![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#4684 closed defect (duplicate)
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-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202104240152 (2021-04-24 01:52:36 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears'-discard.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0137, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 2, values float32
Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 1, values float32
Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown
at level 0.00634, step 1, values float32
Log from Sun May 23 03:46:49 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears-BT.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0137, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 2, values float32
Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 1, values float32
Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown
at level 0.00634, step 1, values float32
Log from Wed May 19 14:45:04 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0137, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 2, values float32
Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 1, values float32
Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown
at level 0.00634, step 1, values float32
Log from Tue May 18 20:24:40 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0181, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 2, values float32
Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 1, values float32
Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown
at level 0.00634, step 1, values float32
Log from Mon May 17 05:23:44 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs format
> session
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0181, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 2, values float32
Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 1, values float32
Log from Mon May 17 03:52:16 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs format
> session
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0181, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00589, step 2, values float32
Log from Mon May 17 03:37:02 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs format
> session
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0179, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00553, step 2, values float32
Log from Sun May 16 01:36:06 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Desktop/paper/Figs2021Apr/20210427_colorB_1.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0179, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown
at level 0.023, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Opened whole-j532post copy.mrc 1 as #6.2, grid size 210,210,210, pixel 1.66,
shown at level 0.014, step 1, values float32
Opened whole-j532post copy.mrc 2 as #6.3, grid size 210,210,210, pixel 1.66,
shown at level 0.0153, step 1, values float32
Opened whole-j532post copy.mrc 3 as #6.4, grid size 210,210,210, pixel 1.66,
shown at level 0.0153, step 1, values float32
Log from Tue Apr 27 22:25:14 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0204, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown
at level 0.0244, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Log from Tue Apr 27 19:58:11 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0204, step 1, values float32
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0314, step 1, values float32
Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown
at level 0.0244, step 1, values float32
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
Log from Tue Apr 27 19:38:10 2021UCSF ChimeraX version: 1.3.dev202104240152
(2021-04-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/miao/Downloads/coot/Figs2021Apr/whole-j532post copy.mrc"
Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown
at level 0.0217, step 1, values float32
> open "/Users/miao/Downloads/coot/Figs2021Apr/core-j577post copy.mrc"
Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown
at level 0.0168, step 1, values float32
> open "/Users/miao/Downloads/coot/Figs2021Apr/Ears-j544post copy.mrc"
Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown
at level 0.017, step 1, values float32
> open "/Users/miao/Downloads/coot/Figs2021Apr/C2E-j542post copy.mrc"
Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown
at level 0.0218, step 1, values float32
> select #4
2 models selected
> select #2
2 models selected
> ~select #2
Nothing selected
> select #2
2 models selected
> ~select #2
Nothing selected
> volume #2 level 0.0255
> hide #!1 models
> hide #!3 models
> hide #!4 models
> volume #1 level 0.02176
> hide #!1 models
> volume #2 level 0.02985
> volume #2 level 0.02923
> volume #2 level 0.0314
> surface dust #2 size 16.6
> show #!4 models
> select #4
2 models selected
> select #2
2 models selected
> ~select #2
Nothing selected
> select #2
2 models selected
> fitmap #2 inMap #4
Fit map core-j577post copy.mrc in map C2E-j542post copy.mrc using 38598 points
correlation = 0.9669, correlation about mean = 0.3607, overlap = 45.22
steps = 48, shift = 0.474, angle = 0.526 degrees
Position of core-j577post copy.mrc (#2) relative to C2E-j542post copy.mrc (#4)
coordinates:
Matrix rotation and translation
0.99998434 0.00483252 -0.00282164 -0.40654303
-0.00481186 0.99996191 0.00728217 -0.04881033
0.00285672 -0.00726848 0.99996950 0.90466921
Axis -0.79264881 -0.30932952 -0.52537901
Axis point 0.00000000 114.43819001 13.16112241
Rotation angle (degrees) 0.52589670
Shift along axis -0.13794989
> ~select #2
Nothing selected
> select #3
2 models selected
> hide #!2 models
> show #!3 models
> hide #!4 models
> volume #3 level 0.02268
> volume #3 level 0.02438
> surface dust #3 size 16.6
> select #4
2 models selected
> show #!4 models
> ~select #4
Nothing selected
> select #4
2 models selected
> ~select #3
2 models selected
> select #3
2 models selected
> fitmap #3 inMap #4
Fit map Ears-j544post copy.mrc in map C2E-j542post copy.mrc using 35585 points
correlation = 0.9916, correlation about mean = 0.6487, overlap = 29.37
steps = 44, shift = 0.351, angle = 0.267 degrees
Position of Ears-j544post copy.mrc (#3) relative to C2E-j542post copy.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999306 0.00243421 -0.00281987 -0.02007499
-0.00244208 0.99999313 -0.00278912 0.39707369
0.00281306 0.00279599 0.99999213 -0.85931214
Axis 0.59981627 -0.60495218 -0.52369200
Axis point 268.51643092 0.00000000 -49.84611442
Rotation angle (degrees) 0.26675196
Shift along axis 0.19776299
> ~select #3
Nothing selected
> hide #!3 models
> show #!1 models
> select #1
2 models selected
> hide #!4 models
> volume #1 level 0.02077
> volume #1 level 0.02037
> show #!4 models
> select #4
2 models selected
> ~select #4
Nothing selected
> select #4
2 models selected
> ~select #1
2 models selected
> select #1
2 models selected
> fitmap #1 inMap #4
Fit map whole-j532post copy.mrc in map C2E-j542post copy.mrc using 128057
points
correlation = 0.8969, correlation about mean = 0.05034, overlap = 52.69
steps = 88, shift = 0.852, angle = 5.6 degrees
Position of whole-j532post copy.mrc (#1) relative to C2E-j542post copy.mrc
(#4) coordinates:
Matrix rotation and translation
0.99626467 -0.06341774 0.05860803 2.02692477
0.06067742 0.99703082 0.04741101 -18.37332373
-0.06144072 -0.04367773 0.99715460 18.85954601
Axis -0.46660987 0.61496004 0.63568811
Axis point 300.81511332 12.36084184 0.00000000
Rotation angle (degrees) 5.60138469
Shift along axis -0.25585376
> ~select #1
Nothing selected
> select #1
2 models selected
> ~select #1
Nothing selected
> save /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs
——— End of log from Tue Apr 27 19:38:10 2021 ———
opened ChimeraX session
> open "/Users/miao/Downloads/coot/Figs2021Apr/j532_fitall copy.pdb"
Summary of feedback from opening
/Users/miao/Downloads/coot/Figs2021Apr/j532_fitall copy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 24
SER A 39 1 16
Start residue of secondary structure not found: HELIX 2 2 GLY A 44 LYS A 54 1
11
Start residue of secondary structure not found: HELIX 3 3 THR A 58 LEU A 67 1
10
Start residue of secondary structure not found: HELIX 4 4 VAL A 119 SER A 123
1 5
Start residue of secondary structure not found: HELIX 5 5 GLY A 125 GLY A 143
1 19
160 messages similar to the above omitted
End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B
354 0
Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B
391 0
Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B
432 0
Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B
451 0
Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B
458 0
Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B
514 0
231 messages similar to the above omitted
End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B
354 0
Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B
391 0
Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B
432 0
Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B
451 0
Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B
458 0
Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B
514 0
468 messages similar to the above omitted
End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B
354 0
Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B
391 0
Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B
432 0
Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B
451 0
Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B
458 0
Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B
514 0
468 messages similar to the above omitted
End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B
354 0
Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B
391 0
Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B
432 0
Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B
451 0
Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B
458 0
Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B
514 0
66 messages similar to the above omitted
j532_fitall copy.pdb title:
Crystal structure of the acyl-coa carboxylase, ACCD5, from mycobacterium
tuberculosis [more info...]
