Opened 6 years ago

Closed 6 years ago

#2128 closed defect (duplicate)

'view' command: model is None

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: General Controls Version: 0.8
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.20.0-1.el7.elrepo.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/software/graphics/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/software/graphics/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/software/graphics/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/software/graphics/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: 'list' object has no attribute
'split'  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 1584, resource id:
29946155, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/TK_mods_by_rate.cxs

opened ChimeraX session  

> color
#2/a:211,1171,1058,1304,1162,490,1278,1244,418,136,537,663,207,265,435,396,1211,977,1007,830,682,501,936,82,605,807,229,615,5,569,827,1125,358,1020,1217,41,697,818,298,373,525,847,1459,458,730
tomato target a

> color
#1/A:1352,1026,1571,1366,1278,310,1497,2008,2457,746,1431,2876,1256,1986,1739,114,1305,925,1142,1238,1059,1357,967,2780,2992,1314,1414,1697,2207,1613,1972,2917,1069,1631,819,2273,2201,2071,392,227,2942,1955,1120,88,1750,1600,1757,2417,942,945,739,799,579,478,2864,778,2797,358,719,1996,1745,1656,2478,2121,1873,685,730,138,27,1834,526,2838,640,2819,713,2737,1492,1092,342,1427,1396,433,335,1934,228,2590,1641,805,484,418,651,1337,2514,1543,2832,1099,150,2420,1375,2955,201,376,1434,1470,1538,1810,106,501,2159,244,56,617,124,2442,1899,858
tomato target a

> color #1/B:62,90,32 tomato target a

> ui mousemode rightMode zoom

QXcbConnection: XCB error: 3 (BadWindow), sequence: 13073, resource id:
29953024, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/TK_mods_by_temp.cxs

opened ChimeraX session  

> select #1/A:277

20 atoms, 21 bonds selected  

> view name start

> view start

> hide selAtoms

> select #1/A:277

20 atoms, 21 bonds selected  

> show selAtoms

> select #1/A:227

20 atoms, 21 bonds selected  

> select #1/A:227

20 atoms, 21 bonds selected  

> view start

> color #1/A:277 tomato target a

> select #1/A:277

20 atoms, 21 bonds selected  

> view start

> color #2/a:
5,41,136,229,298,358,373,458,501,525,569,605,682,697,730,818,847,1020,1459
steel blue target a

> color #2/a:
5,41,136,229,298,358,373,458,501,525,569,605,682,697,730,818,847,1020,1459
deep sky blue target a

> color #2/a:
5,41,136,229,298,358,373,458,501,525,569,605,682,697,730,818,847,1020,1459
royal blue target a

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color
#1/A:27,56,124,201,224,335,376,418,433,501,526,617,713,730,778,799,805,858,925,1069,1305,1337,1357,1375,1396,1427,1431,1434,1470,1543,1641,1810,1899,1934,1955,1972,2071,2121,2159,2457,2478,2590,2780,2797,2832,2838,2955
royal blue target a

> color #1/A:819,2992,2997,3009,3023 lime green target a

> select #1/A:819,2992,2997,3009,3023

100 atoms, 105 bonds selected  

> show selAtoms

> color #1/A:819,2992,2997,3009,3023 green target a

> color #1/A:819,2992,2997,3009,3023 medium spring green target a

> color #1/A:819,2992,2997,3009,3023 spring green target a

> color #1/A:819,2992,2997,3009,3023 lime target a

> color #1/A:819,2992,2997,3009,3023 lime green target a

> color #1/A:819,2992,2997,3009,3023 yellow green target a

> color #1/A:819,2992,2997,3009,3023 green yellow target a

> color #1/A:819,2992,2997,3009,3023 lime green target a

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> save /users/donna/T_Kodakarensis/Figs/Shragi_vs_cryo_vs_MS.png supersample 4
transparentBackground true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 43193, resource id:
29967914, major code: 40 (TranslateCoords), minor code: 0  

