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#6151 closed defect (fixed)

MatchMaker: wrapped C/C++ object of type QPushButton has been deleted

Reported by:	martti.tolvanen@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.4.dev202202030703 (2022-02-03 07:03:08 UTC)
Description
I was trying to change alignment algorithm from NW to SW in matchmaker

Log:
UCSF ChimeraX version: 1.4.dev202202030703 (2022-02-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Thu Feb 10 12:36:32 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\Users\meetol\Dropbox\CA_projects_Martti\CA6\AF-based models\glyc
> dimer.cxs" format session

Log from Sat Feb 5 13:32:34 2022UCSF ChimeraX version: 1.4.dev202202030703
(2022-02-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/AF orig
> ja oma.cxs"

Log from Thu Feb 3 09:37:28 2022 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7262 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.4.dev202201282313 (2022-01-28)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based
> models/ca6_cd.fasta"

Summary of feedback from opening
C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/ca6_cd.fasta  
---  
note | Alignment identifier is ca6_cd.fasta  
  
Opened 1 sequences from ca6_cd.fasta  

> alphafold predict ca6_cd.fasta:1,ca6_cd.fasta:1 prokaryote false

Running AlphaFold prediction  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Associated best_model.pdb chain A to ca6_cat 18-278 with 0 mismatches  
Associated best_model.pdb chain B to ca6_cat 18-278 with 0 mismatches  
AlphaFold prediction finished  
Results in C:\Users\meetol/Downloads\ChimeraX\AlphaFold\prediction_5  

> surface

> surface hidePatches

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based
> models/alphafold human ca6 dimer.cxs"

> ui tool show Matchmaker

> split

Split best_model.pdb (#1) into 2 models  
Chain information for best_model.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for best_model.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Associated best_model.pdb A (1.1) chain A to ca6_cat 18-278 with 0 mismatches  
Associated best_model.pdb B (1.2) chain B to ca6_cat 18-278 with 0 mismatches  

> matchmaker #1.2 to #1.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb A, chain A (#1.1) with best_model.pdb B, chain B
(#1.2), sequence alignment score = 1353.6  
RMSD between 261 pruned atom pairs is 0.104 angstroms; (across all 261 pairs:
0.104)  
  

> undo

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/AF
> dimer chains superimposed.cxs"

> open 3fe4

Summary of feedback from opening 3fe4 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3fe4 from
http://files.rcsb.org/download/3fe4.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
3fe4 title:  
Crystal Structure of Human Carbonic Anhydrase vi [more info...]  
  
Chain information for 3fe4 #2  
---  
Chain | Description | UniProt  
A B | Carbonic anhydrase 6 | CAH6_HUMAN  
  
Non-standard residues in 3fe4 #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
  
3fe4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #1.1 to #2/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3fe4, chain A (#2) with best_model.pdb A, chain A (#1.1), sequence
alignment score = 1284.8  
RMSD between 216 pruned atom pairs is 0.629 angstroms; (across all 243 pairs:
1.252)  
  

> ui tool show Matchmaker

> matchmaker #1.2 to #2/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3fe4, chain B (#2) with best_model.pdb B, chain B (#1.2), sequence
alignment score = 1284.2  
RMSD between 215 pruned atom pairs is 0.630 angstroms; (across all 243 pairs:
1.216)  
  

> focus

Unknown command: focus  

> ui tool show "Selection Inspector"

> help help:user/tools/inspector.html

> select all

12543 atoms, 12351 bonds, 14 pseudobonds, 1442 residues, 6 models selected  

> cofr sel

> view sel

> select clear

> surface #1

> ~ribbon #2

> delete :gol

> select

12531 atoms, 12341 bonds, 14 pseudobonds, 1440 residues, 6 models selected  

> cofr sel

> ui mousemode right rotate

> ui mousemode right zoom

> select :278

22 atoms, 22 bonds, 2 residues, 1 model selected  

> color green selected

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel lime

> color sel lime surfaces

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A #1.2/B

Alignment identifier is 1  

> select #1:262

Nothing selected  

> select #1:261

42 atoms, 42 bonds, 2 residues, 2 models selected  

> color (#!1.1-2 & sel) lime

> ui tool show Clashes

> clashes ignoreHiddenModels true

27879 clashes  

> select clear

> surface hidePatches

> show target ab

> ~display #2

> hide target a

> open "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based
> models/AF-P23280-F1-model_v2.pdb"

AF-P23280-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase 6 (P23280) [more
info...]  
  
