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Opened 13 months ago
Closed 13 months ago
#16200 closed defect (duplicate)
MatchMaker: 'NoneType' object has no attribute 'setChecked'
| 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/abubakrsangare/Desktop/Deletion_test_BIO45.cxs
Not registering illegal selector name "resi.R110.close"
Log from Fri Oct 25 17:23:06 2024UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/abubakrsangare/Desktop/BIO 45 TA Helpful
> Information/Mut1_DG_Structure.cxs"
Not registering illegal selector name "resi.R110.close"
Log from Mon Oct 21 11:37:12 2024UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3KMD
3kmd title:
Crystal structure of the p53 core domain bound to a full consensus site as a
self-assembled tetramer [more info...]
Chain information for 3kmd #1
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN
E F | 5'-D(*GP*GP*GP*CP*ap*TP*GP*CP*CP*TP*ap*GP*GP*CP*ap*TP*GP*CP*C)-3' |
Non-standard residues in 3kmd #1
---
ZN — zinc ion
> hide target a
> cartoon
> select /A
1728 atoms, 1607 bonds, 4 pseudobonds, 357 residues, 2 models selected
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #b7b768ff
> select /A
1728 atoms, 1607 bonds, 4 pseudobonds, 357 residues, 2 models selected
> select /B
1656 atoms, 1607 bonds, 4 pseudobonds, 285 residues, 2 models selected
> color (#!1 & sel) #8db985ff
> select /C
1673 atoms, 1607 bonds, 4 pseudobonds, 302 residues, 2 models selected
> color (#!1 & sel) #b79195ff
> select /D
1700 atoms, 1607 bonds, 4 pseudobonds, 329 residues, 2 models selected
> color (#!1 & sel) #9ea9cfff
> select clear
> select /E
418 atoms, 435 bonds, 49 residues, 1 model selected
> color sel medium blue
> select /F
412 atoms, 435 bonds, 43 residues, 1 model selected
> color sel red
> select /E
418 atoms, 435 bonds, 49 residues, 1 model selected
> style sel stick
Changed 418 atom styles
> show sel target ab
> color sel byhetero
> select /F
412 atoms, 435 bonds, 43 residues, 1 model selected
> style sel stick
Changed 412 atom styles
> show sel target ab
> color sel byhetero
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> select /F : HOH
24 atoms, 24 residues, 1 model selected
> hide sel
> select /E : HOH
30 atoms, 30 residues, 1 model selected
> hide sel
> select /E
418 atoms, 435 bonds, 49 residues, 1 model selected
> color sel #a0b6cfff
> color sel #a0b5cfff
> color sel #9fb4cfff
> color sel #9db0cfff
> color sel #93a3cfff
> color sel #8f9ecfff
> color sel #8d9ccfff
> color sel #8c9acfff
> color sel #8b99cfff
[Repeated 1 time(s)]
> color sel #8a99cfff
> color sel #8997cfff
> color sel #8896cfff
> color sel #8693cfff
> color sel #828fcfff
> color sel #808dcfff
> color sel #7e8bcfff
> color sel #7a86cfff
> color sel #7580cfff
> color sel #747fcfff
> color sel #727ccfff
> color sel #707acfff
> color sel #6f78cfff
> color sel #6d74cfff
> color sel #6a70cfff
> color sel #676dcfff
> color sel #676ccfff
> color sel #6568cfff
> color sel #6466cfff
> color sel #6163cfff
> color sel #6062cfff
> color sel #5f5fcfff
> color sel #5e5ecfff
> color sel #5e5dcfff
> color sel #5d5bcfff
> color sel #5c5acfff
> color sel #5c58cfff
> color sel #5b58cfff
> color sel #5a56cfff
> color sel #5a54cfff
[Repeated 1 time(s)]
> color sel #5954cfff
[Repeated 1 time(s)]
> color sel #5953cfff
[Repeated 1 time(s)]
> color sel #5a53cfff
[Repeated 1 time(s)]
> color sel #5952cfff
[Repeated 1 time(s)]
> color sel #5951cfff
> color sel #574ecfff
> color sel #574dcfff
> color sel #564bcfff
[Repeated 1 time(s)]
> color sel #574bcfff