Chain information for j532_fitall copy.pdb
---
Chain | Description
5.4/? 5.6/? | No description available
5.1/A 5.1/B 5.1/C 5.1/D 5.1/E 5.1/F | probable propionyl-coa carboxylase β
chain 5
5.2/A 5.3/A 5.5/A 5.7/A 5.2/B 5.3/B 5.5/B 5.7/B | probable propionyl-coa
carboxylase β chain 5
> hide #!1 models
> hide #!4 models
> color bychain
> color byhetero
> color bychain
> style sphere
Changed 56388 atom styles
> style sphere
Changed 56388 atom styles
> color bychain
> hide #5.1 models
> show #5.1 models
> color #5.1 #fffb00
> hide #5.1 models
> show #5.1 models
> hide #!5.2 models
> show #!5.2 models
> color #5.1 #8efa00
> color #5.1 #fffb00
> hide #!5.2 models
> show #!5.2 models
> color #5.2 #d4fb79
> color #5.2 #8efa00
> hide #!5.3 models
> show #!5.3 models
> hide #!5.3 models
> show #!5.3 models
> color #5.2 #4f8f00
> color #5.2 #8efa00
> color #5.3 #008f00
> color #5.3 #4f8f00
> color #5.3 #008f00
> color #5.3 #009051
> color #5.3 #008f00
> hide #5.4 models
> show #5.4 models
> hide #!5.5 models
> show #!5.5 models
> color #5.5 #7a81ff
> hide #5.6 models
> show #5.6 models
> hide #!5.7 models
> show #!5.7 models
> color #5.7 #0433ff
> color #5.7 #9437ff
> hide #!5.5 models
> show #!5.5 models
> color #5.5 #d783ff
> color #5.5 #ff85ff
> color #5.5 #ff8ad8
> color #5.5 #ff2f92
> color #5.5 #d783ff
> hide #5.6 models
> show #5.6 models
> color #5.6 #ff9300
> color #5.6 #ffd479
> color #5.6 #ff9300
> color #5.6 #ffd479
> color #5.6 #d4fb79
> color #5.6 #ffd479
> color #5.6 #ff7e79
> color #5.6 #ff9300
> set bgColor white
> hide #5.4 models
> show #5.4 models
> color #5.6 #0096ff
> color #5.6 #ff9300
> hide #5.4 models
> show #5.4 models
> color #5.4 #0096ff
> color #5.4 #9437ff
> color #5.4 #0433ff
> color #5.4 #0096ff
> hide #!5.5 models
> show #!5.5 models
> color #5.5 #0433ff
> hide #!5.7 models
> show #!5.7 models
> color #5.7 #0096ff
> hide #5.4 models
> color #5.4 #9437ff
> show #5.4 models
> undo
[Repeated 8 time(s)]
> color #5.4 #7a81ff
> save /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs
> color #5.2 #73fa79
> color #5.2 #00f900
> color #5.2 #00fa92
> color #5.2 #00f900
> color #5.3 #009051
> color #5.3 #008f00
> save /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs
——— End of log from Tue Apr 27 19:58:11 2021 ———
opened ChimeraX session
> hide #!5 models
> show #!5 models
> color bychain
> show #!1 models
> volume #1 level 0.01991
> hide #!1 models
> show #!3 models
> hide #!3 models
Drag select of 1894 residues, 8 pseudobonds
> select up
14615 atoms, 14927 bonds, 8 pseudobonds, 1919 residues, 5 models selected
> show #!3 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 7 atomic
models, 1 maps.
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> color zone #3 near sel & #5.3 distance 9.96
> ui tool show "Color Zone"
> color zone #3 near #5.1 distance 1.66
> color zone #3 near #5.3 distance 14.15
> color zone #3 near #5.4 distance 14.15
> color zone #3 near #5.3 distance 14.15
> color zone #3 near #5.3 distance 13.15
> color zone #3 near #5.3 distance 12.15
> color zone #3 near #5.3 distance 11.15
> color zone #3 near #5.3 distance 12.15
> color zone #3 near #5.3 distance 13.15
> color zone #3 near #5.3 distance 13.1
> color zone #3 near #5.3 distance 13
> color zone #3 near #5.3 distance 13.5
> color zone #3 near #5.3 distance 13
> color zone #3 near #5.3 distance 14
> ~select #5.3
Nothing selected
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> color zone #3 near #5.4 distance 14
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> color zone #3 near #5.3 distance 14
> ~select #5.3
Nothing selected
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.4
Nothing selected
> select #5.5
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> ~select #5.5
Nothing selected
> select #5.1
25316 atoms, 24642 bonds, 4310 residues, 1 model selected
> ~select #5.1
Nothing selected
> select #5.2
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> color zone #3 near #5.2 distance 14
> hide #!3 models
> select clear
Drag select of 1751 residues, 8 pseudobonds
> select up
14398 atoms, 14699 bonds, 8 pseudobonds, 1891 residues, 5 models selected
> show #!3 models
> color zone #3 near sel distance 14
> select clear
> hide #!3 models
Drag select of 25157 atoms, 13 residues
> select up
25350 atoms, 24591 bonds, 4298 residues, 3 models selected
> select up
25519 atoms, 24864 bonds, 4319 residues, 3 models selected
> select down
25350 atoms, 24591 bonds, 4298 residues, 3 models selected
> select up
25519 atoms, 24864 bonds, 4319 residues, 3 models selected
> select down
25350 atoms, 24591 bonds, 4298 residues, 3 models selected
> show #!2 models
> color zone #2 near sel distance 9.96
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> select #5.1
25316 atoms, 24642 bonds, 4310 residues, 1 model selected
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> color sel bychain
> style sel sphere
Changed 25316 atom styles
> color #5.1 #fffb00
> color zone #2 near sel distance 9.96
> color zone #2 near sel distance 9.78
> color zone #2 near sel distance 17.65
> color zone #2 near sel distance 17.01
> color zone #2 near sel distance 18.32
> color zone #2 near sel distance 18.3
> color zone #2 near sel distance 18
> color zone #2 near sel distance 19
[Repeated 1 time(s)]
> undo
> hide #5.1 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> hide #5.6 models
> show #5.6 models
> hide #5.4 models
> show #5.4 models
> color #5.4 #008f00
> color #5.4 #9437ff
> color #5.4 #0433ff
> show #5.1 models
> color #5.4 #0096ff
> select clear
Drag select of 1789 residues, 8 pseudobonds
> select down
13608 atoms, 8 pseudobonds, 1789 residues, 5 models selected
> select down
13608 atoms, 8 pseudobonds, 1789 residues, 5 models selected
> select down
13608 atoms, 8 pseudobonds, 1789 residues, 5 models selected
> select up
14349 atoms, 14654 bonds, 8 pseudobonds, 1883 residues, 5 models selected
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> show #!1 models
> color zone #1 near sel distance 9.96
> color single #1
> hide #!1 models
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> select up