Chain information for AF-P23280-F1-model_v2.pdb #4  
---  
Chain | Description | UniProt  
A | carbonic anhydrase 6 | CAH6_HUMAN  
  
Associated AF-P23280-F1-model_v2.pdb chain A to ca6_cat 18-278 with 0
mismatches  

> ui tool show Matchmaker

> matchmaker #4 to #1.1/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb A, chain A (#1.1) with AF-P23280-F1-model_v2.pdb,
chain A (#4), sequence alignment score = 1365  
RMSD between 253 pruned atom pairs is 0.463 angstroms; (across all 261 pairs:
0.828)  
  

> alphafold predict LGSEFQFYLHKIEEILDYLRRALN,LGSEFQFYLHKIEEILDYLRRALN
> prokaryote false

Running AlphaFold prediction  

> help copy

No help found for 'copy'  

> help combine

> combine #4

Associated copy of AF-P23280-F1-model_v2.pdb chain A to ca6_cat 18-278 with 0
mismatches  

> ui tool show Matchmaker

> matchmaker #5 to #1.2/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb B, chain B (#1.2) with copy of
AF-P23280-F1-model_v2.pdb, chain A (#5), sequence alignment score = 1357.8  
RMSD between 254 pruned atom pairs is 0.471 angstroms; (across all 261 pairs:
0.812)  
  

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/AF orig
> ja oma.cxs"

> hide #4:1-17

> ribbon off #4:1-17

> cartoon off #4:1-17

Expected an atoms specifier or a keyword  

> ~ribbon #4:1-17

> ~ribbon #5:1-17

Downloaded prediction file not found:
C:\Users\meetol/Downloads\ChimeraX\AlphaFold\prediction_6\best_model.pdb  

AlphaFold prediction finished  
Results in C:\Users\meetol/Downloads\ChimeraX\AlphaFold\prediction_6  

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/AF orig
> ja oma.cxs"

——— End of log from Thu Feb 3 09:37:28 2022 ———

opened ChimeraX session  

> delete #1

> hide #!2 models

> show #!2 models

> ribbon #2

> hide #!2 models

> ~ribbon #5:280-283

> display #5:280-283@n,ca,c,o

> hide #4 models

> ui mousemode right "bond rotation"

> torsion #5/A:281@CA #5/A:281@C #5/A:282@N #5/A:282@CA -15.42

> torsion #5/A:281@C #5/A:282@N #5/A:282@CA #5/A:282@CB 55.42

> ui mousemode right zoom

> ribbon #5:280-283

> ~ribbon #5:1-279

> delete #1-4

> open 3fe4

3fe4 title:  
Crystal Structure of Human Carbonic Anhydrase vi [more info...]  
  
Chain information for 3fe4 #2  
---  
Chain | Description | UniProt  
A B | Carbonic anhydrase 6 | CAH6_HUMAN  
  
Non-standard residues in 3fe4 #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
  
3fe4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> combine #5

Associated copy of copy of AF-P23280-F1-model_v2.pdb chain A to ca6_cat 18-278
with 0 mismatches  

> ui tool show Matchmaker

> matchmaker #4/A to #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 3fe4, chain A (#2) with copy of copy of AF-P23280-F1-model_v2.pdb,
chain A (#4), sequence alignment score = 1328.7  
RMSD between 223 pruned atom pairs is 0.669 angstroms; (across all 244 pairs:
1.132)  
  

> matchmaker #5/A to #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 3fe4, chain B (#2) with copy of AF-P23280-F1-model_v2.pdb, chain A
(#5), sequence alignment score = 1329.9  
RMSD between 225 pruned atom pairs is 0.692 angstroms; (across all 245 pairs:
1.083)  
  

> ~tile

> matchmaker #5/A to #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 3fe4, chain B (#2) with copy of AF-P23280-F1-model_v2.pdb, chain A
(#5), sequence alignment score = 1329.9  
RMSD between 225 pruned atom pairs is 0.692 angstroms; (across all 245 pairs:
1.083)  
  

> matchmaker #4/A to #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 3fe4, chain A (#2) with copy of copy of AF-P23280-F1-model_v2.pdb,
chain A (#4), sequence alignment score = 1328.7  
RMSD between 223 pruned atom pairs is 0.669 angstroms; (across all 244 pairs:
1.132)  
  

> ui mousemode right "move picked models"

> view matrix models
> #2,0.83823,0.097374,-0.53656,17.132,-0.051895,0.99371,0.099266,62.5,0.54285,-0.055363,0.838,76.135

> view matrix models
> #2,0.83823,0.097374,-0.53656,15.848,-0.051895,0.99371,0.099266,63.166,0.54285,-0.055363,0.838,77.526

> ~select #3

Nothing selected  

> matchmaker #4/A to #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 3fe4, chain A (#2) with copy of copy of AF-P23280-F1-model_v2.pdb,
chain A (#4), sequence alignment score = 1328.7  
RMSD between 223 pruned atom pairs is 0.669 angstroms; (across all 244 pairs:
1.132)  
  

> matchmaker #5/A to #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 3fe4, chain B (#2) with copy of AF-P23280-F1-model_v2.pdb, chain A
(#5), sequence alignment score = 1329.9  
RMSD between 225 pruned atom pairs is 0.692 angstroms; (across all 245 pairs:
1.083)  
  

> ui mousemode right "translate selected models"

