Blast from AlphaFold: self.job.model_name is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "C:/Users/Asus/Downloads/ChimeraX/kif2c TAD.cxs"

Log from Thu Aug 24 12:23:29 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Asus\Downloads\ChimeraX\AlphaFold\prediction_8\best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  


> open "C:/Users/Asus/Downloads/tad domain of MLL.ent"

tad domain of MLL.ent title:  
Allosteric communication In the kix domain proceeds through dynamic Re-packing
of the hydrophobic core [more info...]  

Chain information for tad domain of MLL.ent  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | creb-binding protein
| CBP_HUMAN 586-672  
2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.11/B 2.12/B
2.13/B 2.14/B 2.15/B 2.16/B 2.17/B 2.18/B 2.19/B 2.20/B | histone-lysine
N-methyltransferase MLL | MLL1_HUMAN 840-858  


> hide #1 models

> show #1 models

> rename #1 "KIF2A TAD.pdb"

> hide #2.20 models

> hide #2.19 models

> hide #2.18 models

> hide #2.17 models

> hide #2.16 models

> hide #2.15 models

> hide #2.14 models

> hide #2.13 models

> hide #2.12 models

> hide #2.11 models

> hide #2.10 models

> hide #2.5 models

> hide #2.4 models

> hide #2.3 models

> hide #2.2 models

> hide #2.1 models

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select #2.3/A:586-672

1467 atoms, 1482 bonds, 87 residues, 1 model selected  

> select #2.3/A:586-672

1467 atoms, 1482 bonds, 87 residues, 1 model selected  

> select add #2.3

1753 atoms, 1770 bonds, 106 residues, 1 model selected  

> select add #2

35060 atoms, 35400 bonds, 2120 residues, 21 models selected  

> select subtract #2

Nothing selected  

> view #1 clip false

> hide #2.9 models

> hide #2.8 models

> hide #2.7 models

> matchmaker #2 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 KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.1), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.842 angstroms; (across all 28 pairs:
6.059)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.2), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.640 angstroms; (across all 28 pairs:
6.086)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.3), sequence alignment score = 51.7  
RMSD between 24 pruned atom pairs is 0.714 angstroms; (across all 28 pairs:
6.238)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.4), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.657 angstroms; (across all 28 pairs:
5.912)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.5), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.573 angstroms; (across all 28 pairs:
5.790)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.6), sequence alignment score = 48.1  
RMSD between 24 pruned atom pairs is 0.605 angstroms; (across all 28 pairs:
5.960)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.7), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.469 angstroms; (across all 28 pairs:
5.790)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.8), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.639 angstroms; (across all 28 pairs:
6.124)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.9), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.568 angstroms; (across all 28 pairs:
5.863)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.10), sequence alignment score = 51.7  
RMSD between 23 pruned atom pairs is 0.555 angstroms; (across all 28 pairs:
5.995)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.11), sequence alignment score = 51.7  
RMSD between 23 pruned atom pairs is 0.456 angstroms; (across all 28 pairs:
5.729)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.12), sequence alignment score = 51.7  
RMSD between 24 pruned atom pairs is 0.660 angstroms; (across all 28 pairs:
5.930)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.13), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.555 angstroms; (across all 28 pairs:
5.672)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.14), sequence alignment score = 48.7  
RMSD between 24 pruned atom pairs is 0.679 angstroms; (across all 28 pairs:
5.971)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.15), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.479 angstroms; (across all 28 pairs:
5.910)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.16), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.558 angstroms; (across all 28 pairs:
5.989)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.17), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.495 angstroms; (across all 28 pairs:
5.919)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.18), sequence alignment score = 47.3  
RMSD between 19 pruned atom pairs is 0.661 angstroms; (across all 33 pairs:
10.168)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.19), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.621 angstroms; (across all 28 pairs:
5.787)  

