Alphafold contacts trying to create pseudobond involving deleted atoms

[chenhr@…]

The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
I wanted to show the contacts between a predicted protein and RNA molecule. I used command : alphafold contacts /A to /B distance. However, an error occurred.   

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

> open "/Users/huiruchen/ownCloud2/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/PAE_analysis_dis3_desat1_model_1/dis3_desat1_model_1_interaction.cxs"

Log from Wed Jun 12 18:02:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/PAE_analysis_dis3_desat1_model_1/dis3_desat1_model_1_no_interaction.cxs"

Log from Wed Jun 12 13:01:41 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_light
> steel blue.cxs"

Log from Sat Jun 8 10:04:00 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/huiruchen/ownCloud2/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1.cxs

Log from Fri Jun 7 22:23:57 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/huiruchen/ownCloud2/Dis3_FLASH/seed_2123711991_dis3_desat1/dis3_desat1_model_no_mutation.cxs

Log from Fri Jun 7 16:44:46 2024UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_model_0.cif"

Chain information for fold_2024_06_07_dis3_desat1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> color sel bychain

> color sel bynucleotide

> color sel bychain

> color sel bynucleotide

> nucleotides sel stubs

Alignment identifier is 1/A  
Alignment identifier is 1/B  

> select /A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> color sel light sky blue

> color sel light steel blue

> color sel thistle

> select : 144. 183, 494

Expected an objects specifier or a keyword  

> select : 144, 183, 494

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

> color sel medium blue

> label sel text "{0.name} {0.number}{0.insertion_code}"

> label height 2

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> show sel target ab

> select /A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> color sel gray

> color sel light gray

> select : 144, 183, 494

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

> color sel blue

> ui mousemode right "move label"

> select : 144, 183, 494

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

> label height 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> hide #!1 models

> select add #1

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #1

Nothing selected  

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_model_1.cif"

Chain information for fold_2024_06_07_dis3_desat1_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> color #2 bychain

> select #2/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light cyan

> color sel lavender

> color sel bynucleotide

[Repeated 1 time(s)]

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> select subtract #2

Nothing selected  

> color #2 bynucleotide

> select : 144, 183, 494

48 atoms, 42 bonds, 6 residues, 2 models selected  

> show (#2 & sel) target ab

> color (#2 & sel) medium blue

> label (#2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 2

[Repeated 1 time(s)]

> select add #2

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #2

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

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> select : 144, 183, 494

48 atoms, 42 bonds, 6 residues, 2 models selected  

> label height 3

[Repeated 1 time(s)]

> select add #2

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #2

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

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> hide #!2 models

> select add #1

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #1

Nothing selected  

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_model_2.cif"

Chain information for fold_2024_06_07_dis3_desat1_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
  

> color #3 bychain

> select #3/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light blue

> color sel old lace

> color sel light goldenrod yellow

> color sel bynucleotide

> select add #3

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> select subtract #3

Nothing selected  

> color #3 bynucleotide

> select : 144, 183, 494

72 atoms, 63 bonds, 9 residues, 3 models selected  

> show (#3 & sel) target ab

> color (#3 & sel) medium blue

> label (#3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 3

[Repeated 1 time(s)]

> select add #3

9625 atoms, 9964 bonds, 1068 residues, 4 models selected  

> select subtract #3

48 atoms, 42 bonds, 6 residues, 2 models selected  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> save /Users/huiruchen/Desktop/dis3_desat1_model_2.cxs

> hide #!3 models

> show #!2 models

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_model_3.cif"

Chain information for fold_2024_06_07_dis3_desat1_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

> hide #!2 models

> color #4 bychain

> select #4/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light cyan

> color sel pale goldenrod

> color sel bynucleotide

> select add #4

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> select subtract #4

Nothing selected  

> color #4 bynucleotide

> select : 144, 183, 494

96 atoms, 84 bonds, 12 residues, 4 models selected  

> show (#4 & sel) target ab

> color (#4 & sel) medium blue

> label (#4 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> cofr sel

> label height 3

[Repeated 1 time(s)]

> hide #!4 models

> show #!4 models

> select #4/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel plum

> color sel linen

> select add #4

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #4

Nothing selected  

> select : 144, 183, 494

96 atoms, 84 bonds, 12 residues, 4 models selected  

> color (#!4 & sel) medium blue

> select add #4

9649 atoms, 9985 bonds, 1071 residues, 5 models selected  

> select subtract #4

72 atoms, 63 bonds, 9 residues, 3 models selected  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> hide #!4 models

> open
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_model_4.cif"

Chain information for fold_2024_06_07_dis3_desat1_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
  