> select :val,ile,leu,phe,tyr & :285-308

204 atoms, 198 bonds, 22 residues, 2 models selected  

> color maroon sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel maroon

> ~display

> open "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based
> models/af_best_B glycosylated.pdb"

Summary of feedback from opening
C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/af_best_B
glycosylated.pdb  
---  
warnings | Ignored bad PDB record found on line 22  
  
  
Ignored bad PDB record found on line 30  
  
  
Ignored bad PDB record found on line 32  
  
  
Ignored bad PDB record found on line 34  
  
  
Ignored bad PDB record found on line 36  
  
  
8992 messages similar to the above omitted  
  
Chain information for af_best_B glycosylated.pdb #6  
---  
Chain | Description  
B | No description available  
  
Associated af_best_B glycosylated.pdb chain B to ca6_cat 18-278 with 0
mismatches  

> combine #6

Associated copy of af_best_B glycosylated.pdb chain B to ca6_cat 18-278 with 0
mismatches  

> rename #6 "glyco 1"

> rename #7 "glyco 2"

> matchmaker #6/B to #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 3fe4, chain A (#2) with glyco 1, chain B (#6), sequence alignment
score = 1284.2  
RMSD between 215 pruned atom pairs is 0.623 angstroms; (across all 243 pairs:
1.264)  
  

> ui tool show Matchmaker

> matchmaker #7/B to #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 3fe4, chain B (#2) with glyco 2, chain B (#7), sequence alignment
score = 1284.2  
RMSD between 215 pruned atom pairs is 0.630 angstroms; (across all 243 pairs:
1.216)  
  

> hide #!2 models

> color #6 sky blue

> color #6 !protein byhet

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #6 !protein byhetero

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color byhetero #6 !protein

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #6 & !protein byhetero

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #6 & !protein sky blue byhetero

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #6 & !protein lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color (#6 & !protein) lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> select #6 & !protein

Expected a keyword  

> select #6 & ^protein

Expected a keyword  

> help select

> select #6 & ~protein

703 atoms, 728 bonds, 27 residues, 1 model selected  

> color #6 & ~protein byhetero

> color #7 light coral

> color #7 & ~protein byhetero

> select :val,ile,leu,phe,tyr & :285-308

204 atoms, 198 bonds, 22 residues, 2 models selected  

> color #4 & ~sel sky blue

> color #5 & ~sel light coral

> color #4 & sel fire brick

> select clear

> surface #6 & protein

> color #6 & protein sky blue

> surface #7 & protein

> select #6-7 & ~prot

Expected a keyword  

> select #6-7 & ~protein

1406 atoms, 1456 bonds, 54 residues, 2 models selected  

> style sel sphere

Changed 1406 atom styles  

> select clear

> color #6 & protein & :1-14 sandy brown

> color #7 & protein & :1-14 lavender

> transparency surf 30

Missing or invalid "percent" argument: Expected a number  

> transparency 30 surfaces

> transparency 20 surfaces

> rotate x 90

Unknown command: rotate x 90  

> turn x 90

[Repeated 4 time(s)]

> turn x 120

> lighting soft

[Repeated 1 time(s)]

> lighting full

> lighting simple

> turn x 180

[Repeated 19 time(s)]

> ~ribbon #6-7

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color #7 & protein & :1-14 dodger blue

> color #7 & protein & :1-14 lavender

> color #6 & protein & :15-261 dodger blue

> select #7 & ~protein

703 atoms, 728 bonds, 27 residues, 1 model selected  

> color peach puff sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color peachpuff sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color navajowhite sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel pink

> color sel peachpuff

> color sel navajowhite

> color sel light coral

> color #7 & protein coral

> color #7 & protein lignt coral

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #7 & protein ligntcoral

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #7 & protein lightcoral

> color sel light pink

> color sel byhetero

> select clear

> color #7 & protein & :1-14 dodger blue

> color #7 & protein & :1-14 sky blue

> color #7 & protein & :1-14 navajowhite

> transparency 30 surfaces

> transparency 25 surfaces

> color sel navajoselect :val,ile,leu,phe,tyr & :289-308

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> select :val,ile,leu,phe,tyr & :289-308

188 atoms, 184 bonds, 20 residues, 2 models selected  

> select :val,ile,leu,phe,tyr,met & :289-308

188 atoms, 184 bonds, 20 residues, 2 models selected  

> color #4 & ~sel dodger blue

> select clear

> turn x 180

[Repeated 39 time(s)]

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/glyc
> dimer 1.png" width 1079 height 727 supersample 3

> turn x 180

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/glyc
> dimer 2.png" width 1079 height 727 supersample 3

> turn x 180

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/glyc
> dimer.cxs"

> combine #6 #7

Remapping chain ID 'A' in glyco 2 #7 to 'D'  
Remapping chain ID 'B' in glyco 2 #7 to 'E'  
Remapping chain ID 'C' in glyco 2 #7 to 'F'  

> transparency 10 surfaces

> ui tool show "Side View"

> ui mousemode right "translate selected models"

