![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Closed 3 weeks ago
#19319 closed defect (fixed)
AlphaFold JSON drag and drop: pae_path is None
| Reported by: | 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
opening the .json full data file (PAE data) that matches the model that i have open. downloaded from alphafold3
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/fold_full_length_par3_and_psd95_model_0.cif
Chain information for fold_full_length_par3_and_psd95_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/fold_full_length_par3_and_psd95_full_data_0.json
Opened AlphaFold PAE with values for 1990 residues and atoms
> color bychain
> alphafold contacts /A toAtoms /B 8
Expected a keyword
> hide (protein & @bfactor<70)
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> contacts
6959 contacts
> ~hbonds
> close #1.1
> alphafold contacts /A toAtoms /B maxPae 5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> interfaces ~solvent
1 buried areas: A B 9107
> alphafold contacts /A toAtoms /B maxPae 10
Found 22 residue or atom pairs within distance 3 with pae <= 10
> alphafold contacts /A toAtoms /B maxPae 10
Found 17 residue or atom pairs within distance 3 with pae <= 10
> alphafold contacts /A toAtoms /B maxPae 10 outputFile
> /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/contacts-
> AtoB-maxPae10
Found 17 residue or atom pairs within distance 3 with pae <= 10
> alphafold contacts /A toAtoms /B maxPae 5 outputFile
> /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/contacts-
> AtoB-maxPae5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /B toAtoms /A maxPae 5 outputFile
> /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/contacts-
> BtoA-maxPae5
Found 0 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /B toAtoms /A maxPae 10
Found 11 residue or atom pairs within distance 3 with pae <= 10
> alphafold contacts /A toAtoms /B maxPae 5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> show sel surfaces
[Repeated 1 time(s)]
> help help:user/commands/interfaces.html#diagram
> hide #1.2 models
> hide #1.3 models
> select subtract #1.2
1459 atoms, 172 residues, 3 models selected
> select subtract #1.3
1 model selected
> show cartoons
> hide surfaces
[Repeated 1 time(s)]
> ~hbonds
> hide atoms
> show #1.2 models
> hide #1.2 models
> hide atoms
> hide surfaces
> show cartoons
> hide #1.1 models
> show #1.1 models
> color (#!1 & sel) magenta
> select subtract #1.2
1 model selected
> color (#!1 & sel) cyan
> color (#!1 & sel) dim gray
> color (#!1 & sel) white
> select subtract #1.3
1 model selected
> show #1.3 models
> hide #1.3 models
> select add #1.3
5672 atoms, 724 residues, 1 model selected
> select subtract #1.3
1 model selected
> select add #1.2
9913 atoms, 1266 residues, 1 model selected
> select subtract #1.2
1 model selected
> color #1.2 #ff00ff3e
> color #1.2 #ff00ffa8
> show #1.2 models
> color #1 #ff00ff80
> color #1 magenta
[Repeated 1 time(s)]
> color #1.1 #f7d0d8ff models
> close #1.2
> close
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/fold_full_length_par3_and_psd95_full_data_0.json
> format pae
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/hannacaiola/Library/CloudStorage/Box-
Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/fold_full_length_par3_and_psd95_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/fold_full_length_par3_and_psd95_model_0.cif
> format mmcif
Chain information for fold_full_length_par3_and_psd95_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> alphafold contacts /A toAtoms /B maxPae 5
Structure fold_full_length_par3_and_psd95_model_0.cif #1 does not have PAE
data opened
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-FL_PSD95-FL/fold_full_length_par3_and_psd95_full_data_0.json
Opened AlphaFold PAE with values for 1990 residues and atoms
> alphafold contacts /A toAtoms /B maxPae 5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Find Cavities"
> kvfinder replace false
77 cavities found for fold_full_length_par3_and_psd95_model_0.cif #1
fold_full_length_par3_and_psd95_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.7 | | 7742.3 | 5073.72 | 35844 | 9.69 | 2.43
1.2.57 | | 2500.85 | 1746.59 | 11578 | 7.85 | 2.35
1.2.24 | | 816.48 | 566.87 | 3780 | 5.97 | 1.85
1.2.46 | | 761.62 | 567.23 | 3526 | 8.76 | 2.5
1.2.64 | | 623.16 | 647.23 | 2885 | 9.62 | 3.22
1.2.49 | | 538.7 | 379.21 | 2494 | 7.4 | 1.31
1.2.17 | | 242.14 | 261.02 | 1121 | 6.21 | 2.36
1.2.66 | | 231.98 | 157.58 | 1074 | 4.02 | 1.24
1.2.59 | | 216 | 140.91 | 1000 | 2.68 | 0.68
1.2.38 | | 178.63 | 151.85 | 827 | 2.55 | 0.66
1.2.4 | | 162.65 | 142.84 | 753 | 3 | 0.89
1.2.65 | | 158.11 | 148.43 | 732 | 1.7 | 0.42
1.2.74 | | 135.65 | 139.9 | 628 | 4.8 | 1.59
1.2.52 | | 89.42 | 106.04 | 414 | 0 | 0
1.2.61 | | 85.97 | 94.17 | 398 | 3 | 0.89
1.2.6 | | 68.26 | 92.92 | 316 | 0 | 0
1.2.1 | | 65.66 | 58.62 | 304 | 2.47 | 0.71
1.2.5 | | 65.23 | 63.54 | 302 | 1.47 | 0.41
1.2.44 | | 61.13 | 87.02 | 283 | 0 | 0
1.2.27 | | 55.08 | 72.37 | 255 | 3.55 | 1.28
1.2.55 | | 49.46 | 62.04 | 229 | 3.65 | 1.29
1.2.47 | | 44.93 | 47.9 | 208 | 2.16 | 0.59
