id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16075	QWebEngine crash	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs""

Log from Sun Oct 6 15:21:54 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant2_zoom.cxs""

Log from Sun Oct 6 13:09:19 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5.cxs""

Log from Fri Oct 4 15:32:18 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/TOPview.cxs""

Log from Fri Oct 4 15:13:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Top.cxs""

Log from Wed Sep 18 22:21:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 5.cxs""

Log from Wed Sep 18 22:00:52 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs""

Log from Wed Sep 18 21:35:21 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/lks559/Desktop/CINP-c1orf109_refine_13-coot.pdb

Chain information for CINP-c1orf109_refine_13-coot.pdb #1  
---  
Chain | Description  
A C | No description available  
B D | No description available  


> set bgColor white

> lighting soft

> color #1 #678ad7ff

> select /A:2-203

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> select /C:2-203

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]

> show sel cartoons

> ui tool show ""Unit Cell""

> ui tool show ""Crystal Contacts""

> crystalcontacts #1

8 pairs of asymmetric units of CINP-c1orf109_refine_13-coot.pdb contact at
distance 3.0 A



     Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        6     0      1     -1  1 -1      0         1
        5     0      3      0  0  1      0         1
        5     0      1     -1  1  0      0         1
        4     0      3     -1  0  1      0         1
        3     0      1      0  1  0      0         1
        3     0      1      0  1 -1      0         1
        1     0      0      1  0  0      0         1
        1     0      0     -1  0  0      0         1




> select /D:17-212

14319 atoms, 14607 bonds, 1764 residues, 9 models selected  

> select /C:2-203

14751 atoms, 15012 bonds, 1818 residues, 9 models selected  

> select /D:17-212

14319 atoms, 14607 bonds, 1764 residues, 9 models selected  

> select /C:2-203

14751 atoms, 15012 bonds, 1818 residues, 9 models selected  

> select /D:17-212

14319 atoms, 14607 bonds, 1764 residues, 9 models selected  

> select #2.1/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> hide sel cartoons

> select #1/B#2.1/B#2.2/B#2.3/B#2.4/B#2.5/B#2.6/B#2.7/B#2.8/B

14319 atoms, 14607 bonds, 1764 residues, 9 models selected  

> hide sel cartoons

> select #1/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A

14751 atoms, 15012 bonds, 1818 residues, 9 models selected  

> hide sel cartoons

> select #2.1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide sel cartoons

> select #2.2/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide sel cartoons

> select #2.3/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide sel cartoons

> select #2.4/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide sel cartoons

> select #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C

14751 atoms, 15012 bonds, 1818 residues, 9 models selected  

> hide sel cartoons

> select #2.2/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> show sel cartoons

> select #1/D#2.1/D#2.2/D#2.3/D#2.4/D#2.5/D#2.6/D#2.7/D#2.8/D

14319 atoms, 14607 bonds, 1764 residues, 9 models selected  

> hide sel cartoons

> select #2.2/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> show sel cartoons

> select #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C

14751 atoms, 15012 bonds, 1818 residues, 9 models selected  

> show sel cartoons

> select #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C

14751 atoms, 15012 bonds, 1818 residues, 9 models selected  

> hide sel cartoons

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> show sel cartoons

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel dim gray

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/biological unit.cxs""

> color #2 #356abfff models

> select #2.2/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color sel orange

> select add #2

51680 atoms, 52656 bonds, 6368 residues, 9 models selected  

> select subtract #2

Nothing selected  

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel hot pink

> open /Users/lks559/Desktop/CINP-c1orf109_refine_13-coot.pdb

Chain information for CINP-c1orf109_refine_13-coot.pdb #3  
---  
Chain | Description  
A C | No description available  
B D | No description available  


> select #3/B

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> hide sel cartoons

> select #3/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color sel medium blue

> select #3/A

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel lime

> select #3/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color midnight blue

> color sel #ffffffff

> color sel #011993ff

> color midnightblue blueselect #3/A

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

> select #3/A

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #73fa79ff

> color sel #0096ffff

> color sel #0433ffff

> color sel #0096ffff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #73fa79ff