> save session
/users/donna/T_Kodakarensis/Figs/TK_mods_shragi_vs_cryoEM_vs_MS.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 44582, resource id:
29966725, major code: 40 (TranslateCoords), minor code: 0  

> close session

QXcbConnection: XCB error: 3 (BadWindow), sequence: 48229, resource id:
29969675, major code: 40 (TranslateCoords), minor code: 0  

> open
/users/donna/T_Kodakarensis/coot/TK85/phenix/RealSpaceRefine_23/TK85_50S_refine23_real_space_refined.pdb

Chain information for TK85_50S_refine23_real_space_refined.pdb #1  
---  
Chain | Description  
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 I | No description available  
J | No description available  
K | No description available  
L | No description available  
M 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  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 50827, resource id:
29973019, major code: 40 (TranslateCoords), minor code: 0  

> open
/users/donna/T_Kodakarensis/coot/TK85/phenix/RealSpaceRefine_5/TK85_30S_real_space_refined-
coot-1.pdb

Summary of feedback from opening
/users/donna/T_Kodakarensis/coot/TK85/phenix/RealSpaceRefine_5/TK85_30S_real_space_refined-
coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
422 messages similar to the above omitted  
Ignored bad PDB record found on line 58218  
  
Chain information for TK85_30S_real_space_refined-coot-1.pdb #2  
---  
Chain | Description  
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  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

Expected an objects specifier or a view name or a keyword  

> color #1 dark gray

> lighting soft

> lighting full

> lighting flat

> lighting flat

> set silhouettes false

> set silhouettes true

> set silhouettes false

> lighting simple

> lighting shadows true

> lighting soft

> color #2 dark gray

> color #2 gray

> color #1 gray

> select #1:C-Z

77030 atoms, 82276 bonds, 5 pseudobonds, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> select #1:a-m

79679 atoms, 85187 bonds, 4 pseudobonds, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> select #1:A-B

22831 atoms, 23462 bonds selected  

> hide selAtoms

> hide selAtoms surfaces

> show selAtoms

> select #2:b-z

45436 atoms, 47996 bonds, 4 pseudobonds, 1 model selected  

> select #1:A-B

22831 atoms, 23462 bonds selected  

> select #1

101297 atoms, 109832 bonds, 9 pseudobonds, 1 model selected  

> hide selAtoms surfaces

> show selAtoms

> select #1:B

Nothing selected  

> select #1/A-B

66049 atoms, 73907 bonds, 5 pseudobonds, 1 model selected  

> select #1/C-Z

27743 atoms, 28252 bonds, 4 pseudobonds, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> select #1/a-m

7505 atoms, 7673 bonds selected  

> hide selAtoms

> show selAtoms surfaces

> select #1/F

1489 atoms, 1513 bonds selected  

> color #1/F red

> color #1/F orange red

> select #1/O

1152 atoms, 1174 bonds selected  

> select #1/E

2028 atoms, 2068 bonds selected  

> color #1/F coral

> color #1/F orange red

> color #1/E coral

> color #1/F orange

> color #1/F dark orange

> color #1/F orange

> select #2/a-z

58196 atoms, 62421 bonds, 6 pseudobonds, 1 model selected  

> select #2/b-z

26732 atoms, 27209 bonds, 1 pseudobond, 1 model selected  

> select #2/b-z

26732 atoms, 27209 bonds, 1 pseudobond, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> set silhouettes true

