Opened 3 years ago
Closed 3 years ago
#8450 closed defect (can't reproduce)
MatchMaker: 'NoneType' object has no attribute 'setChecked'
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Comparison | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
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. > matchmaker #!3 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 (#3), sequence alignment score = 568.5 RMSD between 94 pruned atom pairs is 0.976 angstroms; (across all 104 pairs: 1.568) > close #3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer H2AH2B RKK comparison 1.tif" width > 704 height 533 supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer H2AH2B RKK comparison 2.tif" width > 704 height 533 supersample 3 > select #2/C:1-15 260 atoms, 263 bonds, 15 residues, 1 model selected > show sel atoms > select /I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > show sel atoms > select clear > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer H2AH2B RKK comparison 3.tif" width > 704 height 533 supersample 3 > select #2/C:1-15 260 atoms, 263 bonds, 15 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #1/I:8 24 atoms, 23 bonds, 1 residue, 1 model selected > select add #1/I:9 46 atoms, 44 bonds, 2 residues, 2 models selected > select add #1/I:10 68 atoms, 65 bonds, 3 residues, 2 models selected > select add #1/I:11 92 atoms, 88 bonds, 4 residues, 2 models selected > select add #1/I:12 102 atoms, 97 bonds, 5 residues, 2 models selected > select add #1/I:13 126 atoms, 120 bonds, 6 residues, 2 models selected > label (#!1 & sel) attribute name > label height 1 > ui tool show "Color Actions" > color sel black target l > color sel light gray target l > color sel dark gray target l > color sel lime target l > color sel orange red target l > color sel yellow target l > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer RKK 1.tif" width 704 height 533 > supersample 3 > select clear > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer RKK 2.tif" width 704 height 533 > supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer RKK 3.tif" width 704 height 533 > supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone Octamer RKK 4.tif" width 704 height 533 > supersample 3 > 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 > 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 > 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, -18.85, mean -3.64, maximum 9.54 To also show corresponding color key, enter the above coulombic command and add key true > select /B:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected Alignment identifier is 1/B > select /B:4 10 atoms, 9 bonds, 1 residue, 1 model selected > select /B:4-6 41 atoms, 40 bonds, 3 residues, 1 model selected > select /B:33 14 atoms, 14 bonds, 1 residue, 1 model selected > select /B:33-42 153 atoms, 155 bonds, 10 residues, 1 model selected > select /B:74 11 atoms, 10 bonds, 1 residue, 1 model selected > select /B:74-84 182 atoms, 184 bonds, 11 residues, 1 model selected > select /B:87-88 34 atoms, 33 bonds, 2 residues, 1 model selected > select /B:87-95 140 atoms, 140 bonds, 9 residues, 1 model selected > select /B:109 15 atoms, 14 bonds, 1 residue, 1 model selected > select /B:109-116 140 atoms, 139 bonds, 8 residues, 1 model selected > select /B:53 24 atoms, 23 bonds, 1 residue, 1 model selected > select /B:53-68 283 atoms, 286 bonds, 16 residues, 1 model selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > select /B:105 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:105-108 69 atoms, 70 bonds, 4 residues, 1 model selected > show sel atoms > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-BRD8/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 -26.17, mean -2.868, maximum 26.88 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 cornflower blue Alignment identifier is 1/B > select /B:28 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:28-29 38 atoms, 37 bonds, 2 residues, 1 model selected > select /B:27 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:27-30 72 atoms, 73 bonds, 4 residues, 1 model selected > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-BRD8/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 /C:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected > select /A:1-168 2756 atoms, 2792 bonds, 168 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface "ranked_1.pdb_A SES surface": minimum -26.28, mean -2.805, maximum 23.27 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 cornflower blue Alignment identifier is 1/B > select /B:27 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:27-31 88 atoms, 89 bonds, 5 residues, 1 model selected > select /B:1-127 2042 atoms, 2053 bonds, 127 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_B SES surface #1.2: minimum, -19.57, mean -3.44, maximum 10.58 To also show corresponding color key, enter the above coulombic command and add key true > select /C:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected > show sel surfaces > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-BRD8/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 > show sel surfaces > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -25.69, mean -2.822, maximum 22.88 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 cornflower blue > select clear > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-Dimer + 2 AI > Chromo/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A B | No description available C D | 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_0.pdb_A SES surface": minimum -26.23, mean -2.904, maximum 24.13 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-168 2756 atoms, 2792 bonds, 168 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface "ranked_0.pdb_B SES surface": minimum -25.68, mean -3.058, maximum 24.88 To also show corresponding color key, enter the above mlp command and add key true > select clear > select /D:74 20 atoms, 20 bonds, 1 residue, 1 model selected > select /D:75 14 atoms, 14 bonds, 1 residue, 1 model selected > select /D:76 16 atoms, 15 bonds, 1 residue, 1 model selected > select /D:77 14 atoms, 14 bonds, 1 residue, 1 model selected > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-Dimer- > AIChromo/MRGDimer-Chromo.pdb" Chain information for MRGDimer-Chromo.pdb #1 --- Chain | Description A 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 "MRGDimer-Chromo.pdb_A SES surface": minimum -26.93, mean -2.801, maximum 25.03 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-168 2756 atoms, 2792 bonds, 168 residues, 1 model selected > mlp sel Map values for surface "MRGDimer-Chromo.pdb_B SES surface": minimum -25.16, mean -2.832, maximum 22.62 To also show corresponding color key, enter the above mlp command and add key true > 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 > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-MRGBP/ranked_4.pdb" Chain information for ranked_4.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 > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-MRGBP/ranked_3.pdb" Chain information for ranked_3.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > 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 > 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 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 > 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 > select clear > select /B:1-127 2042 atoms, 2053 bonds, 127 residues, 1 model selected > color sel cornflower blue > select clear > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-MRGBP/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_1.pdb, chain C (#1) with ranked_0.pdb, chain C (#2), sequence alignment score = 1009.7 RMSD between 115 pruned atom pairs is 0.680 angstroms; (across all 204 pairs: 18.787) > select #2/B:1-127 2042 atoms, 2053 bonds, 127 residues, 1 model selected > color sel hot pink > select clear > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-BRD8/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 > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -25.69, mean -2.822, maximum 22.88 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 cornflower blue Alignment identifier is 1/B > select /B:27 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:27-30 72 atoms, 73 bonds, 4 residues, 1 model selected > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-BRD8/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 > mlp sel Map values for surface "ranked_1.pdb_A SES surface": minimum -26.28, mean -2.805, maximum 23.27 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 Alignment identifier is 1/B > color sel cornflower blue > select clear > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1/ranked_0.pdb" Chain information for ranked_0.pdb #2 --- Chain | Description A | No description available B | No description available > select #2/A:1-168 2756 atoms, 2792 bonds, 168 residues, 1 model selected > color sel orange > select #2/B:1-127 2042 atoms, 2053 bonds, 127 residues, 1 model selected > color sel hot pink > ui tool show Matchmaker > matchmaker #!1 to #2/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 (#2) with ranked_1.pdb, chain A (#1), sequence alignment score = 846.6 RMSD between 152 pruned atom pairs is 0.674 angstroms; (across all 168 pairs: 1.074) > select clear > select #2/B:27 20 atoms, 20 bonds, 1 residue, 1 model selected > select add #1/B:27 40 atoms, 40 bonds, 2 residues, 2 models selected > select add #2/B:28 59 atoms, 58 bonds, 3 residues, 2 models selected > select add #1/B:28 78 atoms, 76 bonds, 4 residues, 2 models selected > select add #2/B:29 97 atoms, 94 bonds, 5 residues, 2 models selected > select add #2/B:30 111 atoms, 108 bonds, 6 residues, 2 models selected > select add #1/B:29 130 atoms, 126 bonds, 7 residues, 2 models selected > select add #1/B:30 144 atoms, 140 bonds, 8 residues, 2 models selected > show sel atoms > color sel byhetero > select #1/A:2@CE 1 atom, 1 residue, 1 model selected > select clear > 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 > hide atoms > show cartoons > color cornflower blue > select /I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > color sel orange > select clear > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #2 --- 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 cartoons > hide atoms > show cartoons > 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 C (#1) with ranked_0.pdb, chain D (#2), sequence alignment score = 627.4 RMSD between 105 pruned atom pairs is 0.661 angstroms; (across all 126 pairs: 1.964) > select #2/A 2063 atoms, 2075 bonds, 130 residues, 1 model selected > color sel hot pink > select #2/B 2063 atoms, 2075 bonds, 130 residues, 1 model selected > color sel hot pink > select #2/C 2024 atoms, 2039 bonds, 126 residues, 1 model selected > color sel hot pink > select #2/D 2024 atoms, 2039 bonds, 126 residues, 1 model selected > color sel hot pink > select #2/E 1703 atoms, 1714 bonds, 103 residues, 1 model selected > color sel hot pink > select #2/F 1703 atoms, 1714 bonds, 103 residues, 1 model selected > color sel hot pink [Repeated 1 time(s)] > select #2/H 1664 atoms, 1672 bonds, 103 residues, 1 model selected > color sel hot pink > select #2/H 1664 atoms, 1672 bonds, 103 residues, 1 model selected > select clear > select #2/G 1664 atoms, 1672 bonds, 103 residues, 1 model selected > color sel hot pink > select clear > select #2/I 329 atoms, 332 bonds, 20 residues, 1 model selected > color sel yellow > select clear > 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. > matchmaker #2 to #1/I 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 I (#1) with ranked_0.pdb, chain I (#2), sequence alignment score = 86.8 RMSD between 15 pruned atom pairs is 1.213 angstroms; (across all 20 pairs: 1.970) > ui tool show H-Bonds > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 = 626 RMSD between 111 pruned atom pairs is 0.786 angstroms; (across all 130 pairs: 1.652) > show surfaces > coulombic Using Amber 20 recommended default charges and atom types for standard residues [Repeated 1 time(s)]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 Coulombic values for ranked_0.pdb_I SES surface #1.9: minimum, -12.27, mean 2.58, maximum 12.25 Coulombic values for ranked_0.pdb_A SES surface #2.1: minimum, -17.25, mean 4.62, maximum 19.62 Coulombic values for ranked_0.pdb_B SES surface #2.2: minimum, -16.67, mean 4.25, maximum 21.71 Coulombic values for ranked_0.pdb_C SES surface #2.3: minimum, -10.17, mean 5.19, maximum 16.79 Coulombic values for ranked_0.pdb_D SES surface #2.4: minimum, -10.16, mean 5.01, maximum 16.53 Coulombic values for ranked_0.pdb_E SES surface #2.5: minimum, -16.57, mean 2.42, maximum 12.88 Coulombic values for ranked_0.pdb_F SES surface #2.6: minimum, -16.19, mean 2.43, maximum 13.05 Coulombic values for ranked_0.pdb_G SES surface #2.7: minimum, -7.63, mean 6.00, maximum 17.63 Coulombic values for ranked_0.pdb_H SES surface #2.8: minimum, -8.32, mean 5.87, maximum 24.96 Coulombic values for ranked_0.pdb_I SES surface #2.9: minimum, -11.73, mean 2.88, maximum 15.96 To also show corresponding color key, enter the above coulombic command and add key true > select #2/I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > hide sel surfaces > show sel atoms > color sel byhetero > style sel stick Changed 329 atom styles > select /I:1-20 658 atoms, 664 bonds, 40 residues, 2 models selected > hide sel surfaces > show sel atoms > style sel stick Changed 658 atom styles > color sel byhetero > select clear > close #1 > hide surfaces > open 3x1s 3x1s title: Crystal structure of the nucleosome core particle [more info...] Chain information for 3x1s #1 --- 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 #1 --- CL — chloride ion MN — manganese (II) ion > hide cartoons > hide atoms > show cartoons > ui tool show Matchmaker > matchmaker #!1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ranked_0.pdb, chain C (#2) with 3x1s, chain D (#1), sequence alignment score = 565.1 RMSD between 83 pruned atom pairs is 1.259 angstroms; (across all 94 pairs: 2.166) > show surfaces > hide surfaces > close #1 > open 1kx5 Summary of feedback from opening 1kx5 fetched from pdb --- note | Fetching compressed mmCIF 1kx5 from http://files.rcsb.org/download/1kx5.cif 1kx5 title: X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution [more info...] Chain information for 1kx5 #1 --- Chain | Description | UniProt A E | histone H3 | H32_BOVIN B F | histone H4 | H4_HUMANX C G | histone H2A.1 | H2A1_XENLA D H | histone H2B.2 | H2B1_XENLA I | DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3') | J | DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3') | Non-standard residues in 1kx5 #1 --- CL — chloride ion MN — manganese (II) ion > select :CL 4 atoms, 4 residues, 1 model selected > select :CL 4 atoms, 4 residues, 1 model selected > select :MN 14 atoms, 14 residues, 1 model selected > select :CL 4 atoms, 4 residues, 1 model selected > select clear Drag select of 3 residues, 16753 atoms, 410 pseudobonds > color (#!1-2 & sel) cornflower blue > hide sel atoms > show sel cartoons > select clear > 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 1kx5, chain G (#1) with ranked_0.pdb, chain A (#2), sequence alignment score = 535.6 RMSD between 77 pruned atom pairs is 1.313 angstroms; (across all 128 pairs: 7.017) > close > open /Users/Gareth/Documents/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 > show sel surfaces > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -25.35, mean -2.756, maximum 24.2 To also show corresponding color key, enter the above mlp command and add key true > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-BRD8/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/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 = 875.4 RMSD between 168 pruned atom pairs is 0.344 angstroms; (across all 168 pairs: 0.344) > select /B:1-127 4084 atoms, 4106 bonds, 254 residues, 2 models selected > color sel cornflower blue > select clear > select #2/B:1-127 2042 atoms, 2053 bonds, 127 residues, 1 model selected > color sel orange > select clear > close #2 > select #2/A:1-168 Nothing selected > select /B:1-127 2042 atoms, 2053 bonds, 127 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_B SES surface #1.2: minimum, -17.71, mean -3.38, maximum 17.10 To also show corresponding color key, enter the above coulombic command and add key true > select #2/C:1-169 Nothing selected > select #2/C:1-169 Nothing selected > select /C:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected Alignment identifier is 1/C > select /C:7-8 34 atoms, 34 bonds, 2 residues, 1 model selected > select /C:7-11 90 atoms, 90 bonds, 5 residues, 1 model selected > select /C:84 19 atoms, 18 bonds, 1 residue, 1 model selected > select /C:84-92 153 atoms, 152 bonds, 9 residues, 1 model selected > select /C:74 21 atoms, 21 bonds, 1 residue, 1 model selected > select /C:74-77 71 atoms, 71 bonds, 4 residues, 1 model selected > select /C:101 17 atoms, 16 bonds, 1 residue, 1 model selected > select /C:101-116 279 atoms, 281 bonds, 16 residues, 1 model selected > select /C:99 17 atoms, 16 bonds, 1 residue, 1 model selected > select /C:99-116 306 atoms, 308 bonds, 18 residues, 1 model selected > show sel atoms > select clear > select /B:1-127 2042 atoms, 2053 bonds, 127 residues, 1 model selected > hide sel surfaces > select clear > select /B:27 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > select /B:28 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /B:29 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /B:24 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > close > open /Users/Gareth/Documents/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 > open "/Users/Gareth/Documents/DDR > 2022/AlphaFold/MRFAP1/MRFAP1-MRGBP/ranked_0.pdb" Chain information for ranked_0.pdb #2 --- Chain | Description A | No description available B | 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 B (#2), sequence alignment score = 970.1 RMSD between 102 pruned atom pairs is 0.694 angstroms; (across all 204 pairs: 12.546) > close > open /Users/Gareth/Documents/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 > show sel surfaces > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -27.67, mean -2.586, maximum 24.72 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 > select clear > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > MRFAP1-MRGBP/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/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 = 873.6 RMSD between 166 pruned atom pairs is 0.254 angstroms; (across all 168 pairs: 0.367) > select #2/C:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > color sel hot pink > select clear > close > open /Users/Gareth/Documents/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 > hide atoms > show cartoons > select /I:1-323 5271 atoms, 5335 bonds, 323 residues, 1 model selected > color sel cornflower blue > 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, -16.17, mean 4.46, maximum 19.51 Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -13.65, mean 4.36, maximum 19.24 Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -10.36, mean 4.80, maximum 16.39 Coulombic values for ranked_0.pdb_D SES surface #1.4: minimum, -10.42, mean 4.86, maximum 17.37 Coulombic values for ranked_0.pdb_E SES surface #1.5: minimum, -14.07, mean 2.28, maximum 12.93 Coulombic values for ranked_0.pdb_F SES surface #1.6: minimum, -13.53, mean 2.26, maximum 12.79 Coulombic values for ranked_0.pdb_G SES surface #1.7: minimum, -8.63, mean 5.55, maximum 16.43 Coulombic values for ranked_0.pdb_H SES surface #1.8: minimum, -8.19, mean 5.67, maximum 15.08 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select /I:1-323 5271 atoms, 5335 bonds, 323 residues, 1 model selected Alignment identifier is 1/I > select /I:113 14 atoms, 13 bonds, 1 residue, 1 model selected > select /I:113-116 75 atoms, 74 bonds, 4 residues, 1 model selected > select /I:132 14 atoms, 14 bonds, 1 residue, 1 model selected > select /I:132-139 154 atoms, 155 bonds, 8 residues, 1 model selected > select /I:111 22 atoms, 21 bonds, 1 residue, 1 model selected > select /I:111-115 97 atoms, 96 bonds, 5 residues, 1 model selected > select /I:93-94 24 atoms, 24 bonds, 2 residues, 1 model selected > select /I:93-99 100 atoms, 100 bonds, 7 residues, 1 model selected > select /I:106-107 31 atoms, 30 bonds, 2 residues, 1 model selected > select /I:106-118 230 atoms, 230 bonds, 13 residues, 1 model selected > open 1kx5 1kx5 title: X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution [more info...] Chain information for 1kx5 #2 --- Chain | Description | UniProt A E | histone H3 | H32_BOVIN B F | histone H4 | H4_HUMANX C G | histone H2A.1 | H2A1_XENLA D H | histone H2B.2 | H2B1_XENLA I | DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3') | J | DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3') | Non-standard residues in 1kx5 #2 --- CL — chloride ion MN — manganese (II) ion > hide sel atoms [Repeated 1 time(s)] > show sel cartoons [Repeated 1 time(s)] > sequence chain #2/A#2/E Alignment identifier is 1 > select #2/A:1-135 1074 atoms, 1088 bonds, 135 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/E:1-135 1074 atoms, 1088 bonds, 135 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/B:1-102 792 atoms, 800 bonds, 102 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/F:1-102 792 atoms, 800 bonds, 102 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/C:1-128 978 atoms, 988 bonds, 128 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/G:1-128 978 atoms, 988 bonds, 128 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/D:1-122 949 atoms, 962 bonds, 122 residues, 1 model selected > hide sel atoms > show sel cartoons > select :MN 14 atoms, 14 residues, 1 model selected > hide sel atoms > hide sel cartoons > select :CL 4 atoms, 4 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #2/D:1-122 949 atoms, 962 bonds, 122 residues, 1 model selected > select #2/H:1-122 949 atoms, 962 bonds, 122 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/D:1-122 949 atoms, 962 bonds, 122 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/I:-73-73 3011 atoms, 3378 bonds, 147 residues, 1 model selected > hide sel atoms > show sel cartoons > select #2/J:-73-73 3010 atoms, 3376 bonds, 147 residues, 1 model selected > hide sel atoms > show sel cartoons > select clear > select ::name="CL"::name="HOH"::name="MN" 3148 atoms, 55 pseudobonds, 3148 residues, 2 models selected > hide sel atoms > 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 1kx5, chain G (#2), sequence alignment score = 532.6 RMSD between 95 pruned atom pairs is 0.824 angstroms; (across all 128 pairs: 6.767) > hide sel surfaces [Repeated 1 time(s)]Drag select of ranked_0.pdb_A SES surface, ranked_0.pdb_B SES surface, ranked_0.pdb_C SES surface, ranked_0.pdb_D SES surface, ranked_0.pdb_E SES surface, ranked_0.pdb_F SES surface, ranked_0.pdb_G SES surface, ranked_0.pdb_H SES surface, 2515 residues > hide sel surfaces > select clear > show cartoons > close #2 > select /I:1-323 5271 atoms, 5335 bonds, 323 residues, 1 model selected > select ~sel 14908 atoms, 15000 bonds, 924 residues, 1 model selected > color (#!1 & sel) hot pink > show sel surfaces > coulombic sel Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -16.17, mean 4.46, maximum 19.51 Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -13.65, mean 4.36, maximum 19.24 Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -10.36, mean 4.80, maximum 16.39 Coulombic values for ranked_0.pdb_D SES surface #1.4: minimum, -10.42, mean 4.86, maximum 17.37 Coulombic values for ranked_0.pdb_E SES surface #1.5: minimum, -14.07, mean 2.28, maximum 12.93 Coulombic values for ranked_0.pdb_F SES surface #1.6: minimum, -13.53, mean 2.26, maximum 12.79 Coulombic values for ranked_0.pdb_G SES surface #1.7: minimum, -8.63, mean 5.55, maximum 16.43 Coulombic values for ranked_0.pdb_H SES surface #1.8: minimum, -8.19, mean 5.67, maximum 15.08 To also show corresponding color key, enter the above coulombic command and add key true > select clear > close > open /Users/Gareth/Documents/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:1-198 3031 atoms, 3066 bonds, 198 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 -27.67, mean -2.552, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > 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, -29.80, mean -3.95, maximum 10.63 To also show corresponding color key, enter the above coulombic command and add key true > close > open /Users/Gareth/Documents/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 > 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, -19.24, mean -4.27, maximum 9.24 To also show corresponding color key, enter the above coulombic command and add key true > close > open /Users/Gareth/Documents/ranked_2.pdb Chain information for ranked_2.