> color #5 bychain

> select #5/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel misty rose

> color sel light cyan

> color sel bynucleotide

> select add #5

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> select subtract #5

Nothing selected  

> color #5 bynucleotide

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> show (#5 & sel) target ab

> color (#5 & sel) purple

> color (#5 & sel) medium blue

> label (#5 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 3

[Repeated 1 time(s)]

> select add #5

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select subtract #5

96 atoms, 84 bonds, 12 residues, 4 models selected  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> save /Users/huiruchen/Desktop/dis3_desat1_model_no_mutation.cxs

——— End of log from Fri Jun 7 16:44:46 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!5 models

> select add #4

9649 atoms, 9985 bonds, 1071 residues, 5 models selected  

> select subtract #4

72 atoms, 63 bonds, 9 residues, 3 models selected  

> select add #2

9625 atoms, 9964 bonds, 1068 residues, 4 models selected  

> select subtract #2

48 atoms, 42 bonds, 6 residues, 2 models selected  

> select add #3

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #3

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

> select add #1

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #1

Nothing selected  

> ui mousemode right "move label"

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> label height 4

> select add #1

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select subtract #1

96 atoms, 84 bonds, 12 residues, 4 models selected  

> save /Users/huiruchen/Desktop/Desktop_HR/Dis3_desat1_model_0.png width 1134
> height 783 supersample 3

> label height 4

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color : blue

> color : #0000FF

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

> (color, #0000FF)

Unknown command: (color, #0000FF)  

> ui mousemode right label

> cofr sel

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> ~label (#!1 & sel) residues

> select add #1

9673 atoms, 10006 bonds, 1074 residues, 5 models selected  

> select subtract #1

96 atoms, 84 bonds, 12 residues, 4 models selected  

> save /Users/huiruchen/Desktop/Desktop_HR/Dis3_desat1_model_0_no_label.png
> width 1134 height 783 supersample 3

> save /Users/huiruchen/Desktop/Dis3_WT_desat1_model_0.cxs

——— End of log from Fri Jun 7 22:23:57 2024 ———

opened ChimeraX session  

> color #1 bychain

> select #1/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light blue

> color sel pale turquoise

> color sel light steel blue

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#1 & sel) medium blue

> show (#1 & sel) target ab

> label (#1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 4

[Repeated 1 time(s)]

> select add #1

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select add #2

19226 atoms, 19907 bonds, 2133 residues, 7 models selected  

> select add #5

28779 atoms, 29808 bonds, 3192 residues, 8 models selected  

> select add #4

38332 atoms, 39709 bonds, 4251 residues, 9 models selected  

> select subtract #4

28755 atoms, 29787 bonds, 3189 residues, 7 models selected  

> select subtract #5

19178 atoms, 19865 bonds, 2127 residues, 5 models selected  

> select add #3

28731 atoms, 29766 bonds, 3186 residues, 6 models selected  

> select subtract #2

19154 atoms, 19844 bonds, 2124 residues, 4 models selected  

> select subtract #1

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #3

Nothing selected  

> color #!1 bynucleotide

> ui mousemode right "move label"

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#!1 & sel) red

> color (#!1 & sel) orange red

> color (#!1 & sel) orange

> select add #1

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select subtract #1

96 atoms, 84 bonds, 12 residues, 4 models selected  

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#!1 & sel) magenta

> select add #1

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select subtract #1

96 atoms, 84 bonds, 12 residues, 4 models selected  

> save /Users/huiruchen/Desktop/fold_2024_06_07_dis3_desat1_model_0.png width
> 1134 height 783 supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie2.mp4

Movie saved to /Users/huiruchen/Desktop/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie2.mp4

Movie saved to /Users/huiruchen/Desktop/movie2.mp4  
  

> save /Users/huiruchen/Desktop/fold_2024_06_07_dis3_desat1_model_0.png width
> 1134 height 783 supersample 3

> select add #2

9649 atoms, 9985 bonds, 1071 residues, 5 models selected  

> select subtract #2

72 atoms, 63 bonds, 9 residues, 3 models selected  

> select add #3

9625 atoms, 9964 bonds, 1068 residues, 4 models selected  

> select subtract #3

48 atoms, 42 bonds, 6 residues, 2 models selected  

> select add #4

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #4

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

> select add #5

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #5

Nothing selected  

> ~label #1 residues

> save
> /Users/huiruchen/Desktop/fold_2024_06_07_dis3_desat1_model_0_no_label.png
> width 1134 height 783 supersample 3

