Opened 5 years ago

Closed 5 years ago

#3920 closed defect (fixed)

Drawing (map) _colors is None

Reported by: caillancm@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Drawing (map) _colors is None

Reported by Caillan Crowe-McAuliffe

comment:2 by Tom Goddard, 5 years ago

This error saving a session is a bug where it is trying to save a closed volume. The message indicates that a named view is referring to a clipping cap which is referring to the closed VolumeSurface.

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'

I will fix the code so it does not try to save this closed volume.

comment:3 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tonight's daily build. Thanks for reporting the error.

It took a few hours to figure this out. Somehow the clip cap surface was not deleted when a volume was deleted. Turned out the clip cap was "removed" but not closed. This caused the session saving of named views to try to save it. Fixed by making sure clip cap gets closed when clipping turned off.

The steps needed to reproduce this bug were: 1) open volume, 2) use side view and drag far clip plane, 3) name a view ("view name test"), 4) turn off clipping using the "clip far" checkbutton on the side view, 5) close the volume, 6) save a session. Was hard to find since all those steps had to be done in that order to hit this bug.

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