Color map from segmentation: unsupported operand type(s) for *: 'float' and 'NoneType'

[mestroupe@…]

The following bug report has been submitted:
Platform:        macOS-12.6.3-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Attempt to color map from segmentation.

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/mestroupe/Library/Mobile
> Documents/com~apple~CloudDocs/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs"

Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc as #1, grid size
320,320,320, pixel 0.765, shown at level 0.322, step 1, values float32  
Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian as #4, grid
size 320,320,320, pixel 0.765, shown at level 0.279, step 1, values float32  
Log from Mon Feb 5 09:43:42 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs format session

Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc as #1, grid size
320,320,320, pixel 0.765, shown at level 0.322, step 1, values float32  
Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian as #4, grid
size 320,320,320, pixel 0.765, shown at level 0.279, step 1, values float32  
Log from Sun Feb 4 17:53:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs

Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc as #1, grid size
320,320,320, pixel 0.765, shown at level 0.322, step 1, values float32  
Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian as #4, grid
size 320,320,320, pixel 0.765, shown at level 0.279, step 1, values float32  
Log from Sun Feb 4 17:17:25 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc

Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc as #1, grid size
320,320,320, pixel 0.765, shown at level 0.132, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.346

> open /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/closed_dimer3_P15-map80_real_space_refined_025-coot-38_real_space_refined_028.pdb

Chain information for
closed_dimer3_P15-map80_real_space_refined_025-coot-38_real_space_refined_028.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /B

4581 atoms, 4667 bonds, 27 pseudobonds, 574 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lime green

> color sel byhetero

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> hide #!1 models

> set bgColor white

> select /B

4581 atoms, 4667 bonds, 27 pseudobonds, 574 residues, 2 models selected  

> color sel medium spring green target c

> color sel lime target c

> color sel lime green target c

> select /B:590@K

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

[Repeated 1 time(s)]

> hide atoms

> undo

> select /A:64-65

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:64-240

1221 atoms, 1240 bonds, 1 pseudobond, 159 residues, 2 models selected  

> select /A:206-207

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:64-207

1110 atoms, 1126 bonds, 144 residues, 1 model selected  

> color sel pale violet red target c

> select /A:226-227

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select /A:226-599

2988 atoms, 3055 bonds, 374 residues, 1 model selected  

> select clear

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60n-HP.cxs

> show #!1 models

> volume #1 level 0.3537

> select add #1

2 models selected  

> ui tool show "Hide Dust"

> surface dust #1 size 4.59

> select subtract #1

Nothing selected  

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60nx-HP.cxs

> volume #1 color #b2b2b280

> volume style surface

> select add #1

2 models selected  

> volume sel style surface

> lighting simple

> lighting soft

> lighting full

> hide #!2 models

> show #!2 models

> volume #1 color #b2b2b2cc

> lighting soft

> select subtract #1

Nothing selected  

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60nx-HP.cxs

> select /A

4182 atoms, 4274 bonds, 1 pseudobond, 520 residues, 2 models selected  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select /B:2

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60nx-HP.cxs

> volume #1 level 0.2986

> volume #1 level 0.3222

> ui tool show "Color Zone"

> color zone #1 near #2 distance 4.59

> color single #1

> color zone #1 near #2 distance 4.59

> color single #1

> help help:user/tools/colorzone.html

> ui tool show "Segment Map"

Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 5 of 75 regions.  
Showing 5 of 75 region surfaces  
2397 watershed regions, grouped to 75 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 75 regions, 5
surfaces  

> select add #2

8763 atoms, 8941 bonds, 28 pseudobonds, 1094 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select add #3

6 models selected  

> select subtract #3

Nothing selected  

> select add #3

6 models selected  

> select subtract #3

Nothing selected  

> select add #3

6 models selected  
Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 50 of 75 regions.  
Showing 50 of 75 region surfaces  
2397 watershed regions, grouped to 75 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 75 regions, 50
surfaces  
Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 40 of 75 regions.  
Showing 40 of 75 region surfaces  
2397 watershed regions, grouped to 75 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 75 regions, 40
surfaces  
Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 65 of 75 regions.  
Showing 65 of 75 region surfaces  
2397 watershed regions, grouped to 75 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 75 regions, 65
surfaces  

> ui mousemode right "next docked"

Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 90 of 779 regions.  
Showing 90 of 779 region surfaces  
2397 watershed regions, grouped to 779 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 779 regions, 90
surfaces  
Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 90 of 912 regions.  
Showing 90 of 912 region surfaces  
2397 watershed regions, grouped to 912 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 912 regions, 90
surfaces  

> select #3.6

1 model selected  
Drag select of 3812, 3828, 11536 of 14688 triangles, 3840, 3841, 3818, 1116 of
15044 triangles, 3807, 3835, 7949 of 13092 triangles, 3836, 3809, 8003 of
12572 triangles, 3819, 3838, 3869, 11142 of 11152 triangles, 3821, 3837, 10660
of 10696 triangles, 3870, 3839, 11146 of 11220 triangles, 3822, 3854, 3865,
3866, 3856, 3861, 3873, 3834, 4072 of 7460 triangles, 3855, 3820, 3842, 3860,
6008 of 7208 triangles, 3844, 3813, 3877, 2570 of 7004 triangles, 3875, 3867,
3843, 3767, 3878, 3814, 3748, 3787, 3799, 3876, 3874, 1993 of 3368 triangles,
3659, 3671, 3664, 168 of 2136 triangles, 1
cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc , 232 atoms, 496 residues, 1
pseudobonds, 217 bonds  

> select #3.6

1 model selected  

> select add #3.88

2 models selected  

> select add #3.80

3 models selected  

> select add #3.89

4 models selected  

> select add #3.31

5 models selected  

> select add #3.45

6 models selected  

> select add #3.84

7 models selected  

> select add #3.3

8 models selected  

> select add #3.32

9 models selected  

> select add #3.27

10 models selected  

> select subtract #3.32

9 models selected  

> select add #3.8

10 models selected  

> select add #3.71

11 models selected  

> select add #3.81

14 models selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> hide #!2 models

> show #!2 models

> hide #!1 models

> select
> /A:74-89,98-100,103-108,126-135,163-175,191-203,284-293,311-318,326-336,342-344,348-357,360-366,373-379,394-397,420-427,461-476,492-495,499-507,528-534,536-545,555-574,578-590

1646 atoms, 1653 bonds, 208 residues, 1 model selected  

> select /A:206-207

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:64-207

1110 atoms, 1126 bonds, 144 residues, 1 model selected  

> show #!1 models

> show #!3 models

Overlapping 1110 atoms with 912 regions  
Selected 9 regions  
Grouped 9 regions  
Only showing 90 of 904 regions.  
Showing 90 of 904 region surfaces  

> close #3

> select clear

> select /B

4581 atoms, 4667 bonds, 27 pseudobonds, 574 residues, 2 models selected  
Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc, density threshold
0.322197  
Only showing 90 of 912 regions.  
Showing 90 of 912 region surfaces  
2397 watershed regions, grouped to 912 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip.seg - 912 regions, 90
surfaces  
Overlapping 4581 atoms with 912 regions  
Selected 14 regions  

> select clear

> hide #!3 models

> hide #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 2/B  

> select /B:80

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1-80

643 atoms, 654 bonds, 80 residues, 1 model selected  

> color sel medium blue

> select clear

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60nx-HP.cxs

> show #!1 models

> ui tool show "Map Filter"

> volume gaussian #1 sDev 0.38

Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian as #4, grid
size 320,320,320, pixel 0.765, shown at step 1, values float32  

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #4

> show #!1 models

> volume gaussian #1 sDev 0.56

Opened cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian as #4, grid
size 320,320,320, pixel 0.765, shown at step 1, values float32  

> ui tool show "Map Filter"

> ui tool show "Segment Map"

Segmenting cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian, density
threshold 0.279489  
Only showing 90 of 472 regions.  
Showing 90 of 472 region surfaces  
1768 watershed regions, grouped to 472 regions  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip gaussian.seg - 472
regions, 90 surfaces  
Drag select of 2993, 11583 of 14680 triangles, 3029, 3020, 3042, 11565 of
14272 triangles, 3023, 10736 of 14144 triangles, 3009, 4391 of 13716
triangles, 2994, 13392 of 13980 triangles, 3002, 3033, 1442 of 14136
triangles, 3003, 11521 of 13052 triangles, 3021, 12180 of 12844 triangles,
3008, 2997, 3052, 3044, 6320 of 11752 triangles, 2995, 3016, 3017, 3043, 10640
of 10644 triangles, 3022, 3007, 3040, 8742 of 9208 triangles, 2998, 5628 of
9728 triangles, 3018, 3045, 8992 of 9628 triangles, 3053, 3030, 3011, 2888 of
9376 triangles, 3019, 3039, 3041, 3012, 50 of 8052 triangles, 3061, 7630 of
7952 triangles, 3010, 6429 of 7428 triangles, 3031, 3032, 5893 of 5928
triangles, 3058, 3059, 2918, 3060, 2865, 2190 of 2876 triangles, 2569, 2874,
2639, 794, 296 of 772 triangles, 232 atoms, 489 residues, 27 pseudobonds, 197
bonds, 4 cryosparc_P15_J80_009_volume_map_sharp_zflip.mrc gaussian  
Grouped 45 regions  