56388 atoms, 54556 bonds, 8 pseudobonds, 9938 residues, 9 models selected
> select down
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> select down
900 atoms, 913 bonds, 8 pseudobonds, 118 residues, 3 models selected
> select down
14349 atoms, 14654 bonds, 8 pseudobonds, 1883 residues, 5 models selected
> show #!1 models
> color zone #1 near sel distance 9.96
> volume #1 level 0.01787
> color zone #1 near sel distance 12
> color zone #1 near sel distance 13
> color zone #1 near sel distance 14
> color zone #1 near sel distance 15
> hide #!5 models
> volume splitbyzone #1
Opened whole-j532post copy.mrc 0 as #6.1, grid size 210,210,210, pixel 1.66,
shown at level 0.0179, step 1, values float32
Opened whole-j532post copy.mrc 1 as #6.2, grid size 210,210,210, pixel 1.66,
shown at level 0.0179, step 1, values float32
Opened whole-j532post copy.mrc 2 as #6.3, grid size 210,210,210, pixel 1.66,
shown at level 0.0179, step 1, values float32
Opened whole-j532post copy.mrc 3 as #6.4, grid size 210,210,210, pixel 1.66,
shown at level 0.0179, step 1, values float32
> volume #6.3 level 0.01596
> volume #6.4 level 0.016
> volume #6.2 level 0.016
> show #!2 models
> show #!3 models
> volume #6.2 level 0.014
> color #5.4 #805c93
> color #5.4 #f5affe
[Repeated 1 time(s)]
> volume #6.2 color #0096ff
> volume #6.2 color #e3a2fe
> volume #6.3 level 0.01531
> volume #6.4 level 0.0153
> color #2 #00f900 models
> color #2 #8efa00 models
> color #2 #fffb00 models
> color #2 #d4fb79 models
> color #2 #8efa00 models
> color #2 #4f8f00 models
> color #2 #8efa00 models
> color #2 #fffb00 models
> color #2 #00fdff models
> color #2 #0096ff models
> color #2 #005493 models
> color #2 #0096ff models
> lighting soft
> volume #6.2 color #fffb00
> volume #6.2 color #fffc79
> volume #6.2 color #ffd479
> volume #6.2 color #fffc79
> undo
[Repeated 1 time(s)]
> redo
[Repeated 2 time(s)]No redo action is available
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.6
Nothing selected
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.6
Nothing selected
> hide #5.6 models
> show #5.6 models
> hide #5.6 models
> hide #5.4 models
> show #5.4 models
> hide #5.4 models
> show #5.4 models
> hide #5.4 models
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.4
Nothing selected
> hide #!3 models
> show #5.6 models
> color #5.6 #fffc79
> select clear
> hide #!5.3 models
> hide #!5.2 models
> show #!5.2 models
> show #!5.3 models
> hide #5.1 models
> show #!3 models
> hide #!3 models
Drag select of 6.1 whole-j532post copy.mrc 0 , 1798 residues, 8 pseudobonds
> hide #!2 models
> select clear
> select #5.2
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> select clear
Drag select of 6.1 whole-j532post copy.mrc 0 , 1861 residues, 8 pseudobonds
> select clear
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #6.1
Drag select of 1907 residues, 8 pseudobonds
> select up
14615 atoms, 883 bonds, 8 pseudobonds, 1919 residues, 5 models selected
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> show #!3 models
> color zone #3 near sel distance 14
> hide #!5.2 models
> hide #!5.3 models
> ~select #5.2
8218 atoms, 7935 bonds, 4 pseudobonds, 1466 residues, 3 models selected
> ~select #5.3
900 atoms, 913 bonds, 118 residues, 1 model selected
> hide #5.6 models
> hide #!5.5 models
> hide #!5.7 models
> hide #!6 models
> ~select #5.6
Nothing selected
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!6.2 models
> show #!6.2 models
> save /Users/miao/Downloads/coot/Figs2021Apr/20210427_0_colorB.cxs
> save /Users/miao/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/miao/Desktop/movie1.mp4
Movie saved to /Users/miao/Desktop/movie1.mp4
> hide #!2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
No atoms selected for color zoning
[Repeated 1 time(s)]
> show #!5.2 models
> show #5.1 models
> hide #5.1 models
> show #!5.3 models
> show #5.6 models
> hide #!3 models
Drag select of 1907 residues, 8 pseudobonds
> select up
14615 atoms, 883 bonds, 8 pseudobonds, 1919 residues, 5 models selected
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> show #!3 models
> color zone #3 near sel distance 16.7
> color zone #3 near sel distance 15.7
> color zone #3 near sel distance 16
[Repeated 1 time(s)]
> color zone #3 near sel distance 17
> color zone #3 near sel distance 16
> color zone #3 near sel distance 16.6
> color zone #3 near sel distance 16
> color zone #3 near sel distance 16.7
> color zone #3 near sel distance 16
> color zone #3 near sel distance 16.8
> ~select #5.3
8218 atoms, 7935 bonds, 4 pseudobonds, 1466 residues, 3 models selected
> ~select #5.2
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.6
Nothing selected
> hide #5.6 models
> hide #!5.3 models
> hide #!5.2 models
> hide #!5 models
> show #!6 models
> show #!2 models
> save /Users/miao/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/miao/Desktop/movie1.mp4
Movie saved to /Users/miao/Desktop/movie1.mp4
> volume #3 level 0.0237
> volume #3 level 0.02302
> save /Users/miao/Downloads/coot/Figs2021Apr/20210427_0_colorB.cxs
> save /Users/miao/Desktop/image3.png supersample 3
> marker segment #7 position 126.6,166.9,172.9 toPosition 122.2,172.1,180.9
> color yellow radius 0.415 label 10.46 labelHeight 1.046 labelColor yellow
> save /Users/miao/Desktop/image4.png supersample 3
> save /Users/miao/Desktop/image5.png supersample 3
> save /Users/miao/Desktop/image6.png supersample 3
> open /Users/miao/Downloads/coot/Figs2021Apr/built.pdb
Chain information for built.pdb #8
---
Chain | Description
a | No description available
b | No description available
d | No description available
e | No description available
> hide #!6 models
> hide #!6.2 models
> show #!6 models
> show #!6.2 models
> hide #!3 models
> select #8
325 atoms, 321 bonds, 65 residues, 1 model selected
> hide #!7 models
> close #7
> color #8 #ff2600
> hide #!2 models
> show #!2 models
> color zone #2 near #8 distance 9.96
> volume #!2#!6.2-4 style image
> volume #!2#!6.2-4 style surface
> volume #2 change image level -0.004278,0 level 0.0168,0.8 level 0.1241,1
> transparency #2.1#6.2.1#6.3.1#6.4.1 50