Matchmaker KIF2A TAD.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.20), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.620 angstroms; (across all 28 pairs:
5.803)  


> color #1#2.6 bychain

> coulombic #1#2.6

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for KIF2A TAD.pdb_A SES surface #1.1:
minimum, -18.19, mean -5.13, maximum 7.06  
Coulombic values for tad domain of MLL.ent_A SES surface #2.6.1: minimum,
-9.03, mean 3.75, maximum 31.23  
Coulombic values for tad domain of MLL.ent_B SES surface #2.6.2: minimum,
-11.06, mean -1.43, maximum 9.09  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hbonds #!1#!2.6 reveal true

1129 hydrogen bonds found  

> hide #3 models

> rainbow #!1#!2.6

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #!2 models

> show #!2 models

> hide #!2.6 models

> show #!2.6 models

> hide #2.6.2 models

> hide #1.1 models

> hide #!1 models

> show #!1 models

> rainbow #!1#!2.6

> color #!1#!2.6 bychain

> hide #!2 models

> show #!2 models

> hide #!2.6 models

> show #!2.6 models

> hide #2.6.1 models

> ~hbonds

> color bfactor #!1#!2.6

2025 atoms, 139 residues, 3 surfaces, atom bfactor range 0 to 98.5  

> hide #!1#!2.6 atoms

> coulombic #!1#!2.6

Coulombic values for KIF2A TAD.pdb_A SES surface #1.1: minimum, -18.19, mean
-5.13, maximum 7.06  
Coulombic values for tad domain of MLL.ent_A SES surface #2.6.1: minimum,
-9.03, mean 3.75, maximum 31.23  
Coulombic values for tad domain of MLL.ent_B SES surface #2.6.2: minimum,
-11.06, mean -1.43, maximum 9.09  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #2.6.1 models

> hide #2.6.2 models

> hide #1.1 models

> hide #!1 models

> show #!1 models

> close session

> open C:\Users\Asus\Downloads\ChimeraX\AlphaFold\prediction_6\best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  


> matchmaker #2 to #1

No molecules/chains to match specified  

> close session

> close #

Expected a models specifier or a keyword  

> ui tool show AlphaFold

> alphafold predict SDNNNSDDCGNILPSDIMDFVLKNTPSMQALGESPESS

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> open C:\Users\Asus\Downloads\ChimeraX\AlphaFold\prediction_8\best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  


> save "C:/Users/Asus/Downloads/ChimeraX/kif2c TAD.cxs"

\u2014\u2014\u2014 End of log from Thu Aug 24 12:23:29 2023 \u2014\u2014\u2014

opened ChimeraX session  

> open "C:/Users/Asus/Downloads/tad domain of MLL.ent"

tad domain of MLL.ent title:  
Allosteric communication In the kix domain proceeds through dynamic Re-packing
of the hydrophobic core [more info...]  

Chain information for tad domain of MLL.ent  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | creb-binding protein
| CBP_HUMAN 586-672  
2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.11/B 2.12/B
2.13/B 2.14/B 2.15/B 2.16/B 2.17/B 2.18/B 2.19/B 2.20/B | histone-lysine
N-methyltransferase MLL | MLL1_HUMAN 840-858  


