id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5552 morph same true: Execution of 'Structure' object's 'coordset_size' property raised AttributeError am2837@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/closed-arf1-morph.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed- arf1-morph.pdb --- warning | Ignored bad PDB record found on line 41274 END Chain information for closed-arf1-morph.pdb #1 --- Chain | Description A B | No description available C | No description available > set bgColor white > lighting soft > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/compled-FIXED-coot-0.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/compled- FIXED-coot-0.pdb --- warning | Ignored bad PDB record found on line 21237 END Chain information for compled-FIXED-coot-0.pdb #2 --- Chain | Description A C | No description available B | No description available D | No description available > mmaker #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 closed-arf1-morph.pdb, chain A (#1) with compled-FIXED-coot-0.pdb, chain A (#2), sequence alignment score = 5451 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs: 8.396) > select #2/D 1311 atoms, 1334 bonds, 2 pseudobonds, 164 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > morph #1,2 same true Computed 21 frame morph #3 > coordset #3 1,21 > close #3 > show #!2 models > show #1 models > select #1/C#2/C 10772 atoms, 10794 bonds, 22 pseudobonds, 1471 residues, 3 models selected > select clear > close #2 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/complex-morph.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex- morph.pdb --- warning | Ignored bad PDB record found on line 19926 END Chain information for complex-morph.pdb #2 --- Chain | Description A B | No description available C | No description available > mmaker #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 closed-arf1-morph.pdb, chain A (#1) with complex-morph.pdb, chain A (#2), sequence alignment score = 5451 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs: 8.396) > morph #1,2 same true Computed 21 frame morph #3 > coordset #3 1,21 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/1r8s.pdb 1r8s.pdb title: ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the catalytic glutamate to lysine [more info...] Chain information for 1r8s.pdb #4 --- Chain | Description A | adp-ribosylation factor 1 E | ARNO Non-standard residues in 1r8s.pdb #4 --- BME — β-mercaptoethanol FMT — formic acid GDP — guanosine-5'-diphosphate SO3 — sulfite ion SO4 — sulfate ion > mmaker #4 to #3/C 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 Morph - closed-arf1-morph.pdb, chain C (#3) with 1r8s.pdb, chain A (#4), sequence alignment score = 831.5 RMSD between 160 pruned atom pairs is 0.001 angstroms; (across all 160 pairs: 0.001) > select #4/E 1735 atoms, 1559 bonds, 392 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #4#!3 atoms > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/1r8s.pdb 1r8s.pdb title: ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the catalytic glutamate to lysine [more info...] Chain information for 1r8s.pdb #5 --- Chain | Description A | adp-ribosylation factor 1 E | ARNO Non-standard residues in 1r8s.pdb #5 --- BME — β-mercaptoethanol FMT — formic acid GDP — guanosine-5'-diphosphate SO3 — sulfite ion SO4 — sulfate ion > mmaker #5 to #4 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 1r8s.pdb, chain A (#4) with 1r8s.pdb, chain A (#5), sequence alignment score = 846.2 RMSD between 160 pruned atom pairs is 0.000 angstroms; (across all 160 pairs: 0.000) > hide #4-5#!3 atoms > select #5 3206 atoms, 2904 bonds, 704 residues, 1 model selected > ui mousemode right ""translate selected models"" > morph #4,5 same true Computed 21 frame morph #6 > coordset #6 1,21 > close #6 > morph #5,4 same true Computed 21 frame morph #6 > coordset #6 1,21 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/1r8s.pdb 1r8s.pdb title: ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the catalytic glutamate to lysine [more info...] Chain information for 1r8s.pdb #7 --- Chain | Description A | adp-ribosylation factor 1 E | ARNO Non-standard residues in 1r8s.pdb #7 --- BME — β-mercaptoethanol FMT — formic acid GDP — guanosine-5'-diphosphate SO3 — sulfite ion SO4 — sulfate ion > mmaker #7 to #6 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 Morph - 1r8s.pdb, chain A (#6) with 1r8s.pdb, chain A (#7), sequence alignment score = 846.2 RMSD between 160 pruned atom pairs is 0.000 angstroms; (across all 160 pairs: 0.000) > hide #!3 models > hide #6 models > ~select #5 Nothing selected > hide #7 atoms > select #7/E 1735 atoms, 1559 bonds, 392 residues, 1 model selected > delete atoms sel > delete bonds sel > show #7 atoms > hide #7 atoms > show #7 ::name=""GDP"" > ui tool show ""Show Sequence Viewer"" > sequence chain #7/A Alignment identifier is 7/A > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel > show #!3 models > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/1r8s.pdb 1r8s.pdb title: ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the catalytic glutamate to lysine [more info...] Chain information for 1r8s.pdb #8 --- Chain | Description A | adp-ribosylation factor 1 E | ARNO Non-standard residues in 1r8s.pdb #8 --- BME — β-mercaptoethanol FMT — formic acid GDP — guanosine-5'-diphosphate SO3 — sulfite ion SO4 — sulfate ion > mmaker #8 to #7 Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands. > mmaker #8 to #6 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 Morph - 1r8s.pdb, chain A (#6) with 1r8s.pdb, chain A (#8), sequence alignment score = 846.2 RMSD between 160 pruned atom pairs is 0.000 angstroms; (across all 160 pairs: 0.000) > select #8 3206 atoms, 2904 bonds, 704 residues, 1 model selected > morph #7,8 same true Computed 21 frame morph #9 > coordset #9 1,21 > hide #!3 models > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/complex-morph.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex- morph.pdb --- warning | Ignored bad PDB record found on line 19926 END Chain information for complex-morph.pdb #10 --- Chain | Description A B | No description available C | No description available > mmaker #10 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 complex-morph.pdb, chain A (#2) with complex-morph.pdb, chain A (#10), sequence alignment score = 5965.7 RMSD between 1159 pruned atom pairs is 0.000 angstroms; (across all 1159 pairs: 0.000) > select #10/A 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > select #10/C 1320 atoms, 1344 bonds, 165 residues, 1 model selected > select #10/B 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/2KSQ-7.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb --- warnings | Ignored bad PDB record found on line 3843 END Cannot find LINK/SSBOND atom SG in residue MTN /A:182 Cannot find LINK/SSBOND atom SG in residue MTN /A:183 Cannot find LINK/SSBOND atom SG in residue MTN /A:184 Cannot find LINK/SSBOND atom SG in residue MTN /A:185 Cannot find LINK/SSBOND atom SG in residue MTN /A:186 2KSQ-7.pdb title: The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more info...] Chain information for 2KSQ-7.pdb #11 --- Chain | Description A | adp-ribosylation factor 1 Non-standard residues in 2KSQ-7.pdb #11 --- GTP — guanosine-5'-triphosphate MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate (MTSL) MYR — myristic acid > mmaker #11 to #10 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 complex-morph.pdb, chain C (#10) with 2KSQ-7.pdb, chain A (#11), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > hide #9,11#!10 atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #10/C Alignment identifier is 10/C > sequence chain #11/A Alignment identifier is 11/A > delete atoms sel > delete bonds sel > morph #10,11 same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\morph.py"", line 76, in morph color_segments = color_segments, color_core = color_core) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 139, in interpolate nc = sm.coordset_size File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > morph #10,11 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 111, in interpolate results = segment.segmentHingeExact(sm, m, cf, mhs, log=log) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\segment.py"", line 109, in segmentHingeExact % (s0.name, cid0, len(r0list), s1.name, cid1, len(r1list))) chimerax.morph.segment.AtomPairingError: Morph - complex-morph.pdb chain C (165) and 2KSQ-7.pdb chain A (172) have different number of residues During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\morph.py"", line 76, in morph color_segments = color_segments, color_core = color_core) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 114, in interpolate results = segment.segmentHingeApproximate(sm, m, cf, mhs, log=log) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\segment.py"", line 158, in segmentHingeApproximate m1map = dict((s.chain.chain_id, s) for s in m1seqs) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\segment.py"", line 158, in m1map = dict((s.chain.chain_id, s) for s in m1seqs) AttributeError: 'NoneType' object has no attribute 'chain_id' AttributeError: 'NoneType' object has no attribute 'chain_id' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\segment.py"", line 158, in m1map = dict((s.chain.chain_id, s) for s in m1seqs) See log for complete Python traceback. > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP- > Arf1-morph.