id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3920	Drawing (map) _colors is None	caillancm@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202011040611 (2020-11-04 06:11:15 UTC)
Description
I cannot reliably reproduce this bug yet. It seems to occur after some density in a map is deleted with the volume eraser tool, the map is re-opened, and an image is saved with clipped using the side view panel. Closing the maps, side view, etc, doesn't help.

Log:
UCSF ChimeraX version: 1.2.dev202011040611 (2020-11-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/200511_vgaA_ATP-density_02.cxs

Log from Fri Nov 6 18:47:34 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201010_vgaA_ATP-density_01.cxs

Log from Sat Oct 10 17:33:42 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/crowe/Dropbox/ABCF-writing/maps/pp/pp_VgaA-LC_rebox-resamp.mrc

Opened pp_VgaA-LC_rebox-resamp.mrc, grid size 352,352,352, pixel 1.04, shown
at level 0.0148, step 2, values float32  

> open /Users/crowe/Dropbox/ABCF-writing/maps/locally-filtered/LocFilt_VgaA-
> LC_rebox-resamp.mrc

Opened LocFilt_VgaA-LC_rebox-resamp.mrc, grid size 352,352,352, pixel 1.04,
shown at level 0.0107, step 2, values float32  

> open /Users/crowe/Dropbox/ABCF-writing/maps/r3d/r3d_VgaA-LC_rebox-resamp.mrc

Opened r3d_VgaA-LC_rebox-resamp.mrc, grid size 352,352,352, pixel 1.04, shown
at level 0.0107, step 2, values float32  

> set bgColor white

> volume level 1

> volume level 0.008

> volume step 1

> volume level 0.01

> open /Users/crowe/Dropbox/ABCF-writing/models/vgaA-70S/201009_vgaA_chimeraX-
> aligned.pdb

Chain information for 201009_vgaA_chimeraX-aligned.pdb #4  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
D | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> hide #4 atoms