> set silhouettes false

> view name front

> color #1/I

> color #1/l

> color #1/l

> color #1/l

> color #1/I

> select #1/l

Nothing selected  

> select #1/l

Nothing selected  

> select #1/I

928 atoms, 941 bonds selected  

> color #1/A deep pink target s

> color #1/A deep pink target s

> color #1/A deep pink

> color #1 gray

> color #2 gray

> color #1/D deep pink target s

> color #1/G dodger blue target s

> color #1/T lime green target s

> color #1/J orange target s

> color #1/J orange red target s

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1/J orange target s

> color #1/K pale goldenrod surfaces

> color #1/N violet target s

> color #1/a medium turquoise target s

> color #1/L green target s

> color #1/L forest green target s

> color #1/h gold target s

> color #1/h gray target s

> color #1/F crimson target s

> color #1/I medium violet red target s

> color #1/I dark violet target s

> color #1/i sandy brown target s

> color #1/i peru target s

> color #1/i rosy brown target s

> color #1/i indian red target s

> color #2/u steel blue target s

> color #2/o rosy brown target s

> color #2/w spring green target s

> color #2/f sandy brown target s

> color #2/h chocolate target s

> color #2/h peru target s

> color #2/h sienna target s

> color #2/h goldenrod target s

> color #2/h dark goldenrod target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #2/p dark olive green target s

> color #2/p olive target s

> color #2/p olive drab target s

> color #2/p olive target s

> color #2/m dark magenta target s

> color #2/m dark magenta target s

> color #2/m magenta target s

> color #2/m maroon target s

> color #2/e maroon target s

> color #2/c magenta target s

> color #2/v magenta target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #2/c peach puff target s

> color #2/c medium slate blue target s

> color #2/c dark slate blue target s

> color #2/e dark slate blue target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #2/c maroon target s

> color #2/m dark khaki target s

> color #2/m khaki target s

> color #2/m dark khaki target s

> color #2/g peach puff target s

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #2/g midnight blue target s

> color #2/g dark green target s

> color #2/g dark slate gray target s

> color #2/e black target s

> color #2/e indigo target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #2/e midnight blue target s

> color #1/E pale green target s

> color #1/V sky blue target s

> color #1/V powder blue target s

> color #1/X saddle brown target s

> color #1/X sienna target s

> color #1/R yellow target s

> color #1/R gold target s

> color #1/R yellow target s

> color #1/U midnight blue target s

> color #1/U dark slate gray target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1/U teal target s

> color #1/Q teal target s

> color #1/U plum target s

> color #1/U lavender target s

> color #1/U thistle target s

> color #1/U light coral target s

> color #1/U thistle target s

> color #1/c navy target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1/c dark slate blue target s

> color #1/Y powder blue target s

> color #1/Y peach puff target s

> color #1/Y lavender target s

> color #1/Y lavender blush target s

> color #1/Y linen target s

> color #1/Y gainsboro target s

> color #1/Y azure target s

> color #1/d blue violet target s

> color #2/d blue violet target s

> color #1/C lawn green target s

> select #1/O

1152 atoms, 1174 bonds selected  

> select #1/X

991 atoms, 1007 bonds selected  

> select #1/n

Nothing selected  

> select #1/d

1018 atoms, 1040 bonds selected  

> color #1/d pink target s

> select #1/n

Nothing selected  

> select #1/O

1152 atoms, 1174 bonds selected  

> color #1/O cornflower blue target s

> view front

> save /users/donna/T_Kodakarensis/Figs/70S_front_colors.png supersample 4
transparentBackground true

> view name back

> view front

> save session /users/donna/T_Kodakarensis/Figs/colored_proteins.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> view front

> color #1/H dark violet target s

> color #1/M violet target s

> view back

> view front

> save session /users/donna/T_Kodakarensis/Figs/colored_proteins.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 22986, resource id:
30086529, major code: 40 (TranslateCoords), minor code: 0  

> hide target m

> open /users/donna/T_Kodakarensis/maps/TK85/30S_unsharp.mrc

Opened 30S_unsharp.mrc, grid size 480,480,480, pixel 0.85, shown at level
0.0157, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 40339, resource id:
30090639, major code: 40 (TranslateCoords), minor code: 0  

> open
/users/donna/T_Kodakarensis/maps/TK85/Multibody/TK85_LSU_postprocess_MB.mrc

Opened TK85_LSU_postprocess_MB.mrc, grid size 480,480,480, pixel 0.85, shown
at level 0.0285, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 40850, resource id:
30092136, major code: 40 (TranslateCoords), minor code: 0  