[Repeated 2 time(s)]
> color sel #584bcfff
> color sel #594ccfff
> color sel #5a4ccfff
> color sel #5a4dcfff
> color sel #5b4dcfff
[Repeated 1 time(s)]
> color sel #5b4ccfff
[Repeated 1 time(s)]
> color sel #5b4dcfff
> select /F
412 atoms, 435 bonds, 43 residues, 1 model selected
> color sel #5852cfff
[Repeated 1 time(s)]
> color sel #665bcfff
> color sel #9781cfff
> color sel #c09fcfff
> color sel #cfaac7ff
> color sel #cfaabeff
> color sel #cfa9b8ff
> color sel #cfa4abff
> color sel #cf9b97ff
> color sel #cf998eff
> color sel #cf9888ff
> color sel #cf9784ff
> color sel #cf9681ff
[Repeated 1 time(s)]
> color sel #cf957fff
> color sel #cf937cff
> color sel #cf8e75ff
> color sel #cf8a70ff
> color sel #cf876dff
> color sel #cf856bff
> color sel #cf8368ff
> color sel #cf8268ff
> color sel #cf8267ff
[Repeated 1 time(s)]
> color sel #cf8065ff
> color sel #cf7e63ff
> color sel #cf785eff
> color sel #cf7259ff
> color sel #cf7058ff
> color sel #cf6e56ff
[Repeated 1 time(s)]
> color sel #cf6c56ff
> color sel #cf6b55ff
> color sel #cf6854ff
> color sel #cf5a4cff
> color sel #cf5247ff
> color sel #cf4d44ff
> color sel #cf4841ff
> color sel #cf453fff
> color sel #cf433eff
> color sel #cf443fff
[Repeated 1 time(s)]
> color sel #cf4641ff
> color sel #cf4944ff
> color sel #cf4a45ff
> color sel #cf4c47ff
> color sel #cf4d48ff
> color sel #cf4d49ff
> color sel #cf4d4aff
> color sel #cf4c4bff
[Repeated 2 time(s)]
> color sel #cf4c4cff
[Repeated 1 time(s)]
> color sel #cf4d4eff
> color sel #cf4e52ff
> color sel #cf4f54ff
> color sel #cf4f55ff
> color sel #cf5056ff
[Repeated 3 time(s)]
> color sel #cf5057ff
> color sel #cf515aff
> color sel #cf525fff
> color sel #cf5467ff
> color sel #cf5569ff
> color sel #cf556bff
[Repeated 1 time(s)]
> color sel #cf556aff
[Repeated 1 time(s)]
> color sel #cf5569ff
> color sel #cf5467ff
> color sel #cf5365ff
> color sel #cf5364ff
> color sel #cf5362ff
> color sel #cf5260ff
> color sel #cf525dff
> color sel #cf5157ff
> color sel #cf4e4fff
> color sel #cf504bff
> color sel #cf5248ff
> color sel #cf5246ff
> color sel #cf5245ff
> color sel #cf5244ff
> color sel #cf5343ff
> color sel #cf5442ff
> color sel #cf5440ff
> color sel #cf553fff
> color sel #cf553eff
> color sel #cf563dff
[Repeated 2 time(s)]
> color sel #cf573cff
> color sel #cf593cff
> color sel #cf593bff
> color sel #cf5a3aff
[Repeated 1 time(s)]
> color sel #cf5b3bff
> color sel #cf5c3cff
> color sel #cf5d3eff
> color sel #cf5f3fff
> color sel #cf6343ff
> color sel #cf6949ff
> color sel #cf6b4bff
> color sel #cf6b4cff
> color sel #cf6c4eff
> color sel #cf6c50ff
> color sel #cf6b51ff
> color sel #cf6952ff
> color sel #cf6852ff
> color sel #cf6753ff
> color sel #cf6653ff
[Repeated 1 time(s)]
> color sel #cf6553ff
> color sel #cf6454ff
> color sel #cf6154ff
> color sel #cf5e54ff
> color sel #cf5b55ff
> color sel #cf5955ff
> color sel #cf5655ff
> color sel #cf5556ff
> color sel #cf5557ff
> color sel #cf555aff
> color sel #cf555cff
> color sel #cf545eff
[Repeated 2 time(s)]
> color sel #cf535eff
[Repeated 1 time(s)]
> color sel #cf525eff
[Repeated 2 time(s)]
> color sel #cf515eff
> color sel #cf505dff
[Repeated 1 time(s)]
> color sel #cf505cff
> color sel #cf4f5cff
[Repeated 1 time(s)]
> color sel #cf4f5bff
> color sel #cf4d5bff
> color sel #cf4b5bff
> color sel #cf495bff
[Repeated 2 time(s)]
> color sel #cf495cff
[Repeated 1 time(s)]
> color sel #cf495dff
[Repeated 1 time(s)]
> select /F
412 atoms, 435 bonds, 43 residues, 1 model selected
> select /E,F
830 atoms, 870 bonds, 48 pseudobonds, 92 residues, 2 models selected