> ui mousemode right zoom

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/glyc
> dimer.cxs"

——— End of log from Sat Feb 5 13:32:34 2022 ———

opened ChimeraX session  

> set bgColor white

> ui windowfill toggle

[Repeated 1 time(s)]

> ~display #7/a

> ~display #7/c

> lighting depthCue false

> lighting full

> lighting shadows false

> transparency 0 surfaces

> transparency (#7/b:1-14 | #6/b:1-14) 10 surfaces

> ui windowfill toggle

> ui mousemode right zoom

[Repeated 1 time(s)]

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/glyc
> dimer white bg.cxs"

——— End of log from Thu Feb 10 12:36:32 2022 ———

opened ChimeraX session  

> ui mousemode right translate

> ui tool show Clashes

> clashes ignoreHiddenModels true makePseudobonds false

137662 clashes  

> ui mousemode right zoom

> ui mousemode right translate

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/CA6/AF-based models/glyc
> dimer white bg2.cxs"

> delete #8

> display #7 & ~protein

> ui tool show Matchmaker

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> matchmaker #!6 to #2/A pairing bs verbose true cutoffDistance 3.0
> showAlignment true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 3  
  
Matchmaker 3fe4, chain A (#2) with glyco 1, chain B (#6), sequence alignment
score = 1284.2  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 3fe4 #2/A, glyco 1 #6/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 231 pruned atom pairs is 0.886 angstroms; (across all 243 pairs:
1.209)  
  