> show #4 cartoons

> color #4 grey

> color #4/A lightblue

> hide #!4 models

> show #!4 models

> color #4 grey

> color #4/A lightgrey

> color #4/0 hotpink

> color #4/0 deeppink

> color #4/D skyblue

> volume #1 color #b2b2b2e0

> volume #1 color #b2b2b2c9

> volume #1 color #b2b2b2bb

> volume #1 color #b2b2b2af

> volume #1 color #b2b2b2ad

> volume #1 color #b2b2b2aa

> volume #1 color #b2b2b2a3

> volume #1 color #b2b2b2a0

> volume #1 color #b2b2b29c

> volume #1 color #b2b2b297

> volume #1 color #b2b2b295

> volume #1 color #b2b2b293

> volume #1 color #b2b2b290

> volume #1 color #b2b2b28c

> volume #1 color #b2b2b28a

> volume #1 color #b2b2b288

> volume #1 color #b2b2b287

> volume #1 color #b2b2b286

> volume #1 color #b2b2b282

> volume #1 color #b2b2b277

> volume #1 color #b2b2b270

> volume #1 color #b2b2b268

> volume #1 color #b2b2b263

> volume #1 color #b2b2b25f

> volume #1 color #b2b2b25c

> volume #1 color #b2b2b257

> volume #1 color #b2b2b256

> volume #1 color #b2b2b254

> volume #1 color #b2b9b254

> volume #1 color #b2bfb254

> volume #1 color #b2cab254

> volume #1 color #b2d0b254

> volume #1 color #b2d7b254

> volume #1 color #b2ddb254

> volume #1 color #b2deb254

> volume #1 color #b2e3b254

> volume #1 color #b2e7b254

> volume #1 color #b2e8b254

> volume #1 color #b2e9b254

> volume #1 color #b2ecb254

> volume #1 color #b2edb254

> volume #1 color #b2f8b254

> volume #1 color #b2fbb254

> volume #1 color #b2ffb254

> volume #1 color #b2ffb354

> volume #1 color #b2ffb654

> volume #1 color #b2ffc054

> volume #1 color #b2ffd554

> volume #1 color #b2ffdc54

> volume #1 color #b2fff354

> volume #1 color #b2ffff54

> volume #1 color #b2ffff53

> volume #1 color #b2ffff52

> volume #1 color #b2ffff4d

> volume #1 color #b2ffff4c

> volume #1 color #b2ffff4b

> volume #1 color #b2ffff4a

> volume #1 color #b2ffff45

> volume #1 color #b2ffff43

> volume #1 color #b2ffff42

> volume #1 color #b2ffff40

> volume #1 color #b2ffff3f

> volume #1 color #b2ffff3c

> volume #1 color #b2ffff3b

> volume #1 color #b2ffff39

> volume #1 color #b2ffff37

> volume #1 color #b2ffff33

> volume #1 color #b2ffff31

> volume #1 color #b2ffff30

> volume #1 color #b2ffff2d

> show #4/0 atoms

> style stick

Changed 145651 atom styles  

> show #4/D atoms

> color #4 byhetero

> ui tool show ""Side View""

> volume #1 color #b2ffff2e

> volume #1 color #b2ffff33

> volume #1 color #b2ffff3c

> volume #1 color #b2ffff3d

> volume #1 color #b2ffff3f

> volume #1 color #b2ffff42

> volume #1 color #b2ffff46

> volume #1 color #b2ffff47

> volume #1 color #b2ffff49

> volume #1 color #b2ffff4b

> volume #1 color #b2ffff4d

> volume #1 color #b2ffff4e

> volume #1 color #b2ffff50

> volume #1 color #b2ffff4f

> volume #1 color #b2ffff4e

> volume #1 color #b2ffff4d

> volume #1 color #b2ffff4c

> volume #1 color #b2ffff4a

> select /0:468@PA

1 atom, 1 residue, 1 model selected  

> select /0:468@O1A

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> color sel grey

> color sel byhetero

> select clear

> select /0:468@C5'

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> cofr sel

> select clear

> select /0:469@MG

1 atom, 1 residue, 1 model selected  

> size sel ballScale 0.5

Changed 1 ball scales  

> size sel atomRadius 0.5

Changed 1 atom radii  

> style sel sphere

Changed 1 atom style  

> select clear

> select up

127 atoms, 128 bonds, 16 residues, 1 model selected  

> hide sel

> hide sel cartoons

> select up

156 atoms, 156 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select /0:387

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

> select up

127 atoms, 127 bonds, 17 residues, 1 model selected  

> hide sel atoms

> select up

3834 atoms, 3893 bonds, 469 residues, 1 model selected  

> select down

127 atoms, 127 bonds, 17 residues, 1 model selected  

> hide sel cartoons

> volume #1 color #b2ffff4b

> volume #1 color #b2ffff4c

> volume #1 color #b2ffff55

> volume #1 color #b2ffff6b

> volume #1 color #b2ffff70

> volume #1 color #b2ffff74

> volume #1 color #b2ffff79

> volume #1 color #b2ffff7d

> volume #1 color #b2ffff81

> volume #1 color #b2ffff83

> volume #1 color #b2ffff87

> volume #1 color #b2ffff8a

> volume #1 color #b2ffff8f

> volume #1 color #b2ffff93

> volume #1 color #b2ffff9b

> volume #1 color #b2ffff9e

> volume #1 color #b2ffffa4

> volume #1 color #b2ffffaa

> volume #1 color #b2ffffaf

> volume #1 color #b2ffffb1

> volume #1 color #b2ffffb3

> volume #1 color #b2ffffb5

> volume #1 color #b2ffffb6

> volume #1 color #b2ffffb8

> volume #1 color #b2ffffba

> volume #1 color #b2ffffbb

> volume #1 color #b2ffffbd

> volume #1 color #b2ffffbf

> volume #1 color #b2ffffc1

> volume #1 color #b2ffffc3

> volume #1 color #b2ffffc7

> volume #1 color #b2ffffc8

> ui mousemode right ""map eraser""

