ChimeraX bug report submission

[amydelur@…]

The following bug report has been submitted:
Platform:        macOS-15.7.3-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
I wanted to record a spin movie for my protein, but it would not save on my desktop due to a "permission error"

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/EPAC2_F374_All_Interactions.cxs"
> format session

Log from Wed Apr 1 14:31:42 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/EPAC2_F374_All_Interactions.cxs"

Log from Mon Mar 30 12:38:07 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/Interface_Model_Cartoon_Surface.cxs"

Log from Mon Mar 30 11:50:25 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif"

Chain information for fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif"

Chain information for fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif"

Chain information for fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif"

Chain information for fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif"

Chain information for fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  
[Repeated 3 time(s)]

> set bgColor white

> cd "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/Models"

Current working directory is: /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/EPAC2-SUR1
Project/Bioinformatics/Docking/AlphaFold/Point
Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/Models  

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/Models/[NAME].pdb"

> ui tool show "Add Charges"

> view

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif (#1) chain A determined from SEQRES records  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif (#1) chain B
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif #1/A LEU 1,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif #1/B LEU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif #1/A ARG 23,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_0.cif #1/B ARG 108  
Chain-final residues that are not actual C termini:  
88 hydrogen bonds  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif (#2) chain A
determined from SEQRES records  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif (#2) chain B
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif #2/A LEU 1,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif #2/B LEU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif #2/A ARG 23,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_1.cif #2/B ARG 108  
Chain-final residues that are not actual C termini:  
85 hydrogen bonds  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif (#3) chain A
determined from SEQRES records  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif (#3) chain B
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif #3/A LEU 1,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif #3/B LEU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif #3/A ARG 23,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_2.cif #3/B ARG 108  
Chain-final residues that are not actual C termini:  
81 hydrogen bonds  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif (#4) chain A
determined from SEQRES records  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif (#4) chain B
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif #4/A LEU 1,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif #4/B LEU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif #4/A ARG 23,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_3.cif #4/B ARG 108  
Chain-final residues that are not actual C termini:  
88 hydrogen bonds  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif (#5) chain A
determined from SEQRES records  
Termini for fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif (#5) chain B
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif #5/A LEU 1,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif #5/B LEU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif #5/A ARG 23,
fold_2026_03_18_epac2_f374y_sur1_zhao_model_4.cif #5/B ARG 108  
Chain-final residues that are not actual C termini:  
97 hydrogen bonds  
5275 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  

> ui tool show "Add Charges"

> view

Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1 Project/Bioinformatics/Docking/AlphaFold/Point
> Mutants/EPAC2/F374Y/fold_2026_03_18_epac2_f374y_sur1_zhao/Models/[NAME].pdb"

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> ui tool show H-Bonds

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> ui tool show H-Bonds

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hide #!2 models

> show #!3 models

> ui tool show H-Bonds

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hide #!3 models

> show #!4 models

> ui tool show H-Bonds

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> hide #!4 models

> show #!5 models

> ui tool show H-Bonds

> hbonds showDist true interModel false intraMol false intraRes false reveal
> true

0 hydrogen bonds found  

> show #!4 models

> hide #!4 models

> hide #!5 models

> show #!1 models

> close #1-5

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Models/New_Refined_Models/H-Bonds_Charges/fold_2025_05_16_10_11_model_0.cif_H-
> Bonds_Charges.pdb"

Chain information for fold_2025_05_16_10_11_model_0.cif_H-Bonds_Charges.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> surface

> transparency 80

> color target c bybfactor

Expected a keyword  

> color bfactor

2087 atoms, 131 residues, 2 surfaces, atom bfactor range 40.3 to 92.7  

> color tan target s

> transparency 80

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target c

131 residues, atom bfactor range 40.3 to 92.7  

> color bychain target s

> transparency 80

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/Interface_Model_0.tif"
> width 726 height 836 supersample 3

> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Models/New_Refined_Models/H-Bonds_Charges/fold_2025_05_16_10_11_model_1.cif_H-
> Bonds_Charges.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein
> Lab/Klein Lab Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Models/New_Refined_Models/H-Bonds_Charges/fold_2025_05_16_10_11_model_2.cif_H-
> Bonds_Charges.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein
> Lab/Klein Lab Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Models/New_Refined_Models/H-Bonds_Charges/fold_2025_05_16_10_11_model_3.cif_H-
> Bonds_Charges.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein
> Lab/Klein Lab Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Models/New_Refined_Models/H-Bonds_Charges/fold_2025_05_16_10_11_model_4.cif_H-
> Bonds_Charges.pdb"