> rainbow

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> matchmaker #2 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 best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.1), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.842 angstroms; (across all 28 pairs:
6.059)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.2), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.640 angstroms; (across all 28 pairs:
6.086)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.3), sequence alignment score = 51.7  
RMSD between 24 pruned atom pairs is 0.714 angstroms; (across all 28 pairs:
6.238)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.4), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.657 angstroms; (across all 28 pairs:
5.912)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.5), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.573 angstroms; (across all 28 pairs:
5.790)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.6), sequence alignment score = 48.1  
RMSD between 24 pruned atom pairs is 0.605 angstroms; (across all 28 pairs:
5.960)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.7), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.469 angstroms; (across all 28 pairs:
5.790)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.8), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.639 angstroms; (across all 28 pairs:
6.124)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.9), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.568 angstroms; (across all 28 pairs:
5.863)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.10), sequence alignment score = 51.7  
RMSD between 23 pruned atom pairs is 0.555 angstroms; (across all 28 pairs:
5.995)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.11), sequence alignment score = 51.7  
RMSD between 23 pruned atom pairs is 0.456 angstroms; (across all 28 pairs:
5.729)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.12), sequence alignment score = 51.7  
RMSD between 24 pruned atom pairs is 0.660 angstroms; (across all 28 pairs:
5.930)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.13), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.555 angstroms; (across all 28 pairs:
5.672)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.14), sequence alignment score = 48.7  
RMSD between 24 pruned atom pairs is 0.679 angstroms; (across all 28 pairs:
5.971)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.15), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.479 angstroms; (across all 28 pairs:
5.910)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.16), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.558 angstroms; (across all 28 pairs:
5.989)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.17), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.495 angstroms; (across all 28 pairs:
5.919)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.18), sequence alignment score = 47.3  
RMSD between 19 pruned atom pairs is 0.661 angstroms; (across all 33 pairs:
10.168)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.19), sequence alignment score = 48.7  
RMSD between 25 pruned atom pairs is 0.621 angstroms; (across all 28 pairs:
5.787)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain A
(#2.20), sequence alignment score = 51.7  
RMSD between 25 pruned atom pairs is 0.620 angstroms; (across all 28 pairs:
5.803)  


> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!2 models

> close session

> open C:\Users\Asus\Downloads\ChimeraX\AlphaFold\prediction_9\best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  


> color bychain

> open "C:/Users/Asus/Downloads/tad domain of MLL.ent"

tad domain of MLL.ent title:  
Allosteric communication In the kix domain proceeds through dynamic Re-packing
of the hydrophobic core [more info...]  

Chain information for tad domain of MLL.ent  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | creb-binding protein
| CBP_HUMAN 586-672  
2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.11/B 2.12/B
2.13/B 2.14/B 2.15/B 2.16/B 2.17/B 2.18/B 2.19/B 2.20/B | histone-lysine
N-methyltransferase MLL | MLL1_HUMAN 840-858  


> matchmaker #2 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 best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.1), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 1.264 angstroms; (across all 19 pairs:
3.482)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.2), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 1.434 angstroms; (across all 19 pairs:
3.205)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.3), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.710 angstroms; (across all 19 pairs:
4.972)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.4), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.484 angstroms; (across all 19 pairs:
4.288)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.5), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.740 angstroms; (across all 19 pairs:
4.045)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.6), sequence alignment score = 85.1  
RMSD between 11 pruned atom pairs is 0.510 angstroms; (across all 19 pairs:
5.015)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.7), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.514 angstroms; (across all 19 pairs:
3.956)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.8), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.494 angstroms; (across all 19 pairs:
4.333)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.9), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 1.436 angstroms; (across all 19 pairs:
3.605)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.10), sequence alignment score = 85.1  
RMSD between 10 pruned atom pairs is 1.299 angstroms; (across all 19 pairs:
3.241)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.11), sequence alignment score = 85.1  
RMSD between 13 pruned atom pairs is 0.706 angstroms; (across all 19 pairs:
2.876)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.12), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.612 angstroms; (across all 19 pairs:
4.410)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.13), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.575 angstroms; (across all 19 pairs:
4.343)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.14), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.812 angstroms; (across all 19 pairs:
4.161)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.15), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.734 angstroms; (across all 19 pairs:
3.946)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.16), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.344 angstroms; (across all 19 pairs:
5.127)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.17), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.418 angstroms; (across all 19 pairs:
3.850)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.18), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.768 angstroms; (across all 19 pairs:
3.764)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.19), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.738 angstroms; (across all 19 pairs:
4.911)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.20), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.463 angstroms; (across all 19 pairs:
5.277)  


