id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4416 MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted yuhang.wang.19@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description Match maker (align two chains from two proteins) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > help help:quickstart Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3 Installed ChimeraX-AddH (2.1.3) Installed ChimeraX-HKCage (1.3) > open 3uag Summary of feedback from opening 3uag fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""UMA"" near line 4565 notes | Fetching compressed mmCIF 3uag from http://files.rcsb.org/download/3uag.cif Fetching CCD MN from http://ligand-expo.rcsb.org/reports/M/MN/MN.cif Fetching CCD UMA from http://ligand-expo.rcsb.org/reports/U/UMA/UMA.cif Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif Fetching CCD EPE from http://ligand-expo.rcsb.org/reports/E/EPE/EPE.cif Fetching CCD KCX from http://ligand-expo.rcsb.org/reports/K/KCX/KCX.cif 3uag title: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...] Chain information for 3uag #1 --- Chain | Description A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase) Non-standard residues in 3uag #1 --- ADP — adenosine-5'-diphosphate EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) MN — manganese (II) ion > lighting full > style /b stick Changed 0 atom styles Drag select of 32 atoms, 100 residues, 1 pseudobonds, 20 bonds > style /b stick Changed 0 atom styles > select clear > style /a stick Changed 3686 atom styles > delete Missing or invalid ""atoms"" argument: empty atom specifier > close #1 > open 7kkj Summary of feedback from opening 7kkj fetched from pdb --- notes | Fetching compressed mmCIF 7kkj from http://files.rcsb.org/download/7kkj.cif Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif 7kkj title: Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...] Chain information for 7kkj #1 --- Chain | Description A C | Synthetic nanobody mNb6 Non-standard residues in 7kkj #1 --- CL — chloride ion SO4 — sulfate ion 7kkj mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select :CL 1 atom, 1 residue, 1 model selected > select :SO4 20 atoms, 16 bonds, 4 residues, 1 model selected > select :CL 1 atom, 1 residue, 1 model selected > hide sel atoms > hide sel atoms > select :CL 1 atom, 1 residue, 1 model selected > show sel atoms > select :SO4 20 atoms, 16 bonds, 4 residues, 1 model selected > hide sel atoms > show sel atoms > sym #1 assembly 1 > view > sym #1 assembly 2 > view > sym #1 assembly 1 > view > show #1 models > hide #1 models > hide #2 models > hide #3 models > show #3 models > show #2 models > hide #3 models > show #3 models > show #1 models > hide #1 models > close #2 > close #3 > close #4 > show #1 models > select :CL 1 atom, 1 residue, 1 model selected > show sel atoms > show sel atoms > hide sel atoms > show sel atoms > show sel atoms > hide sel atoms > select clear > show atoms > hide atoms > show atoms > select clear > hide atoms > hide atoms > show atoms > hide atoms > show atoms > hide atoms > select clear > show atoms > show atoms > hide atoms > clear Unknown command: clear Drag select of 237 residues > hide sel cartoons > show sel cartoons > style sel stick Changed 3531 atom styles > style sel sphere Changed 3531 atom styles > show sel atoms > style sel ball Changed 3531 atom styles > style sel sphere Changed 3531 atom styles > style sel stick Changed 3531 atom styles > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > style sel sphere Changed 3531 atom styles > style sel stick Changed 3531 atom styles > style sel ball Changed 3531 atom styles > close > open 3uag format mmcif fromDatabase pdb Summary of feedback from opening 3uag fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""UMA"" near line 4565 3uag title: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...] Chain information for 3uag #1 --- Chain | Description A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase) Non-standard residues in 3uag #1 --- ADP — adenosine-5'-diphosphate EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) MN — manganese (II) ion > show atoms > hide atoms > show atoms > show cartoons > hide cartoons > style stick Changed 3686 atom styles > style sphere Changed 3686 atom styles > style ball Changed 3686 atom styles > style sphere Changed 3686 atom styles > open 3uag Summary of feedback from opening 3uag fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""UMA"" near line 4565 3uag title: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...] Chain information for 3uag #2 --- Chain | Description A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase) Non-standard residues in 3uag #2 --- ADP — adenosine-5'-diphosphate EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) MN — manganese (II) ion > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > lighting soft > lighting simple > lighting full > lighting full > lighting soft > hide #!1 atoms > hide #!1 atoms > show #!1 atoms > style #!1 stick Changed 3686 atom styles > show #!1 cartoons > hide #!1 cartoons > show #!1 cartoons > hide #!1 atoms > lighting full > select #1/A:424 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:343 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:343 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:344 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:343 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 46 atoms, 46 bonds, 6 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 46 atoms, 46 bonds, 6 residues, 1 model selected > select up 3686 atoms, 3383 bonds, 793 residues, 1 model selected > select #1/A:120 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 98 atoms, 97 bonds, 14 residues, 1 model selected > color sel yellow > select #1/A:367 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 55 atoms, 56 bonds, 6 residues, 1 model selected > select up 3686 atoms, 3383 bonds, 793 residues, 1 model selected > select down 55 atoms, 56 bonds, 6 residues, 1 model selected > color sel bychain > color sel bychain > rainbow sel > color sel byhetero > coulombic sel Don't know how to assign charges to the following residue types: KCX > mlp sel Map values for surface ""3uag_A SES surface"": minimum -29.38, mean -6.019, maximum 71.59 > color bfactor sel 55 atoms, 6 residues, 1 surfaces, atom bfactor range 14 to 46.7 > color bfactor sel 55 atoms, 6 residues, 1 surfaces, atom bfactor range 14 to 46.7 > color sel bynucleotide > color sel byhetero > color sel bychain > color sel byhetero > select clear > color #!1 bychain > color #!1 byhetero > rainbow #!1 > coulombic #!1 Don't know how to assign charges to the following residue types: KCX > mlp #!1 Map values for surface ""3uag_A SES surface"": minimum -6.634e+05, mean -823.8, maximum 22.21 > color #!1 byhetero > rainbow #!1 > mlp #!1 Map values for surface ""3uag_A SES surface"": minimum -29.38, mean -6.128, maximum 22.21 > rainbow #!1 > hide #!1 atoms > hide #!1 atoms > select clear > hide #!1 atoms > show #!1 atoms > show #!1 cartoons > hide #!1 cartoons > hide #!1 surfaces > show #!1 cartoons > hide #!1 atoms > color #!1 byhetero > select clear > color #!1 byhetero > color #!1 byhetero > rainbow #!1 > rainbow #!1 > hide #!1 atoms > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting soft > preset cartoons/nucleotides cylinders/stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > select clear > ui tool show ViewDockX No suitable models found for ViewDockX > show #!1 surfaces > hide #!1 surfaces > show #!1 surfaces > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 15 atoms, 15 bonds, 1 residue, 1 model selected > delete elected Missing or invalid ""atoms"" argument: invalid atoms specifier > coulombic sel Don't know how to assign charges to the following residue types: EPE > select clear Drag select of 3uag_A SES surface, 324486 of 324758 triangles, 92 atoms, 470 residues, 3 pseudobonds, 95 bonds > coulombic sel Don't know how to assign charges to the following residue types: KCX > delete H > coulombic sel Don't know how to assign charges to the following residue types: KCX Drag select of 3uag_A SES surface, 18939 of 324758 triangles, 26 atoms, 59 residues, 28 bonds > select clear Drag select of 3uag_A SES surface, 92 atoms, 470 residues, 3 pseudobonds, 95 bonds > coulombic sel Don't know how to assign charges to the following residue types: KCX Drag select of 3uag_A SES surface, 92 atoms, 470 residues, 3 pseudobonds, 95 bonds > delete H > coulombic sel Don't know how to assign charges to the following residue types: KCX > open 7kkj 7kkj title: Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...] Chain information for 7kkj #3 --- Chain | Description A C | Synthetic nanobody mNb6 Non-standard residues in 7kkj #3 --- CL — chloride ion SO4 — sulfate ion 7kkj mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > hide #1.3 models > hide #1.2 models > hide #1.1 models > hide #!1 models > lighting soft > delete H > show #3 surfaces > coulombic #!3 The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 7kkj #3/C SER 119 OG > mlp #!3 Map values for surface ""7kkj_A SES surface"": minimum -26.2, mean -6.038, maximum 19.75 Map values for surface ""7kkj_C SES surface"": minimum -25.35, mean -5.999, maximum 20.09 > coulombic #!3 > open 4uag Summary of feedback from opening 4uag fetched from pdb --- notes | Fetching compressed mmCIF 4uag from http://files.rcsb.org/download/4uag.cif Fetching CCD UAG from http://ligand-expo.rcsb.org/reports/U/UAG/UAG.cif Fetching CCD UNX from