> color (#!1 & sel) byhetero
> select clear
> select /A,B,C,D : R110
Nothing selected
> select /A,B,C,D R110
Expected a keyword
> select /A,B,C,D: R110
Nothing selected
> select /A,B,C,D: #110
Expected an objects specifier or a keyword
> select /A,B,C,D: R110
Nothing selected
> select /A,B,C,D: 110
44 atoms, 40 bonds, 4 residues, 1 model selected
> style sel stick
Changed 44 atom styles
> show sel target ab
> color sel orange red
> color sel byhetero
> select clear
> select / A,B,C,D : R110
Nothing selected
> select / A,B,C,D : 110
44 atoms, 40 bonds, 4 residues, 1 model selected
> name sel R110
"sel" is reserved and cannot be redefined
> select name R110
Expected an objects specifier or a keyword
> name frozen R110 sel
> select clear
> select R110
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A : 145, 146, 147
29 atoms, 30 bonds, 3 residues, 1 model selected
> select /B : 145, 146, 147
29 atoms, 30 bonds, 3 residues, 1 model selected
> select /A : 145, 146, 147
29 atoms, 30 bonds, 3 residues, 1 model selected
> select clear
> name view standard
"standard": invalid atom specifier
> view name standard
> sel/A:145,146,147
Unknown command: sel/A:145,146,147
> select /A : 145,146,147
29 atoms, 30 bonds, 3 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 29 atom styles
> select add /A : 148
37 atoms, 37 bonds, 4 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 37 atom styles
> color sel byhetero
> name frozen R110-close
Missing or invalid "objects" argument: empty atom specifier
> name frozen resi.R110.close
Missing or invalid "objects" argument: empty atom specifier
> name frozen resi.R110.close sel
Not registering illegal selector name "resi.R110.close"
> name frozen R110resi_close sel
> select /A : 109, 111
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /A : 109, 111,108
23 atoms, 22 bonds, 3 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 23 atom styles
> select /A : 108
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> select /A : 111,109,108
23 atoms, 22 bonds, 3 residues, 1 model selected
> color sel byhetero
> select R110
44 atoms, 40 bonds, 4 residues, 1 model selected
> color sel orange
> color sel #ff9300ff
> color sel #ff9400ff
> color sel #ff9505ff
> color sel #ff980cff
> color sel #ff990cff
[Repeated 1 time(s)]
> color sel #ff990eff
> color sel #ff9a0fff
> color sel #ff9b12ff
> color sel #ff9c14ff
> color sel #ff9c15ff
> color sel #ff9d16ff
> color sel #ff9d17ff
> color sel #ff9d18ff
> color sel #ff9e18ff
> color sel #ff9e1aff
> color sel #ff9f1cff
> color sel #ffa01eff
> color sel #ffa120ff
> color sel #ffa121ff
> color sel #ffa222ff
> color sel #ffa223ff
> color sel #ffa325ff
> color sel #ffa427ff
> color sel #ffa428ff
> color sel #ffa529ff
[Repeated 2 time(s)]
> color sel #ffa52aff
[Repeated 1 time(s)]
> color sel #ffa52bff
> color sel #ffa62bff
> color sel #ffa72eff
> color sel #ff980cff
> color sel #ff9300ff
> color sel #ffad3cff
[Repeated 1 time(s)]
> color sel #ff9300ff
[Repeated 1 time(s)]
> color sel #fe9300ff
> color sel #fd9200ff
> color sel #f88f00ff
> color sel #e98700ff
> color sel #e48400ff
> color sel #da7e00ff
> color sel #d77d00ff
> color sel #d57b00ff
> color sel #d47b00ff
> color sel #d37a00ff
> color sel #d27900ff
> color sel #d07800ff
> color sel #cf7800ff
[Repeated 1 time(s)]
> color sel #ce7700ff
[Repeated 1 time(s)]
> color sel #cd7700ff
> color sel #cc7600ff
[Repeated 1 time(s)]
> color sel #cb7600ff
> color sel #cb7500ff
> color sel #ca7500ff
> color sel #ca7400ff
> color sel #c97400ff