> volume #!2#!6.2-4 style surface
[Repeated 1 time(s)]
> volume #2
> undo
[Repeated 2 time(s)]
> volume #!2#!6.2-4 showOutlineBox true
> volume #2 color #0096ff13
> volume #2 color #0096ffe6
> volume #2 color #0096ff
> volume #2 color #0096ffc9
> color zone #2 near #8 distance 9.96
> volume #2 color #0096ff
> volume #2 color #0096fff2
> volume #2 color #0096ff
> color zone #2 near #8 distance 9.96
> color zone #2 near #8 distance 4.85
[Repeated 1 time(s)]
> color zone #2 near #8 distance 3.41
[Repeated 1 time(s)]
> ~select #8
Nothing selected
> hide #8 models
> volume #!2#!6.2-4 showOutlineBox false
> show #!3 models
> save /Users/miao/Downloads/coot/Figs2021Apr/20210427_colorB_1.cxs
——— End of log from Tue Apr 27 22:25:14 2021 ———
opened ChimeraX session
> hide #!3 models
> open "/Users/miao/Desktop/paper/Figs2021Apr/Earsj669post copy.mrc"
Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown
at level 0.00553, step 2, values float32
> hide #!2 models
> hide #!6 models
> hide #!6.2 models
> hide #!6.3 models
> hide #!6.4 models
> select #7
2 models selected
> show #!4 models
> fitmap #7 inMap #4
Fit map Earsj669post copy.mrc in map C2E-j542post copy.mrc using 92433 points
correlation = 0.9753, correlation about mean = 0.5301, overlap = 15.78
steps = 2000, shift = 0.787, angle = 1.69 degrees
Position of Earsj669post copy.mrc (#7) relative to C2E-j542post copy.mrc (#4)
coordinates:
Matrix rotation and translation
0.99971969 -0.01913513 0.01394199 0.90271890
0.01888777 0.99966558 0.01766304 -5.00550361
-0.01427531 -0.01739476 0.99974679 5.23562545
Axis -0.59505469 0.47894741 0.64538306
Axis point 277.29100614 56.93511692 0.00000000
Rotation angle (degrees) 1.68804185
Shift along axis 0.44444389
> ~select #7
Nothing selected
> hide #!4 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.3 models
> hide #!6.3 models
> show #!5.7 models
> hide #!5.7 models
> show #!5.5 models
> show #!5.7 models
> hide #!5.7 models
> hide #!5.5 models
> show #!5.3 models
> show #!5.2 models
> transparency #7 50
> lighting simple
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5.3 models
> show #!5.3 models
> hide #!5.3 models
> hide #!5.2 models
> show #!5.2 models
> show #!5.3 models
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> ~select #5.3
Nothing selected
> select #5.2
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5.2,0.99041,-0.075512,-0.11566,24.224,0.092914,0.9838,0.15334,-26.555,0.10221,-0.16262,0.98138,11.092
> ui mousemode right "translate selected models"
> view matrix models
> #5.2,0.99041,-0.075512,-0.11566,25.76,0.092914,0.9838,0.15334,-35.378,0.10221,-0.16262,0.98138,14.12
> view matrix models
> #5.2,0.99041,-0.075512,-0.11566,25.142,0.092914,0.9838,0.15334,-37.472,0.10221,-0.16262,0.98138,15.546
> ui mousemode right "rotate selected models"
> view matrix models
> #5.2,0.97247,-0.12405,0.19726,2.9512,-0.18158,-0.93395,0.30784,267.22,0.14604,-0.33519,-0.93076,229.35
> view matrix models
> #5.2,0.86501,0.00048599,0.50176,-30.928,-0.31526,-0.77743,0.54425,239.34,0.39035,-0.62896,-0.67233,211.09
> view matrix models
> #5.2,0.01246,0.77212,0.63535,-35.514,0.78178,-0.40368,0.47525,34.433,0.62343,0.49078,-0.60866,7.0741
> view matrix models
> #5.2,-0.18397,0.46231,0.86742,14.397,0.50505,-0.71262,0.48692,118.17,0.84326,0.52767,-0.10239,-81.396
> view matrix models
> #5.2,-0.67734,0.28346,0.67887,130.5,0.38395,-0.65094,0.65488,109.37,0.62753,0.70422,0.33207,-120.63
> view matrix models
> #5.2,-0.95484,0.017624,0.2966,248.16,0.20161,-0.69484,0.69033,138.31,0.21826,0.71895,0.65991,-97.553
> view matrix models
> #5.2,-0.9982,-0.02772,0.053127,285.82,0.059007,-0.60923,0.79079,135.96,0.010446,0.79251,0.60977,-73.459
> ui mousemode right "translate selected models"
> view matrix models
> #5.2,-0.9982,-0.02772,0.053127,284.37,0.059007,-0.60923,0.79079,135.41,0.010446,0.79251,0.60977,-72.158
> view matrix models
> #5.2,-0.9982,-0.02772,0.053127,280.99,0.059007,-0.60923,0.79079,137.65,0.010446,0.79251,0.60977,-70.773
> fitmap #5.2 inMap #7
Fit molecule j532_fitall copy.pdb (#5.2) to map Earsj669post copy.mrc (#7)
using 7318 atoms
average map value = 0.007925, steps = 220
shifted from previous position = 4.86
rotated from previous position = 52.8 degrees
atoms outside contour = 1402, contour level = 0.0055322
Position of j532_fitall copy.pdb (#5.2) relative to Earsj669post copy.mrc (#7)
coordinates:
Matrix rotation and translation
-0.59833008 0.28261688 0.74975250 105.27324219
0.26528541 -0.81307900 0.51819512 168.13494361
0.75605871 0.50895012 0.41151549 -117.51792216
Axis -0.44812243 -0.30567365 -0.84008923
Axis point 84.49625073 105.12404280 0.00000000
Rotation angle (degrees) 179.40896873
Shift along axis 0.15581790
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> fitmap #5.3 inMap #7
Fit molecule j532_fitall copy.pdb (#5.3) to map Earsj669post copy.mrc (#7)
using 7318 atoms
average map value = 0.007608, steps = 164
shifted from previous position = 9.63
rotated from previous position = 24.5 degrees
atoms outside contour = 1545, contour level = 0.0055322
Position of j532_fitall copy.pdb (#5.3) relative to Earsj669post copy.mrc (#7)
coordinates:
Matrix rotation and translation
0.92058150 0.36352835 0.14274745 -43.22779944
-0.33016311 0.91963356 -0.21275909 114.29464103
-0.20861931 0.14873214 0.96662130 26.23285224
Axis 0.42155378 0.40974710 -0.80894977
Axis point 290.52764782 190.94936224 0.00000000
Rotation angle (degrees) 25.38892569
Shift along axis 7.38799622
> select clear
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!6.2 models
> show #!6.3 models
> show #!6.4 models
> hide #!5.2 models
> hide #!5.3 models
> show #5.1 models
> select #5.1
25316 atoms, 24642 bonds, 4310 residues, 1 model selected
> ~select #5.1
Nothing selected
> hide #5.1 models
> show #5.6 models
> hide #!6 models
> hide #!6.2 models
> hide #!6.3 models
> hide #!6.4 models
> hide #!7 models
> show #!7 models
> fitmap #5.6 inMap #7
Fit molecule j532_fitall copy.pdb (#5.6) to map Earsj669post copy.mrc (#7)
using 900 atoms
average map value = 0.006734, steps = 112
shifted from previous position = 1.18
rotated from previous position = 33.2 degrees