> open
/users/donna/T_Kodakarensis/maps/TK85/Multibody/TK85_SSU_body_postprocess_MB.mrc

Opened TK85_SSU_body_postprocess_MB.mrc, grid size 480,480,480, pixel 0.85,
shown at level 0.00552, step 2, values float32  

> open
/users/donna/T_Kodakarensis/maps/TK85/Multibody/TK85_SSU_head_postprocess_MB.mrc

Opened TK85_SSU_head_postprocess_MB.mrc, grid size 480,480,480, pixel 0.85,
shown at level -1.26e-05, step 2, values float32  

> surface dust #3 size 5

> surface dust #4 size 5

> surface dust #5 size 5

> save /users/donna/T_Kodakarensis/Figs/TK85_front_map.png supersample 4
transparentBackground true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 8178, resource id:
30109153, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/maps/aligned_maps/TKd85_LSU_MB_onTK85.mrc

Opened TKd85_LSU_MB_onTK85.mrc, grid size 480,480,480, pixel 0.85, shown at
level 0.0239, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 8836, resource id:
30110650, major code: 40 (TranslateCoords), minor code: 0  

> open
/users/donna/T_Kodakarensis/maps/aligned_maps/TKd85_SSU_body_MB_onTK85.mrc

Opened TKd85_SSU_body_MB_onTK85.mrc, grid size 480,480,480, pixel 0.85, shown
at level 0.00485, step 2, values float32  

> open
/users/donna/T_Kodakarensis/maps/aligned_maps/TKd85_SSU_head_MB_onTK85.mrc

Opened TKd85_SSU_head_MB_onTK85.mrc, grid size 480,480,480, pixel 0.85, shown
at level -2.02e-05, step 2, values float32  

> hide #!3 models

> hide #!3.1 models

> hide #!4 models

> hide #!4.1 models

> hide #!5 models

> hide #!5.1 models

> surface dust #6 size 5

> surface dust #7 size 5

> surface dust #8 size 5

> surface dust #6 size 5

> surface dust #6 size 6

> surface dust #6 size 7

> save /users/donna/T_Kodakarensis/Figs/TKd85_front_map.png supersample 4
transparentBackground true

> hide #!6 models

> hide #!6.1 models

> hide #!7 models

> hide #!7.1 models

> hide #!8 models

> hide #!8.1 models

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31276, resource id:
30165952, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/TKd85_LSU_on_TK85.pdb

Summary of feedback from opening
/users/donna/T_Kodakarensis/Figs/TKd85_LSU_on_TK85.pdb  
---  
warnings | Ignored bad PDB record found on line 100533  
TER ***** THR e 89  
  
Ignored bad PDB record found on line 101164  
TER ***** LYS g 85  
  
Ignored bad PDB record found on line 101677  
TER ***** TYR h 63  
  
Ignored bad PDB record found on line 102110  
TER ***** GLU i 51  
  
Ignored bad PDB record found on line 102484  
TER ***** GLY j 48  
  
6 messages similar to the above omitted  
  
Chain information for TKd85_LSU_on_TK85.pdb #9  
---  
Chain | Description  
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 I | No description available  
J | No description available  
K | No description available  
L | No description available  
M 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  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 32130, resource id:
30167461, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/TKd85_SSU_on_TK85.pdb

Chain information for TKd85_SSU_on_TK85.pdb #10  
---  
Chain | Description  
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  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> close #10

> close #9

> open /users/donna/T_Kodakarensis/Figs/TKd85_SSU_on_TK85.pdb

Chain information for TKd85_SSU_on_TK85.pdb #9  
---  
Chain | Description  
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  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open /users/donna/T_Kodakarensis/Figs/TKd85_LSU_on_TK85.pdb

