Matchmaker: 'NoneType' object has no attribute 'setChecked'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/H2AH2B MRGRKK.cxs" format session

Log from Fri Jan 6 13:28:28 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> color sel hot pink

> select /B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> color sel cornflower blue

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> color sel orange

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> style sel sphere

Changed 2063 atom styles  

> style sel sphere

Changed 2063 atom styles  

> show target m

> style sel ball

Changed 2063 atom styles  

> select clear

> style sphere

Changed 4347 atom styles  

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> surface sel

> select /B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> show sel surfaces

> select clear

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -15.50, mean
3.92, maximum 18.48  
Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -8.85, mean
4.00, maximum 21.45  
Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -9.90, mean
4.01, maximum 12.56  
To also show corresponding color key, enter the above coulombic command and
add key true  

> undo

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> hide sel surfaces

> select /B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> coulombic sel

Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -8.85, mean
4.00, maximum 21.45  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> coulombic sel

Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -15.50, mean
3.92, maximum 18.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel ball

Changed 260 atom styles  

> show sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> toolshed show

> select clear

[Repeated 1 time(s)]

> select /C:10@CA

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select /C:10@NH2

1 atom, 1 residue, 1 model selected  

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

> label (#!1 & sel) attribute name

> select clear

> select /C:5@CA

1 atom, 1 residue, 1 model selected  

> label (#!1 & sel) text "ARG 134"

> ui tool show "Color Actions"

> color sel black target l

> label height 3

> undo

> redo

> label height 1

> label height 1.5

> select clear

> select /C:6@CA

1 atom, 1 residue, 1 model selected  

> label (#!1 & sel) text "LYS 135"

> select /C:7@CA

1 atom, 1 residue, 1 model selected  

> label (#!1 & sel) text "LYS 136"

> select /C:8@CA

1 atom, 1 residue, 1 model selected  

> label (#!1 & sel) text "ARG 137"

> select /C:10

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

> select /C:11

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select /C:10

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

> label (#!1 & sel) text ARG139

> select clear

> label height 1.5

> ui tool show "Color Actions"

> color black target l

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Change Chain IDs"

> changechains A H2A

Chain IDs of 130 residues changed  

> changechains C MRG15

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (MRG15/1/)  

> changechains C MRG

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (MRG/1/)  

> help help:user/tools/changechains.html

> changechains C MRG

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (MRG/1/)  

> changechains B H2B

No residues specified  

> changechains B H2B

No residues specified  

> select /A:1-130

Nothing selected  

> ui tool show "Change Chain IDs"

> changechains B H2B

No residues specified  
Cannot change to an empty ID  
[Repeated 1 time(s)]

> select /A:1-130

Nothing selected  

> sequence chain #1/A

Chains must have same sequence  

> sequence chain #1/A

Chains must have same sequence  

> undo

[Repeated 2 time(s)]

> redo

> select /A:1-130

Nothing selected  

> sequence chain #1/A

Chains must have same sequence  

> ui tool show "Change Chain IDs"

Must select one or more chain IDs from the list on the left  

> changechains H2A A

Chain IDs of 130 residues changed  

> sequence chain #1/A

Alignment identifier is 1/A  

> ui mousemode right "move label"

[Repeated 1 time(s)]

> ui mousemode right select

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right translate

> save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/Image1.tif" width 704 height 533 supersample 3

> ui tool show Contacts

> select /C:10@CA

1 atom, 1 residue, 1 model selected  

> select /C:8

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

> select add /C:10

48 atoms, 46 bonds, 2 residues, 2 models selected  

> select add /C:7

70 atoms, 67 bonds, 3 residues, 2 models selected  

> select add /A:61@CB

71 atoms, 67 bonds, 4 residues, 2 models selected  

> select subtract /A:61@CB

70 atoms, 67 bonds, 3 residues, 3 models selected  

> select add /C:6

92 atoms, 88 bonds, 4 residues, 2 models selected  

> select add /C:5@CA

93 atoms, 88 bonds, 5 residues, 2 models selected  

> select subtract /C:5

92 atoms, 88 bonds, 4 residues, 2 models selected  

> select add /C:5

116 atoms, 111 bonds, 5 residues, 2 models selected  

> style sel stick

Changed 116 atom styles  

> show sel cartoons

> hbonds sel reveal true

3 hydrogen bonds found  

> hbonds sel reveal true

3 hydrogen bonds found  

> undo

> ~hbonds

[Repeated 2 time(s)]

> undo

> hbonds sel reveal true

3 hydrogen bonds found  

> ~hbonds

> ui tool show H-Bonds

> hbonds sel interModel false intraModel false saltOnly true intraMol false
> intraRes false reveal true