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP- Arf1-morph.pdb --- warnings | Ignored bad PDB record found on line 3130 END Start residue of secondary structure not found: HELIX 1 1 GLY A 2 ASN A 11 1 10 Start residue of secondary structure not found: HELIX 2 2 LEU A 12 GLY A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 GLY A 29 GLY A 40 1 12 Start residue of secondary structure not found: HELIX 4 4 GLN A 71 SER A 76 1 6 Start residue of secondary structure not found: HELIX 5 5 LEU A 77 TYR A 81 1 5 11 messages similar to the above omitted Cannot find LINK/SSBOND residue MYR (1 ) Cannot find LINK/SSBOND residue CYS (55 ) Cannot find LINK/SSBOND residue CYS (59 ) Cannot find LINK/SSBOND residue CYS (83 ) Cannot find LINK/SSBOND residue CYS (117 ) 1 messages similar to the above omitted GTP-Arf1-morph.pdb title: The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more info...] Chain information for GTP-Arf1-morph.pdb #12 --- Chain | Description D | No description available > mmaker #12 to #11 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 2KSQ-7.pdb, chain A (#11) with GTP-Arf1-morph.pdb, chain D (#12), sequence alignment score = 877.5 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > ui tool show ""Show Sequence Viewer"" > sequence chain #12/D Alignment identifier is 12/D No statusbar messages will be shown due to inadequate OpenGL > close #11 > delete atoms sel > delete bonds sel > morph #10,12 same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\morph.py"", line 76, in morph color_segments = color_segments, color_core = color_core) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 139, in interpolate nc = sm.coordset_size File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > morph #10,12 Computed 21 frame morph #11 > coordset #11 1,21 > show #!3 models > hide #!3 models > show #!10 models > hide #9 models > hide #!11 models > hide #!10 models > show #!2 models > show #12 models > hide #12 models > show #!11 models > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/2KSQ-7.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb --- warnings | Ignored bad PDB record found on line 3843 END Cannot find LINK/SSBOND atom SG in residue MTN /A:182 Cannot find LINK/SSBOND atom SG in residue MTN /A:183 Cannot find LINK/SSBOND atom SG in residue MTN /A:184 Cannot find LINK/SSBOND atom SG in residue MTN /A:185 Cannot find LINK/SSBOND atom SG in residue MTN /A:186 2KSQ-7.pdb title: The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more info...] Chain information for 2KSQ-7.pdb #13 --- Chain | Description A | adp-ribosylation factor 1 Non-standard residues in 2KSQ-7.pdb #13 --- GTP — guanosine-5'-triphosphate MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate (MTSL) MYR — myristic acid > mmaker #13 to #12 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 GTP-Arf1-morph.pdb, chain D (#12) with 2KSQ-7.pdb, chain A (#13), sequence alignment score = 880.5 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #!11 models > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #13/A Alignment identifier is 13/A > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel Drag select of 39 atoms, 38 bonds > delete atoms sel > delete bonds sel Drag select of 36 atoms, 36 bonds > delete atoms sel > delete bonds sel > show #12 models > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/2KSQ-7.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb --- warnings | Ignored bad PDB record found on line 3843 END Cannot find LINK/SSBOND atom SG in residue MTN /A:182 Cannot find LINK/SSBOND atom SG in residue MTN /A:183 Cannot find LINK/SSBOND atom SG in residue MTN /A:184 Cannot find LINK/SSBOND atom SG in residue MTN /A:185 Cannot find LINK/SSBOND atom SG in residue MTN /A:186 2KSQ-7.pdb title: The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more info...] Chain information for 2KSQ-7.pdb #14 --- Chain | Description A | adp-ribosylation factor 1 Non-standard residues in 2KSQ-7.pdb #14 --- GTP — guanosine-5'-triphosphate MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate (MTSL) MYR — myristic acid > mmaker #14 to #13 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 2KSQ-7.pdb, chain A (#13) with 2KSQ-7.pdb, chain A (#14), sequence alignment score = 0 Fewer than 3 residues aligned; cannot