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 > show sel surfaces > hide sel surfaces > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > select /B:1-198 3031 atoms, 3066 bonds, 198 residues, 1 model selected Alignment identifier is 1/B > select /B:5 24 atoms, 23 bonds, 1 residue, 1 model selected > select /B:5-13 127 atoms, 127 bonds, 9 residues, 1 model selected > select /B:51 12 atoms, 11 bonds, 1 residue, 1 model selected > select /B:51-59 143 atoms, 142 bonds, 9 residues, 1 model selected > select /B:61-62 34 atoms, 34 bonds, 2 residues, 1 model selected > select /B:61-65 83 atoms, 84 bonds, 5 residues, 1 model selected > select /B:45 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:45-59 251 atoms, 251 bonds, 15 residues, 1 model selected > select /B:41 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:41-68 480 atoms, 485 bonds, 28 residues, 1 model selected > select /B:30 24 atoms, 23 bonds, 1 residue, 1 model selected > select /B:30-88 982 atoms, 997 bonds, 59 residues, 1 model selected > select /B:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:1-29 430 atoms, 433 bonds, 29 residues, 1 model selected > delete atoms sel > delete bonds sel > select /B:89 21 atoms, 21 bonds, 1 residue, 1 model selected > select /B:89-198 1619 atoms, 1634 bonds, 110 residues, 1 model selected > delete atoms sel > delete bonds sel > select /B:1-198 982 atoms, 997 bonds, 59 residues, 1 model selected > color sel hot pink > select /A:1-127 2042 atoms, 2053 bonds, 127 residues, 1 model selected > color sel cornflower blue > show sel surfaces > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > color sel hot pink > select clear > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected Alignment identifier is 1/A > select /A:168 19 atoms, 18 bonds, 1 residue, 1 model selected > select /A:168-170 37 atoms, 36 bonds, 3 residues, 1 model selected > select /A:104 14 atoms, 13 bonds, 1 residue, 1 model selected > select /A:104-110 113 atoms, 114 bonds, 7 residues, 1 model selected > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > show sel surfaces > select clear > select /B:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected Alignment identifier is 1/B > select clear > select /B:99 17 atoms, 16 bonds, 1 residue, 1 model selected > select /B:99-116 306 atoms, 308 bonds, 18 residues, 1 model selected > show sel atoms > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -27.01, mean -4.49, maximum 23.98 To also show corresponding color key, enter the above mlp command and add key true > 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, -20.86, mean -1.03, maximum 10.53 To also show corresponding color key, enter the above coulombic command and add key true > select clear > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | 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_0.pdb_A SES surface": minimum -25.45, mean -2.812, maximum 24.26 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-364 5612 atoms, 5673 bonds, 364 residues, 1 model selected Alignment identifier is 1/B > select /B:321 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:321-324 69 atoms, 70 bonds, 4 residues, 1 model selected > show sel atoms > select /B:269-270 31 atoms, 32 bonds, 2 residues, 1 model selected > select /B:269-284 233 atoms, 239 bonds, 16 residues, 1 model selected > show sel atoms > close > open /Users/Gareth/Documents/ranked_1.pdb Chain information for ranked_1.pdb #1 --- Chain | Description A | No description available B | No description available > 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 -25.58, mean -2.936, maximum 24.61 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-364 5612 atoms, 5673 bonds, 364 residues, 1 model selected Alignment identifier is 1/B > select /B:259 17 atoms, 16 bonds, 1 residue, 1 model selected > select /B:259-315 830 atoms, 844 bonds, 57 residues, 1 model selected > select /B:321 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:321-325 84 atoms, 85 bonds, 5 residues, 1 model selected > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | 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_0.pdb_A SES surface": minimum -25.45, mean -2.812, maximum 24.26 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/MRGBP/MRGBP- > BRD8/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | 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_0.pdb_A SES surface": minimum -25.45, mean -2.812, maximum 24.26 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-364 5612 atoms, 5673 bonds, 364 residues, 1 model selected Alignment identifier is 1/B > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > HNRPU/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | 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_0.pdb_A SES surface": minimum -27.18, mean -1.674, maximum 25.48 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-825 12459 atoms, 12583 bonds, 825 residues, 1 model selected Alignment identifier is 1/B > select /B:640 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:640-643 67 atoms, 68 bonds, 4 residues, 1 model selected > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG- > HNRPU/ranked_1.pdb" Chain information for ranked_1.pdb #1 --- Chain | Description A | No description available B | 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_1.pdb_A SES surface": minimum -29.07, mean -2.496, maximum 27.08 To also show corresponding color key, enter the above mlp command and add key true > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/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 > hide atoms > show cartoons > select /I:1-20 343 atoms, 343 bonds, 20 residues, 1 model selected > color sel yellow > select ~sel 14908 atoms, 15000 bonds, 924 residues, 1 model selected > color sel cornflower blue > show sel surfaces > hide sel surfaces > 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, -15.47, mean 3.94, maximum 17.14 Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -14.98, mean 3.84, maximum 18.15 Coulombic values for ranked_0.pdb_C SES surface #1.3: minimum, -10.27, mean 4.76, maximum 16.75 Coulombic values for ranked_0.pdb_D SES surface #1.4: minimum, -10.23, mean 4.46, maximum 15.94 Coulombic values for ranked_0.pdb_E SES surface #1.5: minimum, -12.99, mean 2.30, maximum 14.71 Coulombic values for ranked_0.pdb_F SES surface #1.6: minimum, -19.28, mean 2.25, maximum 13.65 Coulombic values for ranked_0.pdb_G SES surface #1.7: minimum, -8.87, mean 5.22, maximum 15.87 Coulombic values for ranked_0.pdb_H SES surface #1.8: minimum, -8.85, mean 5.14, maximum 27.95 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select /I:1-20 343 atoms, 343 bonds, 20 residues, 1 model selected > show sel atoms > style sel stick Changed 343 atom styles > color sel byhetero > select /E:21@NE 1 atom, 1 residue, 1 model selected > select clear > hide surfaces > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/ranked_0.pdb" Chain information for ranked_0.pdb #2 --- 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 > select #2/A:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > color sel hot pink > select #2/B:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > color sel hot pink > select #2/C:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > color sel hot pink > select #2/D:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > color sel hot pink > select #2/E:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > color sel hot pink > select #2/F:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > color sel hot pink > select #2/F:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > select #2/G:1-103 1664 atoms, 1672 bonds, 103 residues, 1 model selected > color sel hot pink > select #2/H:1-103 1664 atoms, 1672 bonds, 103 residues, 1 model selected > color sel hot pink > select #2/I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > color sel light sea green > ui tool show "Color Actions" > color sel orange red target l [Repeated 2 time(s)] > color sel orange red > select clear > select #2/I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > color sel cyan > select clear > select #2/I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > color sel forest green > select clear > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 = 603.2 RMSD between 94 pruned atom pairs is 0.866 angstroms; (across all 130 pairs: 3.895) > select #1/A 2063 atoms, 2075 bonds, 130 residues, 1 model selected > show sel surfaces > hide sel surfaces > select #2/A 2063 atoms, 2075 bonds, 130 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 #2.1: minimum, -15.29, mean 4.32, maximum 18.71 To also show corresponding color key, enter the above coulombic command and add key true > select #2/B 2063 atoms, 2075 bonds, 130 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_B SES surface #2.2: minimum, -17.23, mean 3.98, maximum 19.16 To also show corresponding color key, enter the above coulombic command and add key true > select #2/C 2024 atoms, 2039 bonds, 126 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_C SES surface #2.3: minimum, -9.58, mean 5.06, maximum 15.99 To also show corresponding color key, enter the above coulombic command and add key true > select #2/D 2024 atoms, 2039 bonds, 126 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_D SES surface #2.4: minimum, -10.13, mean 4.57, maximum 16.13 To also show corresponding color key, enter the above coulombic command and add key true > select #2/E 1703 atoms, 1714 bonds, 103 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_E SES surface #2.5: minimum, -16.33, mean 2.45, maximum 16.99 To also show corresponding color key, enter the above coulombic command and add key true > select #2/F 1703 atoms, 1714 bonds, 103 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_F SES surface #2.6: minimum, -14.44, mean 2.30, maximum 14.81 To also show corresponding color key, enter the above coulombic command and add key true > select #2/H 1664 atoms, 1672 bonds, 103 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ranked_0.pdb_H SES surface #2.7: 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 #2/H 1664 atoms, 1672 bonds, 103 residues, 1 model selected > select #2/G 1664 atoms, 1672 bonds, 103 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ranked_0.pdb_G SES surface #2.8: minimum, -9.16, mean 5.77, maximum 16.03 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select #1/I 343 atoms, 343 bonds, 20 residues, 1 model selected > show sel atoms > select #2/I 329 