> color sel #c87300ff
> color sel #c77300ff
> color sel #c67200ff
> color sel #c57200ff
[Repeated 1 time(s)]
> color sel #c67200ff
> color sel #c77300ff
> color sel #c97400ff
> color sel #cb7600ff
> color sel #cc7600ff
> color sel #ce7700ff
> color sel #cf7800ff
> color sel #d07800ff
> color sel #d17900ff
> color sel #d27900ff
> color sel #d37a00ff
> color sel #d57b00ff
> color sel #d77c00ff
> color sel #d87d00ff
> color sel #d97d00ff
> color sel #da7e00ff
[Repeated 3 time(s)]
> color sel #da7f02ff
> color sel #da8005ff
> color sel #da8208ff
> color sel #da840dff
> color sel #da840eff
> color sel #da8510ff
> color sel #da8511ff
[Repeated 1 time(s)]
> color sel #da8612ff
[Repeated 1 time(s)]
> color sel #da8613ff
[Repeated 2 time(s)]
> color sel #da8714ff
[Repeated 4 time(s)]
> color sel #db8715ff
> color sel #dc8815ff
> color sel #df8a15ff
> color sel #e08a15ff
> color sel #e18b15ff
> color sel #e28b15ff
> color sel #e38c15ff
> color sel #e48d15ff
> color sel #e58d15ff
> color sel #e78e16ff
> color sel #e78f16ff
[Repeated 1 time(s)]
> color sel byhetero
> view standars
Expected an objects specifier or a view name or a keyword
> view standard
> select clear
> view name R110close
> view standard
[Repeated 1 time(s)]
> surface
> transparency 80
> surface hidePatches
> select /A
1728 atoms, 1607 bonds, 4 pseudobonds, 357 residues, 2 models selected
> color (#!1 & sel) #d6d67aff
> undo
> surface (#!1 & sel)
> color (#!1 & sel) #d4d479ff
> transparency (#!1 & sel) 60
> select /B
1656 atoms, 1607 bonds, 4 pseudobonds, 285 residues, 2 models selected
> surface (#!1 & sel)
> color (#!1 & sel) #7a9f73ff
> select /C
1673 atoms, 1607 bonds, 4 pseudobonds, 302 residues, 2 models selected
> surface (#!1 & sel)
> color (#!1 & sel) #cfa4a8ff
> select /D
1700 atoms, 1607 bonds, 4 pseudobonds, 329 residues, 2 models selected
> color (#!1 & sel) #8a94b5ff
> surface (#!1 & sel)
> select /E
418 atoms, 435 bonds, 49 residues, 1 model selected
> surface (#!1 & sel)
> color (#!1 & sel) #6958efff
> select /F
412 atoms, 435 bonds, 43 residues, 1 model selected
> surface (#!1 & sel)
> color (#!1 & sel) #bd4355ff
> surface (#!1 & sel)
> transparency (#!1 & sel) 60
> select clear
> surface
> transparency 40
> transparency 80
> select R110
44 atoms, 40 bonds, 4 residues, 1 model selected
> color (#!1 & sel) orange
> color (#!1 & sel) byhetero
> select R110resi_close
37 atoms, 38 bonds, 4 residues, 1 model selected
> show (#!1 & sel) target ab
> color (#!1 & sel) byhetero
> select clear
> surface hidePatches
> ui mousemode right select
> name frozen R110_D148 sel
> distance sel
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0
Drag select of 1 atoms, 2 residues
Drag select of 2 atoms, 3 residues, 1 bonds
> ui mousemode right translate
> select clear
> select R11_D148
Expected an objects specifier or a keyword
> select R110_D148
2 bonds, 1 model selected
> distance sel
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0
> ui mousemode right distance
> distance /A:110@NH2 /A:148@CG
Distance between /A ARG 110 NH2 and ASP 148 CG: 3.680Å
> ui mousemode right translate
> hide distance
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide distance /A:110@NH2/A:148@CG
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> distance /A:110@NH2/A:148@CG
Distance already exists; modify distance properties with 'distance style'
> distance /A:110@NH2 /A:148@CG
Distance already exists; modify distance properties with 'distance style'
> distance delete
> distance / /A:110@NH2 /A:148@OD1