1.2.56 | | 42.77 | 52.03 | 198 | 3.45 | 1.35
1.2.3 | | 42.12 | 60.5 | 195 | 1.9 | 0.42
1.2.75 | | 34.34 | 20.47 | 159 | 1.2 | 0.24
1.2.60 | | 33.26 | 54.73 | 154 | 1.34 | 0.29
1.2.71 | | 28.51 | 32.27 | 132 | 1.8 | 0.48
1.2.31 | | 28.3 | 43.5 | 131 | 3.23 | 1.44
1.2.62 | | 28.3 | 52.36 | 131 | 2.16 | 0.8
1.2.19 | | 28.08 | 38.26 | 130 | 1.04 | 0.23
1.2.50 | | 25.7 | 39.21 | 119 | 1.34 | 0.39
1.2.11 | | 25.27 | 44.31 | 117 | 3.23 | 1.33
1.2.40 | | 25.06 | 31.26 | 116 | 1.2 | 0.21
1.2.69 | | 24.62 | 45.81 | 114 | 0 | 0
1.2.23 | | 22.9 | 41.28 | 106 | 0 | 0
1.2.76 | | 22.03 | 29.76 | 102 | 1.8 | 0.53
1.2.53 | | 21.82 | 28.73 | 101 | 1.7 | 0.63
1.2.45 | | 21.6 | 39.67 | 100 | 2.24 | 0.91
1.2.28 | | 20.74 | 41.19 | 96 | 0 | 0
1.2.41 | | 20.74 | 35.61 | 96 | 2.4 | 0.86
1.2.33 | | 20.52 | 36.87 | 95 | 2.16 | 0.67
1.2.25 | | 19.66 | 22.57 | 91 | 1.47 | 0.43
1.2.18 | | 19.01 | 38.34 | 88 | 0 | 0
1.2.9 | | 17.28 | 36.68 | 80 | 0 | 0
1.2.63 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.39 | | 16.63 | 16.71 | 77 | 0.6 | 0.08
1.2.2 | | 16.2 | 30.37 | 75 | 0.85 | 0.21
1.2.21 | | 15.98 | 22.95 | 74 | 1.34 | 0.44
1.2.15 | | 15.77 | 15.33 | 73 | 0.85 | 0.17
1.2.68 | | 15.34 | 23.78 | 71 | 1.34 | 0.31
1.2.32 | | 14.26 | 13.3 | 66 | 0.85 | 0.13
1.2.42 | | 13.18 | 13.98 | 61 | 0.6 | 0.13
1.2.36 | | 12.74 | 15.83 | 59 | 0.6 | 0.18
1.2.13 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.29 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.30 | | 12.31 | 17.49 | 57 | 0.6 | 0.09
1.2.37 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.51 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.54 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.67 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.70 | | 12.31 | 22.36 | 57 | 1.8 | 0.69
1.2.77 | | 12.31 | 18.65 | 57 | 1.34 | 0.37
1.2.58 | | 12.1 | 20.55 | 56 | 1.2 | 0.43
1.2.16 | | 11.88 | 27.62 | 55 | 2.16 | 1.18
1.2.8 | | 10.58 | 19.36 | 49 | 0.6 | 0.18
1.2.43 | | 10.37 | 23.28 | 48 | 1.7 | 0.74
1.2.12 | | 9.07 | 17.94 | 42 | 0.85 | 0.28
1.2.10 | | 8.42 | 13.39 | 39 | 0.6 | 0.06
1.2.73 | | 8.21 | 19.1 | 38 | 0.6 | 0.16
1.2.20 | | 7.78 | 16.64 | 36 | 0.6 | 0.07
1.2.35 | | 7.34 | 15.78 | 34 | 1.2 | 0.36
1.2.22 | | 6.91 | 16.54 | 32 | 0.6 | 0.11
1.2.34 | | 6.48 | 12.95 | 30 | 0.6 | 0.16
1.2.14 | | 6.26 | 15.73 | 29 | 0.85 | 0.41
1.2.26 | | 5.62 | 10.44 | 26 | 0.6 | 0.09
1.2.48 | | 5.62 | 11.34 | 26 | 0.6 | 0.18
1.2.72 | | 5.18 | 12.28 | 24 | 0.85 | 0.37
Populating font family aliases took 60 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> color bychain
> close #1.2
> show atoms
> hide atoms
> interfaces ~solvent
1 buried areas: A B 9107
> show sel surfaces
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> color (#!1 & sel) light gray
> select subtract #1.2
1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> view orient
> ui tool show "Side View"
> color #1.1 #2ceb00ff models
> color #1.1 #30ff00ff models
> hide #1.2 models
> select add #1.2
9913 atoms, 1266 residues, 1 model selected
> set bgColor white
> color #1.2 #ff40ffff
> color (#!1 & sel) magenta
> color #1.2 #00fdffff
> color sel cyan
> select add #1
15585 atoms, 15884 bonds, 3 pseudobonds, 1990 residues, 2 models selected
> select subtract #1
1 model selected
> close #1.2
> set bgColor gray
> select add #1.1
3 pseudobonds, 1 model selected
> select subtract #1.1
Nothing selected
> view orient
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_full_length_par3_and_psd95_model_0.cif_A SES surface
#1.2: minimum, -19.12, mean -0.58, maximum 15.01
Coulombic values for fold_full_length_par3_and_psd95_model_0.cif_B SES surface
#1.3: minimum, -18.22, mean -2.77, maximum 17.37
To also show corresponding color key, enter the above coulombic command and
add key true
> view orient
> hide #1.1 models
> show #1.1 models
> view orient
> hide #1.2 models
> hide #1.3 models
> set bgColor white
> color (#!1 & sel) purple
> color (#!1 & sel) cornflower blue
> color (#!1 & sel) medium blue
> color (#!1 & sel) forest green
> color (#!1 & sel) purple
> color (#!1 & sel) cornflower blue
> color (#!1 & sel) forest green
> color #1.1 #ff9300ff models
> hide #1.1 models
> show #1.1 models
> alphafold contacts /A toAtoms /B maxPae 5 radius 5
Found 0 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5 radius 5
Found 0 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> view orient
> alphafold contacts /A toAtoms /B maxPae 5 radius 5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5 radius 2
Found 3 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5 radius 1
Found 3 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5 radius .75
Found 3 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5 radius .2
Found 3 residue or atom pairs within distance 3 with pae <= 5
> alphafold contacts /A toAtoms /B maxPae 5 radius .5
Found 3 residue or atom pairs within distance 3 with pae <= 5
> select clear
> color #1.1 #ff9300ff models
> color #1.1 #76d6ffff models
> color #1.1 #73fdffff models
> color #1.1 #0433ffff models
> color #1.1 #ff2600ff models
> color #1.1 #ff9300ff models
> color #1.1 #ff7e79ff models