> color sel #00f900ff

> color sel #73fa79ff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> select #3/A

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #0096ffff

> color sel #0433ffff

> color sel #7a81ffff

> color sel #0096ffff

> color sel #0433ffff

> color sel #0096ffff

> color sel #0433ffff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #ff9300ff

> color sel #ff2600ff

> color sel #ff7e79ff

> color #3 #ff9300ff

> undo

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide #3 models

> show #3 models

> hide #3 models

> color #3 #ff2600ff

> show #3 models

> color #3 #ff9300ff

> color #1 #ff9300ff

> select #3/A

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color #1 #011993ff

> hide #3 models

> show #3 models

> hide #1 models

> show #1 models

> hide #3 models

> color #1 #ff9300ff

> select #3/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide #1#2.1-8 cartoons

> undo

> show #3 models

> hide #!2 models

> hide #1 models

> show #1 models

> show #!2 models

> hide #!2 models

> hide #1 models

> show #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> color #2 #73fa79ff models

> color #2 #ffd479ff models

> color #2 #fffb00ff models

> color #2 #fffc79ff models

> color #2 #ffd479ff models

> hide #!2 models

> hide #1 models

> hide #3 models

> show #1 models

> hide #1 models

> show #3 models

> select #3/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> hide sel cartoons

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> select #3/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #011993ff

[Repeated 2 time(s)]

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> select #3/A

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #005493ff

> color sel #011993ff

> color sel #000000ff

> color sel #212121ff

> color sel #011993ff

> select #3/B

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> show sel cartoons

> show #!2 models

> show #1 models

> color sel #0433ffff

> color sel #0096ffff

> color sel #7a81ffff

> color sel #76d6ffff

> color sel #0096ffff

> color sel #2a53e7ff

> select #3/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> hide sel cartoons

> select #3/A

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #121ea8ff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #ea6e38ff

> select #2.2/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color sel #f3bf4cff

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 mutants/color
> proposals.cxs""

> hide #3 models

> select clear

Drag select of 5 residues  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/biological unit.cxs""

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color #1 #212121ff

> color #1 #424242ff

> color #1 #5e5e5eff

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 1.cxs""

> select sequence GDPDLTLSYLSMWLHQPYVESDSRLHLESMLLETGHRAL

6340 atoms, 6500 bonds, 780 residues, 10 models selected  

> color (#1#2.1-8 & sel) #941100ff

> color (#1#2.1-8 & sel) #212121ff

> color (#1#2.1-8 & sel) #941751ff

> color (#1#2.1-8 & sel) #941100ff

> color (#1#2.1-8 & sel) #ff7e79ff

> select add #1

12166 atoms, 12432 bonds, 1498 residues, 10 models selected  

> select subtract #1

5706 atoms, 5850 bonds, 702 residues, 9 models selected  

> select add #2

52314 atoms, 53306 bonds, 6446 residues, 10 models selected  

> select subtract #2

634 atoms, 650 bonds, 78 residues, 1 model selected  

> select add #3

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #3

Nothing selected  

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting full

> lighting shadows false

> graphics silhouettes true

> lighting simple

[Repeated 2 time(s)]

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> lighting soft

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 1.cxs""

> select sequence GDPDLTLSYLSMWLHQPYVESDSRLHLESMLLETGHRAL

6340 atoms, 6500 bonds, 780 residues, 10 models selected  

> color (#1#2.1-8 & sel) #ecbb4aff

> color (#1#2.1-8 & sel) #f3bf4cff

> select add #3

12166 atoms, 12432 bonds, 1498 residues, 10 models selected  

> select subtract #3

5706 atoms, 5850 bonds, 702 residues, 9 models selected  

> select add #2

52314 atoms, 53306 bonds, 6446 residues, 10 models selected  

> select subtract #2

634 atoms, 650 bonds, 78 residues, 1 model selected  

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> volume hide

No volumes specified  

> select ::name=""ALA""