atoms outside contour = 307, contour level = 0.0055322
Position of j532_fitall copy.pdb (#5.6) relative to Earsj669post copy.mrc (#7)
coordinates:
Matrix rotation and translation
0.85031961 -0.48668234 0.20024198 72.96422939
0.49867852 0.86671607 -0.01109017 -66.86527886
-0.16815555 0.10928656 0.97968370 15.17413794
Axis 0.11368731 0.34792540 0.93060363
Axis point 160.42908477 100.77936831 0.00000000
Rotation angle (degrees) 31.96629376
Shift along axis -0.84791442
> hide #!7 models
> show #!7 models
> hide #5.6 models
> show #!6 models
> show #!6.2 models
> show #!6.3 models
> show #!6.4 models
> show #5.4 models
> hide #5.4 models
> show #!5.3 models
> hide #!5.3 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.5 models
> show #!5.7 models
> hide #!5.7 models
> show #!5.7 models
> select #5.7
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5.7,0.97853,0.024066,0.2047,-57.595,0.029953,0.96601,-0.25675,72.451,-0.20392,0.25737,0.94455,0.92223
> view matrix models
> #5.7,-0.85141,-0.35492,0.38618,291.38,0.3557,-0.93181,-0.072179,336.76,0.38546,0.07591,0.9196,-61.061
> view matrix models
> #5.7,-0.77013,-0.63784,-0.0073969,441.56,0.11852,-0.15447,0.98086,-65.554,-0.62678,0.75452,0.19456,185.82
> view matrix models
> #5.7,-0.32035,-0.88134,0.34729,311.44,-0.73878,0.46191,0.49076,101.03,-0.59295,-0.099357,-0.79909,622.82
> view matrix models
> #5.7,-0.14657,-0.79177,0.59297,194.98,-0.95239,-0.049055,-0.30092,458.59,0.26735,-0.60884,-0.74688,555.92
> view matrix models
> #5.7,-0.16062,-0.74682,0.64533,174.13,-0.95827,-0.038649,-0.28324,452.69,0.23647,-0.6639,-0.70945,561.86
> ui mousemode right "translate selected models"
> view matrix models
> #5.7,-0.16062,-0.74682,0.64533,180.2,-0.95827,-0.038649,-0.28324,458.7,0.23647,-0.6639,-0.70945,561.78
> ui mousemode right "rotate selected models"
> view matrix models
> #5.7,-0.46816,-0.16224,0.86862,57.986,-0.69229,-0.54356,-0.47464,563.79,0.54915,-0.82354,0.14216,301.93
> view matrix models
> #5.7,-0.70891,0.15677,0.68765,88.074,-0.38705,-0.90153,-0.19349,502.19,0.58961,-0.40332,0.69978,57.736
> view matrix models
> #5.7,-0.96699,0.25469,-0.0075131,307.06,-0.23436,-0.87746,0.41849,300.94,0.099995,0.40644,0.90819,-72.327
> view matrix models
> #5.7,-0.87809,-0.16588,-0.44883,496.17,-0.34996,-0.41706,0.8388,114.55,-0.32633,0.89361,0.30816,73.632
> view matrix models
> #5.7,-0.60551,-0.66919,-0.43075,541.78,-0.58828,0.011843,0.80857,80.861,-0.53598,0.743,-0.40085,336.74
> view matrix models
> #5.7,-0.49063,-0.81702,-0.30292,515.08,-0.69961,0.16212,0.69589,102.26,-0.51945,0.55335,-0.65113,440.39
> ui mousemode right "translate selected models"
> view matrix models
> #5.7,-0.49063,-0.81702,-0.30292,515.06,-0.69961,0.16212,0.69589,100.37,-0.51945,0.55335,-0.65113,440.43
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 4 maps.
> hide #!5.5 models
> hide #!7 models
> hide #!6.4 models
> show #!6.4 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> hide #!6 models
> show #!6 models
> hide #!6.3 models
> hide #!6.4 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.3 models
> hide #!6.3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5.7 models
> show #!5.7 models
> show #!6 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.3 models
> show #!6.4 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!6.3 models
> hide #!6.4 models
> show #!1 models
> fitmap #5.7 inMap #1
Fit molecule j532_fitall copy.pdb (#5.7) to map whole-j532post copy.mrc (#1)
using 7318 atoms
average map value = 0.01909, steps = 420
shifted from previous position = 2.21
rotated from previous position = 91.9 degrees
atoms outside contour = 2525, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.7) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
-0.96963736 -0.08046323 -0.23093086 431.05259150
-0.08166871 -0.78355827 0.61592747 194.91585061
-0.23050730 0.61608611 0.75319604 -11.75435461
Axis 0.12321197 -0.32896944 -0.93626808
Axis point 214.78637025 99.44884749 0.00000000
Rotation angle (degrees) 179.96311468
Shift along axis -0.00529075
> view matrix models
> #5.7,-0.97435,0.0056364,-0.22499,420.51,-0.15119,-0.7569,0.6358,201.02,-0.16671,0.6535,0.73834,-28.717
> ui mousemode right "rotate selected models"
> view matrix models
> #5.7,-0.98226,0.098546,0.15957,297.18,-0.075338,-0.98649,0.14548,368.45,0.17175,0.13087,0.97641,-51.905
> view matrix models
> #5.7,-0.83679,-0.069724,0.54306,198.29,-0.20691,-0.87804,-0.43155,530.22,0.50692,-0.47348,0.72031,78.37
> view matrix models
> #5.7,-0.65849,-0.35483,0.66369,189.32,-0.48379,-0.47594,-0.73445,584.13,0.57649,-0.80472,0.14174,291.34
> view matrix models
> #5.7,-0.62452,-0.4786,0.61718,220.51,-0.6163,-0.18341,-0.76586,558.81,0.47974,-0.85866,-0.18041,408.3
> view matrix models
> #5.7,-0.55875,-0.78232,0.27526,363.23,-0.80969,0.44278,-0.38516,364.59,0.17944,-0.43809,-0.88084,572.79
> view matrix models
> #5.7,-0.45466,-0.8568,-0.24326,502.96,-0.86973,0.48596,-0.086078,283.95,0.19197,0.17243,-0.96613,474.13
> view matrix models
> #5.7,-0.60797,-0.75669,-0.24039,509.68,-0.74609,0.44095,0.49891,108.91,-0.27152,0.48268,-0.83265,458.4
> fitmap #5.7 inMap #1
Fit molecule j532_fitall copy.pdb (#5.7) to map whole-j532post copy.mrc (#1)
using 7318 atoms
average map value = 0.01909, steps = 500
shifted from previous position = 4.41
rotated from previous position = 105 degrees
atoms outside contour = 2528, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.7) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
-0.97004321 -0.07975247 -0.22946834 430.58007595
-0.08086523 -0.78470474 0.61457243 195.37143057
-0.22907856 0.61471783 0.75474830 -12.17547658
Axis 0.12238584 -0.32809726 -0.93668239
Axis point 214.52559461 99.74984071 0.00000000
Rotation angle (degrees) 179.96596673
Shift along axis 0.00062730
> transparency #1 50
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs
> hide #!6 models
> show #!6 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> close #6.3
> show #!6.4 models
> hide #!6.4 models
> show #!6.4 models
> close #6.4
> show #!6.2 models
> hide #!6.2 models
> close #6
> show #5.6 models
> hide #5.6 models