> color #1.1 #ff9300ff models
> color #1.1 #ff7e79ff models
> color #1.1 #ff9300ff models
> view orient
> toolshed show
> label #1.1#!1 text "{0.name} {0.number}{0.insertion_code}"
> close #1.4
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select
> /A:23-37,65-67,129-133,224-227,267-270,293-305,316-337,454-458,480-489,540-542,572-576,598-609,677-680,801-812,827-829,833-842,908-910,912-925,930-934,960-998,1060-1076,1115-1121,1123-1128,1187-1208,1249-1254
2082 atoms, 2075 bonds, 249 residues, 1 model selected
> select subtract #1.2
1 model selected
> ui mousemode right "link markers"
[Repeated 2 time(s)]
> view orient
> ribscale 1.5
Unknown command: ribscale 1.5
Unsupported scale factor (0.000000) detected on Display1
[Repeated 3 time(s)]
> ui mousemode right translate
> ui mousemode right zoom
> show #1.2 models
> show #1.3 models
> hide #1.2 models
> hide #1.3 models
> alphafold contacts /A toAtoms /B maxPae 10 radius .5
Found 17 residue or atom pairs within distance 3 with pae <= 10
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-C/fold_par3c_e_and_psd95_c_term_model_0.cif
Chain information for fold_par3c_e_and_psd95_c_term_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #!1 models
> hide #1.1 models
> color #2 bychain
> alphafold contacts /A toAtoms /B maxPae 5 radius .5
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-C/fold_par3c_e_and_psd95_c_term_full_data_0.json
Opened AlphaFold PAE with values for 960 residues and atoms
> color #2/A:55 lime
> color #2/B:168 magenta
> alphafold contacts /A toAtoms /B maxPae 10 radius .5
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> close #1
> alphafold contacts /A toAtoms /B maxPae 10 radius .5
Found 5 residue or atom pairs within distance 3 with pae <= 10
> color bychain
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-N/fold_par3c_e_and_psd95_n_term_model_0.cif
Chain information for fold_par3c_e_and_psd95_n_term_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #1 models
> close #2
> show #1 models
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-N/fold_par3c_e_and_psd95_n_term_full_data_0.json
Opened AlphaFold PAE with values for 1058 residues and atoms
> alphafold contacts /A toAtoms /B maxPae 10 radius .5
Found 6 residue or atom pairs within distance 3 with pae <= 10
> color bychain
> show atoms
> hide atoms
> close #1
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-FL/fold_par3c_e_and_full_length_psd95_model_0.cif
Chain information for fold_par3c_e_and_full_length_psd95_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-FL/fold_par3c_e_and_full_length_psd95_full_data_0.json
Opened AlphaFold PAE with values for 1371 residues and atoms
> alphafold contacts /A toAtoms /B maxPae 10 radius .5
Found 4 residue or atom pairs within distance 3 with pae <= 10
> alphafold contacts /B toAtoms /A maxPae 10 radius .5
Found 9 residue or atom pairs within distance 3 with pae <= 10
> select /A
5672 atoms, 5789 bonds, 724 residues, 1 model selected
> select clear
> alphafold contacts /B toAtoms /A maxPae 10 radius .5 browse
Expected a keyword
> alphafold contacts /B toAtoms /A maxPae 10 radius .5 outputFile
> /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-FL/contacts_BtoA_maxPAE10
Found 9 residue or atom pairs within distance 3 with pae <= 10
> show atoms
> hide surfaces
> hide cartoons
> alphafold contacts /B toAtoms /A maxPae 10 radius .5
Found 9 residue or atom pairs within distance 3 with pae <= 10
> hide atoms
> show surfaces
> lighting simple
> lighting soft
> lighting flat
> lighting simple
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_par3c_e_and_full_length_psd95_model_0.cif_A SES
surface #1.2: minimum, -35.71, mean -2.81, maximum 11.18
Coulombic values for fold_par3c_e_and_full_length_psd95_model_0.cif_B SES
surface #1.3: minimum, -19.71, mean -0.57, maximum 16.81
To also show corresponding color key, enter the above coulombic command and
add key true
> color byhetero
> color bychain
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> hide cartoons
> hide surfaces
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 10822 atom styles
> style sphere
Changed 10822 atom styles
> style ball
Changed 10822 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball
Changed 10822 atom styles
> style sphere
Changed 10822 atom styles
> style sphere
Changed 10822 atom styles
> style stick
Changed 10822 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides tube/slab shape box
> nucleotides ladder
> style ball
Changed 10822 atom styles
> style sphere
Changed 10822 atom styles
> style stick
Changed 10822 atom styles
> nucleotides ladder
[Repeated 1 time(s)]
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball
Changed 10822 atom styles
> style sphere
Changed 10822 atom styles
> style sphere
Changed 10822 atom styles
> hide atoms
> show cartoons
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> hide #1.2 models
> show #1.2 models
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> show #1.3 models
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/Alphafold3/Par3c-E_PSD95-FL/fold_par3c_e_and_full_length_psd95_model_0.cif