http://ligand-expo.rcsb.org/reports/U/UNX/UNX.cif 4uag title: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...] Chain information for 4uag #4 --- Chain | Description A | udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase Non-standard residues in 4uag #4 --- SO4 — sulfate ion UAG — uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine-D-glutamate UNX — unknown atom or ion > hide #!3 models > delete H > show #!4 surfaces > coulombic #!4 Don't know how to assign charges to the following residue types: KCX > delete KCK Missing or invalid ""atoms"" argument: invalid atoms specifier > color bfactor #!4 3623 atoms, 761 residues, 1 surfaces, atom bfactor range 5.94 to 63.8 > show #!2 models > hide #!4 models > hide #4.1 models > hide #4.2 models > mlp #!2 Map values for surface ""3uag_A SES surface"": minimum -29.38, mean -6.128, maximum 22.21 > color #!2 byhetero > color #!2 bychain > rainbow #!2 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2/A #4/A Alignment identifier is 1 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 15 atoms, 15 bonds, 1 residue, 1 model selected Seqview [ID: 1] region 3 chains [168-180] RMSD: 0.306 > hide sel & #!2 surfaces > hide sel & #!2 surfaces > show sel & #!2 surfaces > ui tool show ""Modeller Comparative"" > open 4uag fromDatabase eds Summary of feedback from opening 4uag fetched from eds --- note | Fetching map 4uag from http://www.ebi.ac.uk/pdbe/coordinates/files/4uag.ccp4 Opened 4uag.ccp4, grid size 140,118,116, pixel 0.548,0.548,0.561, shown at level 1.19, step 1, values float32 > volume #5 level 1.198 > style sel & #!2 stick Changed 90 atom styles > select clear > style #!2 stick Changed 3686 atom styles > hide #!2 surfaces > volume #5 level 0.8919 > volume #5 level 0.6055 > volume #5 level 0.803 > volume #5 color #ff55ff > volume #5 color #aaff7f > volume #5 color white > volume showOutlineBox true > volume zone #2 nearAtoms #1 > ui tool show ""Side View"" > volume showOutlineBox false > hide #!2 models > hide #!5 models > show #!4 models > ui tool show ""Modeller Comparative"" No alignments chosen for modeling Drag select of 206 atoms, 429 residues, 158 bonds > ui tool show ""Modeller Comparative"" No alignments chosen for modeling > open 7kkl Summary of feedback from opening 7kkl fetched from pdb --- notes | Fetching compressed mmCIF 7kkl from http://files.rcsb.org/download/7kkl.cif Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif 7kkl title: SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...] Chain information for 7kkl #6 --- Chain | Description A C D | Spike glycoprotein B E F | Synthetic nanobody mNb6 Non-standard residues in 7kkl #6 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 7kkl 7kkl title: SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...] Chain information for 7kkl #7 --- Chain | Description A C D | Spike glycoprotein B E F | Synthetic nanobody mNb6 Non-standard residues in 7kkl #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide #!4 models > hide #!6 models > select #7 53325 atoms, 54012 bonds, 21 pseudobonds, 3423 residues, 2 models selected > ~select #7 Nothing selected > hide #!7 models > close > open 7kkl 7kkl title: SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...] Chain information for 7kkl #1 --- Chain | Description A C D | Spike glycoprotein B E F | Synthetic nanobody mNb6 Non-standard residues in 7kkl #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select /B:13@HG3 1 atom, 1 residue, 1 model selected > select up 52 atoms, 50 bonds, 3 residues, 1 model selected > select up 355 atoms, 354 bonds, 22 residues, 1 model selected > select up 5256 atoms, 5313 bonds, 354 residues, 1 model selected > color sel yellow > color /B,E,F gold > color /B,E,F red Drag select of 53325 atoms, 21 pseudobonds, 1809 bonds > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > save C:\Users\10749\Desktop\image1.png supersample 3 > save C:\Users\10749\Desktop\image2.png supersample 3 > open 3uag format mmcif fromDatabase pdb Summary of feedback from opening 3uag fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""UMA"" near line 4565 3uag title: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...] Chain information for 3uag #2 --- Chain | Description A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase) Non-standard residues in 3uag #2 --- ADP — adenosine-5'-diphosphate EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) MN — manganese (II) ion > save C:\Users\10749/Deskspike.png width 1500 > open 6vxx Summary of feedback from opening 6vxx fetched from pdb --- note | Fetching compressed mmCIF 6vxx from http://files.rcsb.org/download/6vxx.cif 6vxx title: Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...] Chain information for 6vxx #3 --- Chain | Description A B