> volume erase #1 center 125.47,139.39,169.51 radius 8.3164

> volume erase #6 center 122.88,140.23,170.28 radius 8.2447

> volume erase #6 center 128.26,142.83,169.03 radius 5.13

> volume #1 color #b2ffffc7

> volume #1 color #b2ffffc6

> volume #1 color #b2ffffc3

> volume #1 color #b2ffffbf

> volume #1 color #b2ffffbe

> volume #1 color #b2ffffb9

> volume #1 color #b2ffffb4

> volume #1 color #b2ffffb0

> volume #1 color #b2ffffa8

> volume #1 color #b2ffff9f

> volume #1 color #b2ffff9c

> volume #1 color #b2ffff9a

> volume #1 color #b2ffff97

> volume #1 color #b2ffff95

> volume #1 color #b2ffff92

> volume #1 color #b2ffff90

> volume #1 color #b2ffff8c

> volume #1 color #b2ffff89

> volume #1 color #b2ffff86

> volume #1 color #b2ffff84

> volume #1 color #b2ffff7d

> volume #1 color #b2ffff7b

> volume #1 color #b2ffff76

> volume #1 color #b2ffff75

> volume #1 color #b2ffff74

> volume #1 color #b2ffff71

> volume #1 color #b2ffff6e

> volume #1 color #b2ffff6c

> volume #1 color #b2ffff6b

> volume #1 color #b2ffff69

> volume #1 color #b2ffff68

> volume #1 color #b2ffff67

> volume #1 color #b2ffff68

> volume #1 color #b2ffff69

> volume #1 color #b2ffff6b

> volume #1 color #b2ffff6c

> volume #1 color #b2ffff6a

> volume #1 color #b2ffff69

> volume #1 color #b2ffff64

> volume #1 color #b2ffff62

> volume #1 color #b2ffff5f

> volume #1 color #b2ffff5c

> volume #1 color #b2ffff5a

> volume #1 color #b2ffff57

> volume #1 color #b2ffff53

> volume #1 color #b2ffff4f

> volume #1 color #b2ffff4a

> volume #1 color #b2ffff43

> volume #1 color #b2ffff41

> volume #1 color #b2ffff3f

> volume #1 color #b2ffff3a

> volume #1 color #b2ffff38

> volume #1 color #b2ffff33

> volume #1 color #b2ffff31

> volume #1 color #b2ffff2e

> volume #1 color #b2ffff2c

> volume #1 color #b2ffff2b

> volume #1 color #b2ffff2a

> volume #1 color #b2ffff28

> volume #1 color #b2ffff27

> volume #1 color #b2ffff28

> volume #1 color #b2ffff2a

> volume #1 color #b2ffff2f

> volume #1 color #b2ffff39

> volume #1 color #b2ffff41

> volume #1 color #b2ffff44

> volume #1 color #b2ffff48

> volume #1 color #b2ffff4f

> volume #1 color #b2ffff57

> volume #1 color #b2ffff5b

> volume #1 color #b2ffff64

> volume #1 color #b2ffff71

> volume #1 color #b2ffff77

> volume #1 color #b2ffff7c

> volume #1 color #b2ffff7d

> volume #1 color #b2ffff7f

> volume #1 color #b2ffff81

> volume #1 color #b2ffff85

> volume #1 color #b2ffff8a

> volume #1 color #b2ffff8d

> volume #1 color #b2ffff91

> volume #1 color #b2ffff96

> volume #1 color #b2ffff9a

> volume #1 color #b2ffff9e

> volume #1 color #b2ffffa3

> volume #1 color #b2ffffaa

> volume #1 color #b2ffffb0

> volume #1 color #b2ffffb3

> volume #1 color #b2ffffb4

> volume #1 color #b2ffffb5

> volume #1 color #b2ffffb6

> volume #1 color #b2ffffb7

> volume #1 color #b2ffffb8

> volume #1 color #b2ffffba

> volume #1 color #b2ffffbb

> volume #1 color #b2ffffbf

> volume #1 color #b2ffffc2

> volume #1 color #b2ffffbf

> volume #6 color #b2ffffc5

> volume #6 color #b2ffffc2

> volume #6 color #b2ffffb7

> volume #6 color #b2ffff9e

> volume #6 color #b2ffff8d

> volume #6 color #b2ffff79

> volume #6 color #b2ffff71

> volume #6 color #b2ffff67

> volume #6 color #b2ffff65

> volume #6 color #b2ffff60