0 hydrogen bonds found  

> select clear

> ~hbonds

[Repeated 5 time(s)]

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> hide sel surfaces

> select /B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> hide sel surfaces

> ~hbonds

[Repeated 2 time(s)]

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> ~hbonds

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> ~hbonds

[Repeated 1 time(s)]

> select clear

> style stick

Changed 4347 atom styles  

> hide cartoons

> show cartoons

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> hide atoms

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> show sel surfaces

> select /B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> show sel surfaces

> select clear

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 260 atom styles  

> style sel sphere

Changed 260 atom styles  

> style sel ball

Changed 260 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 260 atom styles  

> color sel byhetero

> select clear

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> coulombic sel

Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -9.90, mean
4.01, maximum 12.56  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color sel byhetero

> coulombic sel

Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -9.90, mean
4.01, maximum 12.56  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> color (#!1 & sel) byelement

> undo

> select clear

> select /C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> select clear

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true

No contacts  

> ui tool show H-Bonds

> hbonds interModel false intraModel false saltOnly true intraMol false
> intraRes false reveal true

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel saltOnly true reveal true

Atom specifier selects no atoms  

> ui tool show H-Bonds

> hbonds saltOnly true reveal true

14 hydrogen bonds found  

> ~hbonds

> select clear

> save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/Image2.tif" width 704 height 533 supersample 3

> save /Users/Gareth/Desktop/image1.png supersample 3

> ui tool show Matchmaker

> save /Users/Gareth/Desktop/image2.png supersample 3

> save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/H2AH2B MRGRKK.cxs"

——— End of log from Fri Jan 6 13:28:28 2023 ———

opened ChimeraX session  

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close

> open "/Users/Gareth/Documents/DDR
> 2022/AlphaFold/MRFAP1/MRFAP1-MRGBP/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /A:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> color sel cornflower blue

> select /B:1-204

3097 atoms, 3126 bonds, 204 residues, 1 model selected  

> color sel hot pink

> select clear

> select /A:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> show sel surfaces

> mlp sel

Map values for surface "ranked_0.pdb_A SES surface": minimum -25.57, mean
-2.342, maximum 23.27  
To also show corresponding color key, enter the above mlp command and add key
true  

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-
> MRFAP1-MRGBP/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A:1-168

2756 atoms, 2792 bonds, 168 residues, 1 model selected  

> color sel cornflower blue

> select /B:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> color sel hot pink

> select /C:1-204

3097 atoms, 3126 bonds, 204 residues, 1 model selected  

> color sel light sea green

> select clear

> select /A:1-168

2756 atoms, 2792 bonds, 168 residues, 1 model selected  

> show sel surfaces

> mlp sel

Map values for surface "ranked_0.pdb_A SES surface": minimum -27.56, mean
-2.658, maximum 22.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-
> MRFAP1-MRGBP/ranked_1.pdb"

Chain information for ranked_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A:1-168

2756 atoms, 2792 bonds, 168 residues, 1 model selected  

> color sel hot pink

> select /B:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> color sel medium blue

> select /C:1-204

3097 atoms, 3126 bonds, 204 residues, 1 model selected  

> color sel forest green

> select clear

> select /A:1-168

2756 atoms, 2792 bonds, 168 residues, 1 model selected  

> mlp sel

Map values for surface "ranked_1.pdb_A SES surface": minimum -27.86, mean
-2.711, maximum 24.32  
To also show corresponding color key, enter the above mlp command and add key
true  

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-
> MRFAP1-MRGBP/ranked_2.pdb"

Chain information for ranked_2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A:1-168

2756 atoms, 2792 bonds, 168 residues, 1 model selected  

> show sel surfaces

> mlp sel

Map values for surface "ranked_2.pdb_A SES surface": minimum -26.55, mean
-2.543, maximum 23.83  
To also show corresponding color key, enter the above mlp command and add key
true  

> select /B:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> color sel orange

> select clear

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-
> MRFAP1-MRGBP/ranked_3.pdb"

Chain information for ranked_3.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close #1

> select #2/A:1-168

2756 atoms, 2792 bonds, 168 residues, 1 model selected  

> show sel surfaces

> mlp sel

Map values for surface "ranked_3.pdb_A SES surface": minimum -27.31, mean
-2.509, maximum 23.55  
To also show corresponding color key, enter the above mlp command and add key
true  

> select #2/B:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> color sel orange

> close

> open "/Users/Gareth/Documents/DDR
> 2022/AlphaFold/MRFAP1/MRFAP1-MRGBP/ranked_1.pdb"

Chain information for ranked_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /A:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> select /B:1-204