Sequences:  
3fe4, chain A
..MSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNFPNQEYTLGSEFQAENLYFQ  
glyco 1, chain B
QHVSDWTYSEGALDEAHWPQHYPACGGQRQSPINLQRTKVRYNPSLKGLNMTGYETQAGEFPMVNNGHTVQISLPSTMRMTVADGTVYIAQQMHFHWGGASSEISGSEHTVDGIRHVIEIHIVHYNSKYKSYDIAQDAPDGLAVLAAFVEVKNYPENTYYSNFISHLANIKYPGQRTTLTGLDVQDMLPRNLQHYYTYHGSLTTPPCTENVHWFVLADFVKLSRTQVWKLENSLLDHRNKTIHNDYRRTQPLNHRVVESNF...................  
Residues:  
None, None, None, None, None, None, None, None, None, None, None, None, 3fe4
#2/A GLU 32, 3fe4 #2/A ALA 33, 3fe4 #2/A HIS 34, 3fe4 #2/A TRP 35, 3fe4 #2/A
PRO 36, 3fe4 #2/A GLN 37, 3fe4 #2/A HIS 38, 3fe4 #2/A TYR 39, 3fe4 #2/A PRO
40, 3fe4 #2/A ALA 41, 3fe4 #2/A CYS 42, 3fe4 #2/A GLY 43, 3fe4 #2/A GLY 44,
3fe4 #2/A GLN 45, 3fe4 #2/A ARG 46, 3fe4 #2/A GLN 47, 3fe4 #2/A SER 48, 3fe4
#2/A PRO 49, 3fe4 #2/A ILE 50, 3fe4 #2/A ASN 51, 3fe4 #2/A LEU 52, 3fe4 #2/A
GLN 53, 3fe4 #2/A ARG 54, 3fe4 #2/A THR 55, 3fe4 #2/A LYS 56, 3fe4 #2/A VAL
57, 3fe4 #2/A ARG 58, 3fe4 #2/A TYR 59, 3fe4 #2/A ASN 60, 3fe4 #2/A PRO 61,
3fe4 #2/A SER 62, 3fe4 #2/A LEU 63, 3fe4 #2/A LYS 64, 3fe4 #2/A GLY 65, 3fe4
#2/A LEU 66, 3fe4 #2/A ASN 67, 3fe4 #2/A MET 68, 3fe4 #2/A THR 69, 3fe4 #2/A
GLY 70, 3fe4 #2/A TYR 71, 3fe4 #2/A GLU 72, 3fe4 #2/A THR 73, 3fe4 #2/A GLN
74, 3fe4 #2/A ALA 75, 3fe4 #2/A GLY 76, 3fe4 #2/A GLU 77, 3fe4 #2/A PHE 78,
3fe4 #2/A PRO 79, 3fe4 #2/A MET 80, 3fe4 #2/A VAL 81, 3fe4 #2/A ASN 82, 3fe4
#2/A ASN 83, 3fe4 #2/A GLY 84, 3fe4 #2/A HIS 85, 3fe4 #2/A THR 86, 3fe4 #2/A
VAL 87, 3fe4 #2/A GLN 88, 3fe4 #2/A ILE 89, 3fe4 #2/A SER 90, 3fe4 #2/A LEU
91, 3fe4 #2/A PRO 92, 3fe4 #2/A SER 93, 3fe4 #2/A THR 94, 3fe4 #2/A MET 95,
3fe4 #2/A ARG 96, 3fe4 #2/A MET 97, 3fe4 #2/A THR 98, 3fe4 #2/A VAL 99, 3fe4
#2/A ALA 100, 3fe4 #2/A ASP 101, 3fe4 #2/A GLY 102, 3fe4 #2/A THR 103, 3fe4
#2/A VAL 104, 3fe4 #2/A TYR 105, 3fe4 #2/A ILE 106, 3fe4 #2/A ALA 107, 3fe4
#2/A GLN 108, 3fe4 #2/A GLN 109, 3fe4 #2/A MET 110, 3fe4 #2/A HIS 111, 3fe4
#2/A PHE 112, 3fe4 #2/A HIS 113, 3fe4 #2/A TRP 114, 3fe4 #2/A GLY 115, 3fe4
#2/A GLY 116, None, None, None, None, 3fe4 #2/A ILE 121, 3fe4 #2/A SER 122,
3fe4 #2/A GLY 123, 3fe4 #2/A SER 124, 3fe4 #2/A GLU 125, 3fe4 #2/A HIS 126,
3fe4 #2/A THR 127, 3fe4 #2/A VAL 128, 3fe4 #2/A ASP 129, 3fe4 #2/A GLY 130,
3fe4 #2/A ILE 131, 3fe4 #2/A ARG 132, 3fe4 #2/A HIS 133, 3fe4 #2/A VAL 134,
3fe4 #2/A ILE 135, 3fe4 #2/A GLU 136, 3fe4 #2/A ILE 137, 3fe4 #2/A HIS 138,
3fe4 #2/A ILE 139, 3fe4 #2/A VAL 140, 3fe4 #2/A HIS 141, 3fe4 #2/A TYR 142,
3fe4 #2/A ASN 143, 3fe4 #2/A SER 144, 3fe4 #2/A LYS 145, 3fe4 #2/A TYR 146,
3fe4 #2/A LYS 147, 3fe4 #2/A SER 148, 3fe4 #2/A TYR 149, 3fe4 #2/A ASP 150,
3fe4 #2/A ILE 151, 3fe4 #2/A ALA 152, 3fe4 #2/A GLN 153, 3fe4 #2/A ASP 154,
3fe4 #2/A ALA 155, 3fe4 #2/A PRO 156, 3fe4 #2/A ASP 157, 3fe4 #2/A GLY 158,
3fe4 #2/A LEU 159, 3fe4 #2/A ALA 160, 3fe4 #2/A VAL 161, 3fe4 #2/A LEU 162,
3fe4 #2/A ALA 163, 3fe4 #2/A ALA 164, 3fe4 #2/A PHE 165, 3fe4 #2/A VAL 166,
3fe4 #2/A GLU 167, 3fe4 #2/A VAL 168, 3fe4 #2/A LYS 169, 3fe4 #2/A ASN 170,
3fe4 #2/A TYR 171, 3fe4 #2/A PRO 172, 3fe4 #2/A GLU 173, 3fe4 #2/A ASN 174,
3fe4 #2/A THR 175, 3fe4 #2/A TYR 176, 3fe4 #2/A TYR 177, 3fe4 #2/A SER 178,
3fe4 #2/A ASN 179, 3fe4 #2/A PHE 180, 3fe4 #2/A ILE 181, 3fe4 #2/A SER 182,
3fe4 #2/A HIS 183, 3fe4 #2/A LEU 184, 3fe4 #2/A ALA 185, 3fe4 #2/A ASN 186,
3fe4 #2/A ILE 187, 3fe4 #2/A LYS 188, 3fe4 #2/A TYR 189, 3fe4 #2/A PRO 190,
3fe4 #2/A GLY 191, 3fe4 #2/A GLN 192, 3fe4 #2/A ARG 193, 3fe4 #2/A THR 194,
3fe4 #2/A THR 195, 3fe4 #2/A LEU 196, 3fe4 #2/A THR 197, 3fe4 #2/A GLY 198,
3fe4 #2/A LEU 199, 3fe4 #2/A ASP 200, 3fe4 #2/A VAL 201, 3fe4 #2/A GLN 202,
3fe4 #2/A ASP 203, 3fe4 #2/A MET 204, 3fe4 #2/A LEU 205, 3fe4 #2/A PRO 206,