Chain information for fold_par3c_e_and_full_length_psd95_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #!1 models
> color #2 bychain
> show #2 surfaces
> volume style mesh
No volumes specified
> transparency #2.1-2 50
> volume showOutlineBox true
No volumes specified
> select add #2
10822 atoms, 11033 bonds, 1371 residues, 1 model selected
> volume showOutlineBox true
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume hide
No volumes specified
> volume hide
No volumes specified
> hide #!2 models
> select subtract #2
2 models selected
> show #!1 models
> volume style image
No volumes specified
> select add #1
10822 atoms, 11033 bonds, 9 pseudobonds, 1371 residues, 2 models selected
> transparency sel 50
> select subtract #1
2 models selected
> select add #1.1
9 pseudobonds, 1 model selected
> select add #1
10822 atoms, 11033 bonds, 9 pseudobonds, 1371 residues, 2 models selected
> select subtract #1
2 models selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> color #2.1 #7b68ee38
> color #2.1 #7b68ee52
> color #2.1 #7b68ee4d
> show #2.2 models
> color #2.2 #f080804d
> hide #2.2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> volume hide
No volumes specified
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style image
No volumes specified
> volume planes z style image imageMode "full region"
No volumes specified
> show #!1 models
> hide #!1 models
> show #!1 models
> color #2 #7b68ee7f
> color #2 #7b68ee12
> color #2 #7b68ee00
> color #2 #7b68ee48
> color #2 mediumslateblue
> color #2 #7b68ee00
[Repeated 1 time(s)]
> color #2 #7b68ee80
> color #2 #7b68ee50
[Repeated 1 time(s)]
> color #2 #7b68ee4c
> color #2 #7b68ee4d
> color #2.1 #008f00ff
> color #2.1 #008f003b
> color #2.1 #008f0043
> color #2.1 #008f004b
> color #2.1 #008f004d
> color #2 #008f00ff
> color #2 #008f0080
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1 black
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> undo
[Repeated 9 time(s)]
> color #2.1 #9437ffff
> color #2.1 #7a81ffff
> color #2 #ebebebff
> color #2 #009193ff
> color #2 #009051ff
> color #2 #4f8f00ff
> color #2 #00fdffff
> color #2 #009051ff
> color #2 #009193ff
> hide #2.1 models
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A
Alignment identifier is 1
> sequence chain #1/B #2/B
Alignment identifier is 2
> close #2
> select
> /A:61-69,77-81,94-99,116-120,143-151,157-164,172-176,189-194,211-215,238-245,312-317,325-329,336-341,357-362,385-392,431-435,459-464,470-475,485-489,523-530,537-540,598-604,607-612,646-650,690-692,715-719
1303 atoms, 1309 bonds, 157 residues, 1 model selected
> select /B:1-45
349 atoms, 355 bonds, 45 residues, 1 model selected
> select /B:1-569
4509 atoms, 4585 bonds, 569 residues, 1 model selected
> select /B:604-647
357 atoms, 370 bonds, 44 residues, 1 model selected
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> color (#!1 & sel) #942193ff
> color (#!1 & sel) #ff40ffff
> color (#!1 & sel) #ff85ffff
> color (#!1 & sel) #ff8ad8ff
> color (#!1 & sel) #ff85ffff
> color (#!1 & sel) #f39cf9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #eba0f9ff
> color (#!1 & sel) #e4a3f9ff
> color (#!1 & sel) #dda4f9ff
> color (#!1 & sel) #daa5f9ff
> color (#!1 & sel) #d7a6f9ff
> color (#!1 & sel) #d5a6f9ff
> color (#!1 & sel) #d2a7f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #cfa7f9ff
> color (#!1 & sel) #cda7f9ff
> color (#!1 & sel) #cba7f9ff
> color (#!1 & sel) #c9a7f9ff
> color (#!1 & sel) #c7a7f9ff
> color (#!1 & sel) #c6a6f9ff
> color (#!1 & sel) #c39ef9ff
> color (#!1 & sel) #c296f9ff
> color (#!1 & sel) #c28cf9ff
> color (#!1 & sel) #c087f9ff
> color (#!1 & sel) #bd80f9ff
> color (#!1 & sel) #bb7cf9ff
> color (#!1 & sel) #b877f9ff
> color (#!1 & sel) #b774f9ff
> color (#!1 & sel) #b571f9ff
> color (#!1 & sel) #b36bf9ff
> color (#!1 & sel) #b169f9ff
> color (#!1 & sel) #b066f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #b166f9ff
> color (#!1 & sel) #b467f9ff
> color (#!1 & sel) #b867f9ff
> color (#!1 & sel) #bb67f9ff
> color (#!1 & sel) #bd68f9ff
> color (#!1 & sel) #bf68f9ff
> color (#!1 & sel) #c168f9ff
> color (#!1 & sel) #c46af9ff
> color (#!1 & sel) #c66af9ff
> color (#!1 & sel) #c86bf9ff
> color (#!1 & sel) #c96af9ff
> color (#!1 & sel) #ca6af9ff
> color (#!1 & sel) #cb6af9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #cc6af9ff
> color (#!1 & sel) #cf69f9ff
> color (#!1 & sel) #d069f9ff
> color (#!1 & sel) #d368f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d568f9ff
> color (#!1 & sel) #d567f9ff
> color (#!1 & sel) #d667f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d767f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d867f9ff
> color (#!1 & sel) #d866f9ff
> color (#!1 & sel) #d765f9ff
> color (#!1 & sel) #d663f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d561f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d660f9ff
> color (#!1 & sel) #d55ff9ff
> color (#!1 & sel) #d55ef9ff
> color (#!1 & sel) #d55df9ff
> color (#!1 & sel) #d55cf9ff
> color (#!1 & sel) #d45bf9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d45af9ff
