Opened 3 years ago
Closed 3 years ago
#8393 closed defect (can't reproduce)
Matchmaker: 'NoneType' object has no attribute 'setChecked'
Reported by: | Owned by: | pett | |
---|---|---|---|
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. OpenGL version: 4.1 INTEL-12.10.12 OpenGL renderer: Intel Iris OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro11,1 Processor Name: Intel Core i5 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 156.0.0.0.0 SMC Version (system): 2.16f68 Software: System Software Overview: System Version: macOS 10.14.6 (18G103) Kernel Version: Darwin 18.7.0 Time since boot: 89 days 1:27 Graphics/Displays: Intel Iris: Chipset Model: Intel Iris Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0a2e Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Installed Packages: 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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Tried various things -- couldn't reproduce