> show #!2 models

> hide #1 models

> color #!2 bychain

> select #1/A#1/B#2/A#2/B#3/A#3/B#4/A#4/B#5/A#5/B

47885 atoms, 49610 bonds, 5310 residues, 5 models selected  

> select add #2

47885 atoms, 49610 bonds, 5310 residues, 6 models selected  

> select subtract #1

38308 atoms, 39688 bonds, 4248 residues, 5 models selected  

> select subtract #2

28731 atoms, 29766 bonds, 3186 residues, 3 models selected  

> select add #3

28731 atoms, 29766 bonds, 3186 residues, 4 models selected  

> select subtract #3

19154 atoms, 19844 bonds, 2124 residues, 2 models selected  

> select add #4

19154 atoms, 19844 bonds, 2124 residues, 3 models selected  

> select subtract #4

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> select add #5

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #5

Nothing selected  

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select #2/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light steel blue

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> color #!2 bynucleotide

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#!2 & sel) medium blue

> color (#!2 & sel) magenta

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 4

[Repeated 1 time(s)]

> select add #2

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select subtract #2

96 atoms, 84 bonds, 12 residues, 4 models selected  

> select add #1

9649 atoms, 9985 bonds, 1071 residues, 4 models selected  

> select add #3

19202 atoms, 19886 bonds, 2130 residues, 5 models selected  

> select subtract #3

9625 atoms, 9964 bonds, 1068 residues, 3 models selected  

> select add #4

19178 atoms, 19865 bonds, 2127 residues, 4 models selected  

> select subtract #4

9601 atoms, 9943 bonds, 1065 residues, 2 models selected  

> select add #5

19154 atoms, 19844 bonds, 2124 residues, 3 models selected  

> select subtract #5

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> select subtract #1

Nothing selected  

> ui mousemode right "move label"

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> save /Users/huiruchen/Desktop/fold_2024_06_07_dis3_desat1_model_1.png width
> 1134 height 783 supersample 3

> ~label #2 residues

> save
> /Users/huiruchen/Desktop/fold_2024_06_07_dis3_desat1_model_1_no_label.png
> width 1134 height 783 supersample 3

> label #2 text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> ~label #2 residues

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> label (#2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 4

[Repeated 1 time(s)]

> select add #2

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select add #1

19226 atoms, 19907 bonds, 2133 residues, 6 models selected  

> select subtract #1

9649 atoms, 9985 bonds, 1071 residues, 5 models selected  

> select subtract #2

72 atoms, 63 bonds, 9 residues, 3 models selected  

> select add #3

9625 atoms, 9964 bonds, 1068 residues, 4 models selected  

> select add #4

19178 atoms, 19865 bonds, 2127 residues, 5 models selected  

> select add #5

28731 atoms, 29766 bonds, 3186 residues, 6 models selected  

> select subtract #5

19154 atoms, 19844 bonds, 2124 residues, 4 models selected  

> select subtract #4

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #3

Nothing selected  

> hide #!2 models

> show #!3 models

> color #!3 bychain

> select #3/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light steel blue

> select add #3

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #3

Nothing selected  

> color #!3 bynucleotide

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#!3 & sel) magenta

> select add #3

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select subtract #3

96 atoms, 84 bonds, 12 residues, 4 models selected  

> select add #2

9649 atoms, 9985 bonds, 1071 residues, 5 models selected  

> select subtract #2

72 atoms, 63 bonds, 9 residues, 3 models selected  

> select add #1

9625 atoms, 9964 bonds, 1068 residues, 3 models selected  

> select subtract #1

48 atoms, 42 bonds, 6 residues, 2 models selected  

> select add #4

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #4

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

> select add #5

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #5

Nothing selected  

> ui mousemode right "move label"

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> hide #!3 models

> show #!4 models

> color #!4 bychain

> select #4/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light steel blue

> select add #4

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #4

Nothing selected  

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#!4 & sel) magenta

> label (#!4 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color (#!4 & sel) magenta

> select add #1

9673 atoms, 10006 bonds, 1074 residues, 5 models selected  

> select add #2

19226 atoms, 19907 bonds, 2133 residues, 6 models selected  

> select subtract #2

9649 atoms, 9985 bonds, 1071 residues, 4 models selected  

> select add #3

19202 atoms, 19886 bonds, 2130 residues, 5 models selected  

> select subtract #3

9625 atoms, 9964 bonds, 1068 residues, 3 models selected  

> select subtract #1

48 atoms, 42 bonds, 6 residues, 2 models selected  

> select add #5

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #5

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

> color sel bynucleotide

[Repeated 1 time(s)]

> select add #4

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #4

Nothing selected  

> color #!4 bynucleotide

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!4 models

> color #!5 bychain

> select #5/A

7892 atoms, 8043 bonds, 982 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light steel blue