atoms, 332 bonds, 20 residues, 1 model selected > show sel atoms > color sel byhetero > style sel stick Changed 329 atom styles > color sel cyan > color sel byhetero > select clear > select #2/C 2024 atoms, 2039 bonds, 126 residues, 1 model selected > select #2/G 1664 atoms, 1672 bonds, 103 residues, 1 model selected > select clear > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/comparison with RKK 1.tif" width 704 height 533 > supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/comparison with RKK 2.tif" width 704 height 533 > supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/comparison with RKK 3.tif" width 704 height 533 > supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/Histone-Octamer-RKK-KTKK.cxs" > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/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 > hide atoms > show cartoons > select /I:1-20 343 atoms, 343 bonds, 20 residues, 1 model selected > show sel atoms > style sel stick Changed 343 atom styles > color sel byhetero > select ~sel 14908 atoms, 15000 bonds, 924 residues, 1 model selected > 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, -20.91, mean 3.63, maximum 16.26 Coulombic values for ranked_1.pdb_B SES surface #1.2: minimum, -13.26, mean 3.65, maximum 18.85 Coulombic values for ranked_1.pdb_C SES surface #1.3: minimum, -10.67, mean 4.28, maximum 15.64 Coulombic values for ranked_1.pdb_D SES surface #1.4: minimum, -11.50, mean 3.84, maximum 13.94 Coulombic values for ranked_1.pdb_E SES surface #1.5: minimum, -12.92, mean 2.00, maximum 12.92 Coulombic values for ranked_1.pdb_F SES surface #1.6: minimum, -15.93, mean 2.06, maximum 15.18 Coulombic values for ranked_1.pdb_G SES surface #1.7: minimum, -9.30, mean 4.54, maximum 14.73 Coulombic values for ranked_1.pdb_H SES surface #1.8: minimum, -9.19, mean 4.60, maximum 16.14 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select /C 2024 atoms, 2039 bonds, 126 residues, 1 model selected > select /G 1664 atoms, 1672 bonds, 103 residues, 1 model selected > 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 > hide atoms > show cartoons > select /I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > show sel atoms > color sel byhetero > style sel stick Changed 329 atom styles > select ~sel 14908 atoms, 15000 bonds, 924 residues, 1 model selected > 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-KTKK/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 > hide atoms > show cartoons > select /I:1-20 343 atoms, 343 bonds, 20 residues, 1 model selected > show sel atoms > style sel stick Changed 343 atom styles > color sel byhetero > select ~sel 14908 atoms, 15000 bonds, 924 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ranked_2.pdb_A SES surface #1.1: minimum, -18.56, mean 4.77, maximum 19.89 Coulombic values for ranked_2.pdb_B SES surface #1.2: minimum, -13.98, mean 4.51, maximum 17.22 Coulombic values for ranked_2.pdb_C SES surface #1.3: minimum, -10.01, mean 5.64, maximum 22.21 Coulombic values for ranked_2.pdb_D SES surface #1.4: minimum, -10.50, mean 5.23, maximum 19.20 Coulombic values for ranked_2.pdb_E SES surface #1.5: minimum, -15.11, mean 2.14, maximum 15.16 Coulombic values for ranked_2.pdb_F SES surface #1.6: minimum, -13.75, mean 2.05, maximum 13.10 Coulombic values for ranked_2.pdb_G SES surface #1.7: minimum, -7.80, mean 6.98, maximum 22.67 Coulombic values for ranked_2.pdb_H SES surface #1.8: minimum, -8.45, mean 6.51, maximum 20.32 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/Histone-Octamer-RKK.pdb" Chain information for Histone-Octamer-RKK.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 > style sel stick Changed 329 atom styles > color sel byhetero > select ~sel 14908 atoms, 15000 bonds, 924 residues, 1 model selected > show sel cartoons > hide sel atoms > 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 > color sel cornflower blue > select /I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > color sel yellow > 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 > select #2/A:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > color sel purple > color sel hot pink > select #2/B:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > color sel hot pink > select #2/C:1-15 260 atoms, 263 bonds, 15 residues, 1 model selected > color sel orange > show sel atoms > color sel byhetero > select clear > select #2/A:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 Histone-Octamer-RKK.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 /I:1-20 329 atoms, 332 bonds, 20 residues, 1 model selected > show sel cartoons > select clear > select #2/A:1-130 2063 atoms, 2075 bonds, 130 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 #2.1: minimum, -15.50, mean 3.92, maximum 18.48 To also show corresponding color key, enter the above coulombic command and add key true > close #2 > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGBP/MRGBP- > BRD8/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > show sel surfaces Alignment identifier is 1/A > select /A:105 20 atoms, 20 bonds, 1 residue, 1 model selected > select /A:105-112 137 atoms, 138 bonds, 8 residues, 1 model selected > select /B:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected > show sel atoms > select clear > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > 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, -20.86, mean -1.03, maximum 10.53 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG15/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available > select /A:1-323 5271 atoms, 5335 bonds, 323 residues, 1 model selected Alignment identifier is 1/A > select /A:149 14 atoms, 13 bonds, 1 residue, 1 model selected > select /A:149 14 atoms, 13 bonds, 1 residue, 1 model selected > select /A:92 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:92-94 34 atoms, 34 bonds, 3 residues, 1 model selected > close > open "/Users/Gareth/Documents/DDR > 2022/AlphaFold/MRG15/MRG15-AI_Isoform/AF-Q9UBU8-F1-model_v4.pdb" AF-Q9UBU8-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for mortality factor 4-like protein 1 (Q9UBU8) [more info...] Chain information for AF-Q9UBU8-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | mortality factor 4-like protein 1 | MO4L1_HUMAN > select /A:1-362 2929 atoms, 3002 bonds, 362 residues, 1 model selected Alignment identifier is 1/A > select /A:268 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:268-272 36 atoms, 35 bonds, 5 residues, 1 model selected > select /A:148 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:148 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show "AlphaFold Error Plot" > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone-Octamer-RKK.pdb" Chain information for Histone-Octamer-RKK.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 > ui tool show "AlphaFold Error Plot" > alphafold pae #1 file /Users/Gareth/Documents/result_model_1_multimer.pkl > alphafold pae #1 colorDomains true > help help:user/tools/alphafold.html#pae > hide atoms > show cartoons > color #1/A:119-119 lime > color #1/C:96-96 magenta > color #1/C:69-69 lime > color #1/C:72-72 magenta > color #1/I:9-9 lime > color #1/H:69-69 magenta > color #1/A:88-88 lime > color #1/I:15-15 magenta > color #1/A:93-93 lime > color #1/I:14-14 magenta > color #1/D:61-61 lime > color #1/D:66-66 magenta > color #1/F:61-61 lime > color #1/H:67-67 magenta > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | 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_0.pdb_A SES surface": minimum -26.17, mean -2.324, maximum 24.92 To also show corresponding color key, enter the above mlp command and add key true > select clear > select /B:1-111 1653 atoms, 1666 bonds, 111 residues, 1 model selected Alignment identifier is 1/B > select /B:95 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:95-98 67 atoms, 68 bonds, 4 residues, 1 model selected > select /B:59 11 atoms, 10 bonds, 1 residue, 1 model selected > select /B:59-69 170 atoms, 171 bonds, 11 residues, 1 model selected > select /B:77-78 26 atoms, 25 bonds, 2 residues, 1 model selected > select /B:77-80 61 atoms, 60 bonds, 4 residues, 1 model selected > close > open /Users/Gareth/Documents/ranked_1.pdb Chain information for ranked_1.pdb #1 --- Chain | Description A | No description available B | 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_1.pdb_A SES surface": minimum -26.3, mean -2.42, maximum 27.86 To also show corresponding color key, enter the above mlp command and add key true > close > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | 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_0.pdb_A SES surface": minimum -25.88, mean -2.21, maximum 26.06 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-56 872 atoms, 881 bonds, 56 residues, 1 model selected Alignment identifier is 1/B > select /B:18 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:18-21 67 atoms, 68 bonds, 4 residues, 1 model selected > close > open /Users/Gareth/Documents/ranked_1.pdb Chain information for ranked_1.pdb #1 --- Chain | Description A | No description available B | 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_1.pdb_A SES surface": minimum -26.18, mean -2.31, maximum 24.21 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-56 872 atoms, 881 bonds, 56 residues, 1 model selected > show sel atoms > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG15/ranked_0.pdb" Chain information for ranked_0.pdb #2 --- Chain | Description A | 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_1.pdb, chain A (#1) with ranked_0.pdb, chain A (#2), sequence alignment score = 854.4 RMSD between 151 pruned atom pairs is 0.826 angstroms; (across all 168 pairs: 1.693) > hide sel surfaces > select clear > hide surfaces > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone-Octamer-RKK.pdb" Chain information for Histone-Octamer-RKK.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 > 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 > select clear > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/Histone-Octamer-KTKK.pdb" Chain information for Histone-Octamer-KTKK.pdb #2 --- 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 > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 Histone-Octamer-RKK.pdb, chain A (#1) with Histone-Octamer- KTKK.pdb, chain A (#2), sequence alignment score = 603.2 RMSD between 94 pruned atom pairs is 0.866 angstroms; (across all 130 pairs: 3.895) > select #2/A:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/B:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/C:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/D:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/E:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/E:1-103 Nothing selected > select #2/E:1-103 Nothing selected > select #2/F:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/G:1-103 1664 atoms, 1672 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/H:1-103 1664 atoms, 1672 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show "Add Hydrogens" > addh inIsolation false Summary of feedback from adding hydrogens to multiple structures --- notes | No usable SEQRES records for Histone-Octamer-RKK.pdb (#1) chain A; guessing termini instead No usable SEQRES records for Histone-Octamer-RKK.pdb (#1) chain B; guessing termini instead No usable SEQRES records for Histone-Octamer-RKK.pdb (#1) chain C; guessing termini instead No usable SEQRES records for Histone-Octamer-RKK.pdb (#1) chain D; guessing termini instead No usable SEQRES records for Histone-Octamer-RKK.pdb (#1) chain E; guessing termini instead 5 messages similar to the above omitted Chain-initial residues that are actual N termini: Histone-Octamer-RKK.pdb #1/A MET 1, Histone-Octamer-RKK.pdb #1/B MET 1, Histone-Octamer-RKK.pdb #1/C MET 1, Histone-Octamer-RKK.pdb #1/D MET 1, Histone-Octamer-RKK.pdb #1/E THR 1, Histone-Octamer-RKK.pdb #1/F THR 1, Histone-Octamer-RKK.pdb #1/G MET 1, Histone-Octamer-RKK.pdb #1/H MET 1, Histone-Octamer-RKK.pdb #1/I SER 1, Histone-Octamer-KTKK.pdb #2/I LEU 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Histone-Octamer-RKK.pdb #1/A LYS 130, Histone-Octamer-RKK.pdb #1/B LYS 130, Histone-Octamer-RKK.pdb #1/C LYS 126, Histone-Octamer-RKK.pdb #1/D LYS 126, Histone-Octamer-RKK.pdb #1/E ALA 103, Histone-Octamer-RKK.pdb #1/F ALA 103, Histone-Octamer-RKK.pdb #1/G GLY 103, Histone-Octamer-RKK.pdb #1/H GLY 103, Histone-Octamer-RKK.pdb #1/I ASN 20, Histone-Octamer-KTKK.pdb #2/I ASN 20 Chain-final residues that are not actual C termini: 985 hydrogen bonds 1 hydrogens added > ui tool show "Build Structure" > save /Users/Gareth/Desktop/RKK.pdb > close > open /Users/Gareth/Desktop/RKK.pdb Summary of feedback from opening /Users/Gareth/Desktop/RKK.