> hide #2.20 models

> hide #2.19 models

> hide #2.18 models

> hide #2.17 models

> hide #2.16 models

> hide #2.15 models

> hide #2.14 models

> hide #2.13 models

> hide #2.12 models

> hide #2.11 models

> hide #2.10 models

> hide #2.9 models

> hide #2.8 models

> hide #2.7 models

> hide #2.6 models

> hide #2.2 models

> hide #2.3 models

> hide #2.4 models

> hide #2.1 models

Drag select of 9 residues  

> select add #2

35060 atoms, 35400 bonds, 2120 residues, 21 models selected  

> select subtract #2

Nothing selected  

> select add #2

35060 atoms, 35400 bonds, 2120 residues, 21 models selected  

> select subtract #2

Nothing selected  

> open C:/Users/Asus/Downloads/ChimeraX/AlphaFold/prediction_9/results.zip

Unrecognized file suffix '.zip'  

> open C:/Users/Asus/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  


> hide #!2 models

> open C:/Users/Asus/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb

Chain information for best_model.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  


> matchmaker #2 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 best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.1), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 1.264 angstroms; (across all 19 pairs:
3.482)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.2), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 1.434 angstroms; (across all 19 pairs:
3.205)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.3), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.710 angstroms; (across all 19 pairs:
4.972)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.4), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.484 angstroms; (across all 19 pairs:
4.288)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.5), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.740 angstroms; (across all 19 pairs:
4.045)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.6), sequence alignment score = 85.1  
RMSD between 11 pruned atom pairs is 0.510 angstroms; (across all 19 pairs:
5.015)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.7), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.514 angstroms; (across all 19 pairs:
3.956)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.8), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.494 angstroms; (across all 19 pairs:
4.333)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.9), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 1.436 angstroms; (across all 19 pairs:
3.605)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.10), sequence alignment score = 85.1  
RMSD between 10 pruned atom pairs is 1.299 angstroms; (across all 19 pairs:
3.241)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.11), sequence alignment score = 85.1  
RMSD between 13 pruned atom pairs is 0.706 angstroms; (across all 19 pairs:
2.876)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.12), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.612 angstroms; (across all 19 pairs:
4.410)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.13), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.575 angstroms; (across all 19 pairs:
4.343)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.14), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.812 angstroms; (across all 19 pairs:
4.161)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.15), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.734 angstroms; (across all 19 pairs:
3.946)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.16), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.344 angstroms; (across all 19 pairs:
5.127)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.17), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.418 angstroms; (across all 19 pairs:
3.850)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.18), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.768 angstroms; (across all 19 pairs:
3.764)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.19), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.738 angstroms; (across all 19 pairs:
4.911)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.20), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.463 angstroms; (across all 19 pairs:
5.277)  


> matchmaker #2 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 best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.1), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 1.264 angstroms; (across all 19 pairs:
3.482)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.2), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 1.434 angstroms; (across all 19 pairs:
3.205)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.3), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.710 angstroms; (across all 19 pairs:
4.972)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.4), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.484 angstroms; (across all 19 pairs:
4.288)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.5), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.740 angstroms; (across all 19 pairs:
4.045)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.6), sequence alignment score = 85.1  
RMSD between 11 pruned atom pairs is 0.510 angstroms; (across all 19 pairs:
5.015)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.7), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.514 angstroms; (across all 19 pairs:
3.956)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.8), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.494 angstroms; (across all 19 pairs:
4.333)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.9), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 1.436 angstroms; (across all 19 pairs:
3.605)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.10), sequence alignment score = 85.1  
RMSD between 10 pruned atom pairs is 1.299 angstroms; (across all 19 pairs:
3.241)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.11), sequence alignment score = 85.1  
RMSD between 13 pruned atom pairs is 0.706 angstroms; (across all 19 pairs:
2.876)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.12), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.612 angstroms; (across all 19 pairs:
4.410)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.13), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.575 angstroms; (across all 19 pairs:
4.343)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.14), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.812 angstroms; (across all 19 pairs:
4.161)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.15), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.734 angstroms; (across all 19 pairs:
3.946)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.16), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.344 angstroms; (across all 19 pairs:
5.127)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.17), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.418 angstroms; (across all 19 pairs:
3.850)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.18), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.768 angstroms; (across all 19 pairs:
3.764)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.19), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.738 angstroms; (across all 19 pairs:
4.911)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.20), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.463 angstroms; (across all 19 pairs:
5.277)  