2800 atoms, 2280 bonds, 560 residues, 10 models selected  

> select sequence TGDPD

680 atoms, 680 bonds, 100 residues, 10 models selected  

> select ::name=""ASP""

4000 atoms, 3500 bonds, 500 residues, 10 models selected  

> ui tool show ""Show Sequence Viewer""

[Repeated 1 time(s)]

> sequence chain #2.2/D

Alignment identifier is 2.2/D  

> select add #1

10060 atoms, 9732 bonds, 1246 residues, 10 models selected  

> select add #2

58540 atoms, 59588 bonds, 7214 residues, 11 models selected  

> select subtract #2

6860 atoms, 6932 bonds, 846 residues, 2 models selected  

> select subtract #1

400 atoms, 350 bonds, 50 residues, 1 model selected  

> select add #3

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select #2.2/D:18-65,74-126,144-172,176-187,196-207

1260 atoms, 1275 bonds, 154 residues, 1 model selected  

> ui tool show ""Selection Inspector""

> select add #2

51680 atoms, 52656 bonds, 6368 residues, 9 models selected  

> select subtract #2

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs""

\u2014\u2014\u2014 End of log from Wed Sep 18 21:35:21 2024 \u2014\u2014\u2014

opened ChimeraX session  

> select #1/177

Nothing selected  

> select #1/Asp177

Nothing selected  

> select #1:177

26 atoms, 22 bonds, 4 residues, 1 model selected  

> hide #2.2 models

> show #2.2 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> hide #2.2 models

> show #2.2 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> hide #2.4 models

> hide #2.5 models

> hide #2.6 models

> hide #2.7 models

> hide #2.8 models

> show #3 models

> hide #3 models

> close #2.8

> close #2.7

> close #2.6

> close #2.5

> close #2.4

> show #2.3 models

> hide #2.3 models

> close #2.3

> show #3 models

> hide #3 models

> hide #2.2 models

> show #2.2 models

> hide #2.1 models

> show #2.1 models

> close #2.1

> hide #!2 models

> hide #2.2 models

> show #2.2 models

> select #2.2:177

26 atoms, 22 bonds, 4 residues, 1 model selected  

> color sel #ff7e79ff

> select #2.2:181

28 atoms, 24 bonds, 4 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff7e79ff

> select #2.2:182

36 atoms, 34 bonds, 4 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff7e79ff

> select #2.2:184

28 atoms, 24 bonds, 4 residues, 1 model selected  

> color sel #73fdffff

> color sel #ff7e79ff

> select #2.2:185

34 atoms, 30 bonds, 4 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff7e79ff

> select #2.2:188

36 atoms, 34 bonds, 4 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff7e79ff

> select #2.2:191

42 atoms, 40 bonds, 4 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff7e79ff

> select #2.2:193

34 atoms, 30 bonds, 4 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff7e79ff

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs""

> select #2.2:177,181,182,184,185,188,191,193

264 atoms, 246 bonds, 32 residues, 1 model selected  

> color sel #fffc79ff

> color sel #f3bf4cff

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 3.cxs""

> select #2.2:175-193

646 atoms, 664 bonds, 76 residues, 1 model selected  

> color sel #ff7e79ff

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 3.cxs""

> color sel #f3bf4cff

> hide #1 models

> show #1 models

> select #2.2/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #ffd479ff

> color sel #ff9300ff

> color sel #ea6e38ff

> select #2.2:177,181,182,184,185,188,191,193

264 atoms, 246 bonds, 32 residues, 1 model selected  

> color sel #ff7e79ff

> select add #2.2

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #2.2

Nothing selected  

> lighting flat

> select #2.2:177,181,182,184,185,188,191,193

264 atoms, 246 bonds, 32 residues, 1 model selected  

> color sel #000000ff

> select add #2.2

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #2.2

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs""