3097 atoms, 3126 bonds, 204 residues, 1 model selected  

> show sel surfaces

> close

> open "/Users/Gareth/Documents/DDR
> 2022/AlphaFold/MRFAP1/MRFAP1-MRGBP/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /A:1-127

2042 atoms, 2053 bonds, 127 residues, 1 model selected  

> select /B:1-204

3097 atoms, 3126 bonds, 204 residues, 1 model selected  

> show sel surfaces

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone -
> MRG/Histone-Octamer-RKK/ranked_0.pdb"

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
G H | No description available  
I | No description available  
  

> show cartoons

> hide atoms

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> select ~sel

14908 atoms, 15000 bonds, 924 residues, 1 model selected  

> color sel hot pink

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -15.29, mean
4.32, maximum 18.71  
Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -17.23, mean
3.98, maximum 19.16  
Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -9.58, mean
5.06, maximum 15.99  
Coulombic values for ranked_0.pdb_D SES surface #1.4: minimum, -10.13, mean
4.57, maximum 16.13  
Coulombic values for ranked_0.pdb_E SES surface #1.5: minimum, -16.33, mean
2.45, maximum 16.99  
Coulombic values for ranked_0.pdb_F SES surface #1.6: minimum, -14.44, mean
2.30, maximum 14.81  
Coulombic values for ranked_0.pdb_G SES surface #1.7: minimum, -9.16, mean
5.77, maximum 16.03  
Coulombic values for ranked_0.pdb_H SES surface #1.8: minimum, -8.89, mean
5.66, maximum 16.30  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 329 atom styles  

> color sel byhetero

> select clear

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/ranked_0.pdb"

Chain information for ranked_0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> ui tool show Matchmaker

> 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 ranked_0.pdb, chain B (#1) with ranked_0.pdb, chain A (#2),
sequence alignment score = 608.6  
RMSD between 89 pruned atom pairs is 0.844 angstroms; (across all 130 pairs:
22.712)  
  

> ui tool show Matchmaker

> select /A:1-130

4126 atoms, 4150 bonds, 260 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 ranked_0.pdb, chain A (#1) with ranked_0.pdb, chain A (#2),
sequence alignment score = 591.8  
RMSD between 87 pruned atom pairs is 1.118 angstroms; (across all 130 pairs:
21.387)  
  

> select clear

> select #2/C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> color sel orange

> select clear

> select #2/C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> close #2

> open 3x1s

3x1s title:  
Crystal structure of the nucleosome core particle [more info...]  
  
Chain information for 3x1s #2  
---  
Chain | Description | UniProt  
A E | Histone H3.1 | H31_HUMAN  
B F | Histone H4 | H4_HUMAN  
C G | Histone H2A type 1-B/E | H2A1B_HUMAN  
D H | Histone H2B type 1-B | H2B1B_HUMAN  
I J | DNA (146-MER) |  
  
Non-standard residues in 3x1s #2  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> hide surfaces

> show cartoons

> hide atoms

> ui tool show Matchmaker

> 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 ranked_0.pdb, chain B (#1) with 3x1s, chain G (#2), sequence
alignment score = 568.5  
RMSD between 94 pruned atom pairs is 0.976 angstroms; (across all 104 pairs:
1.568)  
  

> select #1/A

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> show sel surfaces

> select #1/B

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> show sel surfaces

> select #1/C

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> show sel surfaces

> select clear

> select #2/C:14-118

810 atoms, 820 bonds, 105 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> close #2

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone -
> MRG/Histone-Octamer-RKK/ranked_1.pdb"

Chain information for ranked_1.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
G H | No description available  
I | No description available  
  

> show cartoons

> hide atoms

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> select ~sel

14908 atoms, 15000 bonds, 924 residues, 1 model selected  

> color sel yellow

> select clear

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> select ~sel

14908 atoms, 15000 bonds, 924 residues, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ranked_1.pdb_A SES surface #1.1: minimum, -21.67, mean
4.74, maximum 18.97  
Coulombic values for ranked_1.pdb_B SES surface #1.2: minimum, -12.65, mean
4.63, maximum 17.40  
Coulombic values for ranked_1.pdb_C SES surface #1.3: minimum, -9.89, mean
5.22, maximum 18.92  
Coulombic values for ranked_1.pdb_D SES surface #1.4: minimum, -9.69, mean
5.37, maximum 22.95  
Coulombic values for ranked_1.pdb_E SES surface #1.5: minimum, -14.14, mean
2.22, maximum 14.80  
Coulombic values for ranked_1.pdb_F SES surface #1.6: minimum, -15.51, mean
2.19, maximum 16.93  
Coulombic values for ranked_1.pdb_G SES surface #1.7: minimum, -8.06, mean
7.15, maximum 21.55  
Coulombic values for ranked_1.pdb_H SES surface #1.8: minimum, -8.79, mean
6.38, maximum 21.21  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone -
> MRG/Histone-Octamer-RKK/ranked_2.pdb"

