Opened 23 months ago
Closed 23 months ago
#10305 closed defect (duplicate)
KeyError matching selected regions
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: Windows-10-10.0.19045 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:\\\Users\\\sarson-lawrence.k\\\OneDrive - > wehi.edu.au\\\GCSF_paper\\\gp130_figure.cxs" Log from Mon Nov 13 10:50:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8d82 8d82 title: Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full extracellular domains [more info...] Chain information for 8d82 #1 --- Chain | Description | UniProt A E | Interleukin-6 receptor subunit beta | IL6RB_HUMAN 23-700 C G | Soluble interleukin-6 receptor subunit alpha | IL6RA_HUMAN 20-331 D H | Interleukin-6 | IL6_HUMAN 30-212 Non-standard residues in 8d82 #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) > set bgColor white > hide atoms > show cartoons > show surfaces > transparency70 Unknown command: transparency70 > transparency 70 Drag select of 8d82_E SES surface, 137124 of 595960 triangles, 149 residues Drag select of 8d82_A SES surface, 146645 of 599374 triangles, 150 residues > select up 1547 atoms, 1592 bonds, 192 residues, 2 models selected > select up 4803 atoms, 4940 bonds, 595 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 4803 atoms, 4940 bonds, 595 residues, 7 models selected > color (#!1 & sel) #abffb8ff > color (#!1 & sel) #8fffb4ff Drag select of 8d82_E SES surface, 81034 of 595960 triangles, 107 residues > select up 1182 atoms, 1213 bonds, 145 residues, 2 models selected > select up 4803 atoms, 4940 bonds, 595 residues, 2 models selected > color (#!1 & sel) #f6ffbbff > color (#!1 & sel) #bbffdaff > color (#!1 & sel) #bcf4ffff > color (#!1 & sel) #d3f8ffff > color (#!1 & sel) #cddaffff > color (#!1 & sel) #b7cdffff > color (#!1 & sel) #98deffff > color (#!1 & sel) #1d83ffff > color (#!1 & sel) #6557ffff > color (#!1 & sel) #107cffff > color (#!1 & sel) #0f7bffff > color (#!1 & sel) #1e96ffff > color (#!1 & sel) #3a8fffff > color (#!1 & sel) #57ffddff > color (#!1 & sel) #4efff9ff > color (#!1 & sel) #3ec2ffff > select clear > color #92caffff > undo Drag select of 8d82_E SES surface, 106540 of 595960 triangles, 122 residues > select up 1740 atoms, 1785 bonds, 217 residues, 2 models selected > select up 4803 atoms, 4940 bonds, 595 residues, 2 models selected > color (#!1 & sel) #aee9ffff > color (#!1 & sel) #8fe7ffff > color (#!1 & sel) #8fecffff > color (#!1 & sel) #86f5ffff > color (#!1 & sel) #81eaffff > color (#!1 & sel) #75e8ffff Drag select of 8d82_A SES surface, 60902 of 599374 triangles, 75 residues > select up 1076 atoms, 1100 bonds, 130 residues, 2 models selected > select up 4803 atoms, 4940 bonds, 595 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 4803 atoms, 4940 bonds, 595 residues, 7 models selected > color (#!1 & sel) #a1ffbcff > color (#!1 & sel) #89ffbaff > color (#!1 & sel) #6bff90ff > select clear > transparency 70 Drag select of 8d82_D SES surface, 8395 of 180946 triangles, 4 residues > select up 247 atoms, 252 bonds, 30 residues, 2 models selected > select up 1358 atoms, 1376 bonds, 169 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 1358 atoms, 1376 bonds, 169 residues, 7 models selected > color (#!1 & sel) #ff54a1ff Drag select of 8d82_H SES surface, 10887 of 181260 triangles, 14 residues > select up 406 atoms, 410 bonds, 49 residues, 2 models selected > select up 1358 atoms, 1376 bonds, 169 residues, 2 models selected > color (#!1 & sel) #ffb254ff > color (#!1 & sel) #ff54a4ff > color (#!1 & sel) #ffb254ff > color (#!1 & sel) #ff54a1ff > select clear > transparency 70 > save C:\Users\sarson-lawrence.k\Desktop\image38.png supersample 3 > save C:\Users\sarson-lawrence.k\Desktop\image39.png supersample 3 > save "C:/Users/sarson-lawrence.k/OneDrive - > wehi.edu.au/GCSF_paper/gp130_figure.cxs" ——— End of log from Mon Nov 13 10:50:01 2023 ——— opened ChimeraX session > open "C:/Users/sarson-lawrence.k/OneDrive - wehi.edu.au/GCSF_paper/GCSF- > GCSFR_Isolde_kaiseal_11_symmetry.pdb" Chain information for GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb #2 --- Chain | Description A | No description available B | No description available C D | No description available > hide atoms > 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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain B (#2) with 8d82, chain A (#1), sequence alignment score = 814.5 RMSD between 106 pruned atom pairs is 0.844 angstroms; (across all 550 pairs: 11.340) Drag select of 8d82_G SES surface, 70051 of 302790 triangles, 71 residues > select up 667 atoms, 684 bonds, 88 residues, 2 models selected > select up 2382 atoms, 2459 bonds, 