Opened 17 months ago

Closed 17 months ago

#15578 closed defect (nonchimerax)

AlphaFold JSON: Expecting ',' delimiter

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/robertkazmierczak/Desktop/AF3 Models/ChimeraX
> Files/1341-1328delspAF3mod4_may24.cxs"

Log from Mon May 20 11:53:07 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_3.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_3.cif #1  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_2.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_2.cif #2  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_1.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_1.cif #3  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_0.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_0.cif #4  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_4.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_4.cif #5  
---  
Chain | Description  
A | .  
  

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 models

> show #2 models

> hide #2 models

> show #1 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> show #1 models

> hide #1 models

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_20_atu1341_pbp1a_dimer/fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_3.cif

Chain information for fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_3.cif #6  
---  
Chain | Description  
A B | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_20_atu1341_pbp1a_dimer/fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_2.cif

Chain information for fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_2.cif #7  
---  
Chain | Description  
A B | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_20_atu1341_pbp1a_dimer/fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_1.cif

Chain information for fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_1.cif #8  
---  
Chain | Description  
A B | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_20_atu1341_pbp1a_dimer/fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_0.cif

Chain information for fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_0.cif #9  
---  
Chain | Description  
A B | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_20_atu1341_pbp1a_dimer/fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_4.cif

Chain information for fold_2024_05_16_10_20_atu1341_pbp1a_dimer_model_4.cif
#10  
---  
Chain | Description  
A B | .  
  

> hide #10 models

> hide #8 models

> hide #7 models

> hide #6 models

> hide #9 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #10 models

> hide #10 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #10 models

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_3.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_3.cif #11  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_2.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_2.cif #12  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_1.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_1.cif #13  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_0.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_0.cif #14  
---  
Chain | Description  
A | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_13_14_atu1348/fold_2024_05_16_13_14_atu1348_model_4.cif

Chain information for fold_2024_05_16_13_14_atu1348_model_4.cif #15  
---  
Chain | Description  
A | .  
  

> hide #10 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_3.cif

Chain information for
fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_3.cif #16  
---  
Chain | Description  
A B | .  
C D | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_2.cif

Chain information for
fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_2.cif #17  
---  
Chain | Description  
A B | .  
C D | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_1.cif

Chain information for
fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_1.cif #18  
---  
Chain | Description  
A B | .  
C D | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_0.cif

Chain information for
fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_0.cif #19  
---  
Chain | Description  
A B | .  
C D | .  
  

> open
> /Users/robertkazmierczak/Downloads/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer/fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_4.cif

Chain information for
fold_2024_05_16_10_40_atu1341_atu1328_cleaved_dimer_model_4.cif #20  
---  
Chain | Description  
A B | .  
C D | .  
  

> hide #20 models

> hide #18 models

> hide #17 models

> hide #16 models

> hide #19 models

> show #20 models

> hide #20 models

> show #18 models

> hide #18 models

> show #17 models

> hide #17 models

> show #16 models

> hide #16 models

> show #17 models

> show #18 models

> hide #17 models

> hide #18 models

> show #17 models

> show #20 models

> hide #17 models

> hide #20 models

> show #19 models

> hide #19 models

> show #18 models

> hide #18 models

> show #16 models

> hide #16 models

> close #11-15

> show #8 models

> show #18 models

> hide #18 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #20 models

> hide #20 models

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  

> select #6/A-B:55 #7/A-B:55 #8/A-B:55 #9/A-B:55 #10/A-B:55 #16/A-B:55
> #17/A-B:55 #18/A-B:55 #19/A-B:55 #20/A-B:55

160 atoms, 140 bonds, 20 residues, 10 models selected  

> select #6/A-B:55-234 #7/A-B:55-234 #8/A-B:55-234 #9/A-B:55-234
> #10/A-B:55-234 #16/A-B:55-234 #17/A-B:55-234 #18/A-B:55-234 #19/A-B:55-234
> #20/A-B:55-234

28640 atoms, 29220 bonds, 3600 residues, 10 models selected  
. [ID: 2] region 20 chains [55-234] RMSD: 62.522  
  

> color (#8 & sel) blue

> select #6/A-B:322 #7/A-B:322 #8/A-B:322 #9/A-B:322 #10/A-B:322 #16/A-B:322
> #17/A-B:322 #18/A-B:322 #19/A-B:322 #20/A-B:322

220 atoms, 220 bonds, 20 residues, 10 models selected  

> select #6/A-B:322-437 #7/A-B:322-437 #8/A-B:322-437 #9/A-B:322-437
> #10/A-B:322-437 #16/A-B:322-437 #17/A-B:322-437 #18/A-B:322-437
> #19/A-B:322-437 #20/A-B:322-437

17400 atoms, 17740 bonds, 2320 residues, 10 models selected  
. [ID: 2] region 20 chains [322-437] RMSD: 53.788  
  

> color (#8 & sel) cyan

> select #6/A-B:439 #7/A-B:439 #8/A-B:439 #9/A-B:439 #10/A-B:439 #16/A-B:439
> #17/A-B:439 #18/A-B:439 #19/A-B:439 #20/A-B:439

80 atoms, 60 bonds, 20 residues, 10 models selected  

> select #6/A-B:439-634 #7/A-B:439-634 #8/A-B:439-634 #9/A-B:439-634
> #10/A-B:439-634 #16/A-B:439-634 #17/A-B:439-634 #18/A-B:439-634
> #19/A-B:439-634 #20/A-B:439-634

29800 atoms, 30400 bonds, 3920 residues, 10 models selected  
. [ID: 2] region 20 chains [439-634] RMSD: 45.419  
  

> select
> #6/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #7/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #8/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #9/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #10/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #16/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #17/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #18/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #19/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #20/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772

18060 atoms, 17940 bonds, 2360 residues, 10 models selected  

> select #6/A-B:439-634 #7/A-B:439-634 #8/A-B:439-634 #9/A-B:439-634
> #10/A-B:439-634 #16/A-B:439-634 #17/A-B:439-634 #18/A-B:439-634
> #19/A-B:439-634 #20/A-B:439-634

29800 atoms, 30400 bonds, 3920 residues, 10 models selected  

> select #6/A-B:436 #7/A-B:436 #8/A-B:436 #9/A-B:436 #10/A-B:436 #16/A-B:436
> #17/A-B:436 #18/A-B:436 #19/A-B:436 #20/A-B:436

180 atoms, 160 bonds, 20 residues, 10 models selected  

> select #6/A-B:436 #7/A-B:436 #8/A-B:436 #9/A-B:436 #10/A-B:436 #16/A-B:436
> #17/A-B:436 #18/A-B:436 #19/A-B:436 #20/A-B:436

180 atoms, 160 bonds, 20 residues, 10 models selected  
. [ID: 2] region 20 chains [436] RMSD: 37.289  
  

> select #6/A-B:439 #7/A-B:439 #8/A-B:439 #9/A-B:439 #10/A-B:439 #16/A-B:439
> #17/A-B:439 #18/A-B:439 #19/A-B:439 #20/A-B:439

80 atoms, 60 bonds, 20 residues, 10 models selected  

> select #6/A-B:439-730 #7/A-B:439-730 #8/A-B:439-730 #9/A-B:439-730
> #10/A-B:439-730 #16/A-B:439-730 #17/A-B:439-730 #18/A-B:439-730
> #19/A-B:439-730 #20/A-B:439-730

43860 atoms, 44760 bonds, 5840 residues, 10 models selected  
. [ID: 2] region 20 chains [439-730] RMSD: 45.560  
  

> color (#8 & sel) orange

> color (#8 & sel) forest green

> select
> #6/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #7/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #8/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #9/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #10/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #16/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #17/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #18/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #19/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #20/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772

18060 atoms, 17940 bonds, 2360 residues, 10 models selected  

> select #6/A-B:404 #7/A-B:404 #8/A-B:404 #9/A-B:404 #10/A-B:404 #16/A-B:404
> #17/A-B:404 #18/A-B:404 #19/A-B:404 #20/A-B:404

120 atoms, 100 bonds, 20 residues, 10 models selected  

> select #6/A-B:404 #7/A-B:404 #8/A-B:404 #9/A-B:404 #10/A-B:404 #16/A-B:404
> #17/A-B:404 #18/A-B:404 #19/A-B:404 #20/A-B:404

120 atoms, 100 bonds, 20 residues, 10 models selected  
. [ID: 2] region 20 chains [404] RMSD: 64.911  
  

> select #6/A-B:815 #7/A-B:815 #8/A-B:815 #9/A-B:815 #10/A-B:815 #16/A-B:815
> #17/A-B:815 #18/A-B:815 #19/A-B:815 #20/A-B:815

260 atoms, 260 bonds, 20 residues, 10 models selected  

> select #6/A-B:815 #7/A-B:815 #8/A-B:815 #9/A-B:815 #10/A-B:815 #16/A-B:815
> #17/A-B:815 #18/A-B:815 #19/A-B:815 #20/A-B:815

260 atoms, 260 bonds, 20 residues, 10 models selected  
. [ID: 2] region 20 chains [815] RMSD: 89.228  
  

> save /Users/robertkazmierczak/Desktop/Atu1341dimerAF3model1_may2024.cxs

> hide #8 models

> show #7 models

> color #7 #ed90e1ff

> select #6/A-B:730 #7/A-B:730 #8/A-B:730 #9/A-B:730 #10/A-B:730 #16/A-B:730
> #17/A-B:730 #18/A-B:730 #19/A-B:730 #20/A-B:730

100 atoms, 80 bonds, 20 residues, 10 models selected  

> select #6/A-B:439-730 #7/A-B:439-730 #8/A-B:439-730 #9/A-B:439-730
> #10/A-B:439-730 #16/A-B:439-730 #17/A-B:439-730 #18/A-B:439-730
> #19/A-B:439-730 #20/A-B:439-730

43860 atoms, 44760 bonds, 5840 residues, 10 models selected  
. [ID: 2] region 20 chains [439-730] RMSD: 45.560  
  

> color (#7 & sel) forest green

> hide #7 models

> show #10 models

> color (#10 & sel) forest green

> hide #10 models

> show #8 models

> select #6/A-B:408 #7/A-B:408 #8/A-B:408 #9/A-B:408 #10/A-B:408 #16/A-B:408
> #17/A-B:408 #18/A-B:408 #19/A-B:408 #20/A-B:408

140 atoms, 120 bonds, 20 residues, 10 models selected  

> select #6/A-B:408-409 #7/A-B:408-409 #8/A-B:408-409 #9/A-B:408-409
> #10/A-B:408-409 #16/A-B:408-409 #17/A-B:408-409 #18/A-B:408-409
> #19/A-B:408-409 #20/A-B:408-409

220 atoms, 200 bonds, 40 residues, 10 models selected  
. [ID: 2] region 20 chains [408-409] RMSD: 64.427  
  

> hide #8 models

> show #7 models

> select #6/A-B:437 #7/A-B:437 #8/A-B:437 #9/A-B:437 #10/A-B:437 #16/A-B:437
> #17/A-B:437 #18/A-B:437 #19/A-B:437 #20/A-B:437

140 atoms, 120 bonds, 20 residues, 10 models selected  

> select #6/A-B:285-437 #7/A-B:285-437 #8/A-B:285-437 #9/A-B:285-437
> #10/A-B:285-437 #16/A-B:285-437 #17/A-B:285-437 #18/A-B:285-437
> #19/A-B:285-437 #20/A-B:285-437

23200 atoms, 23600 bonds, 3060 residues, 10 models selected  
. [ID: 2] region 20 chains [285-437] RMSD: 50.244  
  

> select
> #6/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #7/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #8/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #9/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #10/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #16/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #17/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #18/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #19/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #20/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772

18060 atoms, 17940 bonds, 2360 residues, 10 models selected  

> select #6/A-B:285-437 #7/A-B:285-437 #8/A-B:285-437 #9/A-B:285-437
> #10/A-B:285-437 #16/A-B:285-437 #17/A-B:285-437 #18/A-B:285-437
> #19/A-B:285-437 #20/A-B:285-437

23200 atoms, 23600 bonds, 3060 residues, 10 models selected  

> select #6/A-B:483-533 #7/A-B:483-533 #8/A-B:483-533 #9/A-B:483-533
> #10/A-B:483-533 #16/A-B:483-533 #17/A-B:483-533 #18/A-B:483-533
> #19/A-B:483-533 #20/A-B:483-533

7340 atoms, 7500 bonds, 1020 residues, 10 models selected  

> select #6/A-B:483-534 #7/A-B:483-534 #8/A-B:483-534 #9/A-B:483-534
> #10/A-B:483-534 #16/A-B:483-534 #17/A-B:483-534 #18/A-B:483-534
> #19/A-B:483-534 #20/A-B:483-534

7460 atoms, 7620 bonds, 1040 residues, 10 models selected  
. [ID: 2] region 20 chains [483-534] RMSD: 58.505  
  

> select #6/A-B:437 #7/A-B:437 #8/A-B:437 #9/A-B:437 #10/A-B:437 #16/A-B:437
> #17/A-B:437 #18/A-B:437 #19/A-B:437 #20/A-B:437

140 atoms, 120 bonds, 20 residues, 10 models selected  

> select #6/A-B:322-437 #7/A-B:322-437 #8/A-B:322-437 #9/A-B:322-437
> #10/A-B:322-437 #16/A-B:322-437 #17/A-B:322-437 #18/A-B:322-437
> #19/A-B:322-437 #20/A-B:322-437

17400 atoms, 17740 bonds, 2320 residues, 10 models selected  
. [ID: 2] region 20 chains [322-437] RMSD: 53.788  
  

> hide #7 models

> show #8 models

> hide #8 models

> show #7 models

> color (#7 & sel) cyan

> hide #7 models

> show #10 models

> color (#10 & sel) cyan

> hide #10 models

> show #8 models

> hide #8 models

> show #20 models

> color (#20 & sel) cyan

> show #17 models

> hide #17 models

> show #10 models

> hide #10 models

> show #17 models

> hide #20 models

> color (#17 & sel) cyan

> select #16/C-D:2-5,7-14,19-26,31-33,36-46,55-63,69-78,92-100
> #17/C-D:2-5,7-14,19-26,31-33,36-46,55-63,69-78,92-100
> #18/C-D:2-5,7-14,19-26,31-33,36-46,55-63,69-78,92-100
> #19/C-D:2-5,7-14,19-26,31-33,36-46,55-63,69-78,92-100
> #20/C-D:2-5,7-14,19-26,31-33,36-46,55-63,69-78,92-100

5180 atoms, 5240 bonds, 620 residues, 5 models selected  

> select #16/C-D:113 #17/C-D:113 #18/C-D:113 #19/C-D:113 #20/C-D:113

100 atoms, 90 bonds, 10 residues, 5 models selected  

> select #16/C-D #17/C-D #18/C-D #19/C-D #20/C-D

8960 atoms, 9140 bonds, 1130 residues, 5 models selected  
. [ID: 3] region 10 chains [1-113] RMSD: 41.576  
  

> color (#17 & sel) red

> show #20 models

> hide #17 models

> color (#20 & sel) red

> select #6/A-B:439 #7/A-B:439 #8/A-B:439 #9/A-B:439 #10/A-B:439 #16/A-B:439
> #17/A-B:439 #18/A-B:439 #19/A-B:439 #20/A-B:439

80 atoms, 60 bonds, 20 residues, 10 models selected  

> select #6/A-B:439-630 #7/A-B:439-630 #8/A-B:439-630 #9/A-B:439-630
> #10/A-B:439-630 #16/A-B:439-630 #17/A-B:439-630 #18/A-B:439-630
> #19/A-B:439-630 #20/A-B:439-630

29140 atoms, 29720 bonds, 3840 residues, 10 models selected  
. [ID: 2] region 20 chains [439-630] RMSD: 45.128  
  

> select
> #6/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #7/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #8/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #9/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #10/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #16/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #17/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #18/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #19/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #20/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772

18060 atoms, 17940 bonds, 2360 residues, 10 models selected  

> select #6/A-B:437 #7/A-B:437 #8/A-B:437 #9/A-B:437 #10/A-B:437 #16/A-B:437
> #17/A-B:437 #18/A-B:437 #19/A-B:437 #20/A-B:437

140 atoms, 120 bonds, 20 residues, 10 models selected  

> select #6/A-B:439 #7/A-B:439 #8/A-B:439 #9/A-B:439 #10/A-B:439 #16/A-B:439
> #17/A-B:439 #18/A-B:439 #19/A-B:439 #20/A-B:439

80 atoms, 60 bonds, 20 residues, 10 models selected  

> select #6/A-B:439-745 #7/A-B:439-745 #8/A-B:439-745 #9/A-B:439-745
> #10/A-B:439-745 #16/A-B:439-745 #17/A-B:439-745 #18/A-B:439-745
> #19/A-B:439-745 #20/A-B:439-745

46140 atoms, 47120 bonds, 6140 residues, 10 models selected  
. [ID: 2] region 20 chains [439-745] RMSD: 45.867  
  

> color (#20 & sel) forest green

> hide #20 models

> show #17 models

> color (#17 & sel) forest green

> color (#17 & sel) orange

> select #6/A-B:234-235 #7/A-B:234-235 #8/A-B:234-235 #9/A-B:234-235
> #10/A-B:234-235 #16/A-B:234-235 #17/A-B:234-235 #18/A-B:234-235
> #19/A-B:234-235 #20/A-B:234-235

280 atoms, 260 bonds, 40 residues, 10 models selected  

> select #6/A-B:231-235 #7/A-B:231-235 #8/A-B:231-235 #9/A-B:231-235
> #10/A-B:231-235 #16/A-B:231-235 #17/A-B:231-235 #18/A-B:231-235
> #19/A-B:231-235 #20/A-B:231-235

820 atoms, 800 bonds, 100 residues, 10 models selected  
. [ID: 2] region 20 chains [231-235] RMSD: 76.234  
  

> select
> #6/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #7/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #8/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #9/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #10/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #16/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #17/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #18/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #19/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814
> #20/A-B:2-32,37-42,72-74,77-87,91-93,99-111,125-134,141-157,160-170,180-188,192-194,197-208,210-213,219-235,241-249,267-288,299-320,335-341,388-394,476-490,527-532,536-546,548-557,568-572,579-590,621-624,646-661,683-685,717-734,793-799,801-814

52880 atoms, 53160 bonds, 6760 residues, 10 models selected  

> select #6/A-B:374 #7/A-B:374 #8/A-B:374 #9/A-B:374 #10/A-B:374 #16/A-B:374
> #17/A-B:374 #18/A-B:374 #19/A-B:374 #20/A-B:374

100 atoms, 80 bonds, 20 residues, 10 models selected  

> select #6/A-B:374 #7/A-B:374 #8/A-B:374 #9/A-B:374 #10/A-B:374 #16/A-B:374
> #17/A-B:374 #18/A-B:374 #19/A-B:374 #20/A-B:374

100 atoms, 80 bonds, 20 residues, 10 models selected  
. [ID: 2] region 20 chains [374] RMSD: 48.537  
  

> select #6/A-B:234-235 #7/A-B:234-235 #8/A-B:234-235 #9/A-B:234-235
> #10/A-B:234-235 #16/A-B:234-235 #17/A-B:234-235 #18/A-B:234-235
> #19/A-B:234-235 #20/A-B:234-235

280 atoms, 260 bonds, 40 residues, 10 models selected  

> select #6/A-B:232-235 #7/A-B:232-235 #8/A-B:232-235 #9/A-B:232-235
> #10/A-B:232-235 #16/A-B:232-235 #17/A-B:232-235 #18/A-B:232-235
> #19/A-B:232-235 #20/A-B:232-235

660 atoms, 640 bonds, 80 residues, 10 models selected  
. [ID: 2] region 20 chains [232-235] RMSD: 76.417  
  

> select #6/A-B:276-326 #7/A-B:276-326 #8/A-B:276-326 #9/A-B:276-326
> #10/A-B:276-326 #16/A-B:276-326 #17/A-B:276-326 #18/A-B:276-326
> #19/A-B:276-326 #20/A-B:276-326

8140 atoms, 8240 bonds, 1020 residues, 10 models selected  

> select #6/A-B:276-325 #7/A-B:276-325 #8/A-B:276-325 #9/A-B:276-325
> #10/A-B:276-325 #16/A-B:276-325 #17/A-B:276-325 #18/A-B:276-325
> #19/A-B:276-325 #20/A-B:276-325

7980 atoms, 8080 bonds, 1000 residues, 10 models selected  
. [ID: 2] region 20 chains [276-325] RMSD: 36.239  
  

> select #6/A-B:234-235 #7/A-B:234-235 #8/A-B:234-235 #9/A-B:234-235
> #10/A-B:234-235 #16/A-B:234-235 #17/A-B:234-235 #18/A-B:234-235
> #19/A-B:234-235 #20/A-B:234-235

280 atoms, 260 bonds, 40 residues, 10 models selected  

> select #6/A-B:234-235 #7/A-B:234-235 #8/A-B:234-235 #9/A-B:234-235
> #10/A-B:234-235 #16/A-B:234-235 #17/A-B:234-235 #18/A-B:234-235
> #19/A-B:234-235 #20/A-B:234-235

280 atoms, 260 bonds, 40 residues, 10 models selected  
. [ID: 2] region 20 chains [234-235] RMSD: 78.973  
  

> select #6/A-B:469 #7/A-B:469 #8/A-B:469 #9/A-B:469 #10/A-B:469 #16/A-B:469
> #17/A-B:469 #18/A-B:469 #19/A-B:469 #20/A-B:469

140 atoms, 120 bonds, 20 residues, 10 models selected  

> select #6/A-B:469-472 #7/A-B:469-472 #8/A-B:469-472 #9/A-B:469-472
> #10/A-B:469-472 #16/A-B:469-472 #17/A-B:469-472 #18/A-B:469-472
> #19/A-B:469-472 #20/A-B:469-472

580 atoms, 560 bonds, 80 residues, 10 models selected  
. [ID: 2] region 20 chains [469-472] RMSD: 23.412  
  

> select #6/A-B:55 #7/A-B:55 #8/A-B:55 #9/A-B:55 #10/A-B:55 #16/A-B:55
> #17/A-B:55 #18/A-B:55 #19/A-B:55 #20/A-B:55

160 atoms, 140 bonds, 20 residues, 10 models selected  

> select #6/A-B:55-234 #7/A-B:55-234 #8/A-B:55-234 #9/A-B:55-234
> #10/A-B:55-234 #16/A-B:55-234 #17/A-B:55-234 #18/A-B:55-234 #19/A-B:55-234
> #20/A-B:55-234

28640 atoms, 29220 bonds, 3600 residues, 10 models selected  
. [ID: 2] region 20 chains [55-234] RMSD: 62.522  
  

> color (#17 & sel) blue

> show #10 models

> hide #17 models

> color (#10 & sel) blue

> select #6/A-B:697-698 #7/A-B:697-698 #8/A-B:697-698 #9/A-B:697-698
> #10/A-B:697-698 #16/A-B:697-698 #17/A-B:697-698 #18/A-B:697-698
> #19/A-B:697-698 #20/A-B:697-698

300 atoms, 280 bonds, 40 residues, 10 models selected  

> select #6/A-B:697-698 #7/A-B:697-698 #8/A-B:697-698 #9/A-B:697-698
> #10/A-B:697-698 #16/A-B:697-698 #17/A-B:697-698 #18/A-B:697-698
> #19/A-B:697-698 #20/A-B:697-698

300 atoms, 280 bonds, 40 residues, 10 models selected  
. [ID: 2] region 20 chains [697-698] RMSD: 37.180  
  

> select #16/C-D:113 #17/C-D:113 #18/C-D:113 #19/C-D:113 #20/C-D:113

100 atoms, 90 bonds, 10 residues, 5 models selected  

> select #16/C-D #17/C-D #18/C-D #19/C-D #20/C-D

8960 atoms, 9140 bonds, 1130 residues, 5 models selected  
. [ID: 3] region 10 chains [1-113] RMSD: 41.576  
  

> select #6/A-B:607 #7/A-B:607 #8/A-B:607 #9/A-B:607 #10/A-B:607 #16/A-B:607
> #17/A-B:607 #18/A-B:607 #19/A-B:607 #20/A-B:607

220 atoms, 200 bonds, 20 residues, 10 models selected  

> select #6/A-B:607 #7/A-B:607 #8/A-B:607 #9/A-B:607 #10/A-B:607 #16/A-B:607
> #17/A-B:607 #18/A-B:607 #19/A-B:607 #20/A-B:607

220 atoms, 200 bonds, 20 residues, 10 models selected  
. [ID: 2] region 20 chains [607] RMSD: 38.993  
  

> select #16/C-D #17/C-D #18/C-D #19/C-D #20/C-D

8960 atoms, 9140 bonds, 1130 residues, 5 models selected  

> select #16/C-D:113 #17/C-D:113 #18/C-D:113 #19/C-D:113 #20/C-D:113

100 atoms, 90 bonds, 10 residues, 5 models selected  

> select #16/C-D:2-113 #17/C-D:2-113 #18/C-D:2-113 #19/C-D:2-113 #20/C-D:2-113

8910 atoms, 9090 bonds, 1120 residues, 5 models selected  
. [ID: 3] region 10 chains [2-113] RMSD: 41.571  
  

> select #16/C-D:1 #17/C-D:1 #18/C-D:1 #19/C-D:1 #20/C-D:1

50 atoms, 40 bonds, 10 residues, 5 models selected  

> select #16/C-D #17/C-D #18/C-D #19/C-D #20/C-D

8960 atoms, 9140 bonds, 1130 residues, 5 models selected  
. [ID: 3] region 10 chains [1-113] RMSD: 41.576  
  

> color #10 red

> undo

> select
> #6/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #7/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #8/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #9/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #10/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #16/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #17/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #18/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #19/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772
> #20/A-B:49-52,58-62,292-295,352-359,363-368,381-386,416-421,429-432,438-444,451-455,497-500,505-507,510-512,523-526,601-605,611-614,618-621,635-638,676-681,687-693,698-704,748-753,767-772

18060 atoms, 17940 bonds, 2360 residues, 10 models selected  

> select #6/A-B:373 #7/A-B:373 #8/A-B:373 #9/A-B:373 #10/A-B:373 #16/A-B:373
> #17/A-B:373 #18/A-B:373 #19/A-B:373 #20/A-B:373

160 atoms, 140 bonds, 20 residues, 10 models selected  

> select #6/A-B:373 #7/A-B:373 #8/A-B:373 #9/A-B:373 #10/A-B:373 #16/A-B:373
> #17/A-B:373 #18/A-B:373 #19/A-B:373 #20/A-B:373

160 atoms, 140 bonds, 20 residues, 10 models selected  
. [ID: 2] region 20 chains [373] RMSD: 44.477  
  

> select #16/C-D:59 #17/C-D:59 #18/C-D:59 #19/C-D:59 #20/C-D:59

90 atoms, 80 bonds, 10 residues, 5 models selected  

> select #16/C-D:59 #17/C-D:59 #18/C-D:59 #19/C-D:59 #20/C-D:59

90 atoms, 80 bonds, 10 residues, 5 models selected  
. [ID: 3] region 10 chains [59] RMSD: 41.251  
  

> select #16/C-D:67 #17/C-D:67 #18/C-D:67 #19/C-D:67 #20/C-D:67

110 atoms, 100 bonds, 10 residues, 5 models selected  

> select #16/C-D:62-67 #17/C-D:62-67 #18/C-D:62-67 #19/C-D:62-67 #20/C-D:62-67

510 atoms, 500 bonds, 60 residues, 5 models selected  
. [ID: 3] region 10 chains [62-67] RMSD: 52.105  
  

> show #17 models

> hide #10 models

> show #20 models

> hide #17 models

> select #6/A-B:55 #7/A-B:55 #8/A-B:55 #9/A-B:55 #10/A-B:55 #16/A-B:55
> #17/A-B:55 #18/A-B:55 #19/A-B:55 #20/A-B:55

160 atoms, 140 bonds, 20 residues, 10 models selected  

> select #6/A-B:55-234 #7/A-B:55-234 #8/A-B:55-234 #9/A-B:55-234
> #10/A-B:55-234 #16/A-B:55-234 #17/A-B:55-234 #18/A-B:55-234 #19/A-B:55-234
> #20/A-B:55-234

28640 atoms, 29220 bonds, 3600 residues, 10 models selected  
. [ID: 2] region 20 chains [55-234] RMSD: 62.522  
  

> color (#20 & sel) blue

> select #16/C-D:113 #17/C-D:113 #18/C-D:113 #19/C-D:113 #20/C-D:113

100 atoms, 90 bonds, 10 residues, 5 models selected  

> select #16/C-D:113 #17/C-D:113 #18/C-D:113 #19/C-D:113 #20/C-D:113

100 atoms, 90 bonds, 10 residues, 5 models selected  
. [ID: 3] region 10 chains [113] RMSD: 53.622  
  

> save /Users/robertkazmierczak/Desktop/1341-1328delspAF3mod4_may24.cxs

——— End of log from Mon May 20 11:53:07 2024 ———

opened ChimeraX session  

> ui tool show "AlphaFold Error Plot"

Must choose path to predicted aligned file  

> alphafold pae #20 file
> /Users/robertkazmierczak/Downloads/ChimeraX/AlphaFold/alphafold_database.json

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 173, in _choose_pae_file  
self._open_pae()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 186, in _open_pae  
self._open_pae_from_file(s)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 210, in _open_pae_from_file  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1405, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 941, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1185, in read_pae_matrix  
return read_json_pae_matrix(path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1198, in read_json_pae_matrix  
j = json.load(f)  
^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 293, in load  
return loads(fp.read(),  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 353, in raw_decode  
obj, end = self.scan_once(s, idx)  
^^^^^^^^^^^^^^^^^^^^^^  
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 6 column 5 (char
256)  
  
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 6 column 5 (char
256)  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 353, in raw_decode  
obj, end = self.scan_once(s, idx)  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> alphafold pae #20 file
> /Users/robertkazmierczak/Downloads/ChimeraX/AlphaFold/alphafold_database.json

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 186, in _open_pae  
self._open_pae_from_file(s)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 210, in _open_pae_from_file  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1405, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 941, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1185, in read_pae_matrix  
return read_json_pae_matrix(path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1198, in read_json_pae_matrix  
j = json.load(f)  
^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 293, in load  
return loads(fp.read(),  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 353, in raw_decode  
obj, end = self.scan_once(s, idx)  
^^^^^^^^^^^^^^^^^^^^^^  
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 6 column 5 (char
256)  
  
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 6 column 5 (char
256)  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 353, in raw_decode  
obj, end = self.scan_once(s, idx)  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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 Air
      Model Identifier: MacBookAir10,1
      Model Number: Z127000FKLL/A
      Chip: Apple M1
      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: 56 days, 1 hour, 53 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          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

Change History (2)

comment:1 by Eric Pettersen, 17 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AlphaFold JSON: Expecting ',' delimiter

comment:2 by Tom Goddard, 17 months ago

Resolution: → nonchimerax
Status: assigned → closed

User tried to open a file called alphafold_database.json that did not even parse as legal JSON using the Python json.load() function.

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