> select #2.2:177,181,182,184,185,188,191,193

264 atoms, 246 bonds, 32 residues, 1 model selected  

> color sel #f3bf4cff

> select #2.2:177,181,182,184,185,188,191,193

264 atoms, 246 bonds, 32 residues, 1 model selected  

> ui tool show ""Show Sequence Viewer""

> select #1:177,181,182,184,185,188,191,193

264 atoms, 246 bonds, 32 residues, 1 model selected  

> sequence chain #1/C

Alignment identifier is 1/C  

> select #1:63,66,68,69,72,73,76,77

258 atoms, 240 bonds, 32 residues, 1 model selected  

> color sel #000000ff

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 5.cxs""

\u2014\u2014\u2014 End of log from Wed Sep 18 22:00:52 2024 \u2014\u2014\u2014

opened ChimeraX session  

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> turn y 90 models #1,#2.2 center #1,#2.2

Invalid ""models"" argument: only initial part ""#1"" of atom specifier valid  

> turn y 90 models #1 center #1

> turn y 90 models #2.2 center #2.2

> turn y -90 models #2.2 center #2.2

> turn y -90 models #1 center #1

> select #1:63,66,68,69,72,73,76,77

258 atoms, 240 bonds, 32 residues, 1 model selected  

> color sel #eb6e37ff

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Top.cxs""

> save /Users/lks559/Desktop/image1.png supersample 3

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Side.cxs""

> turn 90

Expected an axis vector or a keyword  

> turn 90turn y 90

Expected an axis vector or a keyword  

> turn y 90

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/top.cxs""

> turn y 90

[Repeated 6 time(s)]

> save /Users/lks559/Desktop/image2.png supersample 3

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/side.cxs""

> turn y 90

> save /Users/lks559/Desktop/image3.png supersample 3

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/top.cxs""

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Top.cxs""

\u2014\u2014\u2014 End of log from Wed Sep 18 22:21:14 2024 \u2014\u2014\u2014

opened ChimeraX session  

> graphics silhouettes width 1

> lighting model #1 depthCue true

> cartoon style width 1.5

> cartoon style nucleic width 1 thickness 0.5

> cartoon style width 1.5

> lighting multiShadow 600

> graphics silhouettes false

> lighting soft

> select #2.2

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> color sel #f7f2abff

> color sel wheat

> color sel #f7f2abff

> color sel wheat

> color sel #ffffcdff

> color sel #F5DEB3

> select #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> color sel #f7d081ff

> color sel #c6a668ff

> color sel #c5a668ff

> color sel #c2a466ff

> color sel #c3a467ff

> color sel #c8a869ff

> color sel #cbab6bff

> color sel #d1b06eff

> color sel #d2b16eff

> color sel #e0bc76ff

> color sel #f6cf81ff

> color sel #ffd786ff

> color sel #ffdd6aff

> color sel #ffde6bff

> color sel #ffdb68ff

> color sel #ffd762ff

> color sel #ffd15aff

> color sel #ffd059ff

> color sel #ffcf59ff

> color sel #ffce58ff

> color sel #ffc855ff

> color sel #ffc453ff

> color sel #ffc352ff

> color sel #ffc251ff

> color sel #ffc150ff

> color sel #ffbf4cff

> color sel #ffbd47ff

> color sel #ffba44ff

> color sel #ffb841ff

> color sel #ffb53fff

> color sel #ffb03eff

> color sel #ffac3cff

> color sel #ffa83bff

> color sel #ffa53bff

> color sel #ffa43aff

> color sel #ffa439ff

> color sel #ffa539ff

> color sel #ffa537ff

> color sel #ffa632ff

> color sel #ffa731ff

> color sel #ffa630ff

> color sel #ffa730ff

> color sel #ffa72fff

> color sel #ffa82fff

> color sel #ffa82eff

> color sel #ffaa2dff

> color sel #ffab2cff

> color sel #ffab2bff

> color sel #ffac2aff

[Repeated 1 time(s)]

> select subtract #1

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Side.cxs""