3fe4 #2/A ARG 207, 3fe4 #2/A ASN 208, 3fe4 #2/A LEU 209, 3fe4 #2/A GLN 210,
3fe4 #2/A HIS 211, 3fe4 #2/A TYR 212, 3fe4 #2/A TYR 213, 3fe4 #2/A THR 214,
3fe4 #2/A TYR 215, 3fe4 #2/A HIS 216, 3fe4 #2/A GLY 217, 3fe4 #2/A SER 218,
3fe4 #2/A LEU 219, 3fe4 #2/A THR 220, 3fe4 #2/A THR 221, 3fe4 #2/A PRO 222,
3fe4 #2/A PRO 223, 3fe4 #2/A CYS 224, 3fe4 #2/A THR 225, 3fe4 #2/A GLU 226,
3fe4 #2/A ASN 227, 3fe4 #2/A VAL 228, 3fe4 #2/A HIS 229, 3fe4 #2/A TRP 230,
3fe4 #2/A PHE 231, 3fe4 #2/A VAL 232, 3fe4 #2/A LEU 233, 3fe4 #2/A ALA 234,
3fe4 #2/A ASP 235, 3fe4 #2/A PHE 236, 3fe4 #2/A VAL 237, 3fe4 #2/A LYS 238,
3fe4 #2/A LEU 239, 3fe4 #2/A SER 240, 3fe4 #2/A ARG 241, 3fe4 #2/A THR 242,
3fe4 #2/A GLN 243, 3fe4 #2/A VAL 244, 3fe4 #2/A TRP 245, 3fe4 #2/A LYS 246,
3fe4 #2/A LEU 247, 3fe4 #2/A GLU 248, 3fe4 #2/A ASN 249, 3fe4 #2/A SER 250,
3fe4 #2/A LEU 251, 3fe4 #2/A LEU 252, 3fe4 #2/A ASP 253, 3fe4 #2/A HIS 254,
3fe4 #2/A ARG 255, 3fe4 #2/A ASN 256, 3fe4 #2/A LYS 257, 3fe4 #2/A THR 258,
3fe4 #2/A ILE 259, 3fe4 #2/A HIS 260, 3fe4 #2/A ASN 261, 3fe4 #2/A ASP 262,
3fe4 #2/A TYR 263, 3fe4 #2/A ARG 264, 3fe4 #2/A ARG 265, 3fe4 #2/A THR 266,
3fe4 #2/A GLN 267, 3fe4 #2/A PRO 268, 3fe4 #2/A LEU 269, 3fe4 #2/A ASN 270,
3fe4 #2/A HIS 271, 3fe4 #2/A ARG 272, 3fe4 #2/A VAL 273, 3fe4 #2/A VAL 274,
3fe4 #2/A GLU 275, 3fe4 #2/A SER 276, 3fe4 #2/A ASN 277, 3fe4 #2/A PHE 278,
3fe4 #2/A PRO 279, None, None, None, None, None, None, None, None, None, None,
None, None, None, None, None, None, None, None  
glyco 1 #6/B GLN 1, glyco 1 #6/B HIS 2, glyco 1 #6/B VAL 3, glyco 1 #6/B SER
4, glyco 1 #6/B ASP 5, glyco 1 #6/B TRP 6, glyco 1 #6/B THR 7, glyco 1 #6/B
TYR 8, glyco 1 #6/B SER 9, glyco 1 #6/B GLU 10, glyco 1 #6/B GLY 11, glyco 1
#6/B ALA 12, glyco 1 #6/B LEU 13, glyco 1 #6/B ASP 14, glyco 1 #6/B GLU 15,
glyco 1 #6/B ALA 16, glyco 1 #6/B HIS 17, glyco 1 #6/B TRP 18, glyco 1 #6/B
PRO 19, glyco 1 #6/B GLN 20, glyco 1 #6/B HIS 21, glyco 1 #6/B TYR 22, glyco 1
#6/B PRO 23, glyco 1 #6/B ALA 24, glyco 1 #6/B CYS 25, glyco 1 #6/B GLY 26,
glyco 1 #6/B GLY 27, glyco 1 #6/B GLN 28, glyco 1 #6/B ARG 29, glyco 1 #6/B
GLN 30, glyco 1 #6/B SER 31, glyco 1 #6/B PRO 32, glyco 1 #6/B ILE 33, glyco 1
#6/B ASN 34, glyco 1 #6/B LEU 35, glyco 1 #6/B GLN 36, glyco 1 #6/B ARG 37,
glyco 1 #6/B THR 38, glyco 1 #6/B LYS 39, glyco 1 #6/B VAL 40, glyco 1 #6/B
ARG 41, glyco 1 #6/B TYR 42, glyco 1 #6/B ASN 43, glyco 1 #6/B PRO 44, glyco 1
#6/B SER 45, glyco 1 #6/B LEU 46, glyco 1 #6/B LYS 47, glyco 1 #6/B GLY 48,
glyco 1 #6/B LEU 49, glyco 1 #6/B ASN 50, glyco 1 #6/B MET 51, glyco 1 #6/B
THR 52, glyco 1 #6/B GLY 53, glyco 1 #6/B TYR 54, glyco 1 #6/B GLU 55, glyco 1
#6/B THR 56, glyco 1 #6/B GLN 57, glyco 1 #6/B ALA 58, glyco 1 #6/B GLY 59,
glyco 1 #6/B GLU 60, glyco 1 #6/B PHE 61, glyco 1 #6/B PRO 62, glyco 1 #6/B
MET 63, glyco 1 #6/B VAL 64, glyco 1 #6/B ASN 65, glyco 1 #6/B ASN 66, glyco 1
#6/B GLY 67, glyco 1 #6/B HIS 68, glyco 1 #6/B THR 69, glyco 1 #6/B VAL 70,
glyco 1 #6/B GLN 71, glyco 1 #6/B ILE 72, glyco 1 #6/B SER 73, glyco 1 #6/B
LEU 74, glyco 1 #6/B PRO 75, glyco 1 #6/B SER 76, glyco 1 #6/B THR 77, glyco 1
#6/B MET 78, glyco 1 #6/B ARG 79, glyco 1 #6/B MET 80, glyco 1 #6/B THR 81,
glyco 1 #6/B VAL 82, glyco 1 #6/B ALA 83, glyco 1 #6/B ASP 84, glyco 1 #6/B
GLY 85, glyco 1 #6/B THR 86, glyco 1 #6/B VAL 87, glyco 1 #6/B TYR 88, glyco 1
#6/B ILE 89, glyco 1 #6/B ALA 90, glyco 1 #6/B GLN 91, glyco 1 #6/B GLN 92,
glyco 1 #6/B MET 93, glyco 1 #6/B HIS 94, glyco 1 #6/B PHE 95, glyco 1 #6/B
HIS 96, glyco 1 #6/B TRP 97, glyco 1 #6/B GLY 98, glyco 1 #6/B GLY 99, glyco 1
#6/B ALA 100, glyco 1 #6/B SER 101, glyco 1 #6/B SER 102, glyco 1 #6/B GLU
