Surface recomputation: cannot convert float NaN to integer

[chimerax-bug-report@…]

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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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.

[Tom Goddard]

This error occurred due to NaN atom coordinates when recomputing a molecular surface. The atom coordinates changed because of playing a morph. How some frame of the morph got NaN atom coordinates is unclear. The input model could have had NaN or the morph calculation could have generated. Without the input data files it is not possible to tell. The user had over 50 models open.