> color (#!1 & sel) #d459f9ff
> color (#!1 & sel) #d458f9ff
> color (#!1 & sel) #d457f9ff
> color (#!1 & sel) #d455f9ff
> color (#!1 & sel) #d454f9ff
> color (#!1 & sel) #d453f9ff
> color (#!1 & sel) #d452f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d451f9ff
[Repeated 2 time(s)]
> color (#!1 & sel) #d551f9ff
> color (#!1 & sel) #d753f9ff
> color (#!1 & sel) #d954f9ff
> color (#!1 & sel) #db56f9ff
> color (#!1 & sel) #df5af9ff
> color (#!1 & sel) #e25cf9ff
> color (#!1 & sel) #e65ff9ff
> color (#!1 & sel) #e861f9ff
> color (#!1 & sel) #e962f9ff
> color (#!1 & sel) #eb66f9ff
> color (#!1 & sel) #ed6bf9ff
> color (#!1 & sel) #ed6df9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ed6ff9ff
> color (#!1 & sel) #ed70f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ec70f9ff
> color (#!1 & sel) #ec6ff9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #eb6ff9ff
> color (#!1 & sel) #ea6ff9ff
> color (#!1 & sel) #e86ff9ff
> color (#!1 & sel) #e770f9ff
> color (#!1 & sel) #e670f9ff
> color (#!1 & sel) #e571f9ff
> color (#!1 & sel) #e372f9ff
> color (#!1 & sel) #e272f9ff
> color (#!1 & sel) #dd74f9ff
> color (#!1 & sel) #db75f9ff
> color (#!1 & sel) #da75f9ff
> color (#!1 & sel) #d975f9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d774f9ff
> color (#!1 & sel) #d574f9ff
> color (#!1 & sel) #d171f9ff
> color (#!1 & sel) #cd6ff9ff
> color (#!1 & sel) #c96af9ff
> color (#!1 & sel) #c765f9ff
> color (#!1 & sel) #c35ff9ff
> color (#!1 & sel) #c058f9ff
> color (#!1 & sel) #be54f9ff
> color (#!1 & sel) #bc50f9ff
[Repeated 2 time(s)]
> color (#!1 & sel) #bd53f9ff
> color (#!1 & sel) #c25cf9ff
> color (#!1 & sel) #c45ff9ff
> color (#!1 & sel) #c663f9ff
> color (#!1 & sel) #c767f9ff
> color (#!1 & sel) #c96af9ff
> color (#!1 & sel) #cc6cf9ff
> color (#!1 & sel) #cd6ef9ff
> color (#!1 & sel) #ce6ef9ff
> color (#!1 & sel) #ce6ff9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d06ef9ff
> color (#!1 & sel) #d26ef9ff
> color (#!1 & sel) #d36ef9ff
> color (#!1 & sel) #d46df9ff
[Repeated 2 time(s)]
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-477
3660 atoms, 3734 bonds, 477 residues, 1 model selected
> select /A:1-724
5672 atoms, 5789 bonds, 724 residues, 1 model selected
> color (#!1 & sel) #009193ff
> color (#!1 & sel) #00fdffff
> color (#!1 & sel) #73fdffff
> color (#!1 & sel) #00fdffff
> color (#!1 & sel) #0096ffff
> select /B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> color (#!1 & sel) #ff2f92ff
> color (#!1 & sel) #ff2600ff
> color (#!1 & sel) #ff2f92ff
> select add #1
10822 atoms, 11033 bonds, 9 pseudobonds, 1371 residues, 3 models selected
> select subtract #1
2 models selected
> color #1.1 #00f900ff models
> color #1.1 #ff7e79ff models
> color #1.1 black models
> color #1.1 white models
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> color #1.1 #00fa92ff models
> color #1.1 #008f00ff models
> set bgColor white
> set bgColor #ffffff00
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> color #1.1 white models
> view orient
> set bgColor white
> set bgColor #ffffff00
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> select
> /A:104-108,130-139,199-203,225-233,248-251,304-306,346-350,372-380,394-417,441-443,491-506,544-554,586-594,613-621,632-640,655-661,667-687,697-711
1416 atoms, 1415 bonds, 174 residues, 1 model selected
> select /B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> color #1.1 #ff2600ff models
> hide #1.1 models
> show #1.1 models
> undo
[Repeated 3 time(s)]
> select add #1
10822 atoms, 11033 bonds, 9 pseudobonds, 1371 residues, 3 models selected
> select subtract #1
2 models selected
> select /B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> color #1.1 #ffd479ff models
> select add #1
10822 atoms, 11033 bonds, 9 pseudobonds, 1371 residues, 3 models selected
> select subtract #1
2 models selected
> select /B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> color (#!1 & sel) #ff2f92ff
> color (#!1 & sel) #0096ffff
> color (#!1 & sel) #5e5e5eff
> color (#!1 & sel) #919191ff
> color (#!1 & sel) #a9a9a9ff
> color (#!1 & sel) #424242ff
> color (#!1 & sel) #5e5e5eff
> color (#!1 & sel) #008f00ff
> select add #1
10822 atoms, 11033 bonds, 9 pseudobonds, 1371 residues, 3 models selected
> select subtract #1
2 models selected
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> view orient
> graphics silhouettes false
> color #1.1 #ff2f92ff models
> view orient
> view
> view orient
> view
> ui tool show "Side View"
> view orient
> select
> /A:61-69,77-81,94-99,116-120,143-151,157-164,172-176,189-194,211-215,238-245,312-317,325-329,336-341,357-362,385-392,431-435,459-464,470-475,485-489,523-530,537-540,598-604,607-612,646-650,690-692,715-719
1303 atoms, 1309 bonds, 157 residues, 1 model selected
> select /B
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> hide sel cartoons
> select /A:1-477
3660 atoms, 3734 bonds, 477 residues, 1 model selected
> select /A:381-382
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:145-382
1799 atoms, 1833 bonds, 238 residues, 1 model selected
> select /A:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:2-146