103, glyco 1 #6/B ILE 104, glyco 1 #6/B SER 105, glyco 1 #6/B GLY 106, glyco 1
#6/B SER 107, glyco 1 #6/B GLU 108, glyco 1 #6/B HIS 109, glyco 1 #6/B THR
110, glyco 1 #6/B VAL 111, glyco 1 #6/B ASP 112, glyco 1 #6/B GLY 113, glyco 1
#6/B ILE 114, glyco 1 #6/B ARG 115, glyco 1 #6/B HIS 116, glyco 1 #6/B VAL
117, glyco 1 #6/B ILE 118, glyco 1 #6/B GLU 119, glyco 1 #6/B ILE 120, glyco 1
#6/B HIS 121, glyco 1 #6/B ILE 122, glyco 1 #6/B VAL 123, glyco 1 #6/B HIS
124, glyco 1 #6/B TYR 125, glyco 1 #6/B ASN 126, glyco 1 #6/B SER 127, glyco 1
#6/B LYS 128, glyco 1 #6/B TYR 129, glyco 1 #6/B LYS 130, glyco 1 #6/B SER
131, glyco 1 #6/B TYR 132, glyco 1 #6/B ASP 133, glyco 1 #6/B ILE 134, glyco 1
#6/B ALA 135, glyco 1 #6/B GLN 136, glyco 1 #6/B ASP 137, glyco 1 #6/B ALA
138, glyco 1 #6/B PRO 139, glyco 1 #6/B ASP 140, glyco 1 #6/B GLY 141, glyco 1
#6/B LEU 142, glyco 1 #6/B ALA 143, glyco 1 #6/B VAL 144, glyco 1 #6/B LEU
145, glyco 1 #6/B ALA 146, glyco 1 #6/B ALA 147, glyco 1 #6/B PHE 148, glyco 1
#6/B VAL 149, glyco 1 #6/B GLU 150, glyco 1 #6/B VAL 151, glyco 1 #6/B LYS
152, glyco 1 #6/B ASN 153, glyco 1 #6/B TYR 154, glyco 1 #6/B PRO 155, glyco 1
#6/B GLU 156, glyco 1 #6/B ASN 157, glyco 1 #6/B THR 158, glyco 1 #6/B TYR
159, glyco 1 #6/B TYR 160, glyco 1 #6/B SER 161, glyco 1 #6/B ASN 162, glyco 1
#6/B PHE 163, glyco 1 #6/B ILE 164, glyco 1 #6/B SER 165, glyco 1 #6/B HIS
166, glyco 1 #6/B LEU 167, glyco 1 #6/B ALA 168, glyco 1 #6/B ASN 169, glyco 1
#6/B ILE 170, glyco 1 #6/B LYS 171, glyco 1 #6/B TYR 172, glyco 1 #6/B PRO
173, glyco 1 #6/B GLY 174, glyco 1 #6/B GLN 175, glyco 1 #6/B ARG 176, glyco 1
#6/B THR 177, glyco 1 #6/B THR 178, glyco 1 #6/B LEU 179, glyco 1 #6/B THR
180, glyco 1 #6/B GLY 181, glyco 1 #6/B LEU 182, glyco 1 #6/B ASP 183, glyco 1
#6/B VAL 184, glyco 1 #6/B GLN 185, glyco 1 #6/B ASP 186, glyco 1 #6/B MET
187, glyco 1 #6/B LEU 188, glyco 1 #6/B PRO 189, glyco 1 #6/B ARG 190, glyco 1
#6/B ASN 191, glyco 1 #6/B LEU 192, glyco 1 #6/B GLN 193, glyco 1 #6/B HIS
194, glyco 1 #6/B TYR 195, glyco 1 #6/B TYR 196, glyco 1 #6/B THR 197, glyco 1
#6/B TYR 198, glyco 1 #6/B HIS 199, glyco 1 #6/B GLY 200, glyco 1 #6/B SER
201, glyco 1 #6/B LEU 202, glyco 1 #6/B THR 203, glyco 1 #6/B THR 204, glyco 1
#6/B PRO 205, glyco 1 #6/B PRO 206, glyco 1 #6/B CYS 207, glyco 1 #6/B THR
208, glyco 1 #6/B GLU 209, glyco 1 #6/B ASN 210, glyco 1 #6/B VAL 211, glyco 1
#6/B HIS 212, glyco 1 #6/B TRP 213, glyco 1 #6/B PHE 214, glyco 1 #6/B VAL
215, glyco 1 #6/B LEU 216, glyco 1 #6/B ALA 217, glyco 1 #6/B ASP 218, glyco 1
#6/B PHE 219, glyco 1 #6/B VAL 220, glyco 1 #6/B LYS 221, glyco 1 #6/B LEU
222, glyco 1 #6/B SER 223, glyco 1 #6/B ARG 224, glyco 1 #6/B THR 225, glyco 1
#6/B GLN 226, glyco 1 #6/B VAL 227, glyco 1 #6/B TRP 228, glyco 1 #6/B LYS
229, glyco 1 #6/B LEU 230, glyco 1 #6/B GLU 231, glyco 1 #6/B ASN 232, glyco 1
#6/B SER 233, glyco 1 #6/B LEU 234, glyco 1 #6/B LEU 235, glyco 1 #6/B ASP
236, glyco 1 #6/B HIS 237, glyco 1 #6/B ARG 238, glyco 1 #6/B ASN 239, glyco 1
#6/B LYS 240, glyco 1 #6/B THR 241, glyco 1 #6/B ILE 242, glyco 1 #6/B HIS
243, glyco 1 #6/B ASN 244, glyco 1 #6/B ASP 245, glyco 1 #6/B TYR 246, glyco 1
#6/B ARG 247, glyco 1 #6/B ARG 248, glyco 1 #6/B THR 249, glyco 1 #6/B GLN
250, glyco 1 #6/B PRO 251, glyco 1 #6/B LEU 252, glyco 1 #6/B ASN 253, glyco 1
#6/B HIS 254, glyco 1 #6/B ARG 255, glyco 1 #6/B VAL 256, glyco 1 #6/B VAL
257, glyco 1 #6/B GLU 258, glyco 1 #6/B SER 259, glyco 1 #6/B ASN 260, glyco 1
#6/B PHE 261  
Residue usage in match (1=used, 0=unused):  
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0  
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1  