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 13 THR A 17 1 5 Start residue of secondary structure not found: HELIX 2 2 SER A 20 ALA A 22 1 3 Start residue of secondary structure not found: HELIX 3 3 VAL A 28 LYS A 37 1 10 Start residue of secondary structure not found: HELIX 4 4 GLY A 47 ALA A 71 1 25 Start residue of secondary structure not found: HELIX 5 5 ARG A 72 ASN A 74 1 3 58 messages similar to the above omitted End residue of secondary structure not found: HELIX 64 64 LYS I 9 ARG I 11 1 3 Start residue of secondary structure not found: SHEET 1 1 1 VAL A 101 ILE A 103 0 Start residue of secondary structure not found: SHEET 2 2 1 VAL B 101 ILE B 103 0 Start residue of secondary structure not found: SHEET 3 3 1 THR G 97 TYR G 99 0 Start residue of secondary structure not found: SHEET 4 4 1 THR H 97 TYR H 99 0 Chain information for RKK.pdb --- Chain | Description 1.1/A 1.1/B | No description available 1.1/C 1.1/D | No description available 1.1/E 1.1/F | No description available 1.1/G 1.1/H | No description available 1.1/I | No description available 1.2/I | No description available > hide atoms > show cartoons > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-RKK/Histone-Octamer-RKK.pdb" Chain information for Histone-Octamer-RKK.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 > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/Histone - > MRG/Histone-Octamer-KTKK/Histone-Octamer-KTKK.pdb" Chain information for Histone-Octamer-KTKK.pdb #2 --- 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 > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 Histone-Octamer-RKK.pdb, chain A (#1) with Histone-Octamer- KTKK.pdb, chain A (#2), sequence alignment score = 603.2 RMSD between 94 pruned atom pairs is 0.866 angstroms; (across all 130 pairs: 3.895) > select #2/A:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/B:1-130 2063 atoms, 2075 bonds, 130 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/C:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/D:1-126 2024 atoms, 2039 bonds, 126 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/E:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/F:1-103 1703 atoms, 1714 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/G:1-103 1664 atoms, 1672 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/H:1-103 1664 atoms, 1672 bonds, 103 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/F:1-103 Nothing selected > select add #1 15237 atoms, 15332 bonds, 944 residues, 1 model selected > select add #2 15580 atoms, 15675 bonds, 964 residues, 2 models selected > select subtract #2 15237 atoms, 15332 bonds, 944 residues, 1 model selected > select add #2 15580 atoms, 15675 bonds, 964 residues, 2 models selected > select subtract #2 15237 atoms, 15332 bonds, 944 residues, 1 model selected > select subtract #1 Nothing selected > ui tool show "Change Chain IDs" > view clip false > select add #1 15237 atoms, 15332 bonds, 944 residues, 1 model selected > select add #2 15580 atoms, 15675 bonds, 964 residues, 2 models selected > Incomplete command: modeller > join models Unknown command: join models > combine Remapping chain ID 'I' in Histone-Octamer-KTKK.pdb #2 to 'J' > close #1 > close #2 > save /Users/Gareth/Desktop/RKK.pdb relModel #3 > close > open /Users/Gareth/Downloads/step1_pdbreader.pdb Summary of feedback from opening /Users/Gareth/Downloads/step1_pdbreader.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON FEB, 02. 2023. JOB Ignored bad PDB record found on line 2 REMARK READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE Ignored bad PDB record found on line 3 REMARK DATE: 2/ 2/23 11:37:31 CREATED BY USER: apache Chain information for step1_pdbreader.pdb #1 --- Chain | Description P | No description available > close > open /Users/Gareth/Desktop/MD/RKK.pdb Summary of feedback from opening /Users/Gareth/Desktop/MD/RKK.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON FEB, 03. 2023. JOB Ignored bad PDB record found on line 2 REMARK READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE Ignored bad PDB record found on line 3 REMARK DATE: 2/ 3/23 7:23: 2 CREATED BY USER: apache Chain information for RKK.pdb #1 --- Chain | Description P | No description available Alignment identifier is 1/P > select clear > select /P:130 46 atoms, 44 bonds, 2 residues, 1 model selected > select /P:130 46 atoms, 44 bonds, 2 residues, 1 model selected > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGBP/MRGBP- > BRD8/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > show sel surfaces > select /A:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > close > close # Expected a models specifier or a keyword > open /Users/Gareth/Documents/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:1-168 2756 atoms, 2792 bonds, 168 residues, 1 model selected > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -25.88, mean -2.21, maximum 26.06 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-56 872 atoms, 881 bonds, 56 residues, 1 model selected Alignment identifier is 1/B > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG-MRGBP- > BRD8/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 > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -26.9, mean -2.559, maximum 25.42 To also show corresponding color key, enter the above mlp command and add key true > select /B:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > color sel cornflower blue > select clear > select /C:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected > color sel hot pink > select /B:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected Alignment identifier is 1/B > select /B:105 20 atoms, 20 bonds, 1 residue, 1 model selected > select /B:105-108 69 atoms, 70 bonds, 4 residues, 1 model selected > select /C:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ranked_0.pdb_C SES surface #1.2: minimum, -14.15, mean 0.59, maximum 16.76 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select /B:33 14 atoms, 14 bonds, 1 residue, 1 model selected > select /B:33-42 153 atoms, 155 bonds, 10 residues, 1 model selected > show sel atoms > style sel stick Changed 153 atom styles > color sel byhetero > select /B:74 11 atoms, 10 bonds, 1 residue, 1 model selected > select /B:74-83 165 atoms, 167 bonds, 10 residues, 1 model selected > show sel atoms > color sel byhetero > select /B:84 17 atoms, 16 bonds, 1 residue, 1 model selected > select /B:84-89 94 atoms, 94 bonds, 6 residues, 1 model selected > color sel byhetero > show sel atoms > select /C:111@C 1 atom, 1 residue, 1 model selected > select /B:43-44 36 atoms, 35 bonds, 2 residues, 1 model selected > select /B:43-49 112 atoms, 113 bonds, 7 residues, 1 model selected > show sel atoms > color sel byhetero > select /B:33-42,50-68,74-83,87-93,109-133,176-186,198-200 1409 atoms, 1413 bonds, 85 residues, 1 model selected > select /B:96-97 33 atoms, 33 bonds, 2 residues, 1 model selected > select /B:96-99 67 atoms, 69 bonds, 4 residues, 1 model selected > select /B:54 17 atoms, 17 bonds, 1 residue, 1 model selected > select /B:54-67 240 atoms, 243 bonds, 14 residues, 1 model selected > show sel atoms > color sel byhetero > select /B:1-204 3097 atoms, 3126 bonds, 204 residues, 1 model selected > hide sel cartoons > hide sel atoms > select /C:1-169 2723 atoms, 2753 bonds, 169 residues, 1 model selected > hide sel surfaces > hide sel cartoons > close > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG15/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available > mlp Map values for surface "ranked_0.pdb_A SES surface": minimum -25.17, mean -3.564, maximum 24.96 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > show surfaces > hide surfaces > show surfaces > select /A:265@O 1 atom, 1 residue, 1 model selected > select /A:233@CA 1 atom, 1 residue, 1 model selected > select add /A:265@CA 2 atoms, 2 residues, 2 models selected > select add /A:233@CD2 3 atoms, 2 residues, 2 models selected > select add /A:265@HB2 4 atoms, 2 residues, 2 models selected > select add /A:268@HG23 5 atoms, 3 residues, 2 models selected > select add /A:268@HG11 6 atoms, 3 residues, 2 models selected > select add /A:160@HG12 7 atoms, 4 residues, 2 models selected > select add /A:168@HB3 8 atoms, 5 residues, 2 models selected > select add /A:168@CD2 9 atoms, 5 residues, 2 models selected > select add /A:168@HD11 10 atoms, 5 residues, 2 models selected > select add /A:168@HD12 11 atoms, 5 residues, 2 models selected > select add /A:160@HG13 12 atoms, 5 residues, 2 models selected > select add /A:160@CB 13 atoms, 5 residues, 2 models selected > select add /A:165@HG3 14 atoms, 6 residues, 2 models selected > select add /A:168@CD1 15 atoms, 6 residues, 2 models selected > select add /A:268@CG2 16 atoms, 6 residues, 2 models selected > select add /A:268@CG1 17 atoms, 6 residues, 2 models selected > select add /A:265@CG 18 atoms, 6 residues, 2 models selected > select add /A:265@O 19 atoms, 6 residues, 2 models selected > select add /A:265@HD2 20 atoms, 6 residues, 2 models selected > select add /A:265@CB 21 atoms, 6 residues, 2 models selected > select add /A:233@O 22 atoms, 6 residues, 2 models selected > select add /A:233@C 23 atoms, 6 residues, 2 models selected > select add /A:233@HA 24 atoms, 6 residues, 2 models selected > select add /A:265@CD 25 atoms, 6 residues, 2 models selected > select add /A:265@HG2 26 atoms, 6 residues, 2 models selected > select add /A:168@HD23 27 atoms, 6 residues, 2 models selected > select add /A:265@HA 28 atoms, 6 residues, 2 models selected > select add /A:268@HB 29 atoms, 6 residues, 2 models selected > select add /A:268@CB 30 atoms, 6 residues, 2 models selected > select add /A:268@HG13 31 atoms, 6 residues, 2 models selected > select add /A:268@HG12 32 atoms, 6 residues, 2 models selected > select add /A:160@CG1 33 atoms, 6 residues, 2 models selected > select add /A:268@HG21 34 atoms, 6 residues, 2 models selected > select subtract /A:165@HG3 33 atoms, 5 residues, 2 models selected > select add /A:165@CA 34 atoms, 6 residues, 2 models selected > select add /A:165@CG 35 atoms, 6 residues, 2 models selected > select add /A:165@HG3 36 atoms, 6 residues, 2 models selected > select add /A:165@HA 37 atoms, 6 residues, 2 models selected > select add /A:160@CG2 38 atoms, 6 residues, 2 models selected > select add /A:160@HB 39 atoms, 6 residues, 2 models selected > select add /A:168@CB 40 atoms, 6 residues, 2 models selected > select add /A:168@HB2 41 atoms, 6 residues, 2 models selected > select add /A:172@HB2 42 atoms, 7 residues, 2 models selected > select add /A:235@CE1 43 atoms, 8 residues, 2 models selected > select add /A:235@HH 44 atoms, 8 residues, 2 models selected > select subtract /A:235@HH 43 atoms, 8 residues, 2 models selected > select add /A:235@OH 44 atoms, 8 residues, 2 models selected > select add /A:235@HH 45 atoms, 8 residues, 2 models selected > select add /A:235@HE1 46 atoms, 8 residues, 2 models selected > select add /A:168@O 47 atoms, 8 residues, 2 models selected > select add /A:169@N 48 atoms, 9 residues, 2 models selected > select add /A:172@CE3 49 atoms, 9 residues, 2 models selected > select add /A:172@CE2 50 atoms, 9 residues, 2 models selected > select add /A:172@CD2 51 atoms, 9 residues, 2 models selected > select add /A:172@CB 52 atoms, 9 residues, 2 models selected > select subtract /A:172@CE3 51 atoms, 9 residues, 2 models selected > select add /A:172@CZ3 52 atoms, 9 residues, 2 models selected > select add /A:172@CH2 53 atoms, 9 residues, 2 models selected > select add /A:172@CZ2 54 atoms, 9 residues, 2 models selected > select add /A:172@NE1 55 atoms, 9 residues, 2 models selected > select add /A:172@CD1 56 atoms, 9 residues, 2 models selected > select add /A:172@CG 57 atoms, 9 residues, 2 models selected > select add /A:169@CG2 58 atoms, 9 residues, 2 models selected > select add /A:169@HG11 59 atoms, 9 residues, 2 models selected > select add /A:172@CE3 60 atoms, 9 residues, 2 models selected > select add /A:169@HA 61 atoms, 9 residues, 2 models selected > select add /A:169@HG21 62 atoms, 9 residues, 2 models selected > select subtract /A:169@HG11 61 atoms, 9 residues, 2 models selected > select add /A:169@CG1 62 atoms, 9 residues, 2 models selected > select add /A:169@HG11 63 atoms, 9 residues, 2 models selected > select subtract /A:169@HA 62 atoms, 9 residues, 2 models selected > select subtract /A:169@N 61 atoms, 9 residues, 2 models selected > select add /A:169@N 62 atoms, 9 residues, 2 models selected > select add /A:169@HA 63 atoms, 9 residues, 2 models selected > select add /A:168@C 64 atoms, 9 residues, 2 models selected > select add /A:169@CA 65 atoms, 9 residues, 2 models selected > show sel atoms > hide sel surfaces Alignment identifier is 1/A > select /A:250@HB2 1 atom, 1 residue, 1 model selected > hide sel surfaces [Repeated 5 time(s)] > select /A:1-323 5271 atoms, 5335 bonds, 323 residues, 1 model selected > hide sel surfaces > select clear > show cartoons [Repeated 1 time(s)] > select /A 5271 atoms, 5335 bonds, 323 residues, 1 model selected > show sel cartoons > select clear > select /A:172 24 atoms, 25 bonds, 1 residue, 1 model selected > style sel stick Changed 24 atom styles > show sel atoms > select /A:265 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > select /A:268 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select /A:160 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:165 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select /A:168 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:169 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select /A:235 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select /A:233 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:235 21 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:233 40 atoms, 39 bonds, 2 residues, 2 models selected > select add /A:265 64 atoms, 62 bonds, 3 residues, 2 models selected > select add /A:268 80 atoms, 77 bonds, 4 residues, 2 models selected > select add /A:160 99 atoms, 95 bonds, 5 residues, 2 models selected > select add /A:168 118 atoms, 113 bonds, 6 residues, 2 models selected > select add /A:169 134 atoms, 128 bonds, 7 residues, 2 models selected > select add /A:172 158 atoms, 153 bonds, 8 residues, 2 models selected > select add /A:165 180 atoms, 174 bonds, 9 residues, 2 models selected > select clear > show surfaces > select /A:286@CD2 1 atom, 1 residue, 1 model selected > select /A:286@CD1 1 atom, 1 residue, 1 model selected > select add /A:286@CD2 2 atoms, 1 residue, 2 models selected > select add /A:290@HH 3 atoms, 2 residues, 2 models selected > select add /A:212@CD1 4 atoms, 3 residues, 2 models selected > select add /A:217@CG2 5 atoms, 4 residues, 2 models selected > select add /A:270@HD13 6 atoms, 5 residues, 2 models selected > select add /A:287@HD23 7 atoms, 6 residues, 2 models selected > select add /A:279@CD2 8 atoms, 7 residues, 2 models selected > select add /A:277@CG2 9 atoms, 8 residues, 2 models selected > select add /A:224@CE2 10 atoms, 9 residues, 2 models selected > select add /A:224@CG 11 atoms, 9 residues, 2 models selected > select add /A:270@CD1 12 atoms, 9 residues, 2 models selected > select add /A:287@HD11 13 atoms, 9 residues, 2 models selected > select add /A:287@CB 14 atoms, 9 residues, 2 models selected > select add /A:290@CE2 15 atoms, 9 residues, 2 models selected > select add /A:290@CD2 16 atoms, 9 residues, 2 models selected > select add /A:213@HB3 17 atoms, 10 residues, 2 models selected > select add /A:212@HE1 18 atoms, 10 residues, 2 models selected > select add /A:216@OE1 19 atoms, 11 residues, 2 models selected > select add /A:216@OE2 20 atoms, 11 residues, 2 models selected > select add /A:213@O 21 atoms, 11 residues, 2 models selected > select add /A:216@CB 22 atoms, 11 residues, 2 models selected > select add /A:217@CA 23 atoms, 11 residues, 2 models selected > select add /A:221@N 24 atoms, 12 residues, 2 models selected > select add /A:220@CA 25 atoms, 13 residues, 2 models selected > select add /A:224@CD2 26 atoms, 13 residues, 2 models selected > select add /A:283@HA 27 atoms, 14 residues, 2 models selected > select add /A:283@OG 28 atoms, 14 residues, 2 models selected > select add /A:283@HB2 29 atoms, 14 residues, 2 models selected > select add /A:279@HD21 30 atoms, 14 residues, 2 models selected > select add /A:224@OH 31 atoms, 14 residues, 2 models selected > select add /A:287@HA 32 atoms, 14 residues, 2 models selected > select add /A:283@O 33 atoms, 14 residues, 2 models selected > select add /A:279@CD1 34 atoms, 14 residues, 2 models selected > select add /A:287@CD1 35 atoms, 14 residues, 2 models selected > select add /A:274@CD2 36 atoms, 15 residues, 2 models selected > select add /A:291@HD11 37 atoms, 16 residues, 2 models selected > select add /A:291@CD2 38 atoms, 16 residues, 2 models selected > select subtract /A:274@CD2 37 atoms, 15 residues, 2 models selected > select subtract /A:270@CD1 36 atoms, 15 residues, 2 models selected > select add /A:270@CD1 37 atoms, 15 residues, 2 models selected > select add /A:291@CD1 38 atoms, 15 residues, 2 models selected > select add /A:291@HD22 39 atoms, 15 residues, 2 models selected > select add /A:287@HD13 40 atoms, 15 residues, 2 models selected > select add /A:224@HE2 41 atoms, 15 residues, 2 models selected > select add /A:274@CD2 42 atoms, 16 residues, 2 models selected > select add /A:274@HD22 43 atoms, 16 residues, 2 models selected > select add /A:287@CD2 44 atoms, 16 residues, 2 models selected > select add /A:287@HD21 45 atoms, 16 residues, 2 models selected > select add /A:279@HD11 46 atoms, 16 residues, 2 models selected > select add /A:277@HG22 47 atoms, 16 residues, 2 models selected > select add /A:277@HG23 48 atoms, 16 residues, 2 models selected > select add /A:279@HD23 49 atoms, 16 residues, 2 models selected > select subtract /A:283@OG 48 atoms, 16 residues, 2 models selected > select add /A:283@OG 49 atoms, 16 residues, 2 models selected > select add /A:283@CB 50 atoms, 16 residues, 2 models selected > select add /A:283@CA 51 atoms, 16 residues, 2 models selected > select add /A:286@CB 52 atoms, 16 residues, 2 models selected > select add /A:286@HD23 53 atoms, 16 residues, 2 models selected > select add /A:286@HD11 54 atoms, 16 residues, 2 models selected > select add /A:286@HD12 55 atoms, 16 residues, 2 models selected > select add /A:286@HD22 56 atoms, 16 residues, 2 models selected > select subtract /A:213@HB3 55 atoms, 16 residues, 2 models selected > select add /A:209@O 56 atoms, 17 residues, 2 models selected > select add /A:213@CB 57 atoms, 17 residues, 2 models selected > select add /A:213@HB3 58 atoms, 17 residues, 2 models selected > select add /A:213@CA 59 atoms, 17 residues, 2 models selected > select add /A:212@HD1 60 atoms, 17 residues, 2 models selected > select add /A:212@OH 61 atoms, 17 residues, 2 models selected > select add /A:212@CZ 62 atoms, 17 residues, 2 models selected > select add /A:212@CE1 63 atoms, 17 residues, 2 models selected > select add /A:212@CD2 64 atoms, 17 residues, 2 models selected > select add /A:212@CE2 65 atoms, 17 residues, 2 models selected > select add /A:287@HB3 66 atoms, 17 residues, 2 models selected > select add /A:287@N 67 atoms, 17 residues, 2 models selected > select add /A:287@CA 68 atoms, 17 residues, 2 models selected > select add /A:286@C 69 atoms, 17 residues, 2 models selected > select add /A:290@HD2 70 atoms, 17 residues, 2 models selected > select add /A:290@HE2 71 atoms, 17 residues, 2 models selected > select add /A:286@HD21 72 atoms, 17 residues, 2 models selected > select add /A:286@CG 73 atoms, 17 residues, 2 models selected > select add /A:286@HB2 74 atoms, 17 residues, 2 models selected > select add /A:286@HG 75 atoms, 17 residues, 2 models selected > select add /A:279@HD12 76 atoms, 17 residues, 2 models selected > select add /A:283@C 77 atoms, 17 residues, 2 models selected > select add /A:217@HG22 78 atoms, 17 residues, 2 models selected > select add /A:217@N 79 atoms, 17 residues, 2 models selected > select add /A:216@O 80 atoms, 17 residues, 2 models selected > select add /A:216@C 81 atoms, 17 residues, 2 models selected > select add /A:216@HB3 82 atoms, 17 residues, 2 models selected > select add /A:216@CD 83 atoms, 17 residues, 2 models selected > select add /A:213@HA 84 atoms, 17 residues, 2 models selected > select add /A:213@HB1 85 atoms, 17 residues, 2 models selected > select add /A:213@N 86 atoms, 17 residues, 2 models selected > select add /A:220@HA3 87 atoms, 17 residues, 2 models selected > select subtract /A:221@N 86 atoms, 16 residues, 2 models selected > select add /A:221@N 87 atoms, 17 residues, 2 models selected > select subtract /A:291@CD2 86 atoms, 17 residues, 2 models selected > select add /A:221@HG12 87 atoms, 17 residues, 2 models selected > select add /A:217@CG1 88 atoms, 17 residues, 2 models selected > select add /A:217@O 89 atoms, 17 residues, 2 models selected > select add /A:217@HA 90 atoms, 17 residues, 2 models selected > select add /A:217@HG13 91 atoms, 17 residues, 2 models selected > select add /A:217@HG23 92 atoms, 17 residues, 2 models selected > select add /A:221@CG1 93 atoms, 17 residues, 2 models selected > select add /A:291@CD2 94 atoms, 17 residues, 2 models selected > select add /A:221@CA 95 atoms, 17 residues, 2 models selected > select subtract /A:224@CD2 94 atoms, 17 residues, 2 models selected > select add /A:224@CD2 95 atoms, 17 residues, 2 models selected > select add /A:220@C 96 atoms, 17 residues, 2 models selected > select add /A:221@HA 97 atoms, 17 residues, 2 models selected > select add /A:224@HD2 98 atoms, 17 residues, 2 models selected > show sel atoms > select clear > hide surfaces > select /A:213 10 atoms, 9 bonds, 1 residue, 1 model selected > show sel atoms > select /A:212 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select /A:216 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > select /A:286 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:283@CB 1 atom, 1 residue, 1 model selected > show sel atoms > select /A:290 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select /A:287 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:279 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:277 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select /A:224@OH 1 atom, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > select subtract /A:224 1 model selected > select add /A:224 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select /A:217 16 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select /A:221 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:291 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:158 16 atoms, 15 bonds, 1 residue, 1 model selected > select /A:157 22 atoms, 21 