> show #!5.5 models
> hide #!5.7 models
> ~select #5.7
Nothing selected
> select #5.5
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> fitmap #5.5 inMap #1
Fit molecule j532_fitall copy.pdb (#5.5) to map whole-j532post copy.mrc (#1)
using 7318 atoms
average map value = 0.01913, steps = 72
shifted from previous position = 0.423
rotated from previous position = 5.6 degrees
atoms outside contour = 2342, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.5) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
0.99999661 0.00017116 -0.00259673 0.57418855
-0.00016236 0.99999424 0.00338905 -0.78923841
0.00259730 -0.00338861 0.99999089 0.46028784
Axis -0.79312452 -0.60780773 -0.03902901
Axis point 0.00000000 135.28274606 231.97235454
Rotation angle (degrees) 0.24481179
Shift along axis 0.00633761
> show #!5.7 models
> select #5.7
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> hide #!1 models
Drag select of 783 residues, 2 pseudobonds
> select clear
Drag select of 1793 residues, 8 pseudobonds
> select up
13744 atoms, 14044 bonds, 8 pseudobonds, 1804 residues, 4 models selected
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.6 models
> hide #5.6 models
> show #5.1 models
> hide #5.1 models
> show #5.4 models
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> show #!1 models
> fitmap #5.4 inMap #1
Fit molecule j532_fitall copy.pdb (#5.4) to map whole-j532post copy.mrc (#1)
using 900 atoms
average map value = 0.02006, steps = 52
shifted from previous position = 2.91
rotated from previous position = 5.59 degrees
atoms outside contour = 226, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.4) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
0.99999991 0.00040715 0.00014933 -0.11963845
-0.00040716 0.99999991 0.00010627 0.03987865
-0.00014928 -0.00010633 0.99999998 0.04608935
Axis -0.23807271 0.33438276 -0.91187146
Axis point 98.05121057 293.99070369 0.00000000
Rotation angle (degrees) 0.02558290
Shift along axis -0.00021018
> color #5.4 #fffc79
> color #5.4 #fffb00
> show #5.1 models
> color #5.1 #0096ff
> hide sel cartoons
> show sel cartoons
> ~select #5.4
Nothing selected
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.4
Nothing selected
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> select #5.1
25316 atoms, 24642 bonds, 4310 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel surfaces
> hide sel atoms
> show sel surfaces
> hide sel surfaces
> style sel sphere
Changed 25316 atom styles
> show sel cartoons
> show sel atoms
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> style sel stick
Changed 25316 atom styles
> style sel sphere
Changed 25316 atom styles
> style sel ball
Changed 25316 atom styles
> hide sel atoms
> hide #!5.1 models
> ~select #5.1
6 models selected
> hide #5.4 models
> show #5.4 models
> hide #!1 models
Drag select of 1915 residues, 8 pseudobonds
> select up
14644 atoms, 7022 bonds, 8 pseudobonds, 1922 residues, 5 models selected
> select up
15536 atoms, 14044 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near sel distance 10
> transparency #1 50
> hide #!5.5 models
> show #!5.5 models
> view matrix models
> #5.4,0.97722,0.076555,0.19794,-61.387,-0.046814,0.98746,-0.15079,51.477,-0.207,0.13808,0.96855,9.2568,#5.5,0.97778,0.075674,0.1955,-60.69,-0.046987,0.98796,-0.14742,50.563,-0.20431,0.13495,0.96956,9.3998,#5.7,-0.99947,-0.016135,-0.02816,371.99,-0.00024311,-0.86391,0.50364,226.2,-0.032454,0.50338,0.86345,-64.64
> view matrix models
> #5.4,0.99572,-0.08866,0.026102,16.022,0.086095,0.99249,0.086877,-31.51,-0.033609,-0.084258,0.99588,23.73,#5.5,0.99577,-0.08898,0.023076,16.797,0.086576,0.99218,0.089897,-32.237,-0.030894,-0.087518,0.99568,24.189,#5.7,-0.96461,0.0064394,-0.26362,427.15,-0.18405,-0.73236,0.65557,198.55,-0.18884,0.68089,0.70762,-19.302
> hide #!5.5 models
> hide #5.4 models
> ~select #5.4
14636 atoms, 14044 bonds, 8 pseudobonds, 2696 residues, 4 models selected
> ~select #5.5
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> fitmap #5.7 inMap #1
Fit molecule j532_fitall copy.pdb (#5.7) to map whole-j532post copy.mrc (#1)
using 7318 atoms
average map value = 0.01909, steps = 68
shifted from previous position = 2.12
rotated from previous position = 3.26 degrees
atoms outside contour = 2527, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.7) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
-0.97010540 -0.07963360 -0.22924658 430.51178970
-0.08073779 -0.78491803 0.61431677 195.45352357
-0.22886003 0.61446088 0.75502378 -12.25717216
Axis 0.12225873 -0.32793471 -0.93675591
Axis point 214.48677904 99.80451132 0.00000000
Rotation angle (degrees) 179.96623180
Shift along axis 0.01981034
> hide #!5.7 models
> show #!5.5 models
> fitmap #5.5 inMap #1
Fit molecule j532_fitall copy.pdb (#5.5) to map whole-j532post copy.mrc (#1)
using 7318 atoms
average map value = 0.01913, steps = 88
shifted from previous position = 2.48
rotated from previous position = 2.95 degrees
atoms outside contour = 2343, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.5) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
0.99998311 -0.00050226 -0.00578991 1.47082238
0.00054555 0.99997189 0.00747826 -1.80906649
0.00578599 -0.00748129 0.99995528 1.05657988
Axis -0.78965862 -0.61104833 0.05531000
Axis point 0.00000000 139.76351743 242.23773702
Rotation angle (degrees) 0.54272333
Shift along axis 0.00241893
> hide #!5.5 models
> show #5.6 models
> hide #5.6 models
> show #5.4 models
> fitmap #5.4 inMap #1
Fit molecule j532_fitall copy.pdb (#5.4) to map whole-j532post copy.mrc (#1)
using 900 atoms
average map value = 0.02006, steps = 44
shifted from previous position = 1.32
rotated from previous position = 3.22 degrees
atoms outside contour = 226, contour level = 0.017871
Position of j532_fitall copy.pdb (#5.4) relative to whole-j532post copy.mrc
(#1) coordinates:
Matrix rotation and translation
0.99999993 -0.00034182 -0.00016782 0.09944828
0.00034179 0.99999993 -0.00016596 -0.01577008
0.00016788 0.00016590 0.99999997 -0.06501357
Axis 0.39947768 -0.40408887 0.82287895
Axis point 54.95007303 299.57521035 0.00000000
Rotation angle (degrees) 0.02379919