Chain information for ranked_2.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
G H | No description available  
I | No description available  
  

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> select clear

> show cartoons

> hide atoms

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone -
> MRG/Histone-Octamer-RKK/ranked_3.pdb"

Chain information for ranked_3.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
G H | No description available  
I | No description available  
  

> hide atoms

> show cartoons

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone -
> MRG/Histone-Octamer-RKK/ranked_4.pdb"

Chain information for ranked_4.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
G H | No description available  
I | No description available  
  

> hide atoms

> show cartoons

> close

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone -
> MRG/Histone-Octamer-RKK/ranked_0.pdb" format pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
G H | No description available  
I | No description available  
  

> show cartoons

> hide atoms

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> select ~sel

14908 atoms, 15000 bonds, 924 residues, 1 model selected  

> color sel cornflower blue

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> color sel hot pink

> select ~sel

14908 atoms, 15000 bonds, 924 residues, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -15.29, mean
4.32, maximum 18.71  
Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -17.23, mean
3.98, maximum 19.16  
Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -9.58, mean
5.06, maximum 15.99  
Coulombic values for ranked_0.pdb_D SES surface #1.4: minimum, -10.13, mean
4.57, maximum 16.13  
Coulombic values for ranked_0.pdb_E SES surface #1.5: minimum, -16.33, mean
2.45, maximum 16.99  
Coulombic values for ranked_0.pdb_F SES surface #1.6: minimum, -14.44, mean
2.30, maximum 14.81  
Coulombic values for ranked_0.pdb_G SES surface #1.7: minimum, -9.16, mean
5.77, maximum 16.03  
Coulombic values for ranked_0.pdb_H SES surface #1.8: minimum, -8.89, mean
5.66, maximum 16.30  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select /D:28@CG

1 atom, 1 residue, 1 model selected  

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 329 atom styles  

> color sel byhetero

> select clear

> select /B:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> select /A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> select /C:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> select /E:1-103

1703 atoms, 1714 bonds, 103 residues, 1 model selected  

> select clear

> hide surfaces

> open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - MRG/H2AH2B
> + MRG-RKK/ranked_0.pdb"

Chain information for ranked_0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select #2/A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> color sel orange

> select #2/B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> color sel orange

> select #2/C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> color sel light sea green

> show sel atoms

> color sel byhetero

> select clear

> ui tool show Matchmaker

> matchmaker #2 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 ranked_0.pdb, chain A (#1) with ranked_0.pdb, chain A (#2),
sequence alignment score = 591.8  
RMSD between 87 pruned atom pairs is 1.118 angstroms; (across all 130 pairs:
21.387)  
  

> select clear

> show surfaces

> select #2/A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> hide sel surfaces

> select #2/A:1-130

2063 atoms, 2075 bonds, 130 residues, 1 model selected  

> select #2/B:1-126

2024 atoms, 2039 bonds, 126 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select clear

> select #2/C:1-15

260 atoms, 263 bonds, 15 residues, 1 model selected  

> hide sel surfaces

> select clear

> select /I:1-20

329 atoms, 332 bonds, 20 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ranked_0.pdb_I SES surface #1.9: minimum, -12.27, mean
2.58, maximum 12.25  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select clear

> open 3x1s

3x1s title:  
Crystal structure of the nucleosome core particle [more info...]  
  
Chain information for 3x1s #3  
---  
Chain | Description | UniProt  
A E | Histone H3.1 | H31_HUMAN  
B F | Histone H4 | H4_HUMAN  
C G | Histone H2A type 1-B/E | H2A1B_HUMAN  
D H | Histone H2B type 1-B | H2B1B_HUMAN  
I J | DNA (146-MER) |  
  
Non-standard residues in 3x1s #3  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> show cartoons

> hide atoms

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,1
      Processor Name: Intel Core i5
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 156.0.0.0.0
      SMC Version (system): 2.16f68

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G103)
      Kernel Version: Darwin 18.7.0
      Time since boot: 89 days 1:27

Graphics/Displays:

    Intel Iris:

      Chipset Model: Intel Iris
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a2e
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
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    decorator: 5.1.1
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    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
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    Jinja2: 3.1.2
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    kiwisolver: 1.4.4
    line-profiler: 3.5.1
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    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
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    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
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    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

Tried various things -- couldn't reproduce