1153 residues, 10 pseudobonds
> trasparency sel 80 cartoons
Unknown command: trasparency sel 80 cartoons
> transparency sel 80 cartoons
> transparency sel 30 cartoons
> select /R:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 6.08
> volume #1 transparency 0.3
> hide #!2 models
> hide #!1 models
> show #!2 models
> select /P:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #cf6db8ff
> select /R:343
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
122 atoms, 125 bonds, 16 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #8d78cfff
> select clear
> select /A:382
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #1a80cdff
> select /B:71
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select down
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #0080b1ff
> color sel #8bb0f7ff
> color sel #0080b1ff
> select clear
> select /N:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #007986ff
> select clear
> show #!1 models
> color zone #1 near #2 distance 6.08
> hide #!2 models
> show #!2 models
> hide #!1 models
> select /P:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #f8f770ff
> select /R:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
261 atoms, 264 bonds, 33 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #ffac6fff
> color sel #ff8b88ff
> select clear
> select /A:381
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #ffac6fff
> select /B:294
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
43 atoms, 44 bonds, 5 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #cf6db8ff
> select /N:36
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
57 atoms, 58 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #fd75a3ff
> color sel #ff8b88ff
> color sel #ffac6fff
> color sel #fd75a3ff
> select clear
> select /G:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #cf6db8ff
> color sel #ffd264ff
> select clear
> show #!1 models
> color zone #1 near #2 distance 6.08
> volume #1 transparency 0.3
> hide #!1 models
> select /R:442
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
226 atoms, 234 bonds, 26 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select down
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #8ea8dcff
> select clear
> select /P:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> color sel #fe9172ff
> select /A:380
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:218
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:373
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #81af88ff
> select /B:71
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #fec985ff
> select clear
> select /N:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /G:20
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
174 atoms, 173 bonds, 21 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select down
174 atoms, 173 bonds, 21 residues, 1 model selected
> select clear
> select /G:39
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #f3cfc4ff
> select clear
> select /N:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #d4c4bdff
> color sel #679a92ff
> color sel #e9d0f9ff
> select clear
> show #!1 models
> color zone #1 near #2 distance 6.08
> volume #1 transparency 0.3
> hide #!1 models
> hide #!2 models
> show #!2 models
> select /R:43
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
196 atoms, 197 bonds, 23 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select down
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #6dadaeff
> select clear
> select /A:382
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #7081acff
> select /G:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #ccdfdbff
> select clear
> select /B:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:36
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
228 atoms, 228 bonds, 26 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #759d79ff
> select clear
> select /A:374
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #709b9aff
> color sel #898ba2ff
> select clear
> select /N:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #afccaeff
> transparency sel 80 cartoons
Drag select of 1120 residues, 10 pseudobonds
> transparency sel 80 cartoons
> transparency sel 40 cartoons
> select clear
> show #!1 models
> color zone #1 near #2 distance 6.08
> volume #1 transparency 0.3
> select clear
> volume #1 transparency 0.2
> hide #!1 models
> open
> /Users/zhaixiuwen/Desktop/PTH1R-structure/Aba_PTH1R_Gs_j056_j103_combined.mrc
Opened Aba_PTH1R_Gs_j056_j103_combined.mrc as #3, grid size 224,224,224, pixel
1.01, shown at level 0.031, step 1, values float32
> volume #3 level 0.2746
> color zone #1 near #2 distance 6.08
> color zone #1 near #2 distance 6.08
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> color zone #1 near #2 distance 6.08
> hide #!1 models
> hide #!2 models
> open /Users/zhaixiuwen/Desktop/PTH1R-structure/Aba_PTH1R_Gs-
> coot-14_real_space_refined.pdb
Summary of feedback from opening
/Users/zhaixiuwen/Desktop/PTH1R-structure/Aba_PTH1R_Gs-
coot-14_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 3188
TER
Ignored bad PDB record found on line 3462
TER
Ignored bad PDB record found on line 5321
TER
Ignored bad PDB record found on line 7923
TER
Ignored bad PDB record found on line 8369
TER
2 messages similar to the above omitted
Chain information for Aba_PTH1R_Gs-coot-14_real_space_refined.pdb #4
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> style #!4 stick