> hide #!3 models

> show #!3 models

> hide #!4 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3.1

1 model selected  
No visible atoms or bonds selected  
[Repeated 22 time(s)]

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> hide #3.15 models

> show #3.15 models

> hide #!2 models

> show #!2 models

> select add #3

47 models selected  

> select subtract #3.1

46 models selected  

> select add #3

47 models selected  

> select subtract #3

Nothing selected  

> hide #3.1 models

> show #3.1 models

> select add #3.1

1 model selected  

> color #3.1 #d9fdc580

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select add #3.63

2 models selected  
Grouped 2 regions  

> select subtract #3.1

Nothing selected  

> select add #3.1

1 model selected  

> select add #3

46 models selected  

> select subtract #3

Nothing selected  

> select add #3

46 models selected  

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60nx-HP.cxs

> select subtract #3.1

45 models selected  
Grouped 44 regions  

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60nx-HP.cxs

——— End of log from Sun Feb 4 17:17:25 2024 ———

opened ChimeraX session  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip gaussian.seg - 384
regions, 2 surfaces  

> hide #!3 models

> hide target p

> select /B:440@SG

1 atom, 1 residue, 1 model selected  

> select add /B:575@FE2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance /B:440@SG /B:575@FE2

Distance between /B CYS 440 SG and SF4 575 FE2: 2.255Å  

> distance style symbol false

[Repeated 2 time(s)]

> label delete bonds

> label hide bonds

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> distance style decimalPlaces 2

[Repeated 2 time(s)]

> distance style decimalPlaces 1

[Repeated 2 time(s)]

> ~distance /B:440@SG /B:575@FE2

> select /A:161

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add /A:162

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select add /A:153

25 atoms, 23 bonds, 3 residues, 1 model selected  

> select add /A:116

32 atoms, 29 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select /A:75

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add /A:160

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:155

24 atoms, 22 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select /A:74

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /A:72

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select add /A:71@CA

16 atoms, 13 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select /A:71

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add /A:70

15 atoms, 13 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select add /A:158

27 atoms, 25 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select add /A:119

36 atoms, 33 bonds, 4 residues, 1 model selected  

> select add /A:118

43 atoms, 39 bonds, 5 residues, 1 model selected  

> select add /A:117

49 atoms, 44 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select add /A:387

57 atoms, 51 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add /A:599

70 atoms, 64 bonds, 8 residues, 1 model selected  

> hide sel atoms

> select add /A:598

77 atoms, 70 bonds, 9 residues, 1 model selected  

> select add /A:597@CA

78 atoms, 70 bonds, 10 residues, 1 model selected  

> select add /A:597@CB

79 atoms, 70 bonds, 10 residues, 1 model selected  

> select add /A:597@OD1

80 atoms, 71 bonds, 10 residues, 1 model selected  

> select add /A:597@OD2

81 atoms, 71 bonds, 10 residues, 1 model selected  

> select add /A:462

88 atoms, 77 bonds, 11 residues, 1 model selected  

> select subtract /A:462

81 atoms, 71 bonds, 10 residues, 1 model selected  

> select add /A:462@CB

82 atoms, 71 bonds, 11 residues, 1 model selected  

> select add /A:462@OG1

83 atoms, 71 bonds, 11 residues, 1 model selected  

> select add /A:462@CG2

84 atoms, 71 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select add /A:597@CG

85 atoms, 71 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select subtract /A:599

72 atoms, 58 bonds, 10 residues, 1 model selected  

> select add /A:599

85 atoms, 71 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select add /A:388@CA