> volume #6 color #b2ffff5d

> volume #6 color #b2ffff59

> volume #6 color #b2ffff56

> volume #6 color #b2ffff55

> volume #6 color #b2ffff53

> volume #6 color #b2ffff52

> volume #6 color #b2ffff4e

> volume #6 color #b2ffff4c

> volume #6 color #b2ffff47

> volume #6 color #b2ffff4a

> volume #6 color #b2ffff4b

> volume #6 color #b2ffff4a

> volume #6 color #b2ffff48

> volume #6 color #b2ffff49

> volume #6 color #b2ffff4e

> volume #6 color #b2ffff51

> volume #6 color #b2ffff57

> volume #6 color #b2ffff5b

> volume #6 color #b2ffff5c

> volume #6 color #b2ffff60

> volume #6 color #b2ffff64

> volume #6 color #b2ffff65

> volume #6 color #b2ffff67

> volume #6 color #b2ffff69

> volume #6 color #b2ffff6a

> volume #6 color #b2ffff6b

> volume #6 color #b2ffff74

> volume #6 color #b2ffff76

> volume #6 color #b2ffff78

> volume #6 color #b2ffff79

> volume #6 color #b2ffff7a

> volume #6 color #b2ffff7c

> volume #6 color #b2ffff7e

> volume #6 color #b2ffff80

> volume #6 level 0.01455

> volume #6 level 0.01062

> show #4/0 cartoob

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #4/0 cartoons

> select clear

> select /0:387

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

> select up

127 atoms, 127 bonds, 17 residues, 1 model selected  

> hide sel cartoons

> select clear

> select /0:385

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

> select up

29 atoms, 28 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> select clear

> ui mousemode right ""map eraser""

Drag select of 4 atoms, 13 residues, 2 bonds, 6 pp_VgaA-LC_rebox-resamp.mrc
copy  

> select clear

Drag select of eraser sphere, 21 of 1000 triangles, 33 atoms, 65 residues, 29
bonds, 6 pp_VgaA-LC_rebox-resamp.mrc copy  

> select clear

> select /0:73

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

> select up

127 atoms, 128 bonds, 16 residues, 1 model selected  

> show sel atoms

> select #6

4 models selected  

> select clear

> volume erase #6 center 133.02,142.07,165.97 radius 2.2343

> volume erase #6 center 135.09,144.55,169.21 radius 2.2343

> volume erase #6 center 134.83,143.49,168.8 radius 2.2343

> volume erase #6 center 137.09,142.94,169.75 radius 2.2343

> volume erase #6 center 135.91,140.63,169.63 radius 2.2343

> volume erase #6 center 133.55,139.2,172.15 radius 2.2343

> volume erase #6 center 132.04,137.66,166.59 radius 2.2343

> volume erase #6 center 134.77,137.86,169.69 radius 2.2343

> volume erase #6 center 133.47,137.32,166.34 radius 2.2343

> volume erase #6 center 132.81,137.63,174.15 radius 2.2343

> volume #6 level 0.01435

> view name ATP1-1

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201010_lsaA-vgaA_ATP-density_05.cxs

——— End of log from Sat Oct 10 17:33:42 2020 ———

opened ChimeraX session  

> volume #1 level 0.0143

> windowsize 1800 1138

> select /0:73@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> close #3

> save /Users/crowe/Dropbox/ABCF-writing/maps/for-ATP-density-rendering/vgaA-
> strong_ATP-site.mrc models #6

> open /Users/crowe/Dropbox/ABCF-writing/maps/for-ATP-density-rendering/vgaA-
> strong_ATP-site.mrc

Opened vgaA-strong_ATP-site.mrc, grid size 352,352,352, pixel 1.04, shown at
level 0.0148, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.0152