Summary of feedback from opening
/users/donna/T_Kodakarensis/Figs/TKd85_LSU_on_TK85.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 134 134 GLY f
18 GLN f 34 1 17  
Start residue of secondary structure not found: HELIX 135 135 THR f 72 LYS f
85 1 14  
Start residue of secondary structure not found: HELIX 136 136 GLY g 4 ARG g 11
1 8  
Start residue of secondary structure not found: HELIX 137 137 HIS g 53 ASN g
60 1 8  
Start residue of secondary structure not found: HELIX 138 138 PRO h 6 ARG h 21
1 16  
6 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 115 1 GLY f 52 GLN f 57
0  
Start residue of secondary structure not found: SHEET 1 116 1 ALA f 61 GLY f
65 0  
Start residue of secondary structure not found: SHEET 1 117 1 GLN k 6 THR k 9
0  
Start residue of secondary structure not found: SHEET 1 118 1 THR k 18 VAL k
25 0  
Start residue of secondary structure not found: SHEET 1 119 1 ASP k 66 THR k
72 0  
Start residue of secondary structure not found: SHEET 1 120 1 GLY k 75 THR k
79 0  
Cannot find LINK/SSBOND residue CYS (38 )  
Cannot find LINK/SSBOND residue CYS (38 )  
Cannot find LINK/SSBOND residue CYS (38 )  
Cannot find LINK/SSBOND residue CYS (41 )  
Cannot find LINK/SSBOND residue CYS (56 )  
13 messages similar to the above omitted  
  
Chain information for TKd85_LSU_on_TK85.pdb #10  
---  
Chain | Description  
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 I | No description available  
J | No description available  
K | No description available  
L | No description available  
M 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  
  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #9 dark gray

> color #10 dark gray

> color #9/H dark violet target s

> color #9/I dark violet target s

> color #10/I dark violet target s

> select #10:C-Z

81593 atoms, 87004 bonds, 4 pseudobonds, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> hide selAtoms surfaces

> show selAtoms

> select #10/C-Z

27764 atoms, 28274 bonds, 4 pseudobonds, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> select #10/a-s

12042 atoms, 12271 bonds, 1 pseudobond, 1 model selected  

> hide selAtoms

> show selAtoms surfaces

> select #9/a-z

58244 atoms, 62469 bonds, 5 pseudobonds, 1 model selected  

> select #9/b-z

26780 atoms, 27257 bonds selected  

> hide selAtoms

> show selAtoms surfaces

> color #10 dark gray

> color #9 dark gray

> color #10/I dark violet target s

> color #10/H dark violet target s

> color #10/E pale green target s

> color #10/R yellow target s

> color #10/X sienna target s

> color #10/V powder blue target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #10/a medium turquoise target s

> color #10/N violet target s

> color #10/M violet target s

> color #10/K pale goldenrod target s

> color #10/D deep pink target s

> color #10/G dodger blue target s

> color #10/T lime green target s

> color #10/F crimson target s

> color #10/Q teal target s

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #10/U thistle target s

> color #10/O cornflower blue target s

> color #10/i indian red target s

> color #10/J orange target s

> color #10/L forest green target s

> color #10/Y azure target s

> color #10/d pink target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #10/c dark slate gray target s

> color #10/C lawn green target s

> color #9/f sandy brown target s

> color #9/w spring green target s

> color #9/e midnight blue target s

> color #9/o rosy brown target s

> color #9/g dark slate gray target s

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #9/c maroon target s

> color #9/m dark khaki target s

> color #9/v magenta target s

> color #9/u steel blue target s

> color #9/p olive target s

> color #9/e midnight blue surfaces

> color #9/h dark goldenrod target s

> color #9/d blue violet target s

> hide #!9 models

> hide #!10 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!3.1 models

> hide #!4 models

> hide #!3.1 models

> hide #!3 models

> show #1.2-38 target m

> hide #1.2-38 target m

> hide #!1 models

> hide #!2 models

> show #!9 models

> show #!10 models

> color #10/c dark slate blue target s

> hide #!9 models

> hide #!10 models

> show #1 target m

> hide #!1 models

> show #!9 models

> show #!10 models

> color #10/j indian red target s

> color #10/i gray target s

> color #10/n spring green target s

> color #10/f red target s

> color #10/f dark red target s

> color #10/f firebrick target s

> color #10/f red target s

> color #10/m light salmon target s

> color #9/t light salmon target s

> color #10/q chartreuse target s

> select #10/f

534 atoms, 541 bonds selected  

> select #10/o

350 atoms, 356 bonds selected  

> select #10/p

369 atoms, 371 bonds, 1 pseudobond, 1 model selected  

> save /users/donna/T_Kodakarensis/Figs/TKd85_70S_fron_colors.png supersample
4 transparentBackground true