1097 atoms, 1117 bonds, 145 residues, 1 model selected
> select /A:1-477
3660 atoms, 3734 bonds, 477 residues, 1 model selected
> select clear
> select sequence
> YEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRR
673 atoms, 682 bonds, 89 residues, 1 model selected
> volume style surface
No volumes specified
> volume style image
No volumes specified
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> surface :A[63-151]
Expected an atoms specifier or a keyword
> split
Split fold_par3c_e_and_full_length_psd95_model_0.cif (#1) into 2 models
Chain information for fold_par3c_e_and_full_length_psd95_model_0.cif A #1.1
---
Chain | Description
A | No description available
Chain information for fold_par3c_e_and_full_length_psd95_model_0.cif B #1.2
---
Chain | Description
B | No description available
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> show atoms
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> help help:user/menu.html#named-selections
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A
Alignment identifier is 1.1/A
> sequence chain #1.2/B
Alignment identifier is 1.2/B
> select
> #1.1/A:104-108,130-139,199-203,225-233,248-251,304-306,346-350,372-380,394-417,441-443,491-506,544-554,586-594,613-621,632-640,655-661,667-687,697-711
1416 atoms, 1415 bonds, 174 residues, 1 model selected
> select #1.1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:1-66
519 atoms, 531 bonds, 66 residues, 1 model selected
> select #1.1/A:47
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.1/A:45-47
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #1.1/A:46-47
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1.1/A:46-47
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1.1/A:50
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.1/A:48-50
23 atoms, 24 bonds, 3 residues, 1 model selected
> select #1.1/A:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:51-52
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1.1/A:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:53-55
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #1.1/A:60
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:57-60
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #1.1/A:56
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1.1/A:55-56
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1.1/A:56-57
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #1.1/A:1-57
442 atoms, 453 bonds, 57 residues, 1 model selected
> select #1.1/A:59
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1.1/A:1-59
455 atoms, 466 bonds, 59 residues, 1 model selected
> hide sel surfaces
[Repeated 1 time(s)]
> show sel atoms
> show sel cartoons
[Repeated 3 time(s)]
> hide sel surfaces
> style sel stick
Changed 455 atom styles
> hide sel atoms
> show sel cartoons
> select #1.1/A:369-370
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1.1/A:314-370
410 atoms, 414 bonds, 57 residues, 1 model selected
> select #1.1/A:268
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:160-268
814 atoms, 829 bonds, 109 residues, 1 model selected
> select #1.1/A:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:156-160
42 atoms, 41 bonds, 5 residues, 1 model selected
> select #1.1/A:320-321
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1.1/A:317-321
38 atoms, 38 bonds, 5 residues, 1 model selected
> select #1.1/A:315
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:312-315
37 atoms, 36 bonds, 4 residues, 1 model selected
> select #1.1/A:272
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:269-272
33 atoms, 32 bonds, 4 residues, 1 model selected
> select #1.1/A:283-284
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #1.1/A:268-284
134 atoms, 137 bonds, 17 residues, 1 model selected
> select #1.1/A:318
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:260-318
476 atoms, 488 bonds, 59 residues, 1 model selected
> select #1.1/A:260
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:255-260
47 atoms, 49 bonds, 6 residues, 1 model selected
> select #1.1/A:264
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.1/A:260-264
40 atoms, 40 bonds, 5 residues, 1 model selected
> select #1.1/A:264
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.1/A:264-267
37 atoms, 38 bonds, 4 residues, 1 model selected
> select #1.1/A:267
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:267-302
283 atoms, 291 bonds, 36 residues, 1 model selected
> select #1.1/A:267
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:267-291
191 atoms, 197 bonds, 25 residues, 1 model selected
> select #1.1/A:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:152-155
28 atoms, 29 bonds, 4 residues, 1 model selected
> select #1.1/A:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:152-159
61 atoms, 62 bonds, 8 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #1.1/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:205-206
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #1.1/A:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:245-246
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1.1/A:244-245