match 2KSQ-7.pdb, chain A with 2KSQ-7.pdb, chain A > mmaker #14 to #12 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 GTP-Arf1-morph.pdb, chain D (#12) with 2KSQ-7.pdb, chain A (#14), sequence alignment score = 880.5 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #!13 models > hide #12 models > select #14 3045 atoms, 3079 bonds, 187 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > hide #14 models > show #!13 models > morph #13,14 same true Computed 21 frame morph #15 > coordset #15 1,21 > hide #!15 models > ~select #14 Nothing selected > show #12 models > morph #12,14 same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\morph.py"", line 76, in morph color_segments = color_segments, color_core = color_core) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 139, in interpolate nc = sm.coordset_size File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > morph #12,13 same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\morph.py"", line 76, in morph color_segments = color_segments, color_core = color_core) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 139, in interpolate nc = sm.coordset_size File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > morph #12,13 Computed 21 frame morph #16 > coordset #16 1,21 > show #12 models > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP- > Arf1-morph.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP- Arf1-morph.pdb --- warnings | Ignored bad PDB record found on line 3130 END Start residue of secondary structure not found: HELIX 1 1 GLY A 2 ASN A 11 1 10 Start residue of secondary structure not found: HELIX 2 2 LEU A 12 GLY A 14 1 3 Start residue of secondary structure not found: HELIX 3 3 GLY A 29 GLY A 40 1 12 Start residue of secondary structure not found: HELIX 4 4 GLN A 71 SER A 76 1 6 Start residue of secondary structure not found: HELIX 5 5 LEU A 77 TYR A 81 1 5 11 messages similar to the above omitted Cannot find LINK/SSBOND residue MYR (1 ) Cannot find LINK/SSBOND residue CYS (55 ) Cannot find LINK/SSBOND residue CYS (59 ) Cannot find LINK/SSBOND residue CYS (83 ) Cannot find LINK/SSBOND residue CYS (117 ) 1 messages similar to the above omitted GTP-Arf1-morph.pdb title: The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more info...] Chain information for GTP-Arf1-morph.pdb #17 --- Chain | Description D | No description available > mmaker #17 to #12 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 GTP-Arf1-morph.pdb, chain D (#12) with GTP-Arf1-morph.pdb, chain D (#17), sequence alignment score = 905 RMSD between 165 pruned atom pairs is 0.000 angstroms; (across all 165 pairs: 0.000) > select #17 2829 atoms, 2856 bonds, 180 residues, 1 model selected > morph #12,17 Computed 21 frame morph #18 > coordset #18 1,21 > preset cartoons/nucleotides licorice/ovals 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 default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid No statusbar messages will be shown due to inadequate OpenGL No statusbar messages will be shown due to inadequate OpenGL > show #!2 models > 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 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #3/A #3/B Alignment identifier is 1 > show #!3 models > hide #!2 models > select #1 41115 atoms, 41303 bonds, 2756 residues, 1 model selected > ~select #1 Nothing selected > color (#!3 & sel) #d6e7f4ff > color (#!3 & sel) #ccccccff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #9ac2f5ff > color (#!3 & sel) #fdfcf2ff > color (#!3 & sel) #f4e379ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #310064ff > color (#!3 & sel) #ccccccff > color (#!3 & sel) #9ac2f5ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #fdfdffff > color (#!3 & sel) #f2e5dfff > color (#!3 & sel) #f0e6e0ff > color (#!3 & sel) #f0e3dcff > color (#!3 & sel) #e1c4b2ff > color (#!3 & sel) #310000ff > color (#!3 & sel) #b1ccccff > color (#!3 & sel) #ccccccff > color (#!3 & sel) #9ec2e5ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #9ac2f5ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #f0f0f0ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #f0f0f0ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #310000ff > color (#!3 & sel) #f0f0f0ff > color (#!3 & sel) #ffffffff > color (#!3 & sel) #9ac2f5ff > select clear > select #1/C#2/C#3/C#10/C#11/C 6659 atoms, 6625 bonds, 967 residues, 5 models selected > select clear > undo > undo > undo > undo > color (#!3 & sel) #6f7dd5ff > color (#!3 & sel) #9ac2f5ff > select clear > color (#!3 & sel) #e1c4b2ff > color (#!3 & sel) #f4e379ff > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > select clear > lighting soft > select ::name=""GDP"" 196 atoms, 210 bonds, 7 residues, 7 models selected > show ::name=""GDP"" > show #1 models > color (#1 & sel) #ff007fff > color (#1 & sel) #ff00ffff > color sel & #1 byhetero > select clear > hide #1 models > show #4 models > hide #4 models > show #6 models > coordset slider #6 > show #9 models > coordset slider #9 > show #!11 models > coordset slider #11 > show #!15 models > coordset #15 #16 > coordset slider #15 #16 > hide #18 models > show #18 models > coordset slider #18 > select ::name=""GTP"" 129 atoms, 135 bonds, 3 residues, 3 models selected > color (#!15 & sel) #55aa00ff > color sel & #!15 byhetero > hide #18 models > hide #16 models > hide #!15 models > ~select #15 86 atoms, 90 bonds, 2 residues, 2 models selected > select #14 3045 atoms, 3079 bonds, 187 residues, 1 model selected > ~select #14 Nothing selected > hide #!11 models > show #!10 models > hide #9 models > hide #!10 models > hide #6 models > hide #!3 models > show #!3 models > coordset slider #3 > hide #3/C models > show #3 > show #3 models > hide #!3 atoms > select #3/C 1228 atoms, 1248 bonds, 160 residues, 1 model selected > hide sel cartoons > show #6 models > select #6 ::name=""GDP"" 28 atoms, 30 bonds, 1 residue, 1 model selected > color sel #ff00ffff > color sel byhetero > coordset #6 1,21 > select clear > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 > coordset #9 1,21 > show #9 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > coordset #9 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > coordset #9 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > coordset #9 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > coordset #9 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > show #55 ::name=""GDP"" > coordset #55 1,21 No structures specified > show #6 ::name=""GDP"" > coordset #6 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > show #9 ::name=""GDP"" > show #9 > show #9 models > hide #9 models > show #9 models > hide #9 > show #9 ::name=""GDP"" > hide #6 models > show #6 models > hide #9 models > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > coordset #9 1,21 > show #9 models > hide #9 models > show #9 models > hide #9 models > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #9 ::name=""GDP"" > coordset #9 1,21 > hide #!3 models > hide #6 models > show #9 models > show #9 Drag select of 71 atoms, 7 bonds > delete atoms sel > delete bonds sel Drag select of 115 atoms, 30 bonds > select clear Drag select of 115 atoms, 30 bonds > select #9/A:401@PB 1 atom, 1 residue, 1 model selected Drag select of 115 atoms, 30 bonds > select #9/A:401@PB 1 atom, 1 residue, 1 model selected Drag select of 115 atoms, 30 bonds Drag select of 50 atoms > delete atoms sel > delete bonds sel Drag select of 14 atoms > delete atoms sel > delete bonds sel Drag select of 15 atoms > delete atoms sel > delete bonds sel Drag select of 1 atoms > select clear Drag select of 1 atoms Drag select of 1 atoms Drag select of 1 atoms Drag select of 1 atoms Drag select of 1 atoms Drag select of 1 atoms > delete atoms sel > delete bonds sel Drag select of 2 atoms > delete atoms sel > delete bonds sel > hide #9 models > show #6 models > show #!3 models > show #6 ::name=""GDP"" > coordset #6 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #6 ::name=""GDP"" > coordset #6 1,21 > hide #6 ::name=""GDP"" > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 > coordset 1,21 Missing or invalid ""structures"" argument: invalid structures specifier > show #9 models > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset 1,21 Missing or invalid ""structures"" argument: invalid structures specifier > hide #9 models > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 > show #3/C cartoons > coordset #3 1,21 > hide #!3 models > show #!3 models > hide #6 models > show #6 models > hide #3/C models > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > show #!3 models > hide #!3 models > show #!3 models > select #3/C 1228 atoms, 1248 bonds, 160 residues, 1 model selected > hide sel cartoons > show #6 models > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > select clear > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #!11 models > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > coordset #11 1,21 > hide #9 models > hide #!11 models > show #6 models > show #!15 models > hide #!15 models > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > show #18 models > hide #18 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > coordset #18 1,21 > hide #!15 models > hide #!11 models > hide #9 models > show #6 models > movie record Already recording a movie > movie stop > movie reset > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > wait 21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > coordset #18 1,21 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > show #6 models > hide #!15 models > hide #!11 models > hide #9 models > show #18 models > hide #6,18#!3 atoms > coordset #18 1,21 > hide #18 models > show #18 models > coordset slider #18 > hide #18 models > show #17 models > close #18 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/2KSQ-7.pdb Summary of feedback from opening C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb --- warnings | Ignored bad PDB record found on line 3843 END Cannot find LINK/SSBOND atom SG in residue MTN /A:182 Cannot find LINK/SSBOND atom SG in residue MTN /A:183 Cannot find LINK/SSBOND atom SG in residue MTN /A:184 Cannot find LINK/SSBOND atom SG in residue MTN /A:185 Cannot find LINK/SSBOND atom SG in residue MTN /A:186 2KSQ-7.pdb title: The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more info...] Chain information for 2KSQ-7.pdb #18 --- Chain | Description A | adp-ribosylation factor 1 Non-standard residues in 2KSQ-7.pdb #18 --- GTP — guanosine-5'-triphosphate MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate (MTSL) MYR — myristic acid > show #!11 models > hide #!11 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > hide #6,17-18#!3 cartoons > show #6,17-18#!3 cartoons > hide #6,17-18#!3 atoms > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > 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 > morph #18,17 Computed 21 frame morph #19 > coordset #19 1,21 > coordset slider #19 > select #19 ::name=""GTP"" Nothing selected > hide #* target a > show #3,6,19 target ab > hide #6,19#!3 atoms > select #19 ::name=""GTP"" Nothing selected > select #19 ::name=""GTP"" Nothing selected > select #18 ::name=""GTP"" 43 atoms, 45 bonds, 1 residue, 1 model selected > hide #19 models > show #18 models > hide #6 models > hide #!3 models > morph #18,17 same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\morph.py"", line 76, in morph color_segments = color_segments, color_core = color_core) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\morph\motion.py"", line 139, in interpolate nc = sm.coordset_size File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError AttributeError: Execution of 'Structure' object's 'coordset_size' property raised AttributeError File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 67, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > view orient > show #19 models > hide #19 models > show #!3 models > show #18 ::name=""GTP"" > color sel #55aa00ff > color sel #55aa7fff > show #!15 models > color sel #55aa00ff > color sel byhetero > select clear > move x 10 #18 Expected an integer >= 1 or a keyword > move x 10 10 #18 Expected a keyword > move 10 #18 Missing or invalid ""axis"" argument: Expected 3 floats or ""x"", or ""y"", or ""z"" or two atoms > move x 10 #18 models Expected an integer >= 1 or a keyword > move x 10 10 #18 Expected a keyword > move x 10 10 #18 models Expected a keyword > move x 10 25 models #18 > hide #18 models > hide #!15 models > show #!15 models > hide #!15 models > show #18 models > move x -10 25 models #18 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > hide #18 models > select #3/C 1228 atoms, 1248 bonds, 160 residues, 1 model selected > hide sel cartoons > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > move x -10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > select #3 19726 atoms, 20040 bonds, 8 pseudobonds, 2466 residues, 2 models selected > ~select #3 Nothing selected > select #3/C 1228 atoms, 1248 bonds, 160 residues, 1 model selected > select #3/C 1228 atoms, 1248 bonds, 160 residues, 1 model selected > select #3 19726 atoms, 20040 bonds, 8 pseudobonds, 2466 residues, 2 models selected > ~select #3 Nothing selected > hide #9 models > show #9 models > hide #9 models > hide #!15 models > show #!15 models > hide #!11 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > move x -10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > move x -10 25 models #18 > movie stop > show #9 ::name=""GDP"" > hide #9 models > show #9 models > hide #9 models > show #15 models > show #15 ::name=""GTP"" > coordset slider #15 > hide #!11 models > show #6 models > show #3 ::name=""GDP"" > show #6 ::name=""GDP"" > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > move x -10 25 models #18 > show #6 models > hide #!3 models > show #!3 models > hide #!11 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > move x -10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > hide #!15 models > show #!15 models > hide #!11 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 > show #18 > move x 10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #!11 models > hide #9 models > show #6 models > show #18 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > hide #6,18#!3,15 atoms > hide #18 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 models > show #18 > show #18 ::name=""GTP"" > move x 10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #!15 models > show #!15 models > show #15 ::name=""GTP"" > hide #9 models > show #6 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 models > show #18 cartoons > show #18 ::name=""GTP"" > move x 10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #!15 models > show #!15 models > show #17 models > hide #9 models > hide #17 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 models > show #18 cartoons > show #18 ::name=""GTP"" > move x 10 25 models #18 > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > show #18 models > hide #9,18#!3,15 atoms > move x 10 #18 models Expected an integer >= 1 or a keyword > move x 10 25 #18 models Expected a keyword > move x 10 models #18 > move x -100 models #18 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > move x -100 100 models #18 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > move x -100 1 models #18 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > move x -10 100 models #18 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > move x -10 25 models #18 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > select ::name=""GTP"" 172 atoms, 180 bonds, 4 residues, 4 models selected > show sel & #18#!15 atoms > select clear > hide #9 models > show #9 models > hide #18 models > show #18 models > hide #18 models > hide #!15 models > select ::name=""GDP"" 196 atoms, 210 bonds, 7 residues, 7 models selected > show sel & #9 atoms > hide #9 models > select clear > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #11 models > show #18 cartoons > show #18 ::name=""GTP"" > move x 10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #!15 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > show #18 models > hide #18 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 cartoons > show #18 ::name=""GTP"" > move x 10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > show #6 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 cartoons > show #18 ::name=""GTP"" > move x 10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > show #18 cartoons > show #18 ::name=""GTP"" > move x 10 25 models #18 > wait > show #18 models > show #18 ::name=""GTP"" > move x 10 25 models #18 > wait > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #18 models > show #18 models > show #18 ::name=""GTP"" > move x 10 25 models #18 > wait > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #18 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > show #!15 models > hide #!15 models > hide #9 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 cartoons > show #18 ::name=""GTP"" > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > show #18 ::name=""GTP"" > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > show #6 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > hide #18 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 cartoons > show #18 ::name=""GTP"" > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > show #18 models > hide #18 models > show #18 cartoons > show #18 models > hide #18 models > hide #9 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > show #6 models > hide #6 models > show #1 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > volume showOutlineBox true No volumes specified > volume showOutlineBox true No volumes specified > ui mousemode right ""play map series"" > hide #!2 models > hide #1 models > show #!3 models > hide #18 models > select #3/A:780 7 atoms, 6 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B Alignment identifier is 1 > select #2 19922 atoms, 20242 bonds, 44 pseudobonds, 2483 residues, 2 models selected > ~select #2 Nothing selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #3/A #3/B Alignment identifier is 1 > select clear Drag select of 7 residues > color (#!3 & sel) #aa0000ff > select clear > zoom 10 10 > zoom -10 100 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\std_commands\zoom.py"", line 46, in zoom ff = math.pow(factor, 1/frames) ValueError: math domain error ValueError: math