id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2730 Surface recomputation: cannot convert float NaN to integer chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-16.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/chang/Desktop/Borrelia-CW-CCW/For-paper/Segmentation/whole- > motor/Borrelia-swtich3/Borrelia-switch4.cxs format session opened ChimeraX session > hide #!7 models > hide #!8 models > show #!2-6 target m > show #!13 models > show #!28 models > show #!30 models > show #!32 models > show #!27 models > show #!25 models > view orient > lighting soft > turn x -90 > view > color radial #28 palette ""coral:yellow"" center #28 > color radial #30 palette ""coral:yellow"" center #30 > color radial #32 palette ""coral:yellow"" center #32 > turn y -2 180 models #13 center #13 > sym #8.4 C46 center #13 > show #!8 models > hide #!8.3 models > hide #!13 models > hide #!8.4 cartoons > show #!8.4 surfaces > color #8.4/A,B rgb(29,52,245) > color #8.4/C rgb(87,178,249) > color #8.4/D-F springgreen > movie record > turn y 2 180 models #8.4 center #8.4 > movie stop > movie encode output /Users/chang/Desktop/turn-CheY3-Cring.mp4 quality > highest Movie saved to /Users/chang/Desktop/turn-CheY3-Cring.mp4 > save /Users/chang/Desktop/image.png supersample 9 transparentBackground > false > hide #!8.4 models > show #!7 models > hide #!7.4 models > hide #!7.5 models > hide #!7.6 models > show #!12 models > sym #7.1 C46 center #12 > hide #!7 models > show #!7 models > hide #!12 models > show #!21 models > hide #!7.1 cartoons > show #!7.1 surfaces > color #7.1/A,B rgb(29,52,245) > movie record > turn y -2 180 models #7.1 center #7.1 > movie stop > movie encode output /Users/chang/Desktop/turn-CheX-Cring.mp4 quality highest Movie saved to /Users/chang/Desktop/turn-CheX-Cring.mp4 > save /Users/chang/Desktop/image.png supersample 9 transparentBackground > false > open /Users/chang/Desktop/Borrelia-CW-CCW/For-paper/Segmentation/whole- > motor/Borrelia-swtich3/Borrelia-switch4-for-movie.cxs format session opened ChimeraX session Invalid ""center"" argument: Center argument has no object bounds > color radial #28 palette ""coral:yellow"" center #28 > color radial #30 palette ""coral:yellow"" center #30 > show #!28.1-16 target m > color radial #28 palette ""coral:yellow"" center #28 > hide #!28.10-16 target m > show #!30.1-16 target m > color radial #30 palette ""coral:yellow"" center #30 > hide #!30.3-9 target m > color radial #32 palette ""coral:yellow"" center #32 > view p4 > hide #!52 models > view p1 > show #!7.1 models > hide #!7.1 models > show #!7.1 models > hide #!7.1 models > show #!7.1 models > show #!7 target m > hide #!7.1 models > show #!7.1 models > show #!12 models > select #12 2 models selected > ui mousemode rightMode ""crop volume"" > ui mousemode rightMode ""translate selected models"" > volume #12 region all > sym #7.1 C46 center #12 > hide #!7.1 models > sym #7.1 C46 center #12 copies true > hide #!12 models > hide #50 cartoons > show #50 surfaces > color #7.1/A,B rgb(29,52,245) > color #50.*/A,B rgb(29,52,245) > color #50.*/C rgb(87,178,249) > color #50.*/D-F springgreen > color #50.*/Y rgb(255,102,102) > hide #!50.25-46 target m > turn y 90 > turn y 90 > turn y 90 > turn y 90 > hide #!50.25-46 target m > hide #!50 models > show #!50 models > turn y 90 > turn y 90 > turn y 90 > turn y 90 > turn y 90 > turn y 90 > turn y 90 > turn y 90 > hide #!50.2 models > show #!50.2 models > hide #!50.1-24 target m > show #!50.1 models > show #!50.1 target m > open /Users/chang/Desktop/Borrelia-CW-CCW/For-paper/Segmentation/whole- > motor/Borrelia-swtich3/Borrelia-switch4-for-movie.cxs format session opened ChimeraX session > color radial #28 palette ""coral:yellow"" center #28 > color radial #30 palette ""coral:yellow"" center #30 > color radial #32 palette ""coral:yellow"" center #32 > hide #!52 models > show #!12 models > volume #12 region all > sym #7.1 C46 center #12 copies true > hide #!12 models > hide #50 cartoons > show #50 surfaces > color #50.*/A,B rgb(29,52,245) > color #50.*/C rgb(87,178,249) > color #50.*/Y rgb(255,102,102) > color #50.