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1.1/A:245-309
508 atoms, 523 bonds, 65 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select
> #1.1/A:104-108,130-139,199-203,225-233,248-251,304-306,346-350,372-380,394-417,441-443,491-506,544-554,586-594,613-621,632-640,655-661,667-687,697-711
1416 atoms, 1415 bonds, 174 residues, 1 model selected
> select #1.1/A:401
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:401-402
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1.1/A:401
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:401-425
187 atoms, 187 bonds, 25 residues, 1 model selected
> select #1.1/A:401
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:401-429
222 atoms, 223 bonds, 29 residues, 1 model selected
> hide sel atoms
> select
> #1.1/A:104-108,130-139,199-203,225-233,248-251,304-306,346-350,372-380,394-417,441-443,491-506,544-554,586-594,613-621,632-640,655-661,667-687,697-711
1416 atoms, 1415 bonds, 174 residues, 1 model selected
> select #1.1/A:496
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:496
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:496
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.1/A:496-532
300 atoms, 305 bonds, 37 residues, 1 model selected
> hide sel atoms
> select #1.1/A:712
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.1/A:712-724
110 atoms, 114 bonds, 13 residues, 1 model selected
> hide sel atoms
> select sequence
> GFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVE
546 atoms, 560 bonds, 66 residues, 1 model selected
> select clear
> select sequence
> YARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDL
1459 atoms, 1488 bonds, 179 residues, 1 model selected
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> select
> #1.2/B:28-34,38-46,53-63,70-73,92-95,174-176,180-193,208-223,341-383,385-387,441-456,568-591,627-637
1366 atoms, 1368 bonds, 165 residues, 1 model selected
> select #1.2/B:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/B:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.2/B:1-23
170 atoms, 173 bonds, 23 residues, 1 model selected
> select #1.2/B:35
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.2/B:35-44
87 atoms, 88 bonds, 10 residues, 1 model selected
> select #1.2/B:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.2/B:51-63
98 atoms, 98 bonds, 13 residues, 1 model selected
> select #1.2/B:65-66
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1.2/B:65-73
73 atoms, 74 bonds, 9 residues, 1 model selected
> select #1.2/B:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:74-84
87 atoms, 87 bonds, 11 residues, 1 model selected
> select #1.2/B:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:85-93
73 atoms, 76 bonds, 9 residues, 1 model selected
> select #1.2/B:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:85-86
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #1.2/B:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:85-195
810 atoms, 823 bonds, 111 residues, 1 model selected
> select #1.2/B:195-196
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1.2/B:193-196
28 atoms, 27 bonds, 4 residues, 1 model selected
> select #1.2/B:171
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:134-171
289 atoms, 293 bonds, 38 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #1.2/B:133-134
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1.2/B:112-134
159 atoms, 161 bonds, 23 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select
> #1.2/B:28-34,38-46,53-63,70-73,92-95,174-176,180-193,208-223,341-383,385-387,441-456,568-591,627-637
1366 atoms, 1368 bonds, 165 residues, 1 model selected
> select
10822 atoms, 11033 bonds, 1371 residues, 3 models selected
> hide sel & #1.2 atoms
> show sel & #1.2 cartoons
> select #1.2/B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/B:57-172
862 atoms, 878 bonds, 116 residues, 1 model selected
> select
> #1.2/B:28-34,38-46,53-63,70-73,92-95,174-176,180-193,208-223,341-383,385-387,441-456,568-591,627-637
1366 atoms, 1368 bonds, 165 residues, 1 model selected
> hide #!1 models
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/fold_par3c_e_and_full_length_psd95_s799_phosphorylated/fold_par3c_e_and_full_length_psd95_s799_phosphorylated_model_0.cif
Chain information for
fold_par3c_e_and_full_length_psd95_s799_phosphorylated_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> color #2 bychain
> show #!1 models
> hide #!1 models
> view orient
> hide #2 models
> show #!1 models
> view orient
> show #2 models
> hide #2 models
> show #2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> split
Did not split fold_par3c_e_and_full_length_psd95_model_0.cif A, has only one
piece
Did not split fold_par3c_e_and_full_length_psd95_model_0.cif B, has only one
piece
Split fold_par3c_e_and_full_length_psd95_s799_phosphorylated_model_0.cif (#2)
into 2 models
Chain information for
fold_par3c_e_and_full_length_psd95_s799_phosphorylated_model_0.cif A #2.1
---
Chain | Description
A | No description available
Chain information for
fold_par3c_e_and_full_length_psd95_s799_phosphorylated_model_0.cif B #2.2
---