> select protein

17102 atoms, 17481 bonds, 2 pseudobonds, 1627 residues, 6 models selected  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-
packages\chimerax\ui\options\options.py", line 345, in set_value  
self.widget.setText(value)  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-
packages\chimerax\ui\options\options.py", line 345, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7262
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

Locale: fi_FI.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 840 G3
OS: Microsoft Windows 10 Enterprise (Build 17763)
Memory: 8,464,723,968
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.11
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.35
    ChimeraX-AtomicLibrary: 5.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202202030703
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.6
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.5
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    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: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.0.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.26
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    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: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (5)

in reply to: 1 ; follow-up: 1 comment:1 by martti.tolvanen@…, 4 years ago

As further information, ChimeraX did not crash after the message but kept
going seemingly as normal. Later I got similar messages of other parameter
changes in MatchMaker UI as well but again with no harm done.

la 12. helmik. 2022 klo 19.09 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:

comment:2 by pett, 4 years ago

Component:	Unassigned → Structure Analysis
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type QPushButton has been deleted

To reproduce, have to use the red X button on the upper left rather than the Close button on the lower right.

comment:3 by pett, 4 years ago

Resolution:	→ fixed
Status:	accepted → closed

Thanks for reporting this. It is fixed in tomorrow's build.

A memory leak prevented the closed tool window from being completely disposed of, so it still got callbacks which produced the error. The code which fixes the problem is: https://github.com/RBVI/ChimeraX/commit/47a3352241395888390f4629f636d2810e02ba84

in reply to: 4 ; follow-up: 4 comment:4 by martti.tolvanen@…, 4 years ago

Thanks a lot. I'm so happy that even minor bug reports get quick attention
from you guys.

Btw am I right that residue renumbering is not implemented in ChimeraX yet?
I found some documentation of ChimeraX code which stated renumber to be
experimental.

-Martti

ke 16. helmik. 2022 klo 3.56 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:

comment:5 by pett, 4 years ago

No, generic residue renumbering hasn't been implemented, though switching between PDB "author" numbering, PDB internal numbering, and UniProt numbering has been implemented for files that contain the relevant information, if that's of any use to you. I could add you to the ticket for generic renumbering if you'd like to be notified when it gets implemented.

--Eric

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