Chain information for fold_2025_05_16_10_11_model_1.cif_H-Bonds_Charges.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for fold_2025_05_16_10_11_model_2.cif_H-Bonds_Charges.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for fold_2025_05_16_10_11_model_3.cif_H-Bonds_Charges.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for fold_2025_05_16_10_11_model_4.cif_H-Bonds_Charges.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> mmaker #2-5 to #1

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_2025_05_16_10_11_model_0.cif_H-Bonds_Charges.pdb, chain B (#1)
with fold_2025_05_16_10_11_model_1.cif_H-Bonds_Charges.pdb, chain B (#2),
sequence alignment score = 542.2  
RMSD between 100 pruned atom pairs is 0.540 angstroms; (across all 108 pairs:
1.058)  
  
Matchmaker fold_2025_05_16_10_11_model_0.cif_H-Bonds_Charges.pdb, chain B (#1)
with fold_2025_05_16_10_11_model_2.cif_H-Bonds_Charges.pdb, chain B (#3),
sequence alignment score = 536.8  
RMSD between 105 pruned atom pairs is 0.540 angstroms; (across all 108 pairs:
0.747)  
  
Matchmaker fold_2025_05_16_10_11_model_0.cif_H-Bonds_Charges.pdb, chain B (#1)
with fold_2025_05_16_10_11_model_3.cif_H-Bonds_Charges.pdb, chain B (#4),
sequence alignment score = 541.6  
RMSD between 105 pruned atom pairs is 0.466 angstroms; (across all 108 pairs:
0.767)  
  
Matchmaker fold_2025_05_16_10_11_model_0.cif_H-Bonds_Charges.pdb, chain B (#1)
with fold_2025_05_16_10_11_model_4.cif_H-Bonds_Charges.pdb, chain B (#5),
sequence alignment score = 537.4  
RMSD between 106 pruned atom pairs is 0.464 angstroms; (across all 108 pairs:
0.549)  
  

> color bfactor

10435 atoms, 655 residues, 2 surfaces, atom bfactor range 32.7 to 95.1  

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target c

655 residues, atom bfactor range 32.7 to 95.1  

> color #1-5 bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target c

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

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target c

655 residues, atom bfactor range 32.7 to 95.1  

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target c

655 residues, atom bfactor range 32.7 to 95.1  

> color bychain target s

> transparency 80

> surface

> color bychain target s

> transparency 80

> ui tool show "Color Key"

> ui mousemode right "color key"

> key pos 0.0551386,0.0490596 size 0.835417,0.0468235

> key blue-white-red :min : :max white:

> key blue:min darkorange: red:max white:

> key darkorange:min darkorange: red:max white:

> key darkorange:min yellow: red:max white:

> key darkorange:min yellow: lightskyblue:max white:

> key darkorange:min yellow: lightskyblue:max yellow:

> key darkorange:min yellow: lightskyblue:max blue:

> key darkorange:min yellow: lightskyblue: blue:

> key darkorange:min yellow: lightskyblue:5 blue:

> key darkorange:min yellow: lightskyblue:50 blue:

> key darkorange:min yellow: lightskyblue:50- blue:

> key darkorange:min yellow: lightskyblue:50-7 blue:

> key darkorange:min yellow: lightskyblue:50-70 blue:

> key darkorange:min yellow: lightskyblue:50-7 blue:

> key darkorange:min yellow: lightskyblue:50- blue:

> key darkorange:min yellow: lightskyblue:50 blue:

> key darkorange:min yellow: lightskyblue:5 blue:

> key darkorange:min yellow: lightskyblue: blue:

> key darkorange:min yellow: lightskyblue:7 blue:

> key darkorange:min yellow: lightskyblue:70 blue:

> key darkorange:min yellow: lightskyblue:70- blue:

> key darkorange:min yellow: lightskyblue:70-9 blue:

> key darkorange:min yellow: lightskyblue:70-90 blue:

> key darkorange:min yellow:5 lightskyblue:70-90 blue:

> key darkorange:min yellow:50 lightskyblue:70-90 blue:

> key darkorange:min yellow:50- lightskyblue:70-90 blue:

> key darkorange:min yellow:50-7 lightskyblue:70-90 blue:

> key darkorange:min yellow:50-70 lightskyblue:70-90 blue:

> key darkorange:< yellow:50-70 lightskyblue:70-90 blue:

> key "darkorange:< " yellow:50-70 lightskyblue:70-90 blue:

> key "darkorange:< 5" yellow:50-70 lightskyblue:70-90 blue:

> key "darkorange:< 50" yellow:50-70 lightskyblue:70-90 blue:

> key "darkorange:< 50" yellow:50-70 lightskyblue:70-90 blue:>

> key "darkorange:< 50" yellow:50-70 lightskyblue:70-90 "blue:> "

> key "darkorange:< 50" yellow:50-70 lightskyblue:70-90 "blue:> 9"

> key "darkorange:< 50" yellow:50-70 lightskyblue:70-90 "blue:> 90"

> transparency #2-5 50 target c

> transparency #2-5 100 target c

> transparency #2-5 0 target c

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/Interface_Model_Intermodel_Alignment.tif"
> width 726 height 836 supersample 3

> hide surfaces

> transparency #2-5 50 target c

> surface #1

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/Interface_Model_Intermodel_Alignment_Model_0.tif"
> width 726 height 836 supersample 3

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/Interface_Model_Cartoon_Surface.cxs"

——— End of log from Mon Mar 30 11:50:25 2026 ———

> view name session-start

opened ChimeraX session  

> hide #!2-5 target m

> select #1/B:24

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

> atoms

Unknown command: atoms  

> show atoms

> show sel atoms

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select clear

> interfaces #!1 & ~solvent

1 buried areas: B A 509  

> show sel atoms

> color sel byhetero target a

> color sel bybfactor target a

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

> color sel bfactor target a

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

> color sel bfactor

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

> color bfactor target a

10435 atoms, atom bfactor range 32.7 to 95.1  

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target c

655 residues, atom bfactor range 32.7 to 95.1  

> color bfactor palette
> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
> target a

10435 atoms, atom bfactor range 32.7 to 95.1  

> color sel byhetero target a

> undo

> select #1/B:24

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

> view sel

> ui tool show H-Bonds

> hbonds sel showDist true interModel false intraMol false intraRes false
> reveal true

0 hydrogen bonds found  

> contacts #1/B:24@C* restrict #1/A@C distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist true

No distances  

> select clear

> contacts #1/B:24@C* restrict #1/A@C distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist true

No distances  

> contacts #1/B:24@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist true

1663 distances  

> contacts #1/B:24@C* restrict #1/A@C distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist true

No distances  

> redo

[Repeated 1 time(s)]

> close #7

> contacts #1/B:24@C* restrict #1/A distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist true

47 distances  

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist true

9 distances  

> color sel byhetero target a

> color byhetero target a

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color black showDist true

9 distances  

> select #1/B:74

19 atoms, 18 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> select #1/B:24

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

> view sel

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color black showDist false

9 distances  

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist false

9 distances  

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color black showDist false

9 distances  

> clashes #1/B:24 restrict #1/A dashes

Missing "dashes" keyword's argument  

> clashes #1/B:24 restrict #1/A

No clashes  

> select clear

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color gold showDist false

9 distances  

> contacts #1/B:24@C* restrict #1/A@C* distanceOnly 5 reveal true name
> VdW_Interaction_EPAC2_F374 color dark goldenrod showDist false

9 distances  

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/EPAC2_F374_All_Interactions.cxs"

——— End of log from Mon Mar 30 12:38:07 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Color Key"

> ui mousemode right "color key"

> key delete

> select #1/B:374

Nothing selected  

> select #1/B:24

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

> label (#!1 & sel) text "EPAC2 F374"

> label (#!1 & sel) atoms attribute name

> close #1.6

> select #1/B:24

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

> label (#!1 & sel) text "EPAC2 F374"

> select #1/A:7@HB2

1 atom, 1 residue, 1 model selected  

> select #1/A:7@N

1 atom, 1 residue, 1 model selected  

> select #1/A:6@HB2

1 atom, 1 residue, 1 model selected  

> select #1/A:6@CB

1 atom, 1 residue, 1 model selected  

> select #1/A:7@OD2

1 atom, 1 residue, 1 model selected  

> select add #1/A:7@HB2

2 atoms, 1 residue, 2 models selected  

> select add #1/A:7@CB

3 atoms, 1 residue, 2 models selected  

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

> undo

> label (#!1 & sel) text "SUR1 D865"