299 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 2382 atoms, 2459 bonds, 299 residues, 7 models selected > hide sel cartoons > select clear > hide surfaces Drag select of 53 residues > select up 708 atoms, 723 bonds, 95 residues, 2 models selected > select up 2382 atoms, 2459 bonds, 299 residues, 2 models selected > hide sel cartoons Drag select of 3 residues > select up 91 atoms, 91 bonds, 12 residues, 2 models selected > select up 1358 atoms, 1376 bonds, 169 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 1358 atoms, 1376 bonds, 169 residues, 7 models selected > hide sel cartoons Drag select of 3 residues > select up 96 atoms, 95 bonds, 13 residues, 2 models selected > select up 1358 atoms, 1376 bonds, 169 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 1358 atoms, 1376 bonds, 169 residues, 7 models selected > hide sel cartoons > select add #1 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select subtract #1 6 models selected > hide #!1 models Drag select of 41 residues > select up 1159 atoms, 1168 bonds, 80 residues, 1 model selected > select up 2546 atoms, 2570 bonds, 168 residues, 1 model selected > hide sel cartoons Drag select of 11 residues > select up 626 atoms, 631 bonds, 43 residues, 1 model selected > select up 2543 atoms, 2568 bonds, 168 residues, 1 model selected > select up 23503 atoms, 23865 bonds, 1528 residues, 1 model selected > select down 2543 atoms, 2568 bonds, 168 residues, 1 model selected > hide sel cartoons Drag select of 99 residues, 1 pseudobonds > select up 2166 atoms, 2193 bonds, 1 pseudobond, 139 residues, 2 models selected > select up 7902 atoms, 8032 bonds, 1 pseudobond, 502 residues, 2 models selected > select up 8016 atoms, 8149 bonds, 1 pseudobond, 510 residues, 2 models selected > select up 9371 atoms, 9527 bonds, 1 pseudobond, 596 residues, 2 models selected > select up 23503 atoms, 23865 bonds, 4 pseudobonds, 1528 residues, 2 models selected > select down 9371 atoms, 9527 bonds, 1 pseudobond, 596 residues, 2 models selected > hide sel cartoons > show #!1 models > undo > redo > color #2 #2630ebff Drag select of 90 residues > select up 765 atoms, 785 bonds, 96 residues, 2 models selected > select up 4803 atoms, 4940 bonds, 595 residues, 2 models selected > select up 17366 atoms, 17850 bonds, 2146 residues, 2 models selected > select down 4803 atoms, 4940 bonds, 595 residues, 7 models selected > hide sel cartoons > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > color #2 #eb9635ff Drag select of 381 residues > select up 4737 atoms, 4827 bonds, 404 residues, 3 models selected > select up 10895 atoms, 11137 bonds, 1001 residues, 3 models selected > select down 4737 atoms, 4827 bonds, 404 residues, 3 models selected > hide sel cartoons > undo > select clear Drag select of 400 residues > select up 4737 atoms, 3204 bonds, 404 residues, 3 models selected > select down 4683 atoms, 400 residues, 3 models selected > hide sel cartoons > select clear > save "C:/Users/sarson-lawrence.k/OneDrive - > wehi.edu.au/GCSF_paper/GCSF_D3-D4_overlay_gp130.cxs" Drag select of 150 residues > select up 2133 atoms, 2171 bonds, 180 residues, 3 models selected > select up 7754 atoms, 7943 bonds, 785 residues, 3 models selected > select clear Drag select of 15 residues > select up 434 atoms, 439 bonds, 27 residues, 1 model selected > select up 1467 atoms, 1493 bonds, 94 residues, 1 model selected > select up 1485 atoms, 1510 bonds, 96 residues, 1 model selected > select up 2951 atoms, 3003 bonds, 190 residues, 1 model selected > select down 1485 atoms, 1510 bonds, 96 residues, 1 model selected > hide sel cartoons Drag select of 2 residues > select up 150 atoms, 152 bonds, 10 residues, 1 model selected > select up 1484 atoms, 1510 bonds, 96 residues, 1 model selected > select up 1614 atoms, 1642 bonds, 105 residues, 1 model selected > select down 1484 atoms, 1510 bonds, 96 residues, 1 model selected > hide sel cartoons Drag select of 98 residues > hide sel cartoons Drag select of 95 residues > hide sel cartoons > lighting full > hide #!1 models Drag select of 104 residues > show #!1 models > hide #!2 models Drag select of 102 residues > show #!2 models > matchmaker #1/E & sel to #2/A pairing ss Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 169, in <lambda> bbox.button(qbbox.Apply).clicked.connect(lambda *args: self.run_matchmaker(apply=True)) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker run(self.session, cmd) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 730, in cmd_match ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend, File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x000002B0BEB168B0> KeyError: File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, See log for complete Python traceback. > matchmaker #1/E & sel to #2/A pairing ss Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 169, in <lambda> bbox.button(qbbox.Apply).clicked.connect(lambda *args: self.run_matchmaker(apply=True)) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker run(self.session, cmd) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 730, in cmd_match ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend, File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x000002B0C3ED60D0> KeyError: File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, See log for complete Python traceback. > matchmaker #!1 & sel 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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain B (#2) with 8d82, chain E (#1), sequence alignment score = 119 RMSD between 46 pruned atom pairs is 0.974 angstroms; (across all 97 pairs: 3.940) > matchmaker #1/E & sel to #2/A pairing ss Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 169, in <lambda> bbox.button(qbbox.Apply).clicked.connect(lambda *args: self.run_matchmaker(apply=True)) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker run(self.session, cmd) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 730, in cmd_match ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend, File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x000002B0C8F32A60> KeyError: File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, See log for complete Python traceback. > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > select clear Drag select of 34 residues > select up 771 atoms, 780 bonds, 50 residues, 1 model selected > select up 6092 atoms, 6197 bonds, 406 residues, 1 model selected > color #2 #eb1e4bff > color #2 #eb0b47ff > color #2 #eb2056ff > color #2 #eb1e7aff > color #2 #eb124cff > color #2 #eb134dff > select clear > save C:\Users\sarson-lawrence.k\Desktop\image49.png supersample 3 > save "C:/Users/sarson-lawrence.k/OneDrive - > wehi.edu.au/GCSF_paper/GCSF_D3-D4_overlay_gp130.cxs" > style stick Changed 40869 atom styles > hide cartoons > show cartoons > undo [Repeated 1 time(s)]Drag select of 397 residues > style sel stick Changed 4451 atom styles > show sel cartoons > style sel ball Changed 4451 atom styles > select clear > show atoms > hide atoms > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides tube/slab shape box > nucleotides atoms > style nucleic stick Changed 0 atom styles > help help:user Drag select of 397 residues > ribbon > undo > licorice Unknown command: licorice > cartoon style protein modeHelix default arrows false xsection oval width 1 > thickness 1 > select clear > save C:\Users\sarson-lawrence.k\Desktop\image50.png supersample 3 > save "C:/Users/sarson-lawrence.k/OneDrive - > wehi.edu.au/GCSF_paper/GCSF_D3-D4_overlay_gp130.cxs" > style stick Changed 40869 atom styles > show cartoons > hide cartoons > undo [Repeated 1 time(s)] > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > matchmaker #1/E to #2/A pairing ss cutoffDistance 3.0 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 | 3 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 191 pruned atom pairs is 1.481 angstroms; (across all 550 pairs: 13.865) > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > ui tool show Matchmaker > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > show cartoons > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > matchmaker #1/E to #2/A pairing ss cutoffDistance 4.0 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 | 4 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 212 pruned atom pairs is 1.785 angstroms; (across all 550 pairs: 13.707) > matchmaker #1/E to #2/A pairing ss cutoffDistance 1.0 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 | 1 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 65 pruned atom pairs is 0.704 angstroms; (across all 550 pairs: 14.072) > matchmaker #1/E to #2/A pairing ss cutoffDistance 10.0 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 | 10 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 384 pruned atom pairs is 5.512 angstroms; (across all 550 pairs: 9.924) Drag select of 127 residues > select up 1124 atoms, 1152 bonds, 147 residues, 2 models selected > select up 2382 atoms, 2459 bonds, 299 residues, 2 models selected > hide sel cartoons Drag select of 159 residues > select up 1583 atoms, 1628 bonds, 204 residues, 2 models selected > select up 2382 atoms, 2459 bonds, 299 residues, 2 models selected > hide sel cartoons Drag select of 64 residues > select up 1163 atoms, 1180 bonds, 120 residues, 3 models selected > select up 11221 