> save session /users/donna/T_Kodakarensis/Figs/colored_proteins_TKd85.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> color #10 gray

> color #9 gray

> color #9 dark gray

> color #10 dark gray

> hide #!9 models

> color #10/p purple target s

> color #10/n spring green target s

> color #10/f red target s

> color #10/q chartreuse target s

> color #10/m light salmon target s

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #10/o deep sky blue target s

> view front

> show #!9 models

> hide #!9 models

> view name specific_proteins_I

> view name specific_proteins_II

> view name specific_proteins_II

> save /users/donna/T_Kodakarensis/Figs/TKd85_specific_proteins_II.png
supersample 4 transparentBackground true

> view specific_proteins_I

> save /users/donna/T_Kodakarensis/Figs/TKd85_specific_proteins_I.png
supersample 4 transparentBackground true

> save session /users/donna/T_Kodakarensis/Figs/TKd85_specific_proteins.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 33113, resource id:
30298849, major code: 40 (TranslateCoords), minor code: 0  

> view front

> hide #!10 models

> show #!3 models

> show #!3.1 models

> show #!4 models

> show #!4.1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!5.1 models

> hide #!5.1 models

> hide #!5 models

> hide #!4.1 models

> hide #!4 models

> hide #!3.1 models

> hide #!3 models

> show #!2 models

> show #!1 models

> show #!3 models

> hide #!3 models

> show #2 target m

> color #1/a-b dark gray target a

> hide #!1 models

> show #!1 models

> color #1/a-b gray target a

> color #1/a-b gray

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1/a-b medium turquoise

> color #1/b gray

> color #1/A-B dark gray target a

> color #2/a dark gray target a

> save /users/donna/T_Kodakarensis/Figs/70S_front_colors.png supersample 4
transparentBackground true

> select #1/A:2159

23 atoms, 24 bonds selected  

> hide #!2 models

> open /users/donna/T_Kodakarensis/Figs/TK_mods_by_rate.cxs

opened ChimeraX session  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 52746, resource id:
30372406, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/TK_mods_by_rate.cxs

opened ChimeraX session  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 54424, resource id:
30379603, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/TKd85_specific_proteins.cxs

opened ChimeraX session  

> view back

Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 53, in view  
show_view(session, objects, frames)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 128, in show_view  
v2.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
  
See log for complete Python traceback.  
  

> view name front

> view name tunnel

> view name tunnel_front

> save /users/donna/T_Kodakarensis/Figs/TKd85_specific_proteins_tunnel.png
supersample 4 transparentBackground true

> save session
/users/donna/T_Kodakarensis/Figs/TKd85_specific_proteins_tunnel..cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

QXcbConnection: XCB error: 8 (BadMatch), sequence: 8019, resource id:
62914577, major code: 42 (SetInputFocus), minor code: 0  

QXcbConnection: XCB error: 8 (BadMatch), sequence: 8043, resource id:
62914574, major code: 42 (SetInputFocus), minor code: 0  

QXcbConnection: XCB error: 8 (BadMatch), sequence: 8097, resource id:
62914577, major code: 42 (SetInputFocus), minor code: 0  

> view back

Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 53, in view  
show_view(session, objects, frames)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 128, in show_view  
v2.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
  
See log for complete Python traceback.  
  