> select #1/A:6@HB2

1 atom, 1 residue, 1 model selected  

> select #1/A:6@OG

1 atom, 1 residue, 1 model selected  

> select #1/A:7@OD2

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> undo

> show sel surfaces

> select clear

> hide #!1 surfaces

> select #1/A:6

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

> show sel surfaces

[Repeated 1 time(s)]

> label (#!1 & sel) text "SUR1 S864"

> select clear

> select #1/A:10

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label (#!1 & sel) text "SUR1 M868"

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

19 atoms, 18 bonds, 1 residue, 2 models selected  

> label (#!1 & sel) text "SUR1 I861"

> select #1/A:14

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:18

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:92@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> undo

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> undo

> select up

14 atoms, 13 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select #1/B:94

17 atoms, 17 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:25@CA

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select #1/B:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:96

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/B:48@CA

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 18 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select #1/B:19

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:16

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:17

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:21

12 atoms, 11 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:2

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:1

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

> hide sel atoms

> select #1/A:9

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:26@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> undo

> select up

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

> hide sel atoms

> select clear

> show #!1 surfaces

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/EPAC2_F374_All_Interactions.cxs"

——— End of log from Wed Apr 1 14:31:42 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Color Key"

> ui mousemode right "color key"

> ui tool show "Color Key"

> ui mousemode right "color key"

> key size 0.9,0.05000

Key is partially or completely offscreen  

> key size 0.91,0.05000

Key is partially or completely offscreen  

> key size 0.912,0.05000

Key is partially or completely offscreen  

> key size 0.9122,0.05000

Key is partially or completely offscreen  

> key size 0.91226,0.05000

Key is partially or completely offscreen  

> key size 0.91226,0.0

Key is partially or completely offscreen  

> key size 0.91226,0.04

Key is partially or completely offscreen  

> key size 0.91226,0.042

Key is partially or completely offscreen  

> key size 0.91226,0.0423

Key is partially or completely offscreen  

> key size 0.91226,0.04238

Key is partially or completely offscreen  

> key blue-white-red :min : :max white:

> key blue:min white: red:max white:<

> key blue:min white: red:max "white:< "

> key blue:min white: red:max "white:< 5"

> key blue:min white: red:max "white:< 50"

> key blue:min white: red:max "darkorange:< 50"

> key blue:min white: yellow:max "darkorange:< 50"

> key blue:min lightskyblue: yellow:max "darkorange:< 50"

> key blue:min lightskyblue: yellow:5 "darkorange:< 50"

> key blue:min lightskyblue: yellow:50 "darkorange:< 50"

> key blue:min lightskyblue: yellow:50- "darkorange:< 50"

> key blue:min lightskyblue: yellow:50-7 "darkorange:< 50"

> key blue:min lightskyblue: yellow:50-70 "darkorange:< 50"

> key blue:min lightskyblue:7 yellow:50-70 "darkorange:< 50"

> key blue:min lightskyblue:70 yellow:50-70 "darkorange:< 50"

> key blue:min lightskyblue:70- yellow:50-70 "darkorange:< 50"

> key blue:min lightskyblue:70-9 yellow:50-70 "darkorange:< 50"

> key blue:min lightskyblue:70-90 yellow:50-70 "darkorange:< 50"

> key blue:> lightskyblue:70-90 yellow:50-70 "darkorange:< 50"

> key "blue:> " lightskyblue:70-90 yellow:50-70 "darkorange:< 50"

> key "blue:> 9" lightskyblue:70-90 yellow:50-70 "darkorange:< 50"

> key "blue:> 90" lightskyblue:70-90 yellow:50-70 "darkorange:< 50"