> matchmaker #2 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 best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.1), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 1.264 angstroms; (across all 19 pairs:
3.482)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.2), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 1.434 angstroms; (across all 19 pairs:
3.205)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.3), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.710 angstroms; (across all 19 pairs:
4.972)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.4), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.484 angstroms; (across all 19 pairs:
4.288)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.5), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.740 angstroms; (across all 19 pairs:
4.045)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.6), sequence alignment score = 85.1  
RMSD between 11 pruned atom pairs is 0.510 angstroms; (across all 19 pairs:
5.015)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.7), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.514 angstroms; (across all 19 pairs:
3.956)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.8), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.494 angstroms; (across all 19 pairs:
4.333)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.9), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 1.436 angstroms; (across all 19 pairs:
3.605)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.10), sequence alignment score = 85.1  
RMSD between 10 pruned atom pairs is 1.299 angstroms; (across all 19 pairs:
3.241)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.11), sequence alignment score = 85.1  
RMSD between 13 pruned atom pairs is 0.706 angstroms; (across all 19 pairs:
2.876)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.12), sequence alignment score = 85.1  
RMSD between 12 pruned atom pairs is 0.612 angstroms; (across all 19 pairs:
4.410)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.13), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.575 angstroms; (across all 19 pairs:
4.343)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.14), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.812 angstroms; (across all 19 pairs:
4.161)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.15), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.734 angstroms; (across all 19 pairs:
3.946)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.16), sequence alignment score = 88.7  
RMSD between 10 pruned atom pairs is 0.344 angstroms; (across all 19 pairs:
5.127)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.17), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.418 angstroms; (across all 19 pairs:
3.850)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.18), sequence alignment score = 88.7  
RMSD between 13 pruned atom pairs is 0.768 angstroms; (across all 19 pairs:
3.764)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.19), sequence alignment score = 88.7  
RMSD between 12 pruned atom pairs is 0.738 angstroms; (across all 19 pairs:
4.911)  

Matchmaker best_model.pdb, chain A (#1) with tad domain of MLL.ent, chain B
(#2.20), sequence alignment score = 88.7  
RMSD between 11 pruned atom pairs is 0.463 angstroms; (across all 19 pairs:
5.277)  


> close session

> open "C:\Users\Asus\Downloads\tad domain of MLL.ent" format pdb

tad domain of MLL.ent title:  
Allosteric communication In the kix domain proceeds through dynamic Re-packing
of the hydrophobic core [more info...]  

Chain information for tad domain of MLL.ent  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | creb-binding protein
| CBP_HUMAN 586-672  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B | histone-lysine
N-methyltransferase MLL | MLL1_HUMAN 840-858  


> rainbow

> hide #1.20 models

> hide #1.19 models

> hide #1.18 models

> hide #1.17 models

> hide #1.16 models

> hide #1.15 models

> hide #1.14 models

> hide #1.13 models

> hide #1.12 models

> hide #1.11 models

> hide #1.10 models

> hide #1.9 models

> hide #1.8 models

> hide #1.7 models

> hide #1.5 models

> hide #1.4 models

> hide #1.3 models

> hide #1.2 models

> hide #1.1 models

> ui tool show AlphaFold

> alphafold search #1.1/A

Webservices job id: TT3JWXJ8CGIBWVG3  

> ui tool show AlphaFold

> alphafold match #1.1/A

Fetching compressed AlphaFold Q92793 from
https://alphafold.ebi.ac.uk/files/AF-Q92793-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: Q92793 (chain A)  
AlphaFold prediction matching tad domain of MLL.ent  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | Q92793 | CBP_HUMAN | 3.67 | 87 | 87 | 100  