C | Spike glycoprotein Non-standard residues in 6vxx #3 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > select #1/C:533@HB2 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 197 atoms, 197 bonds, 12 residues, 1 model selected > select up 15693 atoms, 15891 bonds, 1011 residues, 1 model selected > select up 53325 atoms, 54012 bonds, 3423 residues, 1 model selected > select up 80705 atoms, 81692 bonds, 7195 residues, 3 models selected > select up 80705 atoms, 81692 bonds, 7195 residues, 3 models selected > select down 53325 atoms, 54012 bonds, 3423 residues, 1 model selected > select clear > select #3/A:594 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 54 atoms, 54 bonds, 8 residues, 1 model selected > select up 7758 atoms, 7949 bonds, 983 residues, 1 model selected > select up 23694 atoms, 24297 bonds, 2979 residues, 1 model selected > hide sel cartoons > show sel atoms > color sel byhetero > show sel surfaces > color sel byhetero > select up 23694 atoms, 24297 bonds, 33 pseudobonds, 2979 residues, 5 models selected > select #1/C:533@CD2 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 197 atoms, 197 bonds, 12 residues, 1 model selected > select up 15693 atoms, 15891 bonds, 1011 residues, 1 model selected > select up 53325 atoms, 54012 bonds, 3423 residues, 1 model selected > color bfactor sel 53325 atoms, 3423 residues, atom bfactor range 62.3 to 225 > color sel bychain > color sel byhetero > color sel bynucleotide > coulombic sel > ui mousemode right ""translate selected models"" > select clear > select #1/C:643@CD1 1 atom, 1 residue, 1 model selected > select up 20 atoms, 20 bonds, 1 residue, 2 models selected > select up 67 atoms, 67 bonds, 4 residues, 2 models selected > select up 15693 atoms, 15891 bonds, 1011 residues, 2 models selected > select up 53325 atoms, 54012 bonds, 3423 residues, 2 models selected > select up 53325 atoms, 54012 bonds, 21 pseudobonds, 3423 residues, 8 models selected Drag select of 7kkl_A SES surface, 3397 of 1157934 triangles, 7kkl_C SES surface, 9957 of 1158332 triangles, 7kkl_D SES surface, 2716 of 1152598 triangles, 156 atoms > select up 683 atoms, 664 bonds, 45 residues, 4 models selected > select up 3074 atoms, 3078 bonds, 202 residues, 4 models selected > select up 47079 atoms, 47673 bonds, 3033 residues, 4 models selected > select up 53325 atoms, 54012 bonds, 3423 residues, 4 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected models"" Drag select of 7kkl_A SES surface, 11916 of 1157934 triangles, 7kkl_C SES surface, 22810 of 1158332 triangles, 7kkl_D SES surface, 25555 of 1152598 triangles, 853 atoms, 2 bonds > ui tool show ""Fit in Map"" > select #3/C:440@O 1 atom, 1 residue, 1 model selected > select #1 53325 atoms, 54012 bonds, 21 pseudobonds, 3423 residues, 2 models selected > select #2 3686 atoms, 3383 bonds, 8 pseudobonds, 793 residues, 3 models selected > select #3 23694 atoms, 24297 bonds, 33 pseudobonds, 2979 residues, 2 models selected > select #2 3686 atoms, 3383 bonds, 8 pseudobonds, 793 residues, 3 models selected > open 7kkj 7kkj title: Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...] Chain information for 7kkj #4 --- Chain | Description A C | Synthetic nanobody mNb6 Non-standard residues in 7kkj #4 --- CL — chloride ion SO4 — sulfate ion 7kkj mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select #4/C 1841 atoms, 1792 bonds, 187 residues, 1 model selected > delete atoms sel > delete bonds sel > undo Undo failed, probably because structures have been modified. > undo > undo > undo > undo > undo > ui tool show Matchmaker > matchmaker #4/A to #1/B 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 7kkl, chain B (#1) with 7kkj, chain A (#4), sequence alignment score = 589.7 RMSD between 90 pruned atom pairs is 0.751 angstroms; (across all 117 pairs: 3.062) Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > mmaker #4/A to #1/B 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 7kkl, chain B (#1) with 7kkj, chain A (#4), sequence alignment score = 589.7 RMSD between 90 pruned atom pairs is 0.751 angstroms; (across all 117 pairs: 3.062) Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > select #1/A:245@CG 1 atom, 1 residue, 1 model selected Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > select #1/A:607@N 1 atom, 1 residue, 1 model selected Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. OpenGL version: 3.3.13559 Core Profile Forward-Compatible Context 26.20.12036.1 OpenGL renderer: Radeon (TM) 540X OpenGL vendor: ATI Technologies Inc. Manufacturer: LENOVO Model: 20QC000HCD OS: Microsoft Windows 10 家庭中文版 (Build 18363) Memory: 8,395,395,072 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 WMI: 1.5.1 }}} " defect closed normal Structure Comparison duplicate all ChimeraX