> volume #3 level 0.0145

> volume #3 style mesh

> volume #3 color #e5bf48

> volume #3 color #e5bf47

> volume #3 color #e5bf45

> volume #3 color #e5bf40

> volume #3 color #e5bf35

> volume #3 color #e5bf33

> volume #3 color #e5bf1e

> volume #3 color #e5bf00

> volume #3 color #e53d00

> volume #3 color #e53b00

> volume #3 color #e52a00

> volume #3 color #e51d00

> volume #3 color #e51800

> volume #3 color #e51100

> volume #3 color #e50700

> volume #3 color #e50000

> volume #3 color #460000

> volume #3 color #410000

> volume #3 color #3a0000

> volume #3 color #290000

> volume #3 color #180000

> volume #3 color black

> volume #3 level 0.01111

> volume #3 level 0.0145

> volume #3 level 0.014

> volume #3 level 0.0142

> volume #3 step 2

> volume #3 step 1

> hide sel atoms

> select clear

> view list

Named views: ATP1-1  

> view ATP1-1

> volume #3 subdivideSurface true

> volume #6 level 0.0153

> volume #3 level 0.0152

> cd /Users/crowe/Dropbox/ABCF-writing/figures/pymol_chimera_pngs/201105_ATP-
> density

Current working directory is: /Users/crowe/Dropbox/ABCF-
writing/figures/pymol_chimera_pngs/201105_ATP-density  

> save 201105_VgaA-strong-site_01.png

> volume #3 squareMesh true

> view name vgaA-strong-ATP-1

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/200511_vgaA_ATP-density_05.cxs includeMaps true

> close #2

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/200511_vgaA_ATP-density_02.cxs includeMaps true

——— End of log from Fri Nov 6 18:47:34 2020 ———

opened ChimeraX session  

> select clear

> select up

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

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> cofr sel

> select add /0:81

37 atoms, 38 bonds, 2 residues, 1 model selected  

> select add /0:80

46 atoms, 46 bonds, 3 residues, 1 model selected  

> hide #!3 models

> select clear

> select add /0:81

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

> select add /0:82

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select up

134 atoms, 134 bonds, 17 residues, 1 model selected  

> select up

3834 atoms, 3893 bonds, 469 residues, 1 model selected  

> select down

134 atoms, 134 bonds, 17 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select /0:80

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

> select up

127 atoms, 128 bonds, 16 residues, 1 model selected  

> select down

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

> select clear

> select add /0:80@CA

1 atom, 1 residue, 1 model selected  

> select add /0:79

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select add /0:78@CA

9 atoms, 6 bonds, 3 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /0:80@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

127 atoms, 128 bonds, 16 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select /0:470@MG

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select clear

> ui mousemode right ""map eraser""

> volume erase #3 center 121.22,133.77,152.62 radius 7.5143

> volume erase #3 center 115.56,131.75,154.4 radius 7.5143

> select /0:467@C6

1 atom, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 1 residue, 1 model selected  

> color sel grey

> color sel byhetero

> select clear

> close #6

> ui tool show ""Side View""

> volume #3 level 0.013

> save /Users/crowe/Dropbox/ABCF-writing/maps/for-ATP-density-rendering/vgaA-
> both_ATP-sites.mrc models #3

> open /Users/crowe/Dropbox/ABCF-writing/maps/for-ATP-density-rendering/vgaL-
> both_ATP-sites.mrc

Opened vgaL-both_ATP-sites.mrc, grid size 352,352,352, pixel 1.04, shown at
level 0.0257, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.0128

> close #2

> open /Users/crowe/Dropbox/ABCF-writing/maps/for-ATP-density-rendering/vgaA-
> both_ATP-sites.mrc

Opened vgaA-both_ATP-sites.mrc, grid size 352,352,352, pixel 1.04, shown at
level 0.0148, step 2, values float32  

> volume #2 level 0.0128

> volume #2 step 1

> volume #2 level 0.0131

> volume #2 color #ffb5b2

> volume #2 color #ffb5df

> volume #2 color #ffb5e0

> volume #2 color #ffb5e2

> volume #2 color #ffb5f2

> volume #2 color #ffb5ff

> volume #2 color #ffbcff

> volume #2 color #ffc6ff

> volume #2 color #ffdaff

> volume #2 color #ffe9ff

> volume #2 color #ffeaff

> volume #2 color #ffecff

> volume #2 color #ffedff

> volume #2 color #fff8ff

> volume #2 color white

> volume #2 color #b1ffff

> volume #2 color #08ffff

> volume #2 color #b2ffff

> volume #2 color #b2fffffe

> volume #2 color #b2ffffe9

> volume #2 color #b2ffffd9

> volume #2 color #b2ffffcd

> volume #2 color #b2ffffc1

> volume #2 color #b2ffffbc

> volume #2 color #b2ffffb8

> volume #2 color #b2ffffaa

> volume #2 color #b2ffff9a

> volume #2 color #b2ffff8c

> volume #2 color #b2ffff84

> volume #2 color #b2ffff80

> volume #2 color #b2ffff71

> volume #2 color #b2ffff69

> volume #2 color #b2ffff65

> volume #2 color #b2ffff63

> volume #2 color #b2ffff62

> volume #2 color #b2ffff60

> volume #2 color #b2ffff5f

> volume #2 color #b2ffff5a

> volume #2 color #b2ffff49

> volume #2 color #b2ffff36

> volume #2 color #b2ffff37

> volume #2 color #b2ffff39

> volume #2 color #b2ffff3a

> volume #2 color #b2ffff3b

> volume #2 color #b2ffff3c

> volume #2 color #b2ffff3d

> select clear

> volume #2 level 0.0141

> volume #3 level 0.014

> view name ATP-weak-1

> pwd

Current working directory is: /Users/crowe/Desktop  

> cd ../Dropbox/

Current working directory is: /Users/crowe/Dropbox  

> cd /Users/crowe/Dropbox/ABCF-writing/figures/pymol_chimera_pngs/201107_vgaA-
> ATP

Current working directory is: /Users/crowe/Dropbox/ABCF-
writing/figures/pymol_chimera_pngs/201107_vgaA-ATP  

> save 201107_VgaA-ATP-weak_01.png

> save 201107_VgaA-ATP-weak_02.png

> view list

Named views: ATP-weak-1, ATP1-1, vgaA-strong-ATP-1  

> view name ATP-weak-2

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201107_vgaA_ATP-density_02.cxs includeMaps true

Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py"", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output
file"",  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 48, in display  
run(session, cmd)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py"", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py"", line 79, in save  
return cxs_save(session, path, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close #3

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201107_vgaA_ATP-density_01.cxs includeMaps true

Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py"", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output
file"",  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 48, in display  
run(session, cmd)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py"", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py"", line 79, in save  
return cxs_save(session, path, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201107_vgaL_ATP-density_02.cxs

Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py"", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output
file"",  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 48, in display  
run(session, cmd)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py"", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py"", line 79, in save  
return cxs_save(session, path, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close #2

> close #1

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201107_vgaA_ATP-density_02.cxs

Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py"", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output
file"",  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 48, in display  
run(session, cmd)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py"", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py"", line 79, in save  
return cxs_save(session, path, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201107_vgaA_ATP-density_02.cxs

Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py"", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output
file"",  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 48, in display  
run(session, cmd)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py"", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py"", line 79, in save  
return cxs_save(session, path, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/crowe/Dropbox/ABCF-writing/figures/chimerax-
> sessions/201107_vgaA_ATP-density_02.cxs

Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2281, in take_snapshot  
'rgba': self.rgba,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 1988, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py"", line 2016, in get_color  
return Surface.get_color(self)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py"", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py"", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output
file"",  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py"", line 48, in display  
run(session, cmd)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py"", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2835, in run  
result = ci.function(session, **kw_args)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py"", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py"", line 79, in save  
return cxs_save(session, path, **kw)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 827, in save  
session.save(output, version=version, include_maps=include_maps)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 583, in save  
mgr.discovery(self._state_containers)  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface': Error
while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x1590ef0d0> ->
<chimerax.std_commands.view.NamedView object at 0x15910ee50> ->
<chimerax.surface.cap.ClipCap object at 0x159085a30> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x159059cd0> 'surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface':
Error while saving session data for 'named views' -> -> -> 'cap far' ->
'surface'  
  
File
""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py"", line 261, in discovery  
raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      Boot ROM Version: 1037.140.50.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1:22

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: YPPY075J05DS
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

Locale: (None, 'UTF-8')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    cached-property: 1.5.2
    certifi: 2020.6.20
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.3
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202011040611
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.2.2
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.0.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.4
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.35.1

}}}
"	defect	closed	normal		Volume Data		fixed						all	ChimeraX