*/D-F springgreen > hide #!50.25-46 target m > view p4 > save /Users/chang/Desktop/image.png supersample 9 transparentBackground > false > view p1 > show #!47 models > hide #!47 models > show #!45 models > hide #!45 models > show #!44 models > select #30.2 2 models selected > view sel > select clear > view name p5 > hide #!44 models > save /Users/chang/Desktop/image.png supersample 9 transparentBackground > false > view p4 > hide #!50 models > show #!7.1 models > hide #!7.1 models > show #!7.1 models > show #!7.1 target m > hide #!7 models > show #!7 models > show #!7.3 models > hide #!7.3 models > show #7.1 target m > hide #!7 models > show #!7 models > hide #!7.1 models > show #!7.1 models > show #!8.1 models > view > view p4 > hide #!7 models > hide #!8 models > show #!50 models > show #!52 models > morph #52,50 frames 10 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (CW-cring-CheY-borrelia.pdb #50.1/A,CW-cring-CheY-borrelia.pdb #50.1/B,CW-cring-CheY-borrelia.pdb #50.1/C,CW-cring-CheY-borrelia.pdb #50.1/D,CW-cring-CheY-borrelia.pdb #50.1/E,CW-cring-CheY-borrelia.pdb #50.1/F,CW-cring-CheY-borrelia.pdb #50.1/Y) > morph #52.2-7,50:1,3-7 frames 10 Computed 51 frame morph #51 > coordset #51 1,51 > movie record > movie encode /Users/chang/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/chang/Desktop/movie.mp4 > hide #!50 models > hide #!52 models > hide #!51 models > show #!51 models > close #51 > save session /Users/chang/Desktop/Borrelia-CW-CCW/For- > paper/Segmentation/whole-motor/Borrelia-swtich3/Borrelia-switch4-for- > movie.cxs > show #!7 models > hide #!7 models > show #!50 models > hide #!50.2-24 target m > show #!52 models > hide #!52.1-25 target m > show #!52.1 target m > morph #52.1 #50.1 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (CW-cring-CheY-borrelia.pdb #50.1/A,CW-cring-CheY-borrelia.pdb #50.1/B,CW-cring-CheY-borrelia.pdb #50.1/C,CW-cring-CheY-borrelia.pdb #50.1/D,CW-cring-CheY-borrelia.pdb #50.1/E,CW-cring-CheY-borrelia.pdb #50.1/F,CW-cring-CheY-borrelia.pdb #50.1/Y) > save /Users/chang/Desktop/test.pdb models #50.1 > hide #!50 models > open /Users/chang/Desktop/test.pdb Chain information for test.pdb #51 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available Y | No description available > hide #51#!52.1 atoms > show #51#!52.1 surfaces > morph #52.1 #51 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (test.pdb #51/A,test.pdb #51/B,test.pdb #51/C,test.pdb #51/D,test.pdb #51/E,test.pdb #51/F,test.pdb #51/Y) > save /Users/chang/Desktop/test.pdb models #50.1:A-F > close #51 > open /Users/chang/Desktop/test.pdb Chain information for test.pdb #51 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available Y | No description available > hide #51#!52.1 atoms > show #51#!52.1 surfaces > morph #52.1 #51 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (test.pdb #51/A,test.pdb #51/B,test.pdb #51/C,test.pdb #51/D,test.pdb #51/E,test.pdb #51/F,test.pdb #51/Y) > hide #51.7 models > show #51.7 models > hide #51.4 models > show #51.4 models > hide #51.2 models > show #51.2 models > close #51.2 > morph #52.1 #51 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (test.pdb #51/A,test.pdb #51/B,test.pdb #51/C,test.pdb #51/D,test.pdb #51/E,test.pdb #51/F,test.pdb #51/Y) > rename #51.1 #51.2 No name or id option specified for renaming > rename #51.1 id #51.2 > morph #52.1 #51 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (test.pdb #51/A,test.pdb #51/B,test.pdb #51/C,test.pdb #51/D,test.pdb #51/E,test.pdb #51/F,test.pdb #51/Y) > close #52.1.1 > morph #52.1 #51 models have different number of chains, 6 (Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/A,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/B,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/C,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/D,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/E,Morph - CCW-cring-borrelia- coot-0_real_space_refined-20200107.pdb #/F) and 7 (test.pdb #51/A,test.pdb #51/B,test.pdb #51/C,test.pdb #51/D,test.pdb #51/E,test.pdb #51/F,test.pdb #51/Y) > close #51 > open /Users/chang/Desktop/test.pdb Summary of feedback from opening /Users/chang/Desktop/test.pdb --- warning | CONECT record for nonexistent atom: 1978 Chain information for test.pdb #51 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > hide #51#!52.1 atoms > show #51#!52.1 surfaces > morph #52.1 #51 Computed 21 frame morph #53 > coordset #53 1,21 > hide #53 models > show #53 models > hide #53 models > show #53 models > view > hide #53 models > show #53 models > hide #53 models > show #53 models > hide #53 models > show #53 models > hide #53 models > show #53 models > view p4 > close #53 > close #51 > open /Users/chang/Desktop/test.pdb Summary of feedback from opening /Users/chang/Desktop/test.pdb --- warning | CONECT record for nonexistent atom: 1978 Chain information for test.pdb #51 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > save /Users/chang/Desktop/test2.pdb models #52.1 > open /Users/chang/Desktop/test2.pdb Chain information for test2.pdb #53 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > show #!10.3 models > hide #!10.3 models > hide #!52 models > morph #53 #51 Computed 21 frame morph #54 > coordset #54 1,21 > hide #54 models > show #51 models > show #53 models > hide #53 models > show #53 models > hide #51 models > show #51 models > hide #51 models > show #51 models > hide #51 models > show #51 models > hide #51 models > show #51 models > hide #51 models > show #54 models > mmaker #53/E to 54/E Invalid ""to"" argument: invalid atoms specifier > hide #53 models > show #53 models > hide #54 models > show #51 models > mmaker #51/E to 53/E Invalid ""to"" argument: invalid atoms specifier > mmaker #51:E to 53:E Invalid ""to"" argument: invalid atoms specifier > split #51 Chain information for test.pdb A #51.1 --- Chain | Description A | No description available Chain information for test.pdb B #51.2 --- Chain | Description B | No description available Chain information for test.pdb C #51.3 --- Chain | Description C | No description available Chain information for test.pdb D #51.4 --- Chain | Description D | No description available Chain information for test.pdb E #51.5 --- Chain | Description E | No description available Chain information for test.pdb F #51.6 --- Chain | Description F | No description available Split test.pdb (#51) into 6 models > split #53 Chain information for test2.pdb A #53.1 --- Chain | Description A | No description available Chain information for test2.pdb B #53.2 --- Chain | Description B | No description available Chain information for test2.pdb C #53.3 --- Chain | Description C | No description available Chain information for test2.pdb D #53.4 --- Chain | Description D | No description available Chain information for test2.pdb E #53.5 --- Chain | Description E | No description available Chain information for test2.pdb F #53.6 --- Chain | Description F | No description available Split test2.pdb (#53) into 6 models > mmaker #51:E to 53:E Invalid ""to"" argument: invalid atoms specifier > mmaker #51/E to 53/E Invalid ""to"" argument: invalid atoms specifier > hide #53.4 models > show #53.4 models > hide #53.5 models > show #53.5 models > mmaker #51.5 to 53.5 Invalid ""to"" argument: invalid atoms specifier > hide #53.5 models > show #53.5 models > mmaker #51 to 53 Invalid ""to"" argument: invalid atoms specifier > mmaker #51.5 to #53.5 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 test2.pdb E, chain E (#53.5) with test.pdb E, chain E (#51.5), sequence alignment score = 313.1 RMSD between 69 pruned atom pairs is 0.575 angstroms; (across all 69 pairs: 0.575) > hide #53.6 models > show #53.6 models > mmaker #51.6 to #53.6 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 test2.pdb F, chain F (#53.6) with test.pdb F, chain F (#51.6), sequence alignment score = 313.1 RMSD between 69 pruned atom pairs is 0.575 angstroms; (across all 69 pairs: 0.575) > hide #!53 models > show #!53 models > hide #!53 models > show #!53 models > hide #!53 models > show #!50 models > select #53.5-6 1294 atoms, 1296 bonds, 2 models selected > select #51.5-6 1294 atoms, 1296 bonds, 2 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > mmaker #51.5 to #50.1.5 rotate false Expected a keyword > select clear > select #51.5-6 1294 atoms, 1296 bonds, 2 models selected > ui mousemode rightMode ""translate selected models"" > hide #!50 models > show #!53 models > hide #!53 models > show #!53 models > hide #!51 models > show #!51 models > hide #!53 models > show #!10.1 models > hide #!10.1 models > show #!50 models > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > mmaker #51.5 to #50.1.6 bring #51.6 No 'to' model specified > hide #50.1.6 models > show #50.1.6 models > mmaker #51.5 to #50.1/E bring #51.6 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 CW-cring-CheY-borrelia.pdb, chain E (#50.1) with test.pdb E, chain E (#51.5), sequence alignment score = 322.1 RMSD between 69 pruned atom pairs is 0.001 angstroms; (across all 69 pairs: 0.001) > mmaker #51.5 to #50.1/E bring #51.6 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 CW-cring-CheY-borrelia.pdb, chain E (#50.1) with test.pdb E, chain E (#51.5), sequence alignment score = 322.1 RMSD between 69 pruned atom pairs is 0.001 angstroms; (across all 69 pairs: 0.001) > hide #!50 models > select clear > view p4 > show #!53 models > close #54 > hide #!53 models > show #!53 models > morph #53 #51 Computed 221 frame morph #54 > coordset #54 1,221 > close #54 > show #!51 target m > show #51.1-6 target m > save /Users/chang/Desktop/CheX-modified-FliN.pdb models #51 > hide #!51 models > hide #!53 models > close #53 > open /Users/chang/Desktop/CheX-modified-FliN.pdb Chain information for CheX-modified-FliN.pdb --- Chain | Description 53.1/A | No description available 53.2/B | No description available 53.3/C | No description available 53.4/D 53.5/E 53.6/F | No description available > open /Users/chang/Desktop/test2.pdb Chain information for test2.pdb #54 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > hide #!53 models > show #!53 models > morph #54 #53 models have different number of chains, 6 (Morph - test2.pdb #/A,Morph - test2.pdb #/B,Morph - test2.pdb #/C,Morph - test2.pdb #/D,Morph - test2.pdb #/E,Morph - test2.pdb #/F) and 1 (CheX-modified-FliN.pdb #53.1/A) > close #53 > open /Users/chang/Desktop/CheX-modified-FliN.pdb Chain information for CheX-modified-FliN.pdb --- Chain | Description 53.1/A | No description available 53.2/B | No description available 53.3/C | No description available 53.4/D 53.5/E 53.6/F | No description available > close #53 > open /Users/chang/Desktop/test2.pdb Chain information for test2.pdb #53 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > close #53 > open /Users/chang/Desktop/CheX-modified-FliN.pdb Chain information for CheX-modified-FliN.pdb --- Chain | Description 53.1/A | No description available 53.2/B | No description available 53.3/C | No description available 53.4/D 53.5/E 53.6/F | No description available > show #!51 models > hide #!53 models > close #51 > close #53-54 > open /Users/chang/Desktop/test.pdb /Users/chang/Desktop/test2.pdb Summary of feedback from opening files --- warning | CONECT record for nonexistent atom: 1978 Chain information for test.pdb #51.1 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available Chain information for test2.pdb #51.2 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > hide #!51 models > show #!51 models > hide #51.1 models > show #51.1 models > mmaker #51.1/E to #51.2/E 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 test2.pdb, chain E (#51.2) with test.pdb, chain E (#51.1), sequence alignment score = 304.1 RMSD between 69 pruned atom pairs is 0.575 angstroms; (across all 69 pairs: 0.575) > close #51 > open /Users/chang/Desktop/CheX-modified-FliN.pdb > /Users/chang/Desktop/test2.pdb Summary of feedback from opening files --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 4865 messages similar to the above omitted Chain information for CheX-modified-FliN.pdb #51.1 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available Chain information for test2.pdb #51.2 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > morph #51.2 #51.1 Computed 21 frame morph #53 > coordset #53 1,21 > hide #53 models > show #51.1 models > show #51.2 models > hide #51.2 models > show #51.2 models > hide #51.2 models > close #51 > close #53 > open /Users/chang/Desktop/test.pdb /Users/chang/Desktop/test2.pdb Summary of feedback from opening files --- warning | CONECT record for nonexistent atom: 1978 Chain information for test.pdb #51.1 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available Chain information