\u2014\u2014\u2014 End of log from Fri Oct 4 15:13:12 2024 \u2014\u2014\u2014

opened ChimeraX session  

> select #2.2/D:177,181,182,184,185,188,191,193

71 atoms, 68 bonds, 8 residues, 1 model selected  

> color sel tomato

> show sel atoms

> style sel ball

Changed 71 atom styles  

> hide sel atoms

> style sel ball

Changed 71 atom styles  

> show sel atoms

> style sel sphere

Changed 71 atom styles  

> style sel ball

Changed 71 atom styles  

> color sel byhetero

> select add #2.2

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select add #2

6460 atoms, 6582 bonds, 796 residues, 2 models selected  

> select subtract #2

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant2.cxs""

> save /Users/lks559/Desktop/image5.png supersample 3

> select #2.2/D:177,181,182,184,185,188,191,193

71 atoms, 68 bonds, 8 residues, 1 model selected  

> hide sel atoms

> color sel #F5DEB3

> select #2.2/D:177,181,182,184,185,188,191,193

71 atoms, 68 bonds, 8 residues, 1 model selected  

> select #1/C:63,66,68,69,72,73,76,77

72 atoms, 68 bonds, 8 residues, 1 model selected  

> color sel tomato

> style sel ball

Changed 72 atom styles  

> show sel atoms

> color sel byhetero

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5.cxs""

\u2014\u2014\u2014 End of log from Fri Oct 4 15:32:18 2024 \u2014\u2014\u2014

opened ChimeraX session  

> transparency 80 target c

> select #2.2/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color sel #ecbed6ff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #e9ebb8ff

> select #1/C:63,66,68,69,72,73,76,77

72 atoms, 68 bonds, 8 residues, 1 model selected  

> color sel tomato

> color sel byhetero

> transparency 80 target c

> graphics silhouettes true

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5_zoom.cxs""

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5_zoom.cxs""

> save /Users/lks559/Desktop/image6.png supersample 3

> select #2.2/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color sel #ecbed6ff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #e9ebb8ff

> hide sel atoms

> select #2.2/D:177,181,182,184,185,188,191,193

71 atoms, 68 bonds, 8 residues, 1 model selected  

> color sel tomato

> style sel ball

Changed 71 atom styles  

> show sel atoms

> color sel byhetero

> transparency 80 target c

> select add #2

6460 atoms, 6582 bonds, 796 residues, 2 models selected  

> select subtract #2

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant2_zoom.cxs""

\u2014\u2014\u2014 End of log from Sun Oct 6 13:09:19 2024 \u2014\u2014\u2014

opened ChimeraX session  

> select #2.2/D

1591 atoms, 1623 bonds, 196 residues, 1 model selected  

> color sel #ecbed6ff

> select #1/C

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> color sel #e9ebb8ff

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide #1#2.2 atoms

> select #2.2/D:177,184,190

21 atoms, 19 bonds, 3 residues, 1 model selected  

> hbonds sel reveal true

14 hydrogen bonds found  

> color sel byhetero

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs""

> select add #2

6460 atoms, 6582 bonds, 4 pseudobonds, 796 residues, 3 models selected  

> select subtract #2

Nothing selected  

> transparency 80 target c

> select #1/C:60-68

69 atoms, 71 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs""

[Repeated 1 time(s)]

> hide #4 models

> show #4 models

> color #4 black models

> save /Users/lks559/Desktop/image9.png supersample 3

> select #2.2/D:188

10 atoms, 10 bonds, 1 residue, 1 model selected  

> ~hbonds

> undo

> select up

124 atoms, 127 bonds, 15 residues, 1 model selected  

> select up

1639 atoms, 1668 bonds, 202 residues, 1 model selected  

> select #2.2/D:177,184,190

21 atoms, 19 bonds, 3 residues, 1 model selected  

> hbonds sel reveal true

14 hydrogen bonds found  

> color #4 black models

> interfaces select & ~solvent

Missing or invalid ""atoms"" argument: invalid atoms specifier  

> select add #2

6460 atoms, 6582 bonds, 4 pseudobonds, 796 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select #2.2/D:188