Chain | Description
B | No description available
> hide #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> ui tool show Matchmaker
> matchmaker #2.2 to #1.2
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_par3c_e_and_full_length_psd95_model_0.cif B, chain B (#1.2)
with fold_par3c_e_and_full_length_psd95_s799_phosphorylated_model_0.cif B,
chain B (#2.2), sequence alignment score = 3002.1
RMSD between 33 pruned atom pairs is 0.963 angstroms; (across all 647 pairs:
74.449)
> select add #1.2
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> select subtract #1.2
Nothing selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #2.2 models
> show #2.2 models
> hide #1.2 models
> hide #2.2 models
> show #1.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> show #1.2#2.2 surfaces
> hide #!2.2 models
> select add #1.2
5150 atoms, 5244 bonds, 647 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select subtract #1.2
1 model selected
> show #1.1 models
> select add #1.1
5672 atoms, 5789 bonds, 724 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select subtract #1.1
1 model selected
> color #1.2 #ff40ffff
> select #1.2/B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/B:57-73
128 atoms, 129 bonds, 17 residues, 1 model selected
> select add #1.2
5150 atoms, 5244 bonds, 647 residues, 2 models selected
> select subtract #1.2
1 model selected
> hide #!1 models
> show #2.1 models
> show #!2.2 models
> hide #!2.2 models
> select sequence
> YEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRR
1346 atoms, 1364 bonds, 178 residues, 2 models selected
> show sel & #2.1 surfaces
> select sequence
> EIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVA
1254 atoms, 1270 bonds, 170 residues, 2 models selected
> show sel & #!2.1 surfaces
> select sequence
> EPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF
1370 atoms, 1390 bonds, 182 residues, 2 models selected
> show sel & #!2.1 surfaces
> select sequence
> GFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVE
1092 atoms, 1120 bonds, 132 residues, 2 models selected
> show sel & #!2.1 surfaces
> select sequence
> YARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDL
2918 atoms, 2976 bonds, 358 residues, 2 models selected
> show sel & #!2.1 surfaces
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 surfaces
> show #!2.1 models
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/fold_par3c_e_and_full_length_psd95_s799_phosphorylated/fold_par3c_e_and_full_length_psd95_s799_phosphorylated_full_data_0.json
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 768, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2154, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
pae = alphafold_pae(session, file = path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1457, in alphafold_pae
structure = _guess_pae_associated_structure(session, file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1516, in
_guess_pae_associated_structure
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1517, in <listcomp>
if hasattr(m, 'filename') and dirname(m.filename) == dirname(pae_path)]
^^^^^^^^^^^^^^^^^^^
File "<frozen posixpath>", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
> open /Users/hannacaiola/Library/CloudStorage/Box-
> Box/Zhang_Lab/Hanna/_Par3/Alphafold/fold_par3c_e_and_full_length_psd95_s799_phosphorylated/fold_par3c_e_and_full_length_psd95_s799_phosphorylated_full_data_0.json
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 768, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2154, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
pae = alphafold_pae(session, file = path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1457, in alphafold_pae
structure = _guess_pae_associated_structure(session, file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1516, in
_guess_pae_associated_structure
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1517, in <listcomp>
if hasattr(m, 'filename') and dirname(m.filename) == dirname(pae_path)]
^^^^^^^^^^^^^^^^^^^
File "<frozen posixpath>", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN73LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 24 days, 8 hours, 34 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
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: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 2.5.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.3.3
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
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: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.3.0
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.2
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.3
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → AlphaFold JSON drag and drop: pae_path is None |
comment:2 by , 3 weeks ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Fixed.
User opened AlphaFold 3 structure then split it by chain then tried to open the PAE .json file for the structure. The code assumed mol.filename was not None, but split made the filename None. Added check for mol.filename = None.