Opened 1 AlphaFold model  

> close session

> ui tool show AlphaFold

> alphafold predict DDLKLLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHRA630VFQESIRWLED

Missing or invalid "sequences" argument: Sequences argument
"DDLKLLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHRA630VFQESIRWLED" is not a chain
specifier, alignment id, UniProt id, or sequence characters  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 665, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 97, in on_finish  
BlastProteinResults.from_job(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 90, in from_job  
return cls(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 86, in __init__  
self._build_ui()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 229, in _build_ui  
param_str = self._format_param_str()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
TypeError: sequence item 0: expected str instance, NoneType found  

TypeError: sequence item 0: expected str instance, NoneType found  

File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  

See log for complete Python traceback.  





OpenGL version: 3.3.0 NVIDIA 537.13
OpenGL renderer: NVIDIA GeForce GTX 950M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_IN.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: GL552JX
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 8,473,518,080
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4750HQ CPU @ 2.00GHz
OSLanguage: en-US

Installed Packages:
   alabaster: 0.7.13
   appdirs: 1.4.4
   asttokens: 2.2.1
   Babel: 2.12.1
   backcall: 0.2.0
   beautifulsoup4: 4.11.2
   blockdiag: 3.0.0
   build: 0.10.0
   certifi: 2023.5.7
   cftime: 1.6.2
   charset-normalizer: 3.1.0
   ChimeraX-AddCharge: 1.5.9.1
   ChimeraX-AddH: 2.2.5
   ChimeraX-AlignmentAlgorithms: 2.0.1
   ChimeraX-AlignmentHdrs: 3.3.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.9.3
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.0.3
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.43.10
   ChimeraX-AtomicLibrary: 10.0.6
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.3.2
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.1.2
   ChimeraX-BondRot: 2.0.1
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.8
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.2
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.3.2
   ChimeraX-ChangeChains: 1.0.2
   ChimeraX-CheckWaters: 1.3.1
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.2.4
   ChimeraX-ColorActions: 1.0.3
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.3
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.6.1
   ChimeraX-CoreFormats: 1.1
   ChimeraX-coulombic: 1.4.2
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2
   ChimeraX-DistMonitor: 1.4
   ChimeraX-DockPrep: 1.1.1
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ESMFold: 1.0
   ChimeraX-FileHistory: 1.0.1
   ChimeraX-FunctionKey: 1.0.1
   ChimeraX-Geometry: 1.3
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 1.1.1
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.1
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-Label: 1.1.7
   ChimeraX-ListInfo: 1.1.1
   ChimeraX-Log: 1.1.5
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.8.2
   ChimeraX-Map: 1.1.4
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0.1
   ChimeraX-MapFilter: 2.0.1
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.1.1
   ChimeraX-Markers: 1.0.1
   ChimeraX-Mask: 1.0.2
   ChimeraX-MatchMaker: 2.0.12
   ChimeraX-MDcrds: 2.6
   ChimeraX-MedicalToolbar: 1.0.2
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.12
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.9
   ChimeraX-ModelPanel: 1.3.7