86 atoms, 71 bonds, 12 residues, 1 model selected  

> select add /A:389

92 atoms, 76 bonds, 13 residues, 1 model selected  

> hide sel atoms

> select add /A:388@CG

93 atoms, 76 bonds, 13 residues, 1 model selected  

> select add /A:388@CD1

94 atoms, 76 bonds, 13 residues, 1 model selected  

> select add /A:388@CE1

95 atoms, 76 bonds, 13 residues, 1 model selected  

> select add /A:388@CZ

96 atoms, 76 bonds, 13 residues, 1 model selected  

> select add /A:388@OH

97 atoms, 76 bonds, 13 residues, 1 model selected  

> select add /A:388@CE2

98 atoms, 76 bonds, 13 residues, 1 model selected  

> select add /A:388@CD2

99 atoms, 76 bonds, 13 residues, 1 model selected  

> hide sel atoms

> select add /A:388@CB

100 atoms, 76 bonds, 13 residues, 1 model selected  

> hide sel atoms

> select add /A:404@CB

101 atoms, 76 bonds, 14 residues, 1 model selected  

> select add /A:404@CA

102 atoms, 76 bonds, 14 residues, 1 model selected  

> select add /A:404@CG2

103 atoms, 76 bonds, 14 residues, 1 model selected  

> select add /A:404@OG1

104 atoms, 76 bonds, 14 residues, 1 model selected  

> hide sel atoms

> select add /A:386

115 atoms, 86 bonds, 15 residues, 1 model selected  

> hide sel atoms

> select add /A:357@CA

116 atoms, 86 bonds, 16 residues, 1 model selected  

> select add /A:357@CG2

117 atoms, 87 bonds, 16 residues, 1 model selected  

> select add /A:357@OG1

118 atoms, 87 bonds, 16 residues, 1 model selected  

> hide sel atoms

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs

> select add /A:357@CB

119 atoms, 87 bonds, 16 residues, 1 model selected  

> select /A:357@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select add /A:410

13 atoms, 12 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select add /A:322

20 atoms, 18 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select /B:362

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:396

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add /B:397

17 atoms, 15 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select add /B:395@CA

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select /B:395@CA

1 atom, 1 residue, 1 model selected  

> select add /B:395@CG

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /B:395@OD1

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:395@ND2

3 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select /B:395@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select /B:435

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:113

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:123@CA

1 atom, 1 residue, 1 model selected  

> select add /B:123@CG

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /B:123@CE1

2 atoms, 2 bonds, 1 residue, 1 model selected  

> select add /B:123@NE2

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select add /B:123@CD2

4 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add /B:60@CG

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /B:60@CD

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:60@OE1

3 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:60@NE2

4 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:123@ND1

5 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:123@CB

6 atoms, 1 bond, 2 residues, 1 model selected  

> hide sel atoms

> select clear

[Repeated 1 time(s)]

> select add /B:81@CB

1 atom, 1 residue, 1 model selected  

> select add /B:81@CD1

2 atoms, 1 residue, 1 model selected  

> select add /B:81@CD2

3 atoms, 1 residue, 1 model selected  

> select add /B:121@CB

4 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:121@CG

5 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:121@CD

6 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:121@OE1

7 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:121@NE2

8 atoms, 1 bond, 2 residues, 1 model selected  

> hide sel atoms

> select /B:81@CG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select add /B:439@CG2

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /B:439@OG1

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:580@O1A

3 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:580@O2A

4 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:580@CCA

5 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:580@CBA

6 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:580@CAA

7 atoms, 1 bond, 2 residues, 1 model selected  

> select add /B:580@CMA

8 atoms, 1 bond, 2 residues, 1 model selected  

> hide sel atoms

> select /B:439@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /B:58

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:83

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:153

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:115

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:119

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:306

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:286

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:214

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:258

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:433@CA

1 atom, 1 residue, 1 model selected  

> select /B:429

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:433@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /B:115