Shift along axis -0.00739842
> select #5.4
900 atoms, 913 bonds, 118 residues, 1 model selected
> show #!5.5 models
> hide #!5.5 models
> show #!5.5 models
> show #!5.3 models
> hide #!5.3 models
> show #5.6 models
> hide #5.6 models
> show #!5.3 models
> hide #!5.3 models
> show #!5.7 models
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs
> show #!5.3 models
> show #!5.2 models
> ui mousemode right select
> show #!5.1 models
> hide #!5.1 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.3 models
> show #!5.3 models
> hide #!5.5 models
> show #!5.5 models
> hide #!5.7 models
> show #!5.7 models
> hide #!5.7 models
> hide #!5.5 models
> hide #5.4 models
> ~select #5.4
Nothing selected
> hide #!5.3 models
> show #!5.3 models
> save /Users/miao/Desktop/paper/Figs2021Apr/5.3fitsum.pdb relModel #7
> hide #!5.3 models
> hide #!5.2 models
> show #!5.2 models
> show #!7 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!5 models
> show #!5 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5 models
> hide #!5.2 models
> show #!5.2 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!1 models
> fitmap #5.2 inMap #7
Fit molecule j532_fitall copy.pdb (#5.2) to map Earsj669post copy.mrc (#7)
using 7318 atoms
average map value = 0.007925, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.0138 degrees
atoms outside contour = 1397, contour level = 0.0055322
Position of j532_fitall copy.pdb (#5.2) relative to Earsj669post copy.mrc (#7)
coordinates:
Matrix rotation and translation
-0.59836780 0.28274589 0.74967375 105.26779962
0.26505309 -0.81312864 0.51823612 168.15902185
0.75611033 0.50879915 0.41160732 -117.52190001
Axis -0.44810038 -0.30563139 -0.84011636
Axis point 84.50285188 105.12644030 0.00000000
Rotation angle (degrees) 179.39666609
Shift along axis 0.16685388
> save /Users/miao/Desktop/paper/Figs2021Apr/5.2fitsum.pdb relModel #7
> show #5.4 models
> hide #5.4 models
> show #5.4 models
> save /Users/miao/Desktop/paper/Figs2021Apr/5.4fitsum.pdb relModel #7
> hide #5.4 models
> show #5.6 models
> save /Users/miao/Desktop/paper/Figs2021Apr/5.6fitsum.pdb relModel #7
> close #3
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs
——— End of log from Sun May 16 01:36:06 2021 ———
opened ChimeraX session
> color #7 #929292 models
> color #7 darkgrey models
> volume #1 level 0.01807
> volume #7 level 0.005889
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs
> show #!5.7 models
> hide #!5.7 models
> show #!5.7 models
> hide #!5.7 models
> show #!5.5 models
> hide #!5.5 models
> show #5.4 models
> hide #5.4 models
> show #!5.3 models
> surface dust #7 size 8.3
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> hide #!7 models
Drag select of 1678 residues, 8 pseudobonds
> select up
13893 atoms, 14180 bonds, 8 pseudobonds, 1822 residues, 5 models selected
> select up
15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected
> ui tool show "Color Zone"
> color zone #7 near sel distance 4.98
> show #!7 models
> color zone #7 near sel distance 6
> color zone #7 near sel distance 1
> color zone #7 near sel distance 10
> color zone #7 near sel distance 1
> color zone #7 near sel distance 8
> color single #7
> select down
13893 atoms, 14180 bonds, 8 pseudobonds, 1822 residues, 5 models selected
> color zone #7 near sel distance 8
> color zone #7 near sel distance 1
> color zone #7 near sel distance 10
> color single #7
> hide #!7 models
> select clear
Drag select of 1912 residues, 8 pseudobonds
> show #!7 models
> color zone #7 near sel distance 10
> hide #7.1 models
> hide #!7 models
> show #!7 models
> show #7.1 models
> transparency #7 50
> transparency #7 80
> transparency #7 20
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> select #5
56388 atoms, 54556 bonds, 16 pseudobonds, 9938 residues, 12 models selected
> ~select #5
6 models selected
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs
——— End of log from Mon May 17 03:37:02 2021 ———
opened ChimeraX session
> ui mousemode right "map eraser"
> volume erase #7 center 174.29,174.12,181.36 radius 40.882
Opened Earsj669post copy.mrc copy as #6, grid size 420,420,420, pixel 0.83,
shown at step 1, values float32
> volume erase #6 center 187.07,184.64,187.49 radius 40.786
> volume erase #6 center 155.85,162.89,182.48 radius 40.786
> volume erase #6 center 193.07,175.65,196.29 radius 40.786
> volume erase #6 center 160.09,214,176.05 radius 40.786
> volume erase #6 center 164.98,200.54,164.01 radius 40.786
> volume erase #6 center 137.84,203.92,176.11 radius 40.786
> surface dust #6 size 8.3
> ui mousemode right select
> save /Users/miao/Desktop/paper/Figs2021Apr/Earsj669post_erased.mrc models #6
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> select #5.3
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> select #5.2
7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected
> ~select #5.2
Nothing selected
> hide #!6 models
Drag select of 180 residues, 2 pseudobonds
> select clear
Drag select of 1912 residues, 8 pseudobonds
> ui tool show "Color Zone"
> color zone #6 near sel distance 4.98
> show #!6 models
> color zone #6 near sel distance 4.9
> color zone #6 near sel distance 4
> color zone #6 near sel distance 1
> color zone #6 near sel distance 10
> color zone #6 near sel distance 1
> color zone #6 near sel distance 8
> color zone #6 near sel distance 1
> color zone #6 near sel distance 10
> transparency #7 20
> transparency #6 20
> select #5.6
900 atoms, 913 bonds, 118 residues, 1 model selected
> ~select #5.6
Nothing selected
> hide #!5.3 models
> show #!5.3 models
> hide #!5.3 models
> hide #!5.2 models
> hide #5.6 models
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs
——— End of log from Mon May 17 03:52:16 2021 ———
opened ChimeraX session
> open /Users/miao/Desktop/paper/Figs2021Apr/5.6fitsum-coot-2.pdb
Summary of feedback from opening
/Users/miao/Desktop/paper/Figs2021Apr/5.6fitsum-coot-2.pdb
---
warning | End residue of secondary structure not found: HELIX 2 2 ARG 540 ARG
542 1 3
5.6fitsum-coot-2.pdb title:
Crystal structure of the acyl-coa carboxylase, ACCD5, from mycobacterium
tuberculosis [more info...]