   ChimeraX-ModelSeries: 1.0.1
   ChimeraX-Mol2: 2.0
   ChimeraX-Mole: 1.0
   ChimeraX-Morph: 1.0.2
   ChimeraX-MouseModes: 1.2
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.0
   ChimeraX-NRRD: 1.0
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.10.1
   ChimeraX-PDB: 2.7.2
   ChimeraX-PDBBio: 1.0
   ChimeraX-PDBLibrary: 1.0.2
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1
   ChimeraX-PubChem: 2.1
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.1
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.1
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 3.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0.1
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.8.3
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.1
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.10.3
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.1.2
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.2.1
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.1
   ChimeraX-Topography: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.28.4
   ChimeraX-uniprot: 2.2.2
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.2
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0.1
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.2
   ChimeraX-WebServices: 1.1.1
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.1.3
   comtypes: 1.1.14
   contourpy: 1.0.7
   cxservices: 1.2.2
   cycler: 0.11.0
   Cython: 0.29.33
   debugpy: 1.6.7
   decorator: 5.1.1
   docutils: 0.19
   executing: 1.2.0
   filelock: 3.9.0
   fonttools: 4.39.3
   funcparserlib: 1.0.1
   grako: 3.16.5
   h5py: 3.8.0
   html2text: 2020.1.16
   idna: 3.4
   ihm: 0.35
   imagecodecs: 2022.9.26
   imagesize: 1.4.1
   importlib-metadata: 6.6.0
   ipykernel: 6.21.1
   ipython: 8.10.0
   ipython-genutils: 0.2.0
   ipywidgets: 8.0.6
   jedi: 0.18.2
   Jinja2: 3.1.2
   jupyter-client: 8.0.2
   jupyter-core: 5.3.0
   jupyterlab-widgets: 3.0.7
   kiwisolver: 1.4.4
   line-profiler: 4.0.2
   lxml: 4.9.2
   lz4: 4.3.2
   MarkupSafe: 2.1.2
   matplotlib: 3.6.3
   matplotlib-inline: 0.1.6
   msgpack: 1.0.4
   nest-asyncio: 1.5.6
   netCDF4: 1.6.2
   networkx: 2.8.8
   nibabel: 5.0.1
   nptyping: 2.5.0
   numexpr: 2.8.4
   numpy: 1.23.5
   openvr: 1.23.701
   packaging: 23.1
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pickleshare: 0.7.5
   Pillow: 9.3.0
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 3.5.0
   prompt-toolkit: 3.0.38
   psutil: 5.9.4
   pure-eval: 0.2.2
   pycollada: 0.7.2
   pydicom: 2.3.0
   Pygments: 2.14.0
   pynrrd: 1.0.0
   PyOpenGL: 3.1.5
   PyOpenGL-accelerate: 3.1.5
   pyparsing: 3.0.9
   pyproject-hooks: 1.0.0
   PyQt6-commercial: 6.4.2
   PyQt6-Qt6: 6.4.3
   PyQt6-sip: 13.4.1
   PyQt6-WebEngine-commercial: 6.4.0
   PyQt6-WebEngine-Qt6: 6.4.3
   python-dateutil: 2.8.2
   pytz: 2023.3
   pywin32: 305
   pyzmq: 25.0.2
   qtconsole: 5.4.0
   QtPy: 2.3.1
   RandomWords: 0.4.0
   requests: 2.28.2
   scipy: 1.9.3
   setuptools: 67.4.0
   sfftk-rw: 0.7.3
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.4.1
   sphinx: 6.1.3
   sphinx-autodoc-typehints: 1.22
   sphinxcontrib-applehelp: 1.0.4
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.2
   sphinxcontrib-htmlhelp: 2.0.1
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.3
   sphinxcontrib-serializinghtml: 1.1.5
   stack-data: 0.6.2
   tables: 3.7.0
   tcia-utils: 1.2.0
   tifffile: 2022.10.10
   tinyarray: 1.2.4
   tomli: 2.0.1
   tornado: 6.3.1
   traitlets: 5.9.0
   typing-extensions: 4.5.0
   tzdata: 2023.3
   urllib3: 1.26.15
   wcwidth: 0.2.6
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.7
   WMI: 1.5.1
   zipp: 3.15.0

[Zach Pearson]

Should already be fixed in the daily builds.