Missing or invalid "objects" argument: invalid objects specifier
> distance /A:110@NH2 /A:148@OD1
Distance between /A ARG 110 NH2 and ASP 148 OD1: 2.869Å
> view standard
[Repeated 1 time(s)]
> cd "/Users/abubakrsangare/Desktop/BIO 45 TA Helpful Information"
Current working directory is: /Users/abubakrsangare/Desktop/BIO 45 TA Helpful
Information
> save "/Users/abubakrsangare/Desktop/BIO 45 TA Helpful
> Information/Mut1_DG_Structure.cxs"
——— End of log from Mon Oct 21 11:37:12 2024 ———
opened ChimeraX session
> select clear
> ui mousemode right select
> select /A:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> undo
> select clear
> view name electric_int
> turn y 1 45
[Repeated 8 time(s)]
> view electric_int
> turn y 1 180
[Repeated 1 time(s)]
> turn y 1 90
> turn y 1 -90
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn y 1 270
> turn y 1 45
[Repeated 19 time(s)]
> view electric_int
> select R110resi_close
37 atoms, 38 bonds, 4 residues, 1 model selected
> hide (#!1 & sel) target a
> select R110_D148
2 bonds, 1 model selected
> select /A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /A:111
19 atoms, 18 bonds, 2 residues, 1 model selected
> name frozen resi_next sel
> hide (#!1 & sel) target a
> vire electric_int
Unknown command: vire electric_int
> view electric_int
> select R110
44 atoms, 40 bonds, 4 residues, 1 model selected
> hide (#!1 & sel) target a
> turn y 1 45
> turn y -1 45
> view electric int
Expected an objects specifier or a view name or a keyword
> view electric_int
> select clear
> turn y 1 45
> turn y -1 45
> turn y 1 180
[Repeated 1 time(s)]
> turn y 1 90
> turn y 1 145
> view electric_int
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> view electric_int
> view turn y 1 45
Expected an objects specifier or a view name or a keyword
> turn y 1 45
[Repeated 10 time(s)]
> view electric_int
> turn y 1 45
> turn y -1 45
> view name 1
> turn y 1 45
> view name 2
> turn y 1 45
> view name 3
> turn y 1 90
> turn y -1 90
> view 3
> turn y 1 45
> turn y -1 455
> view 3
> view 2
> view 3
> view 2
> view 1
[Repeated 1 time(s)]
> select R110
44 atoms, 40 bonds, 4 residues, 1 model selected
> cartoon hide (#!1 & sel)
> show (#!1 & sel) target ab
> cartoon (#!1 & sel)
> select resi_next
1571 atoms, 18 bonds, 200 residues, 1 model selected
> view 1
> select clear
> ui mousemode right select
> select /A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /A:111
19 atoms, 18 bonds, 2 residues, 1 model selected
> view 1
> name frozen next sel
> select nect
Expected an objects specifier or a keyword
> select next
1571 atoms, 18 bonds, 200 residues, 1 model selected
> select clear
> select A/109 ; sel add A/111
Expected an objects specifier or a keyword
> select A/109 : sel add A/111
Expected an objects specifier or a keyword
> select A/109
Expected an objects specifier or a keyword
> select /A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /A:111
19 atoms, 18 bonds, 2 residues, 1 model selected
> show (#!1 & sel) target ab
> cartoon hide (#!1 & sel)
> select /A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /A:111
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add /A:110
30 atoms, 28 bonds, 3 residues, 1 model selected
> select add /A:108
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add /A:112
38 atoms, 34 bonds, 5 residues, 1 model selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> hide #!2 models
> show #!2 models
> open 3kmd
3kmd title:
Crystal structure of the p53 core domain bound to a full consensus site as a
self-assembled tetramer [more info...]