> view front

> save /users/donna/T_Kodakarensis/Figs/TKd85_maturation_factor_front.png
supersample 4 transparentBackground true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 17655, resource id:
30869318, major code: 40 (TranslateCoords), minor code: 0  

> save session
/users/donna/T_Kodakarensis/Figs/TKd85_maturation_factor_front.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 19569, resource id:
30868129, major code: 40 (TranslateCoords), minor code: 0  

QXcbConnection: XCB error: 8 (BadMatch), sequence: 19608, resource id:
62914577, major code: 42 (SetInputFocus), minor code: 0  

> color #10/f dark gray target a

> color #10/f dark gray target s

> color #10/m dark gray target s

> color #10/n dark gray target s

> show #!9 models

> show #!8 models

> show #!7 models

> view name side

> hide #!10 models

> show #!10 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #9 target m

> show #9 target m

> hide #!10 models

> show #!10 models

> hide #!9 models

> hide #!8 models

> hide #!10 models

> show #!2 models

> show #2 target m

> show #!1 models

> show #!10 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> select #1

101297 atoms, 109832 bonds, 9 pseudobonds, 1 model selected  

> select #2

58196 atoms, 62421 bonds, 6 pseudobonds, 1 model selected  

> select #1

101297 atoms, 109832 bonds, 9 pseudobonds, 1 model selected  

> select #2

58196 atoms, 62421 bonds, 6 pseudobonds, 1 model selected  

> ~select #6

58196 atoms, 62421 bonds, 6 pseudobonds, 1 model selected  

> ~select #5

58196 atoms, 62421 bonds, 6 pseudobonds, 1 model selected  

> ~select #6

58196 atoms, 62421 bonds, 6 pseudobonds, 1 model selected  

> select #1

101297 atoms, 109832 bonds, 9 pseudobonds, 1 model selected  

> show #1 target m

> show selAtoms

QXcbConnection: XCB error: 3 (BadWindow), sequence: 46309, resource id:
30908317, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/colored_proteins_TKd85.cxs

Summary of feedback from opening
/users/donna/T_Kodakarensis/Figs/colored_proteins_TKd85.cxs  
---  
warning | QXcbConnection: XCB error: 8 (BadMatch), sequence: 46364, resource
id: 62914577, major code: 42 (SetInputFocus), minor code: 0  
  
opened ChimeraX session  

> color #10/gray target s

> color #10 gray target s

> color #9 gray target s

> color #9 dark gray target s

> color #10 dark gray target s

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #10/q chartreuse target s

> hide #!9 models

> show #!9 models

> hide #!10 models

> lighting soft

> set silhouettes true

> lighting flat

> lighting flat

> set silhouettes false

> save /users/donna/T_Kodakarensis/Figs/TKd85_maturation_side_SSU_sil.png
supersample 4 transparentBackground true

> show #!10 models

> hide #!9 models

> lighting full

> lighting soft

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> save /users/donna/T_Kodakarensis/Figs/TKd85_maturation_side_LSU.png
supersample 4 transparentBackground true

> save session
/users/donna/T_Kodakarensis/Figs/TKd85_maturation_factor_side.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

Error in saving session for "NamedView":  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 206, in take_snapshot  
self.remove_deleted_models()  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models  
if m.deleted:  
AttributeError: 'NoneType' object has no attribute 'deleted'  
  

Unable to save "NamedView". Session might not restore properly.  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 62037, resource id:
30948498, major code: 40 (TranslateCoords), minor code: 0  

> open /users/donna/T_Kodakarensis/Figs/colored_proteins.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 593, in restore  
obj = sm.restore_snapshot(self, data)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/std_commands/view.py", line 214, in restore_snapshot  
for k,v in data['view attrs'].items():  
TypeError: 'NoneType' object is not subscriptable  
  
opened ChimeraX session  
Traceback (most recent call last):  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 3370, in _update_drawings  
if v.display:  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "graphics update": object of type 'NoneType' has no
len():  
TypeError: object of type 'NoneType' has no len()  
  
File "/software/graphics/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 410.93
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → General Controls
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 'view' command: model is None
Version: → 0.8

comment:2 by Tom Goddard, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Bug in 0.8 fixed long ago.

Note: See TracTickets for help on using tickets.