Changed 9203 atom styles
> show #!4 cartoons
> hide #!4 atoms
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> ui tool show "Model Panel"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #4/R:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
241 atoms, 244 bonds, 31 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
Drag select of 1153 residues, 10 pseudobonds
> transparency sel 0 cartoons
> select clear
> color #2 #89d2d3ff
> select clear
> undo
> undo
> undo
> show #!4 models
> hide #!2 models
> select #4/R:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
278 atoms, 288 bonds, 33 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> color sel #6dadaeff
> select clear
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!4 models
> color #2 #ffffffff
> undo
> select clear
> hide #!2 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
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> show #!2 models
> hide #!2 models
> show #!4 models
> select #4/B:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
171 atoms, 170 bonds, 20 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel #fcd578ff
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> select #4/G:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 14 residues, 1 model selected
> select up
445 atoms, 451 bonds, 58 residues, 1 model selected
> color sel #a2b2bfff
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> select #4/N:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
961 atoms, 983 bonds, 126 residues, 1 model selected
> color sel #8db384ff
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!2 models
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> show #!2 models
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> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> select #4/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
226 atoms, 226 bonds, 26 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> color sel #898ba2ff
> select clear
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> show #!3 models
> color zone #1 near #2 distance 6.08
> color zone #3 near #4 distance 6.08
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> select #4/P:14
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
244 atoms, 245 bonds, 29 residues, 1 model selected
> select up
273 atoms, 275 bonds, 33 residues, 1 model selected
> color sel #8588efff
> color sel #ebcff8ff
> color sel #ff8063ff
> show #!2 models
> hide #!2 models
> color sel #759d79ff
> color sel #f0a592ff
> show #!2 models
> hide #!2 models
> color sel #bbadc6ff
> show #!2 models
> select clear
> ui tool show Matchmaker
> matchmaker #!4 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 Terip_PTH1R_Gs-coot-17_real_space_refined.pdb, chain R (#2) with
Aba_PTH1R_Gs-coot-14_real_space_refined.pdb, chain R (#4), sequence alignment
score = 1983.7
RMSD between 318 pruned atom pairs is 0.613 angstroms; (across all 373 pairs:
1.419)
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> color zone #3 near #4 distance 6.08
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> select #2/P:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> select ~sel
18133 atoms, 18545 bonds, 20 pseudobonds, 2271 residues, 8 models selected
> transparency sel 1000 cartoons
> select clear
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> show #!4 models
> undo
> show #!4 models
Drag select of 2253 residues, 20 pseudobonds
> transparency sel 30 cartoons
> select clear
> hide #!4 models
> select #2/P:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> select clear
> select #2/R:146
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
49 atoms, 50 bonds, 5 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select subtract #2/P:29
9209 atoms, 9420 bonds, 1152 residues, 1 model selected
> select down
9209 atoms, 9420 bonds, 1152 residues, 1 model selected
> select down
9209 atoms, 9420 bonds, 1152 residues, 1 model selected
> select clear
> select #2/P:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
Drag select of 911 residues, 8 pseudobonds
> hide sel cartoons
> select #2/R:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
261 atoms, 264 bonds, 33 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
Drag select of 1186 residues, 10 pseudobonds
> transparency sel 0 cartoons
> select clear
> save /Users/zhaixiuwen/Desktop/文章图/fig1/cartoons.cxs
> save /Users/zhaixiuwen/Desktop/文章图/fig1/cartoons.tif width 991 height 859
> supersample 3
Drag select of 1186 residues, 10 pseudobonds
> transparency sel 0 cartoons
> select clear
> hide #!2 models
> save /Users/zhaixiuwen/Desktop/文章图/fig1/abl-pth1r.tif width 991 height 859
> supersample 3
> hide #!4 models
> show #!2 models
Drag select of 34 residues
> show sel cartoons
> show sel cartoons
> select #2/P
288 atoms, 293 bonds, 34 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
Drag select of 34 residues
> select #2/R
3065 atoms, 3161 bonds, 4 pseudobonds, 373 residues, 2 models selected
> show sel cartoons
> transparency sel 0 cartoons
> select clear
> save /Users/zhaixiuwen/Desktop/文章图/fig1/ter-pth1r.tif width 991 height 859
> supersample 3
> select #2/R
3065 atoms, 3161 bonds, 4 pseudobonds, 373 residues, 2 models selected
> hide sel cartoons
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> color zone #3 near #4 distance 6.08
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.278
> hide #!1 models