Chain information for 3kmd #3
---
Chain | Description | UniProt
A B C D | Cellular tumor antigen p53 | P53_HUMAN
E F | 5'-D(*GP*GP*GP*CP*ap*TP*GP*CP*CP*TP*ap*GP*GP*CP*ap*TP*GP*CP*C)-3' |
Non-standard residues in 3kmd #3
---
ZN — zinc ion
> rename #3 Background_model
> save /Users/abubakrsangare/Desktop/WORKING_BIO45_Structure.cxs
> select #3 /A
1728 atoms, 1607 bonds, 4 pseudobonds, 357 residues, 2 models selected
> select #3 /B,C,D,E,F
5859 atoms, 5691 bonds, 60 pseudobonds, 1008 residues, 3 models selected
> delete sel
> select #3 : HOH
156 atoms, 156 residues, 1 model selected
> delete sel
> select #3
1572 atoms, 1607 bonds, 4 pseudobonds, 201 residues, 2 models selected
> hide (#!3 & sel) target a
> cartoon (#!3 & sel)
Drag select of 6 residues
> ui mousemode right translate
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #3
1572 atoms, 1607 bonds, 4 pseudobonds, 201 residues, 2 models selected
> color #1-2 #ebeb86ff
> color #3 #ebeb86ff
> show #!3 models
> select subtract #3
Nothing selected
> hide #!1 models
> select add #3
1572 atoms, 1607 bonds, 4 pseudobonds, 201 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3 A
Expected a keyword
> select #3/A
1572 atoms, 1607 bonds, 4 pseudobonds, 201 residues, 2 models selected
> select #3/A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:109
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:109,108
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/A:109,108,110,111
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/A:109,108,110,111,145,146,147,148
71 atoms, 72 bonds, 8 residues, 1 model selected
> name frozen bkgnd_resi sel
> select clear
> select bkgnd_resi
71 atoms, 72 bonds, 8 residues, 1 model selected
> view 1
> save /Users/abubakrsangare/Desktop/Deletion_test_BIO45.cxs
——— End of log from Fri Oct 25 17:23:06 2024 ———
opened ChimeraX session
> select ~sel
9088 atoms, 8829 bonds, 69 pseudobonds, 1558 residues, 7 models selected
> show #!1 models
> select subtract #1
1501 atoms, 1531 bonds, 4 pseudobonds, 193 residues, 9 models selected
> select add #2
1501 atoms, 1531 bonds, 5 pseudobonds, 193 residues, 4 models selected
> select subtract #2.1
1501 atoms, 1531 bonds, 5 pseudobonds, 193 residues, 3 models selected
> select add #2
1501 atoms, 1531 bonds, 5 pseudobonds, 193 residues, 4 models selected
> select subtract #2
1501 atoms, 1531 bonds, 4 pseudobonds, 193 residues, 2 models selected
> select ~sel
7658 atoms, 7370 bonds, 65 pseudobonds, 1373 residues, 6 models selected
> select bkgnd_resi
71 atoms, 72 bonds, 8 residues, 1 model selected
> select ~sel
9088 atoms, 8829 bonds, 69 pseudobonds, 1558 residues, 7 models selected
> select ~#2
9159 atoms, 8905 bonds, 69 pseudobonds, 1566 residues, 6 models selected
> select bkgnd_resi
71 atoms, 72 bonds, 8 residues, 1 model selected
> select ~sel
9088 atoms, 8829 bonds, 69 pseudobonds, 1558 residues, 7 models selected
> ~select #1
1501 atoms, 1531 bonds, 4 pseudobonds, 193 residues, 9 models selected
> ~select #2
1501 atoms, 1531 bonds, 4 pseudobonds, 193 residues, 2 models selected
> hide #!1 models
> delete sel
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!3 to #1 & sel
No 'to' model specified
> ui tool show Matchmaker
Traceback (most recent call last):
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Populating font family aliases took 352 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Users/abubakrsangare/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 85 days, 1 hour, 11 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: 'NoneType' object has no attribute 'setChecked' |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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