bonds, 1 residue, 1 model selected > select /A:274 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select /A:270@CD1 1 atom, 1 residue, 1 model selected > select /A:269 24 atoms, 23 bonds, 1 residue, 1 model selected > select /A:270 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select /A:212 21 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:213 31 atoms, 30 bonds, 2 residues, 2 models selected > select add /A:216 46 atoms, 44 bonds, 3 residues, 2 models selected > select add /A:286 65 atoms, 62 bonds, 4 residues, 2 models selected > select add /A:290 86 atoms, 83 bonds, 5 residues, 2 models selected > select add /A:217 102 atoms, 98 bonds, 6 residues, 2 models selected > select add /A:220 109 atoms, 104 bonds, 7 residues, 2 models selected > select subtract /A:220 102 atoms, 98 bonds, 6 residues, 2 models selected > select add /A:221 121 atoms, 116 bonds, 7 residues, 2 models selected > select add /A:224 142 atoms, 137 bonds, 8 residues, 2 models selected > select add /A:279@CA 143 atoms, 137 bonds, 9 residues, 2 models selected > select add /A:278 157 atoms, 152 bonds, 10 residues, 2 models selected > select subtract /A:278 143 atoms, 138 bonds, 9 residues, 2 models selected > select add /A:280 155 atoms, 149 bonds, 10 residues, 2 models selected > select subtract /A:279 154 atoms, 148 bonds, 9 residues, 2 models selected > select subtract /A:280 142 atoms, 137 bonds, 8 residues, 2 models selected > select add /A:279 161 atoms, 155 bonds, 9 residues, 2 models selected > select add /A:283 172 atoms, 165 bonds, 10 residues, 2 models selected > select add /A:277 186 atoms, 178 bonds, 11 residues, 2 models selected > select add /A:287 205 atoms, 196 bonds, 12 residues, 2 models selected > select add /A:291 224 atoms, 214 bonds, 13 residues, 2 models selected > select add /A:274 243 atoms, 232 bonds, 14 residues, 2 models selected > select add /A:270 262 atoms, 250 bonds, 15 residues, 2 models selected > select add /A:233 281 atoms, 268 bonds, 16 residues, 2 models selected > select subtract /A:233 262 atoms, 250 bonds, 15 residues, 2 models selected > select /A 5271 atoms, 5335 bonds, 323 residues, 1 model selected > color (#!1 & sel) blue > color (#!1 & sel) cornflower blue > color sel byhetero > select clear > open "/Users/Gareth/Documents/DDR > 2022/AlphaFold/MRGX/AF-Q15014-F1-model_v4.pdb" AF-Q15014-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for mortality factor 4-like protein 2 (Q15014) [more info...] Chain information for AF-Q15014-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | mortality factor 4-like protein 2 | MO4L2_HUMAN > sequence chain #2/A Alignment identifier is 2/A > select #2/A:1-288 2275 atoms, 2323 bonds, 288 residues, 1 model selected > color sel hot pink > 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 A (#1) with AF-Q15014-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1033.9 RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 267 pairs: 31.035) > select clear > select #2/A:1-288 2275 atoms, 2323 bonds, 288 residues, 1 model selected > mlp sel Map values for surface "AF-Q15014-F1-model_v4.pdb_A SES surface": minimum -26.64, mean -5.47, maximum 23.64 To also show corresponding color key, enter the above mlp command and add key true > select #1/A 5271 atoms, 5335 bonds, 323 residues, 1 model selected > show sel surfaces > color (#!1 & sel) cornflower blue > hide sel surfaces > select clear > hide surfaces > select #2/A:1-288 2275 atoms, 2323 bonds, 288 residues, 1 model selected Alignment identifier is 2/A > select clear > hide atoms > select #2/A:76 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:76 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:170 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:170 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:135 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:135 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:140 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:140 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:175 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:175 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:140 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:140 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel byhetero > show sel atoms > hide sel atoms > show sel atoms > color sel byhetero > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 7 atom styles > color sel byhetero > select #1/A:183 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:183 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:148 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:148-149 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:147-148 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/A:147-148 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/A:149-150 15 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:149-151 20 atoms, 20 bonds, 3 residues, 1 model selected > select #2/A:148 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:148 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:157 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:157 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero [Repeated 1 time(s)] > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > select #1/A:192 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:192 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:161 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:161 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:196 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:196 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:200 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:200 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:165 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:165 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:169 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:169 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:204 24 atoms, 23 bonds, 1 residue, 1 model selected > select #1/A:204 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:207 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:207 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:172 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:172 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:213 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:213 5 atoms, 4 bonds, 1 residue, 1 model selected > select > #2/A:112-116,127-129,131-141,155-169,173-198,201-203,205-213,219-221,225-241,246-265,267-270,273-275,281-287 1019 atoms, 1029 bonds, 126 residues, 1 model selected > select #2/A:212 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:212-213 13 atoms, 12 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > addH Unknown command: addH > addcharge H Using Amber 20 recommended default charges and atom types for standard residues > show sel atoms > color sel byhetero > show H > undo > ui tool show H-Bonds > select #1/A:247 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:247-248 22 atoms, 21 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select #2/A:254 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:254 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > show sel atoms [Repeated 1 time(s)] > select #1/A:289 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:289 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:269 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:269 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:304 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:304 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:307 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:307 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:272 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:272 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:277 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:277 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:312 15 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:312 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:315 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:315-316 28 atoms, 29 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select #2/A:280 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:280-281 11 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select #1/A:323 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:323 17 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:288 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A 2275 atoms, 2323 bonds, 288 residues, 1 model selected > select #2/A:126 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:126-288 1318 atoms, 1350 bonds, 163 residues, 1 model selected > select #2/A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:112-288 1437 atoms, 1470 bonds, 177 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-Q15014-F1-model_v4.pdb_A SES surface #2.1: minimum, -17.15, mean 0.84, maximum 16.70 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select #1/A:212 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:212 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:200 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:200 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel surfaces > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -25.17, mean -3.564, maximum 24.96 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -15.58, mean 1.22, maximum 17.31 To also show corresponding color key, enter the above coulombic command and add key true > select #1/A:202 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:202 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:204 24 atoms, 23 bonds, 1 residue, 1 model selected > select #1/A:204 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > show sel surfaces > select #1/A:200 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:200 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:200,204 45 atoms, 44 bonds, 2 residues, 1 model selected > hide sel surfaces > select #1/A:289 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:289 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:200,289 35 atoms, 34 bonds, 2 residues, 1 model selected > select #1/A:200,204,289 59 atoms, 57 bonds, 3 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > select #2/A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:112-288 1437 atoms, 1470 bonds, 177 residues, 1 model selected > hide sel surfaces > select clear > select #2/A:60 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:60-62 19 atoms, 18 bonds, 3 residues, 1 model selected > select #2/A:273-274 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2/A:273-288 128 atoms, 130 bonds, 16 residues, 1 model selected > select #2/A:267 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:267-288 171 atoms, 174 bonds, 22 residues, 1 model selected > show sel surfaces > select > #2/A:112-116,127-129,131-141,155-169,173-198,201-203,205-213,219-221,225-241,246-265,267-270,273-275,281-287 1019 atoms, 1029 bonds, 126 residues, 1 model selected > select #2/A:155 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:155-160 45 atoms, 44 bonds, 6 residues, 1 model selected > select #2/A:145 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:145-149 45 atoms, 45 bonds, 5 residues, 1 model selected > select #2/A:142 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:142-155 119 atoms, 120 bonds, 14 residues, 1 model selected > select #2/A:137-138 22 atoms, 23 bonds, 2 residues, 1 model selected > select #2/A:137-154 156 atoms, 159 bonds, 18 residues, 1 model selected > show sel surfaces > select clear > select #2/A:156 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:156 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:131-132 21 atoms, 23 bonds, 2 residues, 1 model selected > select #2/A:131-141 97 atoms, 101 bonds, 11 residues, 1 model selected > show sel surfaces > select clear > select #1/A:170 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:170-177 136 atoms, 137 bonds, 8 residues, 1 model selected > show sel surfaces > select #1/A:302 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:302-323 334 atoms, 339 bonds, 22 residues, 1 model selected > show sel surfaces > select #1/A:290-291 40 atoms, 40 bonds, 2 residues, 1 model selected > select #1/A:290-323 550 atoms, 559 bonds, 34 residues, 1 model selected > show sel surfaces > select #1/A:271 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:271-323 841 atoms, 852 bonds, 53 residues, 1 model selected > show sel surfaces > select #2/A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:112-288 1437 atoms, 1470 bonds, 177 residues, 1 model selected > hide sel surfaces > select #1/A:166-167 38 atoms, 40 bonds, 2 residues, 1 model selected > select #1/A:166-192 465 atoms, 472 bonds, 27 residues, 1 model selected > show sel surfaces > select #1/A:248 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #2/A:212 20 atoms, 18 bonds, 2 residues, 3 models selected > select subtract #2/A:212 12 atoms, 11 bonds, 1 residue, 3 models selected > select add #2/A:212 20 atoms, 18 bonds, 2 residues, 3 models selected > select add #1/A:247 30 atoms, 27 bonds, 3 residues, 4 models selected > select #2/A:112-288 1437 atoms, 1470 bonds, 177 residues, 1 model selected > select #1/A:247 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:247-248 22 atoms, 21 bonds, 2 residues, 1 model selected > show sel surfaces > hide sel surfaces > select #1/A:236-237 42 atoms, 42 bonds, 2 residues, 1 model selected > select #1/A:236-248 218 atoms, 220 bonds, 13 residues, 1 model selected > show sel surfaces > select #1/A:207 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:207-323 1878 atoms, 1903 bonds, 117 residues, 1 model selected > hide sel surfaces > select #1/A:162-163 30 atoms, 29 bonds, 2 residues, 1 model selected > select #1/A:162-323 2645 atoms, 2680 bonds, 162 residues, 1 model selected > hide sel surfaces > select clear Drag select of 21 atoms, 18 residues, 17 bonds Drag select of 11 atoms, 26 residues, 6 bonds Drag select of 31 atoms, 18 residues, 30 bonds Drag select of 6 residues, 1 atoms > select add #1/A:321 516 atoms, 57 bonds, 41 residues, 4 models selected > select add #1/A:183 537 atoms, 78 bonds, 42 residues, 4 models selected > select add #2/A:149 545 atoms, 85 bonds, 43 residues, 4 models selected > show sel surfaces > select clear [Repeated 2 time(s)] > select #1/A:50 14 atoms, 13 bonds, 1 residue, 1 model selected > select clear > select #2/A:280 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel surfaces > select clear > hide surfaces > select #1/A:154 16 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:154 16 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:302 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:302-323 334 atoms, 339 bonds, 22 residues, 1 model selected > show sel surfaces > select #1/A:170 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:170-189 353 atoms, 357 bonds, 20 residues, 1 model selected > show sel surfaces > select clear > select #2/A:78 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:78-81 35 atoms, 34 bonds, 4 residues, 1 model selected > select #2/A:135 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:135-154 173 atoms, 176 bonds, 20 residues, 1 model selected > select #2/A:262 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:262-288 213 atoms, 217 bonds, 27 residues, 1 model selected > select #2/A:266 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:266-288 179 atoms, 182 bonds, 23 residues, 1 model selected > select #2/A:267 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:267-288 171 atoms, 174 bonds, 22 residues, 1 model selected > select #2/A:131,267-288 178 atoms, 181 bonds, 23 residues, 1 model selected > select #2/A:131,267-288 178 atoms, 181 bonds, 23 residues, 1 model selected > select #2/A:131,267-288 178 atoms, 181 bonds, 23 residues, 1 model selected > select #2/A:131,135-154,267-288 351 atoms, 357 bonds, 43 residues, 1 model selected > select #2/A:131,135-154,267-288 351 atoms, 357 bonds, 43 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces [Repeated 1 time(s)] > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces No map chosen to save [Repeated 1 time(s)] > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRG15 Surface 1.tif" width 749 height 533 supersample 3 > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > select #1/A:170-171 24 atoms, 23 bonds, 2 residues, 1 model selected > select #1/A:170-196 457 atoms, 461 bonds, 27 residues, 1 model selected > hide sel surfaces > select #1/A:295 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:295-323 461 atoms, 467 bonds, 29 residues, 1 model selected > hide sel surfaces > select clear > select #2/A:131-154,267-288 380 atoms, 389 bonds, 46 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > select #1/A:166 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:166-189 426 atoms, 433 bonds, 24 residues, 1 model selected > select #1/A:166-189,307-323 686 atoms, 697 bonds, 41 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > select clear > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRGX Surface 1.tif" width 749 height 533 supersample 3 > select #1/A:166 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:166-323 2574 atoms, 2609 bonds, 158 residues, 1 model selected > show sel surfaces > select #2/A:127 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:127-288 1311 atoms, 1342 bonds, 162 residues, 1 model selected > hide sel surfaces > select clear > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > show sel surfaces > select clear > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRG15 Surface 2.tif" width 749 height 533 supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRG15 Surface 3.tif" width 749 height 533 supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRG15 Surface 4.tif" width 749 height 533 supersample 3 > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > hide sel surfaces > select #2/A:126-127 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:126-288 1318 atoms, 1350 bonds, 163 residues, 1 model selected > show sel surfaces > select clear > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRGX Surface 2.tif" width 749 height 533 supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRGX Surface 3.tif" width 749 height 533 supersample 3 > save "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRGX/MRG15 MRGX Comparison > MRGX Surface 4.tif" width 749 height 533 supersample 3 > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > select #2/A:126 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:126-288 1318 atoms, 1350 bonds, 163 residues, 1 model selected > hide sel surfaces > select clear > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > mlp sel Map values for surface "ranked_0.pdb_A SES surface": minimum -25.17, mean -3.564, maximum 24.96 To also show corresponding color key, enter the above mlp command and add key true > select clear > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > hide sel surfaces > select #2/A:126 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:126-288 1318 atoms, 1350 bonds, 163 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface "AF-Q15014-F1-model_v4.pdb_A SES surface": minimum -26.64, mean -5.47, maximum 23.64 To also show corresponding color key, enter the above mlp command and add key true > select clear > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > select clear > select #1/A:161 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:161-323 2659 atoms, 2695 bonds, 163 residues, 1 model selected > hide sel surfaces > select #2/A:126 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:126-288 1318 atoms, 1350 bonds, 163 residues, 1 model selected > hide sel surfaces > select clear > select #1/A:140-141 28 atoms, 27 bonds, 2 residues, 1 model selected > select #1/A:140-141 28 atoms, 27 bonds, 2 residues, 1 model selected > select #2/A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:112-116 43 atoms, 43 bonds, 5 residues, 1 model selected > select #1/A:89 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:89-93 68 atoms, 67 bonds, 5 residues, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-33 265 atoms, 267 bonds, 33 residues, 1 model selected > select #2/A:56-57 11 atoms, 11 bonds, 2 residues, 1 model selected > select #2/A:56-62 55 atoms, 57 bonds, 7 residues, 1 model selected > select #2/A:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:34-111 573 atoms, 584 bonds, 78 residues, 1 model selected > mlp sel Map values for surface "AF-Q15014-F1-model_v4.pdb_A SES surface": minimum -26.64, mean -5.47, maximum 23.64 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for AF-Q15014-F1-model_v4.pdb_A SES surface #2.1: minimum, -17.15, mean 0.84, maximum 16.70 To also show corresponding color key, enter the above coulombic command and add key true > select #2/A:53 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:53-71 133 atoms, 138 bonds, 19 residues, 1 model selected > mlp sel Map values for surface "AF-Q15014-F1-model_v4.pdb_A SES surface": minimum -26.64, mean -5.47, maximum 23.64 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for AF-Q15014-F1-model_v4.pdb_A SES surface #2.1: minimum, -17.15, mean 0.84, maximum 16.70 To also show corresponding color key, enter the above coulombic command and add key true > select #1/A:88 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:88-161 1170 atoms, 1177 bonds, 74 residues, 1 model selected > hide sel surfaces > select #2/A:53 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:53-115 470 atoms, 481 bonds, 63 residues, 1 model selected > hide sel surfaces > select clear > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-33 265 atoms, 267 bonds, 33 residues, 1 model selected > show sel surfaces > hide sel surfaces > select clear > close session > open "/Users/Gareth/Documents/DDR 2022/AlphaFold/MRG15/MRG15/ranked_0.pdb" Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available > select /A:1-323 5271 atoms, 5335 bonds, 323 residues, 1 model selected > color sel cornflower blue > open "/Users/Gareth/Documents/DDR > 2022/AlphaFold/MSLH3/AF-Q8N5Y2-F1-model_v4.pdb" AF-Q8N5Y2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for male-specific lethal 3 homolog (Q8N5Y2) [more info...] Chain information for AF-Q8N5Y2-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | male-specific lethal 3 homolog | MS3L1_HUMAN > select #2/A:1-521 4212 atoms, 4311 bonds, 521 residues, 1 model selected > color sel hot pink > 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 A (#1) with AF-Q8N5Y2-F1-model_v4.pdb, chain A (#2), sequence alignment score = 494.6 RMSD between 136 pruned atom pairs is 0.606 angstroms; (across all 320 pairs: 37.193) > select clear > 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: 96 days 3:37 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: alabaster: 0.7.12 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 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 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 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 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 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 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
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Structure Comparison |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → MatchMaker: 'NoneType' object has no attribute 'setChecked' |
comment:2 by , 3 years ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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