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:117

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:485

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add /B:481@CG

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /B:481@ND2

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:481@CB

3 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:481@OD1

4 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select add /B:217@CB

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /B:217@CG

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:217@CD

3 atoms, 1 bond, 1 residue, 1 model selected  

> select add /B:217@CE

4 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select /B:217@NZ

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /B:215@CG

1 atom, 1 residue, 1 model selected  

> select /B:215@CG

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:215@CG

1 atom, 1 residue, 1 model selected  

> select add /B:215@CD

2 atoms, 1 residue, 1 model selected  

> select add /B:215@CE

3 atoms, 1 residue, 1 model selected  

> select add /B:215@NZ

4 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> select /B:215@CB

1 atom, 1 residue, 1 model selected  

> select /B:215

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:442

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /B:443

5 atoms, 4 bonds, 1 residue, 1 model selected  

> hide sel atoms

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs

> select /B:483@SG

1 atom, 1 residue, 1 model selected  

> select add /B:580@FE

2 atoms, 2 residues, 1 model selected  

> hbonds #2,580@fe #2,483@sg

6 hydrogen bonds found  

> ~hbonds #2,580@fe #2,483@sg

Expected a keyword  

> bond #2,580@fe #2,483@sg

Created 1 bond  

> hide hbonds

> bond #2,574@fe4 #2,483@sg

Created 1 bond  

> bond #2,574@fe4 #2,574@s1

Created 1 bond  

> select /B:483@SG

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> select /B:575@S2

1 atom, 1 residue, 1 model selected  

> select add /B:575@S1

2 atoms, 1 residue, 1 model selected  

> select add /B:479@SG

3 atoms, 2 residues, 1 model selected  

> select add /B:440@SG

4 atoms, 3 residues, 1 model selected  

> style sel ball

Changed 4 atom styles  

> select /B:575@S3

1 atom, 1 residue, 1 model selected  

> select add /B:434@SG

2 atoms, 2 residues, 1 model selected  

> style sel ball

Changed 2 atom styles  

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs

> bond #2,574@fe3 #2,574@s1

Created 1 bond  

> bond #2,574@fe2 #2,574@s1

Created 1 bond  

> bond #2,574@fe2 #2,574@s3

Created 1 bond  

> bond #2,574@fe4 #2,574@s3

Created 1 bond  

> bond #2,574@fe1 #2,574@s3

Created 1 bond  

> bond #2,574@fe1 #2,574@s2

Created 1 bond  

> bond #2,574@fe4 #2,574@s2

Created 1 bond  

> bond #2,574@fe3 #2,574@s2

Created 1 bond  

> select /B:575@S4

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> bond #2,574@fe3 #2,574@s1

Created 0 bonds  

> bond #2,574@fe3 #2,574@s1

Created 0 bonds  

> bond #2,574@fe3 #2,574@s4

Created 1 bond  

> bond #2,574@fe1 #2,574@s4

Created 1 bond  

> bond #2,574@fe2 #2,574@s4

Created 1 bond  

> bond #2,574@fe2 #2,440@sg

Created 1 bond  

> bond #2,574@fe3 #2,479@sg

Created 1 bond  

> bond #2,574@fe1 #2,434@sg

Created 1 bond  

> select clear

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs

[Repeated 1 time(s)]

——— End of log from Sun Feb 4 17:53:17 2024 ———

opened ChimeraX session  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip gaussian.seg - 384
regions, 2 surfaces  

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3.1

1 model selected  

> ui tool show "Color Actions"

> color sel lime green

> hide #!3 models

> select /B:81

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:81-570

3861 atoms, 3942 bonds, 3 pseudobonds, 490 residues, 2 models selected  

> select /B:386-440

415 atoms, 420 bonds, 55 residues, 1 model selected  

> select /B:386-495

820 atoms, 832 bonds, 1 pseudobond, 110 residues, 2 models selected  

> select /B:81-82

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /B:81-570

3861 atoms, 3942 bonds, 3 pseudobonds, 490 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel pale green

> ui tool show "Color Actions"

> color sel light green

> ui tool show "Color Actions"

> color sel lime green

> select clear

> color #3.1 #32cd3299

> show #!3 models

> select #3.1

1 model selected  

> ui tool show "Color Actions"

> color sel light green

> color #3.1 #90ee9080

> select #3.2

1 model selected  

> select #3.2

1 model selected  

> hide #3.2 models

> show #3.2 models

Ungrouped to 44 regions  

> select #3.17

1 model selected  

> select add #3.40

2 models selected  

> select add #3.8

3 models selected  

> select add #3.10

4 models selected  

> select add #3.24

5 models selected  

> select add #3.32

6 models selected  
Grouped 6 regions  

> select add #3.28

2 models selected  

> select add #3.41

3 models selected  
Grouped 3 regions  

> select #3.2

1 model selected  

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> select subtract #3.2

Nothing selected  

> select add #3.2

1 model selected  

> select subtract #3.2

Nothing selected  

> select add #3.2

1 model selected  

> select add #3.33

2 models selected  
Grouped 2 regions  

> select subtract #3.2

Nothing selected  

> select add #3.3

1 model selected  

> select subtract #3.3

Nothing selected  

> select add #3.2

1 model selected  

> ui tool show "Color Actions"