> select : 144, 183, 494

120 atoms, 105 bonds, 15 residues, 5 models selected  

> color (#!5 & sel) magenta

> select add #4

9673 atoms, 10006 bonds, 1074 residues, 6 models selected  

> select add #3

19226 atoms, 19907 bonds, 2133 residues, 7 models selected  

> select add #2

28779 atoms, 29808 bonds, 3192 residues, 8 models selected  

> select subtract #2

19202 atoms, 19886 bonds, 2130 residues, 6 models selected  

> select add #1

28755 atoms, 29787 bonds, 3189 residues, 6 models selected  

> select subtract #1

19178 atoms, 19865 bonds, 2127 residues, 5 models selected  

> select subtract #3

9601 atoms, 9943 bonds, 1065 residues, 3 models selected  

> select subtract #4

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

> select add #5

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #5

Nothing selected  

> color #!5 bynucleotide

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/huiruchen/Desktop/movie1.mp4

Movie saved to /Users/huiruchen/Desktop/movie1.mp4  
  
No map chosen to save  

> save /Users/huiruchen/Desktop/fold_2024_06_07_dis3_desat1.cxs

——— End of log from Sat Jun 8 10:04:00 2024 ———

opened ChimeraX session  

> hide #!3 target m

> close #4

> close #5

> close #1

> close #3

> show #!2 models

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_full_data_1.json"

> hide #2.1 models

> color #2/A:424-856 lime

> color #2/B:61-72 magenta

> color #2/A:617-617 lime

> color #2/B:33-33 magenta

> select : 432-851

3344 atoms, 3412 bonds, 420 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select : 144, 183, 494

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

> ui tool show "Color Actions"

> color sel dark orange

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> color #2/A:430-850 lime

> color #2/B:68-74 magenta

> select : 432-851494

4391 atoms, 4478 bonds, 551 residues, 1 model selected  

> select : 432-851

3344 atoms, 3412 bonds, 420 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select : 431-851

3348 atoms, 3416 bonds, 421 residues, 1 model selected  

> select : 431-852

3357 atoms, 3425 bonds, 422 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select : 431-851

3348 atoms, 3416 bonds, 421 residues, 1 model selected  

> select : 430-851

3356 atoms, 3424 bonds, 422 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel steel blue

> color sel cornflower blue

> select : 144, 183, 494

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

> ui tool show "Color Actions"

> color sel dark orange

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> save /Users/huiruchen/Desktop/dis3_desat1_full_data_1.cxs

——— End of log from Wed Jun 12 13:01:41 2024 ———

opened ChimeraX session  
Alignment identifier is 2/A  
Alignment identifier is 2/B  

> select /B:66

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /B:66-76

231 atoms, 257 bonds, 11 residues, 1 model selected  

> select /B:77

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /B:64-77

293 atoms, 326 bonds, 14 residues, 1 model selected  

> select /B:66

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /B:66-77

251 atoms, 279 bonds, 12 residues, 1 model selected  

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

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

> select : 432-851494

4391 atoms, 4478 bonds, 551 residues, 1 model selected  

> select clear

> select : 432-851

3344 atoms, 3412 bonds, 420 residues, 1 model selected  

> ui tool show "Color Actions"

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> save
> "/Users/huiruchen/Desktop/Desktop_HR/AALab/experiments/Alphafold3/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/PAE_analysis_dis3_desat1_model_1/dis3_desat1_model_1_interaction.cxs"

——— End of log from Wed Jun 12 18:02:40 2024 ———

opened ChimeraX session  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file "/Users/huiruchen/ownCloud2/Dis3&Rrp6
> project/Dis3_FLASH/seed_2123711991_dis3_desat1/fold_2024_06_07_dis3_desat1_full_data_1.json"

> alphafold pae #2 colorDomains true

> alphafold contacts #1/A toResidues #1/B distance 4

No residues specified for alphafold contacts  

> color #1 lightgray ribbons

> color #A lightgray ribbon

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

> color #1 lightgray ribbons

> select /A/B

9577 atoms, 9922 bonds, 1062 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light gray

> color #1 lightgray ribbons

> select add #2

9577 atoms, 9922 bonds, 1062 residues, 2 models selected  

> select subtract #2

Nothing selected  

> alphafold contacts #1/A toResidues #1/B distance 4

No residues specified for alphafold contacts  

> alphafold contacts /A toResidues /B distance 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/contacts.py", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,2
      Model Number: Z16000016TA/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 12 hours, 37 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NIHPresets: 1.1.19
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Hui-Ru Chen

[Tom Goddard]

AlphaFold 3 has predicted aligned error that includes atoms which AlphaFold 2 did not have. So you need to get a newer ChimeraX to handle AlphaFold 3 output, such as ChimeraX 1.8.