domain error File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\std_commands\zoom.py"", line 46, in zoom ff = math.pow(factor, 1/frames) See log for complete Python traceback. > zoom -10 > zoom 0.01 > zoom 10 > zoom 0.01 > zoom 100 > view orient > view > view orient > turn x 180 > turn x -90 20 > turn x 1 90 20 Expected a keyword > turn x 1-90 20 Expected a number or a keyword > turn x 1 90 > turn x 1 90 > turn x 1 90 > turn x 1 90 > turn x 90 1 > turn x 270 360 > turn x 90 > turn x 180 > turn x -1 90 > turn y 90 > view orient > turn x90 Expected an axis vector or a keyword > turn x 90 > turn x 90 > turn x 1 90 > turn y 1 90 > view > view orient > turn x 90 > turn x 90 > turn x -1 90 > turn y 1 90 > view orient > turn x -1 90 > turn y 1 90 > zoom 2 > turn z 20 > turn > turn > view orient > turn x 180 > turn x -1 90 > turn y -1 90 > move x 10 > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 1 > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > hide #18 models > show #6 models > mmaker #18 to 11 > matchmaker #18 to 11 Invalid ""to"" argument: invalid atoms specifier > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 1 > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #9 models > show #6 models > hide #18 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 5 > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #18 models > hide #9 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 5 > move x -10 25 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #18 models > hide #9 models > show #6 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 10 > move x -10 35 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #18 models > hide #9 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 3 > move x -5 30 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 3 > move x -5 30 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #18 models > hide #9 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 3 > move x -5 30 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > hide #18 models > hide #9 models > show #6 models > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 728.4 RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs: 4.525) > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 3 > move x -5 30 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > mmaker #18 to #11 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 Morph - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A (#18), sequence alignment score = 828 RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs: 0.001) > hide #18 models > hide #9 models > show #6 models > movie record > show #6 ::name=""GDP"" > coordset #6 1,21 > wait 21 > hide #6 ::name=""GDP"" > show #9 models > coordset #9 1,21 > hide #6 models > show #3/C cartoons > coordset #3 1,21 > wait 21 > hide #3/C cartoons > show #11 models > show #15 models > coordset #15 21,1 > wait 21 > coordset #11 1,21 > wait 21 > hide #!11 models > hide #15 models > show #18 models > wait 3 > move x -5 30 models #18 > wait > movie stop > movie encode framerate 10 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for- > figures/moprh.cxs 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""begin save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""begin save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""begin save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""begin save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""begin save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""end save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""end save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""end save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""end save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. 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\atomic\structure.py"", line 69, in lambda *args, qual=ses_func: self._ses_call(qual))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1792, in _ses_call f(self._c_pointer) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute '_c_pointer' Error processing trigger ""end save session"": AttributeError: 'Structure' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 69, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 456.71 OpenGL renderer: GeForce GTX 1660/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: OriginPC Model: NEURON OS: Microsoft Windows 10 Home (Build 19042) Memory: 17,093,591,040 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9600K CPU @ 3.70GHz"" 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 Eric Pettersen all ChimeraX