> save /Users/zhaixiuwen/Desktop/文章图/fig1/ter-map.tif width 991 height 859
> supersample 3
> hide #!3 models
> show #!1 models
> save /Users/zhaixiuwen/Desktop/文章图/fig1/ter-map.tif width 991 height 859
> supersample 3
> hide #!1 models
> show #!3 models
> save /Users/zhaixiuwen/Desktop/文章图/fig1/abl-map.tif width 991 height 859
> supersample 3
> save /Users/zhaixiuwen/Desktop/文章图/fig1/cartoons.cxs
——— End of log from Fri Sep 17 14:01:39 2021 ———
opened ChimeraX session
> hide #!3 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> select #2/P:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> show sel cartoons
> select clear
> select #2/P:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
264 atoms, 268 bonds, 31 residues, 1 model selected
> select up
288 atoms, 293 bonds, 34 residues, 1 model selected
> select up
9218 atoms, 9428 bonds, 1153 residues, 1 model selected
> select up
18421 atoms, 18838 bonds, 2305 residues, 6 models selected
> transparency sel 0 cartoons
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
Drag select of 1440 residues, 12 pseudobonds
> hide sel cartoons
> select #2/A:382
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
207 atoms, 209 bonds, 23 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> hide sel cartoons
> select #4/A:381
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
195 atoms, 196 bonds, 22 residues, 1 model selected
> select up
1858 atoms, 1892 bonds, 224 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> select #4/R:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
216 atoms, 217 bonds, 25 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> show #!2 models
> select clear
> hide #!4 models
> select #2/R:145
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!4 models
> select clear
> select #4/R:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
241 atoms, 244 bonds, 31 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9203 atoms, 9410 bonds, 1152 residues, 1 model selected
> select up
18421 atoms, 18838 bonds, 2305 residues, 6 models selected
> select down
9203 atoms, 9410 bonds, 1152 residues, 1 model selected
> show sel cartoons
> undo
> select clear
> select #2/R:467
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
135 atoms, 138 bonds, 16 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> show sel cartoons
> hide #!2 models
> select #4/R:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
241 atoms, 244 bonds, 31 residues, 1 model selected
> select up
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> select up
9203 atoms, 9410 bonds, 1152 residues, 1 model selected
> select down
3065 atoms, 3161 bonds, 373 residues, 1 model selected
> show sel cartoons
> select clear
> show #!2 models
> save /Users/zhaixiuwen/Desktop/文章图/fig3/构象-1.cxs
——— End of log from Fri Sep 17 21:16:27 2021 ———
opened ChimeraX session
> select #1
2 models selected
> close #1
> close #3
> open /Users/zhaixiuwen/Desktop/PTH1R-structure/LAPTH-PTH1R-DNGs.pdb
LAPTH-PTH1R-DNGs.pdb title:
Cryo-em structure of parathyroid hormone receptor type 1 In complex with A
long-acting parathyroid hormone analog and G protein [more info...]
Chain information for LAPTH-PTH1R-DNGs.pdb #1
---
Chain | Description
A | GS protein α subunit
B | transducin β chain 1
G | G γ-I
N | nanobody-35
P | long-acting parathyroid hormone analog
R | parathyroid hormone/parathyroid hormone-related peptide receptor
Non-standard residues in LAPTH-PTH1R-DNGs.pdb #1
---
CLR — cholesterol
PLM — palmitic acid
> show cartoons
> hide atoms
> select clear
> ui tool show Matchmaker
> matchmaker #4/R to #1/R 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 LAPTH-PTH1R-DNGs.pdb, chain R (#1) with Aba_PTH1R_Gs-
coot-14_real_space_refined.pdb, chain R (#4), sequence alignment score =
1791.7
RMSD between 262 pruned atom pairs is 0.496 angstroms; (across all 368 pairs:
2.343)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #4/R to #2/R 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 Terip_PTH1R_Gs-coot-17_real_space_refined.pdb, chain R (#2) with
Aba_PTH1R_Gs-coot-14_real_space_refined.pdb, chain R (#4), sequence alignment
score = 1983.7
RMSD between 318 pruned atom pairs is 0.613 angstroms; (across all 373 pairs:
1.419)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> select clear
> close session
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 11.6 (20G165)
Kernel Version: Darwin 20.6.0
Time since boot: 1 day 22:02
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Acer EH273U:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 941007943LAJ
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: DVI or HDMI
Adapter Firmware Version: 2.55
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: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.4
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.11.2
ChimeraX-AtomicLibrary: 2.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202103170256
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0.1
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
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.3
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3
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: 1.0.1
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.17
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (1)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted |
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