for test2.pdb #51.2 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > split #51.1 Chain information for test.pdb A #51.1.1 --- Chain | Description A | No description available Chain information for test.pdb B #51.1.2 --- Chain | Description B | No description available Chain information for test.pdb C #51.1.3 --- Chain | Description C | No description available Chain information for test.pdb D #51.1.4 --- Chain | Description D | No description available Chain information for test.pdb E #51.1.5 --- Chain | Description E | No description available Chain information for test.pdb F #51.1.6 --- Chain | Description F | No description available Split test.pdb (#51.1) into 6 models > mmaker #51.1.5 to #51.2/F 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 test2.pdb, chain F (#51.2) with test.pdb E, chain E (#51.1.5), sequence alignment score = 313.1 RMSD between 69 pruned atom pairs is 0.575 angstroms; (across all 69 pairs: 0.575) > mmaker #51.1.6 to #51.2/E 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 test2.pdb, chain E (#51.2) with test.pdb F, chain F (#51.1.6), sequence alignment score = 313.1 RMSD between 69 pruned atom pairs is 0.575 angstroms; (across all 69 pairs: 0.575) > mmaker #51.1.6 to #51.2/E 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 test2.pdb, chain E (#51.2) with test.pdb F, chain F (#51.1.6), sequence alignment score = 313.1 RMSD between 69 pruned atom pairs is 0.575 angstroms; (across all 69 pairs: 0.575) > hide #!51.1 models > show #!51.1 models > hide #!51.1 models > show #!51.1 models > hide #51.2 models > show #51.2 models > save /Users/chang/Desktop/test3.pdb models #51.1 > open /Users/chang/Desktop/test3.pdb Summary of feedback from opening /Users/chang/Desktop/test3.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 4865 messages similar to the above omitted Chain information for test3.pdb #53 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > hide #!51.1 models > morph #51.2 #53 Computed 21 frame morph #54 > coordset #54 1,21 > show #!51.1 models > close #54 > close #53 > show #51.2 models > hide #51.2 models > save /Users/chang/Desktop/test3.pdb models #51.1 > open /Users/chang/Desktop/test3.pdb Summary of feedback from opening /Users/chang/Desktop/test3.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 4865 messages similar to the above omitted Chain information for test3.pdb #53 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > hide #!51.1 models > show #51.2 models > morph #51.2 #53 Computed 21 frame morph #54 > coordset #54 1,21 > close #53-54#51 > open /Users/chang/Desktop/test.pdb /Users/chang/Desktop/test2.pdb Summary of feedback from opening files --- warning | CONECT record for nonexistent atom: 1978 Chain information for test.pdb #51.1 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available Chain information for test2.pdb #51.2 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available > hide #51.1 models > show #51.1 models > morph #51.2 #51.1 Computed 21 frame morph #53 > coordset #53 1,21 > hide #!51 models > color #53/A,B rgb(29,52,245) > color #53/C rgb(87,178,249) > color #53/D-F springgreen > hide #53 atoms > show #53 surfaces > color #53/D-F springgreen > color #53/C rgb(87,178,249) > color #53/A,B rgb(29,52,245) Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 152, in _atoms_changed self._recompute_shape() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 185, in _recompute_shape self.calculate_surface_geometry() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 209, in calculate_surface_geometry va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius, self.grid_spacing) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in ses_surface_geometry for a in (2,1,0)] File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] ValueError: cannot convert float NaN to integer Error processing trigger ""changes"": ValueError: cannot convert float NaN to integer File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/surface/gridsurf.py"", line 30, in for a in (2,1,0)] See log for complete Python traceback. > close #53 OpenGL version: 4.1 ATI-1.51.8 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Surface can't reproduce all ChimeraX