> color sel pale violet red

> color #3.2 #ae96c299

> select add #3.3

2 models selected  

> select subtract #3.2

1 model selected  

> select add #3.2

2 models selected  

> select subtract #3.3

1 model selected  

> ui tool show "Color Actions"

> color sel pale violet red

> color sel violet

> color sel pink

> select add #3.3

2 models selected  

> select subtract #3.2

1 model selected  

> select add #3.4

2 models selected  

> select add #3.5

3 models selected  

> select add #3.6

4 models selected  

> select add #3.7

5 models selected  

> select add #3.9

6 models selected  

> select add #3.11

7 models selected  

> select add #3.12

8 models selected  

> select add #3.13

9 models selected  

> select add #3.14

10 models selected  

> select add #3.15

11 models selected  

> select add #3.16

12 models selected  

> select add #3.18

13 models selected  

> select add #3.19

14 models selected  

> select add #3.20

15 models selected  

> select add #3.21

16 models selected  

> select add #3.22

17 models selected  

> select add #3.23

18 models selected  

> select add #3.25

19 models selected  

> select add #3.26

20 models selected  

> select add #3.27

21 models selected  

> select add #3.29

22 models selected  

> select add #3.30

23 models selected  

> select add #3.31

24 models selected  

> select add #3.34

25 models selected  

> select add #3.35

26 models selected  

> select add #3.36

27 models selected  

> select add #3.37

28 models selected  

> select add #3.38

29 models selected  

> select add #3.39

30 models selected  

> select add #3.42

31 models selected  

> select add #3.43

32 models selected  

> select add #3.44

33 models selected  

> select add #3.45

34 models selected  

> select add #3.46

35 models selected  
Grouped 35 regions  

> ui tool show "Color Actions"

> color sel powder blue

> ui tool show "Color Actions"

No visible atoms or bonds selected  

> color #3.3 #b0e0e699

> select clear

> save /Users/mestroupe/Desktop/SiRFP-60-HP_2024/chimera-
> mother_session/FP60x-HP.cxs

[Repeated 1 time(s)]

——— End of log from Mon Feb 5 09:43:42 2024 ———

opened ChimeraX session  
Showing cryosparc_P15_J80_009_volume_map_sharp_zflip gaussian.seg - 385
regions, 3 surfaces  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 954, in ColorDensity  
smod.color_density()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 851, in color_density  
color_surface_pieces(d.surfaces, m, ijk_to_xyz, offset, cmap)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1884, in color_surface_pieces  
xyz = v - offset*n  
~~~~~~^~  
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'  
  
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1884, in color_surface_pieces  
xyz = v - offset*n  
~~~~~~^~  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      System Firmware Version: 1916.60.2.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 12.6.3 (21G419)
      Kernel Version: Darwin 21.6.0
      Time since boot: 198 days 5:54

Graphics/Displays:

    Radeon Pro 575X:

      Chipset Model: Radeon Pro 575X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A14GP-003
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        SMB2330H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: HCLZA00206  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C VGA Adapter
          Adapter Firmware Version: 1.91


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
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File attachment: 3-seg_60c-HP.seg

3-seg_60c-HP.seg​

[mestroupe@…]

Added by email2trac

[Eric Pettersen]

Reported by Beth Stroupe

[Tom Goddard]

This error is a bug in Segger. It is trying to color a volume surface but that surface was never computed. It was not computed because it the surfaces are only computed when the volume is shown. This volume came from opening a session and it was not being displayed so it was not computed.

You could work around this problem by using command "volume all show style surface" so that all surfaces are shown. You only really need to show the surface for the volume that you are trying to color.

I will fix the Segger code so that it does not generate an error coloring volume surfaces that have not been computed.

[Tom Goddard]

Fixed.

Attempting to color uncomputed volume surfaces now gives no error, but also doesn't color the non-existent surface.