Chain information for 5.6fitsum-coot-2.pdb #3
---
Chain | Description
? | No description available
> open /Users/miao/Desktop/paper/Figs2021Apr/Earsj669post_erased.mrc
Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown
at level 0.00315, step 2, values float32
> volume #9 level 0.005719
> hide #!6 models
> color #9 #ebebeb models
> color #9 #d6d6d6 models
> color #9 silver models
> transparency #9 40
> transparency #9 50
> show #!5.2 models
> show #!5.3 models
> color #3 #ffd479
> color #3 #ff7e79
> color #3 #ffd479
> surface dust #9 size 8.3
> volume #9 step 1
> volume #9 level 0.00623
> surface dust #9 size 8.3
[Repeated 1 time(s)]
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs
> transparency #9 80
> transparency #9 60
> transparency #9 90
> transparency #9 80
> volume #9 color darkgrey
> volume #9 color silver
> transparency #9 80
> volume #9 color darkgrey
> transparency #9 80
> volume #9 color #929292
> transparency #9 80
> volume #9 color #919191
> transparency #9 80
> volume #9 color #929292
> transparency #9 80
> volume #9 color #919191
> transparency #9 80
> show #!3#!5.2-3 atoms
> hide #!3#!5.2-3 atoms
> show #!3#!5.2-3 atoms
> nucleotides #!3#!5.2-3 atoms
> style nucleic & #!3#!5.2-3 stick
Changed 0 atom styles
> style #!3#!5.2-3 stick
Changed 15418 atom styles
> style #!3#!5.2-3 sphere
Changed 15418 atom styles
> style #!3#!5.2-3 ball
Changed 15418 atom styles
> style #!3#!5.2-3 stick
Changed 15418 atom styles
> hide #!3#!5.2-3 atoms
> show #!3#!5.2-3 cartoons
> nucleotides #!3#!5.2-3 atoms
> style nucleic & #!3#!5.2-3 stick
Changed 0 atom styles
> style #!3#!5.2-3 stick
Changed 15418 atom styles
> style #!3#!5.2-3 sphere
Changed 15418 atom styles
> style #!3#!5.2-3 ball
Changed 15418 atom styles
> show #!3#!5.2-3 surfaces
> hide #!3#!5.2-3 surfaces
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs
> transparency #3.2#9.1#5.2.2-3#5.3.2-3 0
> transparency #3.2#9.1#5.2.2-3#5.3.2-3 50
> transparency #9 80
> volume #!9 style image
> volume #!9 style mesh
> volume #!9 style surface
> ui mousemode right "contour level"
> volume #9 level 0.007048
> volume #9 level 0.006338
> hide #!5.3 models
> show #!5.3 models
> hide #!5.2 models
> hide #!3 models
> show #!3 models
> show #!5.2 models
> hide #!5.3 models
> show #!5.3 models
> hide #!5.2 models
> save /Users/miao/Desktop/image10.png supersample 3
> turn x 90
> turn x -90
> save /Users/miao/Desktop/image11.png supersample 3
> save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs
——— End of log from Mon May 17 05:23:44 2021 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.01372
> show #!5.2 models
> show #!5.5 models
> show #!5.7 models
> hide #!5.7 models
> show #!4 models
> hide #!1 models
> hide #!5.5 models
> hide #!5.3 models
> hide #!5.2 models
> hide #!5 models
> show #!1 models
> hide #!3 models
> select #1
2 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.
> hide #!9 models
> fitmap #1 inMap #4
Fit map whole-j532post copy.mrc in map C2E-j542post copy.mrc using 267974
points
correlation = 0.8925, correlation about mean = 0.233, overlap = 88.55
steps = 52, shift = 0.0745, angle = 0.823 degrees
Position of whole-j532post copy.mrc (#1) relative to C2E-j542post copy.mrc
(#4) coordinates:
Matrix rotation and translation
0.99605318 -0.06260193 0.06292113 1.10025049
0.06056904 0.99759447 0.03371449 -15.97237620
-0.06488036 -0.02977035 0.99744888 16.83278718
Axis -0.33677830 0.67796924 0.65340500
Axis point 261.46509857 0.00000000 -0.01120204
Rotation angle (degrees) 5.40833613
Shift along axis -0.20069295
> hide #!4 models
> hide #!1 models
> ~select #1
Nothing selected
> show #!1 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> show #8 models
> hide #8 models
> show #!9 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> hide #!1 models
> hide #!6 models
> show #!9 models
> show #!5.7 models
> hide #!5.7 models
> show #!5.5 models
> hide #!5.5 models
> show #!5.3 models
> show #!5.2 models
> show #5.4 models
> hide #5.4 models
> show #5.6 models
> hide #5.6 models
> show #!3 models
> save /Users/miao/Desktop/paper/Figs2021Apr/20210518_mergeB_ears.cxs
——— End of log from Tue May 18 20:24:40 2021 ———
opened ChimeraX session
> show #!4 models
> hide #!9 models
> color #4 silver models
> transparency #4 50
> save /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears-BT.cxs
——— End of log from Wed May 19 14:45:04 2021 ———
opened ChimeraX session
> open /Users/miao/Desktop/paper/Figs2021Apr/AccA_Phyre.pdb
Chain information for AccA_Phyre.pdb #10
---
Chain | Description
? | No description available
> ui tool show Matchmaker
> matchmaker #10 to #5.2
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 j532_fitall copy.pdb, chain A (#5.2) with AccA_Phyre.pdb, chain
(blank) (#10), sequence alignment score = 1919.8
RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs:
6.902)
[Repeated 1 time(s)]
> select #10
4440 atoms, 4522 bonds, 597 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.51245,0.38099,0.76957,236.6,0.52009,-0.85082,0.074882,85.912,0.6833,0.36188,-0.63416,110.19
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.49506,-0.23949,0.8352,188.08,0.63051,-0.56235,-0.53499,93.526,0.5978,0.79146,-0.12739,158.02
> view matrix models
> #10,0.30136,-0.57379,-0.76154,114.73,0.38514,0.80388,-0.45327,203.55,0.87227,-0.1567,0.46324,100.73
> view matrix models
> #10,0.27538,-0.38807,-0.87953,126.19,0.396,0.87947,-0.26405,215.01,0.87598,-0.27558,0.39586,89.297
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.27538,-0.38807,-0.87953,99.696,0.396,0.87947,-0.26405,223.68,0.87598,-0.27558,0.39586,100.45
> view matrix models
> #10,0.27538,-0.38807,-0.87953,98.938,0.396,0.87947,-0.26405,223.18,0.87598,-0.27558,0.39586,99.648
> view matrix models
> #10,0.27538,-0.38807,-0.87953,99.074,0.396,0.87947,-0.26405,223.31,0.87598,-0.27558,0.39586,99.854
> matchmaker #10 to #5.2
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 j532_fitall copy.pdb, chain A (#5.2) with AccA_Phyre.pdb, chain
(blank) (#10), sequence alignment score = 1919.8
RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs:
6.902)
[Repeated 1 time(s)]
> save /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears'-discard.cxs
——— End of log from Sun May 23 03:46:49 2021 ———
opened ChimeraX session
> open /Users/miao/Desktop/paper/Figs2021Apr/AccA_Phyre.pdb
Chain information for AccA_Phyre.pdb #11
---
Chain | Description
? | No description available
> ui tool show Matchmaker
> matchmaker #11/? to #5.2/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 j532_fitall copy.pdb, chain A (#5.2) with AccA_Phyre.pdb, chain
(blank) (#11), sequence alignment score = 1919.8
RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs:
6.902)
[Repeated 1 time(s)]No reference and/or match structure/chain chosen
> matchmaker #11/? to #5.2/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 j532_fitall copy.pdb, chain B (#5.2) with AccA_Phyre.pdb, chain
(blank) (#11), sequence alignment score = 1919.8
RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs:
6.902)
[Repeated 1 time(s)]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-12.10.14
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Intel Core i5
Processor Speed: 2.3 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
Boot ROM Version: 203.0.0.0.0
SMC Version (system): 2.43f6
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G2022)
Kernel Version: Darwin 18.7.0
Time since boot: 1 day 1:39
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
U28D590:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
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: 1.1.1
ChimeraX-AddH: 2.1.6
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: 1.18
ChimeraX-AtomicLibrary: 3.2
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: 2.5.2
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: 1.3
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202104240152
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.2.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.1
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: 1.1
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.3
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: 1.2
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.4
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: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.5
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: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.8
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: 5.0.7
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: 3.0.18
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 (2)
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 |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Miao,
--Eric