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2.2/D:181

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2.2/D:185

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select add #2

6460 atoms, 6582 bonds, 4 pseudobonds, 796 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select #1/C:60-68

69 atoms, 71 bonds, 9 residues, 1 model selected  

> show sel cartoons

> select add #1

6460 atoms, 6582 bonds, 796 residues, 1 model selected  

> select subtract #1

Nothing selected  

> save ""/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs""

\u2014\u2014\u2014 End of log from Sun Oct 6 15:21:54 2024 \u2014\u2014\u2014

opened ChimeraX session  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Pro
     Model Identifier: MacBookPro16,1
     Processor Name: 8-Core Intel Core i9
     Processor Speed: 2,3 GHz
     Number of Processors: 1
     Total Number of Cores: 8
     L2 Cache (per Core): 256 KB
     L3 Cache: 16 MB
     Hyper-Threading Technology: Enabled
     Memory: 16 GB
     System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
     OS Loader Version: 580.140.1~8

Software:

   System Software Overview:

     System Version: macOS 14.6.1 (23G93)
     Kernel Version: Darwin 23.6.0
     Time since boot: 2 days, 4 hours, 6 minutes

Graphics/Displays:

   Intel UHD Graphics 630:

     Chipset Model: Intel UHD Graphics 630
     Type: GPU
     Bus: Built-In
     VRAM (Dynamic, Max): 1536 MB
     Vendor: Intel
     Device ID: 0x3e9b
     Revision ID: 0x0002
     Automatic Graphics Switching: Supported
     gMux Version: 5.0.0
     Metal Support: Metal 3

   AMD Radeon Pro 5500M:

     Chipset Model: AMD Radeon Pro 5500M
     Type: GPU
     Bus: PCIe
     PCIe Lane Width: x16
     VRAM (Total): 4 GB
     Vendor: AMD (0x1002)
     Device ID: 0x7340
     Revision ID: 0x0040
     ROM Revision: 113-D3220E-190
     VBIOS Version: 113-D32206U1-020
     Option ROM Version: 113-D32206U1-020
     EFI Driver Version: 01.A1.190
     Automatic Graphics Switching: Supported
     gMux Version: 5.0.0
     Metal Support: Metal 3
     Displays:
       Color LCD:
         Display Type: Built-In Retina LCD
         Resolution: 3072 x 1920 Retina
         Framebuffer Depth: 24-Bit Color (ARGB8888)
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal


Installed Packages:
   alabaster: 0.7.16
   appdirs: 1.4.4
   appnope: 0.1.4
   asttokens: 2.4.1
   Babel: 2.15.0
   beautifulsoup4: 4.12.3
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 1.2.1
   certifi: 2023.11.17
   cftime: 1.6.4
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.17
   ChimeraX-AddH: 2.2.6
   ChimeraX-AlignmentAlgorithms: 2.0.2
   ChimeraX-AlignmentHdrs: 3.5
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.7
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.57.1
   ChimeraX-AtomicLibrary: 14.0.6
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.4.6
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.12.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.7
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.4
   ChimeraX-ChangeChains: 1.1
   ChimeraX-CheckWaters: 1.4
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.2.4
   ChimeraX-ColorActions: 1.0.5
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.6
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.8
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.3
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2.4
   ChimeraX-DiffPlot: 1.0
   ChimeraX-DistMonitor: 1.4.2
   ChimeraX-DockPrep: 1.1.3
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ESMFold: 1.0
   ChimeraX-FileHistory: 1.0.1
   ChimeraX-FunctionKey: 1.0.1
   ChimeraX-Geometry: 1.3
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 1.1.1
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.2
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-Label: 1.1.10
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.1.6
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.2
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0.1
   ChimeraX-MapFilter: 2.0.1
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.1.1
   ChimeraX-Markers: 1.0.1
   ChimeraX-Mask: 1.0.2
   ChimeraX-MatchMaker: 2.1.3
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.7.1
   ChimeraX-MedicalToolbar: 1.0.3
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.14.1
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.17
   ChimeraX-ModelPanel: 1.5
   ChimeraX-ModelSeries: 1.0.1
   ChimeraX-Mol2: 2.0.3
   ChimeraX-Mole: 1.0
   ChimeraX-Morph: 1.0.2
   ChimeraX-MouseModes: 1.2
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.2
   ChimeraX-NMRSTAR: 1.0.2
   ChimeraX-NRRD: 1.2
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.13.5
   ChimeraX-PDB: 2.7.5
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1.1
   ChimeraX-PubChem: 2.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.4.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.2
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 4.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0.2
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-Segmentations: 3.0.15
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.11.2
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.3
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.16.5
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.2.1
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.5
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-TaskManager: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.39.1
   ChimeraX-uniprot: 2.3
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.4.3
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0.1
   ChimeraX-vrml: 1.0
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.2
   ChimeraX-WebServices: 1.1.4
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.2
   contourpy: 1.2.1
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 3.0.10
   debugpy: 1.8.1
   decorator: 5.1.1
   docutils: 0.20.1
   executing: 2.0.1
   filelock: 3.13.4
   fonttools: 4.53.0
   funcparserlib: 2.0.0a0
   glfw: 2.7.0
   grako: 3.16.5
   h5py: 3.11.0
   html2text: 2024.2.26
   idna: 3.7
   ihm: 1.0
   imagecodecs: 2024.1.1
   imagesize: 1.4.1
   ipykernel: 6.29.2
   ipython: 8.21.0
   ipywidgets: 8.1.3
   jedi: 0.19.1
   jinja2: 3.1.4
   jupyter-client: 8.6.0
   jupyter-core: 5.7.2
   jupyterlab-widgets: 3.0.11
   kiwisolver: 1.4.5
   line-profiler: 4.1.2
   lxml: 5.2.1
   lz4: 4.3.3
   MarkupSafe: 2.1.5
   matplotlib: 3.8.4
   matplotlib-inline: 0.1.7
   msgpack: 1.0.8
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.10.0
   numpy: 1.26.4
   openvr: 1.26.701
   packaging: 23.2
   ParmEd: 4.2.2
   parso: 0.8.4
   pep517: 0.13.1
   pexpect: 4.9.0
   pillow: 10.3.0
   pip: 24.0
   pkginfo: 1.10.0
   platformdirs: 4.2.2
   prompt-toolkit: 3.0.47
   psutil: 5.9.8
   ptyprocess: 0.7.0
   pure-eval: 0.2.2
   py-cpuinfo: 9.0.0
   pycollada: 0.8
   pydicom: 2.4.4
   pygments: 2.17.2
   pynmrstar: 3.3.4
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.3401
   pyparsing: 3.1.2
   pyproject-hooks: 1.1.0
   PyQt6-commercial: 6.6.1
   PyQt6-Qt6: 6.6.3
   PyQt6-sip: 13.6.0
   PyQt6-WebEngine-commercial: 6.6.0
   PyQt6-WebEngine-Qt6: 6.6.3
   python-dateutil: 2.9.0.post0
   pytz: 2024.1
   pyzmq: 26.0.3
   qtconsole: 5.5.1
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.13.0
   setuptools: 69.5.1
   setuptools-scm: 8.0.4
   sfftk-rw: 0.8.1
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.5
   sphinx: 7.2.6
   sphinx-autodoc-typehints: 2.0.1
   sphinxcontrib-applehelp: 1.0.8
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.6
   sphinxcontrib-htmlhelp: 2.0.5
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.7
   sphinxcontrib-serializinghtml: 1.1.10
   stack-data: 0.6.3
   superqt: 0.6.3
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2024.1.30
   tinyarray: 1.2.4
   tornado: 6.4.1
   traitlets: 5.14.2
   typing-extensions: 4.12.2
   tzdata: 2024.1
   urllib3: 2.2.1
   wcwidth: 0.2.13
   webcolors: 1.13
   wheel: 0.43.0
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.11

}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX