The following bug report has been submitted:
Platform: macOS-12.0.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202501170719 (2025-01-17 07:19:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"name" : "QtWidgets"
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"
},
{
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"arch" : "arm64",
"base" : 4303994880,
"CFBundleShortVersionString" : "1.10.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
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"path" : "\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1408K 11 \nActivity Tracing 256K 1 \nCG backing stores 3136K 8 \nCG image 1952K 68 \nColorSync 576K 29 \nCoreAnimation 5216K 123 \nCoreGraphics 48K 3 \nCoreUI image data 5776K 57 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.5G 259 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 576.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 464K 29 \nStack 128.2M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 240.6M 172 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__AUTH 2619K 337 \n__AUTH_CONST 20.4M 542 \n__CTF 759 1 \n__DATA 27.3M 696 \n__DATA_CONST 29.5M 705 \n__DATA_DIRTY 1949K 242 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 601.0M 161 \n__OBJC_CONST 3921K 311 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3088K 1 \n__TEXT 762.9M 722 \n__UNICODE 588K 1 \ndyld private memory 1072K 3 \nmapped file 234.6M 60 \nshared memory 1440K 19 \n=========== ======= ======= \nTOTAL 4.5G 4622 \nTOTAL, minus reserved VM space 3.7G 4622 \n",
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Log:
UCSF ChimeraX version: 1.10.dev202501170719 (2025-01-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2_paegreen5.cxs
Log from Sat Jul 26 18:22:59 2025UCSF ChimeraX version: 1.8rc202405312319
(2024-05-31)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/usuario/Desktop/fragmentoG160/F2.cxs
Log from Fri Jul 25 10:55:12 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/usuario/Downloads/fold_g160_1copia/fold_g160_1copia_model_0.cif
Chain information for fold_g160_1copia_model_0.cif #1
---
Chain | Description
A | .
> set bgColor white
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui tool show "Color Actions"
> color indian red
[Repeated 1 time(s)]
> color fire brick
> color indian red
> transparency 80 target ac
> transparency 50 target ac
> transparency 60 target ac
> transparency 80 target ac
> select :1-393
2937 atoms, 2990 bonds, 393 residues, 1 model selected
> ui tool show "Color Actions"
> color sel red
> color sel medium violet red
[Repeated 2 time(s)]
> color sel medium orchid
> color sel medium violet red
> transparency sel 0 target ac
> select add #1
11715 atoms, 11835 bonds, 1498 residues, 1 model selected
> select subtract #1
Nothing selected
> select :1-393
2937 atoms, 2990 bonds, 393 residues, 1 model selected
> color sel purple
> graphics selection color black width 0.8
> graphics selection color black width 3
> graphics selection color black width 1.2
> save /Users/usuario/Desktop/fragmentoG160/F2.cxs
——— End of log from Fri Jul 25 10:55:12 2025 ———
opened ChimeraX session
> save /Users/usuario/Desktop/fragmentoG160/f2.png width 864 height 611
> supersample 3
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_0.cif"
Chain information for fold_ak1b_2short_f6_2_model_0.cif #2
---
Chain | Description
A B | .
C D | .
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_1.cif"
Chain information for fold_ak1b_2short_f6_2_model_1.cif #3
---
Chain | Description
A B | .
C D | .
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_2.cif"
Chain information for fold_ak1b_2short_f6_2_model_2.cif #4
---
Chain | Description
A B | .
C D | .
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_3.cif"
Chain information for fold_ak1b_2short_f6_2_model_3.cif #5
---
Chain | Description
A B | .
C D | .
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_4.cif"
Chain information for fold_ak1b_2short_f6_2_model_4.cif #6
---
Chain | Description
A B | .
C D | .
> close #1
> ui tool show Matchmaker
> matchmaker #3-6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with
fold_ak1b_2short_f6_2_model_1.cif, chain C (#3), sequence alignment score =
651
RMSD between 78 pruned atom pairs is 0.606 angstroms; (across all 128 pairs:
6.488)
Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with
fold_ak1b_2short_f6_2_model_2.cif, chain C (#4), sequence alignment score =
651
RMSD between 72 pruned atom pairs is 0.524 angstroms; (across all 128 pairs:
12.583)
Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with
fold_ak1b_2short_f6_2_model_3.cif, chain C (#5), sequence alignment score =
651
RMSD between 73 pruned atom pairs is 0.577 angstroms; (across all 128 pairs:
8.942)
Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with
fold_ak1b_2short_f6_2_model_4.cif, chain C (#6), sequence alignment score =
651
RMSD between 72 pruned atom pairs is 0.483 angstroms; (across all 128 pairs:
17.400)
> select #2/A
980 atoms, 986 bonds, 120 residues, 1 model selected
> select #2/A:1-120
980 atoms, 986 bonds, 120 residues, 1 model selected
> select #2/A:1-120
980 atoms, 986 bonds, 120 residues, 1 model selected
> select :A,B
Nothing selected
> select /A,/B
Expected an objects specifier or a keyword
> select A,B
Expected an objects specifier or a keyword
> select A
Expected an objects specifier or a keyword
> color bychain
> color bypolymer
> select
> #2/A#2/B#2/C#2/D#3/A#3/B#3/C#3/D#4/A#4/B#4/C#4/D#5/A#5/B#5/C#5/D#6/A#6/B#6/C#6/D
19470 atoms, 19760 bonds, 2480 residues, 5 models selected
> color sel bypolymer
Alignment identifier is 1
Alignment identifier is 2
> select #2/A-B:1 #3/A-B:1 #4/A-B:1 #5/A-B:1 #6/A-B:1
80 atoms, 70 bonds, 10 residues, 5 models selected
> select #2/A-B #3/A-B #4/A-B #5/A-B #6/A-B
9800 atoms, 9860 bonds, 1200 residues, 5 models selected
. [ID: 1] region 10 chains [1-120] RMSD: 1.517
> color sel cornflower blue
> transparency sel 30
> transparency sel 80
> transparency sel 30 target ac
> select #2/C-D:1 #3/C-D:1 #4/C-D:1 #5/C-D:1 #6/C-D:1
90 atoms, 80 bonds, 10 residues, 5 models selected
> select #2/C-D #3/C-D #4/C-D #5/C-D #6/C-D
9670 atoms, 9900 bonds, 1280 residues, 5 models selected
. [ID: 2] region 10 chains [1-128] RMSD: 12.546
> ui tool show "Color Actions"
> color sel gold
> color sel yellow
> color sel royal blue
> color sel light pink
[Repeated 1 time(s)]
> color sel light coral
> color sel violet
> color sel light goldenrod yellow
> color sel old lace
> color sel light yellow
> color sel lemon chiffon
> color sel moccasin
> color sel pale green
> color sel moccasin
> color sel navajo white
> color sel peach puff
[Repeated 1 time(s)]
> color sel navajo white
> color sel moccasin
> transparency sel 30 target ac
> graphics silhouettes true color black width 1 depthJump 0.01
> hide #3 models
> show #3 models
> select add #3
11630 atoms, 11872 bonds, 1520 residues, 5 models selected
> select subtract #3
7736 atoms, 7920 bonds, 1024 residues, 4 models selected
> select add #4
9696 atoms, 9892 bonds, 1264 residues, 4 models selected
> select subtract #4
5802 atoms, 5940 bonds, 768 residues, 3 models selected
> select add #3
9696 atoms, 9892 bonds, 1264 residues, 4 models selected
> select add #4
13590 atoms, 13844 bonds, 1760 residues, 5 models selected
> select add #5
15550 atoms, 15816 bonds, 2000 residues, 5 models selected
> select add #6
17510 atoms, 17788 bonds, 2240 residues, 5 models selected
> select subtract #6
13616 atoms, 13836 bonds, 1744 residues, 4 models selected
> select add #6
17510 atoms, 17788 bonds, 2240 residues, 5 models selected
> select subtract #6
13616 atoms, 13836 bonds, 1744 residues, 4 models selected
> select subtract #5
9722 atoms, 9884 bonds, 1248 residues, 3 models selected
> select subtract #4
5828 atoms, 5932 bonds, 752 residues, 2 models selected
> select subtract #3
1934 atoms, 1980 bonds, 256 residues, 1 model selected
> select add #3
5828 atoms, 5932 bonds, 752 residues, 2 models selected
> select add #2
7788 atoms, 7904 bonds, 992 residues, 2 models selected
> select subtract #3
3894 atoms, 3952 bonds, 496 residues, 1 model selected
> select add #3
7788 atoms, 7904 bonds, 992 residues, 2 models selected
> select add #4
11682 atoms, 11856 bonds, 1488 residues, 3 models selected
> select add #5
15576 atoms, 15808 bonds, 1984 residues, 4 models selected
> select add #6
19470 atoms, 19760 bonds, 2480 residues, 5 models selected
> graphics silhouettes true color black width 1 depthJump 0.01
> graphics silhouettes true color black width 5 depthJump 0.01
> graphics silhouettes true color black width 1.2 depthJump 0.01
> graphics silhouettes true color black width 1.2 depthJump 0.03
> graphics silhouettes true color black width 1.2 depthJump 0.4
> graphics silhouettes true color black width 1.2 depthJump 6
> graphics silhouettes true color black width 1.2 depthJump 0.01
> save /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2.cxs
> color bfactor palette
> 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6
> key true
> key #ff7d45:0 #ff7d45:50 #ffdb13:50 #ffdb13:70 #65cbf3:70 #65cbf3:90
> #0053d6:90 #0053d6:100 showTool true
> ui mousemode right "color key"
19470 atoms, 2480 residues, atom bfactor range 17.7 to 95.2
> key size 0.26000,0.05000
> key size 0.27000,0.05000
> key size 0.28000,0.05000
> key size 0.29000,0.05000
> key size 0.30000,0.05000
> key size 0.31000,0.05000
Key is partially or completely offscreen
> key size 0.32000,0.05000
Key is partially or completely offscreen
> key size 0.32000,0.04000
Key is partially or completely offscreen
> key size 0.32000,0.03000
Key is partially or completely offscreen
> key pos 0.69000,0.08000
Key is partially or completely offscreen
> key pos 0.68000,0.08000
> key pos 0.69000,0.08000
Key is partially or completely offscreen
> key pos 0.70000,0.08000
Key is partially or completely offscreen
> key pos 0.71000,0.08000
Key is partially or completely offscreen
> key pos 0.72000,0.08000
Key is partially or completely offscreen
> key pos 0.73000,0.08000
Key is partially or completely offscreen
> key pos 0.73000,0.07000
Key is partially or completely offscreen
> key pos 0.73000,0.06000
Key is partially or completely offscreen
> key pos 0.73000,0.05000
Key is partially or completely offscreen
> key pos 0.73000,0.04000
Key is partially or completely offscreen
> key pos 0.73000,0.03000
Key is partially or completely offscreen
> key pos 0.73000,0.02000
Key is partially or completely offscreen
> key pos 0.73000,0.01000
Key is partially or completely offscreen
> key pos 0.73000,0.00000
Key is partially or completely offscreen
> key pos 0.73000,-0.01000
Key is partially or completely offscreen
> key pos 0.73000,-0.02000
Key is partially or completely offscreen
> key pos 0.73000,-0.03000
Key is partially or completely offscreen
> key pos 0.73000,-0.04000
Key is partially or completely offscreen
> key pos 0.73000,-0.05000
Key is partially or completely offscreen
> key pos 0.73000,-0.06000
Key is partially or completely offscreen
> key pos 0.73000,-0.07000
Key is partially or completely offscreen
> key pos 0.73000,-0.08000
Key is partially or completely offscreen
> save /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2bfactor.cxs
> undo
> alphafold contacts #1/A toAtoms #1/D distance 5 maxPae 5 palette paegreen
No alphafold specified for alphafold contacts
> rename #1.1 "AB contacts"
> alphafold contacts #1/B toAtoms #1/C distance 5 maxPae 5 palette paegreen
No alphafold specified for alphafold contacts
> rename #1.2 "BC contacts"
> alphafold contacts #1/A toAtoms #1/C distance 5 maxPae 5 palette paegreen
No alphafold specified for alphafold contacts
> rename #1.3 "CD contacts"
> alphafold contacts #1/B toAtoms #1/D distance 5 maxPae 5 palette paegreen
No alphafold specified for alphafold contacts
> alphafold contacts #2/A toAtoms #2/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened
> rename #2.1 "AB contacts"
> alphafold contacts #2/B toAtoms #2/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened
> rename #2.2 "BC contacts"
> alphafold contacts #2/A toAtoms #2/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened
> rename #2.3 "CD contacts"
> alphafold contacts #2/B toAtoms #2/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened
> alphafold contacts #3/A toAtoms #3/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened
> rename #3.1 "AB contacts"
> alphafold contacts #3/B toAtoms #3/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened
> rename #3.2 "BC contacts"
> alphafold contacts #3/A toAtoms #3/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened
> rename #3.3 "CD contacts"
> alphafold contacts #3/B toAtoms #3/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened
> alphafold contacts #4/A toAtoms #4/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened
> rename #4.1 "AB contacts"
> alphafold contacts #4/B toAtoms #4/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened
> rename #4.2 "BC contacts"
> alphafold contacts #4/A toAtoms #4/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened
> rename #4.3 "CD contacts"
> alphafold contacts #4/B toAtoms #4/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened
> alphafold contacts #5/A toAtoms #5/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened
> rename #5.1 "AB contacts"
> alphafold contacts #5/B toAtoms #5/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened
> rename #5.2 "BC contacts"
> alphafold contacts #5/A toAtoms #5/C distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened
> rename #5.3 "CD contacts"
> alphafold contacts #5/B toAtoms #5/D distance 5 maxPae 5 palette paegreen
Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json"
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"
> alphafold pae #2 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"
> alphafold pae #2 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json"
> alphafold pae #3 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"
> alphafold pae #3 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"
Failed opening file /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json:
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json
format pae structure #1
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"
Failed opening file /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json:
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json
format pae structure #1
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json"
Failed opening file /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json:
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json
format pae structure #1
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json"
Failed opening file /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json:
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json
format pae structure #1
> open "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json"
Failed opening file /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json:
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/usuario/Dropbox
(Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json
format pae structure #1
> alphafold pae #3 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"
> alphafold pae #4 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"
> alphafold pae #5 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json"
> alphafold pae #6 file "/Users/usuario/Dropbox
> (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json"
> close #1
> ui mousemode right translate
> alphafold contacts #2/A toAtoms #2/D distance 5 maxPae 5 palette paegreen
Found 56 residue or atom pairs within distance 5 with pae <= 5
> rename #2.1 "AB contacts"
> alphafold contacts #2/B toAtoms #2/C distance 5 maxPae 5 palette paegreen
Found 57 residue or atom pairs within distance 5 with pae <= 5
> rename #2.2 "BC contacts"
> alphafold contacts #2/A toAtoms #2/C distance 5 maxPae 5 palette paegreen
Found 50 residue or atom pairs within distance 5 with pae <= 5
> rename #2.3 "CD contacts"
> alphafold contacts #2/B toAtoms #2/D distance 5 maxPae 5 palette paegreen
Found 49 residue or atom pairs within distance 5 with pae <= 5
> alphafold contacts #3/A toAtoms #3/D distance 5 maxPae 5 palette paegreen
Found 55 residue or atom pairs within distance 5 with pae <= 5
> rename #3.1 "AB contacts"
> alphafold contacts #3/B toAtoms #3/C distance 5 maxPae 5 palette paegreen
Found 55 residue or atom pairs within distance 5 with pae <= 5
> rename #3.2 "BC contacts"
> alphafold contacts #3/A toAtoms #3/C distance 5 maxPae 5 palette paegreen
Found 49 residue or atom pairs within distance 5 with pae <= 5
> rename #3.3 "CD contacts"
> alphafold contacts #3/B toAtoms #3/D distance 5 maxPae 5 palette paegreen
Found 49 residue or atom pairs within distance 5 with pae <= 5
> alphafold contacts #4/A toAtoms #4/D distance 5 maxPae 5 palette paegreen
Found 52 residue or atom pairs within distance 5 with pae <= 5
> rename #4.1 "AB contacts"
> alphafold contacts #4/B toAtoms #4/C distance 5 maxPae 5 palette paegreen
Found 55 residue or atom pairs within distance 5 with pae <= 5
> rename #4.2 "BC contacts"
> alphafold contacts #4/A toAtoms #4/C distance 5 maxPae 5 palette paegreen
Found 48 residue or atom pairs within distance 5 with pae <= 5
> rename #4.3 "CD contacts"
> alphafold contacts #4/B toAtoms #4/D distance 5 maxPae 5 palette paegreen
Found 47 residue or atom pairs within distance 5 with pae <= 5
> alphafold contacts #5/A toAtoms #5/D distance 5 maxPae 5 palette paegreen
Found 51 residue or atom pairs within distance 5 with pae <= 5
> rename #5.1 "AB contacts"
> alphafold contacts #5/B toAtoms #5/C distance 5 maxPae 5 palette paegreen
Found 54 residue or atom pairs within distance 5 with pae <= 5
> rename #5.2 "BC contacts"
> alphafold contacts #5/A toAtoms #5/C distance 5 maxPae 5 palette paegreen
Found 50 residue or atom pairs within distance 5 with pae <= 5
> rename #5.3 "CD contacts"
> alphafold contacts #5/B toAtoms #5/D distance 5 maxPae 5 palette paegreen
Found 49 residue or atom pairs within distance 5 with pae <= 5
> alphafold contacts #6/A toAtoms #6/D distance 5 maxPae 5 palette paegreen
Found 53 residue or atom pairs within distance 5 with pae <= 5
> rename #5.1 "AB contacts"
> alphafold contacts #6/B toAtoms #6/C distance 5 maxPae 5 palette paegreen
Found 55 residue or atom pairs within distance 5 with pae <= 5
> rename #5.2 "BC contacts"
> alphafold contacts #6/A toAtoms #6/C distance 5 maxPae 5 palette paegreen
Found 48 residue or atom pairs within distance 5 with pae <= 5
> rename #5.3 "CD contacts"
> alphafold contacts #6/B toAtoms #6/D distance 5 maxPae 5 palette paegreen
Found 48 residue or atom pairs within distance 5 with pae <= 5
> select #2/A-B:1 #3/A-B:1 #4/A-B:1 #5/A-B:1 #6/A-B:1
80 atoms, 70 bonds, 10 residues, 5 models selected
> select #2/A-B #3/A-B #4/A-B #5/A-B #6/A-B
9800 atoms, 9860 bonds, 1200 residues, 5 models selected
. [ID: 1] region 10 chains [1-120] RMSD: 1.517
> ui tool show "Color Actions"
> color sel misty rose
> color sel plum
> color sel light salmon
> color sel plum
> color sel violet
> select #2/C-D:1 #3/C-D:1 #4/C-D:1 #5/C-D:1 #6/C-D:1
90 atoms, 80 bonds, 10 residues, 5 models selected
> select #2/C-D #3/C-D #4/C-D #5/C-D #6/C-D
9670 atoms, 9900 bonds, 1280 residues, 5 models selected
. [ID: 2] region 10 chains [1-128] RMSD: 12.546
> transparency sel 0 target ac
> save /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2_paegreen5.cxs
——— End of log from Sat Jul 26 18:22:59 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 7429.41.5
OS Loader Version: 7429.41.5
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 5 days 21:16
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
VA2715-QHD:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501170719
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
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: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.43
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.0
PyQt6-Qt6: 6.8.1
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.1
PyQt6_sip: 13.9.1
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
From before the workaround went in