atoms, 11462 bonds, 1001 residues, 3 models selected > select up 11453 atoms, 11695 bonds, 1018 residues, 3 models selected > select up 12705 atoms, 12972 bonds, 1097 residues, 3 models selected > select up 12819 atoms, 13089 bonds, 1105 residues, 3 models selected > select up 14174 atoms, 14467 bonds, 1191 residues, 3 models selected > select up 40869 atoms, 41715 bonds, 3674 residues, 3 models selected > select down 14174 atoms, 14467 bonds, 1191 residues, 8 models selected > hide sel cartoons Drag select of 150 residues > select up 3229 atoms, 3259 bonds, 273 residues, 3 models selected > select up 3904 atoms, 3946 bonds, 337 residues, 3 models selected > select up 40869 atoms, 41715 bonds, 3674 residues, 3 models selected > select down 3904 atoms, 3946 bonds, 337 residues, 8 models selected > hide sel cartoons Drag select of 97 residues > select up 2675 atoms, 2698 bonds, 220 residues, 3 models selected > select up 3901 atoms, 3944 bonds, 337 residues, 3 models selected > select up 40869 atoms, 41715 bonds, 3674 residues, 3 models selected > select down 3901 atoms, 3944 bonds, 337 residues, 8 models selected > hide sel cartoons > ui tool show Matchmaker > matchmaker #1/E to #2/A pairing ss cutoffDistance 10.0 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 | 10 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 384 pruned atom pairs is 5.512 angstroms; (across all 550 pairs: 9.924) > matchmaker #1/E to #2/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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs: 13.959) > matchmaker #1/E to #2/A pairing ss cutoffDistance 3.0 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 | 3 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 191 pruned atom pairs is 1.481 angstroms; (across all 550 pairs: 13.865) > save C:\Users\sarson-lawrence.k\Desktop\image53.png supersample 3 Drag select of 594 residues Drag select of 607 residues > matchmaker #1/E to #2/A pairing ss cutoffDistance 3.0 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 | 3 Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 191 pruned atom pairs is 1.481 angstroms; (across all 550 pairs: 13.865) > matchmaker #1/E to #2/A pairing ss cutoffDistance none 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 No iteration Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 803.3 RMSD between 550 atom pairs is 9.350 angstroms > matchmaker #1/E & sel to #2/A & sel pairing ss cutoffDistance none Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 169, in <lambda> bbox.button(qbbox.Apply).clicked.connect(lambda *args: self.run_matchmaker(apply=True)) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker run(self.session, cmd) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 730, in cmd_match ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend, File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x000002B0C7C42340> KeyError: File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, See log for complete Python traceback. > matchmaker #1/E to #2/A & sel pairing ss cutoffDistance none 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 No iteration Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82, chain E (#1), sequence alignment score = 411.3 RMSD between 285 atom pairs is 4.210 angstroms > matchmaker #1/E & sel to #2/A pairing ss cutoffDistance none Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 169, in <lambda> bbox.button(qbbox.Apply).clicked.connect(lambda *args: self.run_matchmaker(apply=True)) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker run(self.session, cmd) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 730, in cmd_match ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend, File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x000002B0C7C59310> KeyError: File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\match_maker\match.py", line 314, in match score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, See log for complete Python traceback. OpenGL version: 3.3.0 - Build 20.19.15.5063 OpenGL renderer: Intel(R) HD Graphics 4600 OpenGL vendor: Intel Python: 3.9.11 Locale: en_AU.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: Dell Inc. Model: OptiPlex 9020 OS: Microsoft Windows 10 Pro (Build 19045) Memory: 8,493,617,152 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 zipp: 3.15.0
Change History (2)
comment:1 by , 23 months ago
Component: | Unassigned → Structure Comparison |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → KeyError matching selected regions |
comment:2 by , 23 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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