> key pos 0.69000,0.08000

Key is partially or completely offscreen  

> key pos 0.68000,0.08000

Key is partially or completely offscreen  

> key pos 0.67000,0.08000

Key is partially or completely offscreen  

> key pos 0.66000,0.08000

Key is partially or completely offscreen  

> key pos 0.65000,0.08000

Key is partially or completely offscreen  

> key pos 0.64000,0.08000

Key is partially or completely offscreen  

> key pos 0.63000,0.08000

Key is partially or completely offscreen  

> key pos 0.62000,0.08000

Key is partially or completely offscreen  

> key pos 0.61000,0.08000

Key is partially or completely offscreen  

> key pos 0.60000,0.08000

Key is partially or completely offscreen  

> key pos 0.59000,0.08000

Key is partially or completely offscreen  

> key pos 0.58000,0.08000

Key is partially or completely offscreen  

> key pos 0.57000,0.08000

Key is partially or completely offscreen  

> key pos 0.56000,0.08000

Key is partially or completely offscreen  

> key pos 0.55000,0.08000

Key is partially or completely offscreen  

> key pos 0.54000,0.08000

Key is partially or completely offscreen  

> key pos 0.53000,0.08000

Key is partially or completely offscreen  

> key pos 0.52000,0.08000

Key is partially or completely offscreen  

> key pos 0.51000,0.08000

Key is partially or completely offscreen  

> key pos 0.50000,0.08000

Key is partially or completely offscreen  

> key pos 0.30000,0.08000

Key is partially or completely offscreen  

> key pos 0.30000,0.08000

Key is partially or completely offscreen  

> key pos 0.20000,0.08000

Key is partially or completely offscreen  

> key pos 0.10000,0.08000

Key is partially or completely offscreen  

> key pos 0.0000,0.08000

> key pos 0.05000,0.08000

> key pos 0.641572,0.700678 size 0.0271158,0.00219046

> ui tool show "Color Key"

> key size 0.9,0.00219

Key is partially or completely offscreen  

> key size 0.91,0.00219

Key is partially or completely offscreen  

> key size 0.912,0.00219

Key is partially or completely offscreen  

> key size 0.9122,0.00219

Key is partially or completely offscreen  

> key size 0.91226,0.00219

Key is partially or completely offscreen  

> key size 0.91226,0.04

Key is partially or completely offscreen  

> key size 0.91226,0.042

Key is partially or completely offscreen  

> key size 0.91226,0.0423

Key is partially or completely offscreen  

> key size 0.91226,0.04238

Key is partially or completely offscreen  

> key pos 0.63157,0.70068

Key is partially or completely offscreen  

> key pos 0.63157,0.20068

Key is partially or completely offscreen  

> key pos 0.63157,0.10068

Key is partially or completely offscreen  

> key pos 0.63157,0.5068

Key is partially or completely offscreen  

> key pos 0.63157,0.0680

Key is partially or completely offscreen  

> key pos 0.63157,0.05800

Key is partially or completely offscreen  

> key pos 0.63157,0.05000

Key is partially or completely offscreen  

> key pos 0.0,0.05000

> key pos 0.05,0.05000

> cd "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Figures"

Current working directory is: /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/EPAC2-SUR1
Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Figures  

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Figures/EPAC2_F374_Interactions.tif"
> width 1776 height 875 supersample 3

> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/EPAC2-SUR1
> Project/Bioinformatics/Docking/AlphaFold/20250516_EPAC2_SUR1_Zhao_2013_Fragments/Pics:Movie/EPAC2_F374_All_Interactions.cxs"

> movie encode /Users/AmyDeLury/Downloads/EPAC2_F374.mp4

No frames have been recorded  

> movie encode /Users/AmyDeLury/Downloads/EPAC2_F374.mp4

No frames have been recorded  

> movie record

> select clear

> movie record

Already recording a movie  

> movie stop

> select ~sel & ##selected

Nothing selected  

> ui tool show Log

> movie record

> turn

> movie stop

> movie record

> turn y 2 180

> wait 180

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

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run  
f(s)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.10.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode  
encode_op(session, output[-1], format, quality, qscale, bitrate,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op  
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding  
self.encoder.run(Status_Reporter())  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run  
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-7.0.24
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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 Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 2094.40.1.0.0 (iBridge: 23.16.12048.0.0,0)
      OS Loader Version: 583~2317

Software:

    System Software Overview:

      System Version: macOS 15.7.3 (24G419)
      Kernel Version: Darwin 24.6.0
      Time since boot: 4 days, 22 hours, 14 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

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

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    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: 14.1.18
    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
    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: 1.1.2
    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: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    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: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    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: 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
    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
    pyelftools: 0.32
    Pygments: 2.18.0
    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
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    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