The following bug report has been submitted:
Platform: Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-06-29)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-06-29)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> volume #1 level 0.4 step 1
> volume #3 level 0.25 step 1
> volume #3 color #ffddff
> volume #1 color #55aaff
> lighting full
> set silhouettes false
> surface dust #1 size 10
> surface dust #3 size 10
> transparency #3 75
> set bgColor white
> view matrix camera
-0.044385,0.44748,-0.89319,252.04,0.48128,-0.7739,-0.41163,-531.6,-0.87544,-0.44815,-0.18101,-101.17
models
#1,0.80436,0.33909,0.48788,476.44,0.58831,-0.33978,-0.73378,-184.93,-0.083046,0.87725,-0.4728,-65.323,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.80436,0.33909,0.48788,476.44,0.58831,-0.33978,-0.73378,-184.93,-0.083046,0.87725,-0.4728,-65.323,#3,0.80436,0.33909,0.48788,476.44,0.58831,-0.33978,-0.73378,-184.93,-0.083046,0.87725,-0.4728,-65.323,#3.1,1,0,0,0,0,1,0,0,0,0,1,0
executed chimeraX_desensitized_state.cxc
> hide #!3 models
> hide #!1 models
> close session
incomplete quoted text
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
Invalid "models" argument: No models specified by "#3"
Invalid "models" argument: No models specified by "#3"
> hide #1
Expected ',' or a keyword
Expected an atoms specifier or a keyword
Expected an atoms specifier or a keyword
> surface #2/a,b
> transparency #2.2 75
> select #2/b
3563 atoms, 3654 bonds, 1 model selected
> color #2/b lightgrey cartoons
> color #2.2 lightgrey surfaces
> transparency #2.2 75
> transparency #2/b 75
> transparency #2/b 75 cartoons
> transparency #2.2 80
> transparency #2/b 50 cartoons
> transparency #2/b 15 All
> transparency #2/b 35 All
> transparency #2/b 55 All
> transparency #2/b 75 All
> color #2.1 lightgrey
> transparency #2.1 35
> toolshed show "Side View"
> clip list
Clipping is off
Expected a keyword
> clip list
Using 1 clip planes: far -20.929
> ~select
Nothing selected
> transparency #2.1 15
> transparency #2.1 5
> transparency #2.1 5
> transparency #2.1 0
> transparency #2.2 95
> transparency #2/a 50 cartoons
> transparency #2.1 5
> transparency #2.2 80
> transparency #2.1 80
> lighting shadows false
> set silhouettes false
> set silhouettes true
> color #2.1 grey
> transparency #2.1 80
> hide atoms
> view matrix
camera position:
-0.96758,0.025358,0.25128,278.24,0.25176,0.017891,0.96762,490.43,0.020041,0.99952,-0.023696,182.82
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.2,1,0,0,0,0,1,0,0,0,0,1,0
> lighting shadows true
> lighting shadows false
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
Expected a keyword
Expected a keyword
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> surface #2/a,b
> color #2.1 grey
> color #2.1 lightgrey
> transparency #2.2 80
> transparency #2.1 60
> hide atoms
Invalid "models" argument: No models specified by "#2.1.1"
Invalid "models" argument: No models specified by "#2.1.1"
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> surface #2/a,b
> color #2.1 grey
> color #2.2 lightgrey
> transparency #2.2 80
> transparency #2.1 60
> hide atoms
executed chimeraX_desensitized_state_cartoon_view.cxc
Expected ',' or a keyword
> hide #2/a cartoons
> hide #2/b cartoons
> clip far -40
> clip far 40
> clip list
Using 1 clip planes: far 1.1168e-05
> toolshed show "Side View"
> cartoon style modeHelix tube sides 24
Missing or invalid "percent" argument: Expected a number
> transparency #2/c 100 target c
> undo
> cartoon style modeHelix tube sides 24
Expected ',' or a keyword
> hide #!2.1 models
> hide #!2.2 models
> select up
Nothing selected
> select up
Nothing selected
> transparency #2/c 0 target c
> show #2/a,b cartoons
> transparency #2/a,b 100 target c
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> set silhouettes false
> set silhouettes true
> cartoon style modeHelix tube sides 20
> cartoon style modeHelix tube sides 10
Invalid "sides" argument: Expected an even integer
Invalid "sides" argument: Must be greater than or equal to 3
> cartoon style modeHelix tube sides 4
Invalid "sides" argument: Must be less than or equal to 24
> cartoon style modeHelix tube sides 24
> clip list
Using 2 clip planes: far -25.658, near -62.773
> view matrix
camera position:
-0.98733,0.011805,0.15825,240.96,0.15864,0.10035,0.98222,445.98,-0.0042869,0.99488,-0.10096,163.29
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1,1,0,0,0,0,1,0,0,0,0,1,0
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> clip near -62 far -26
Invalid "models" argument: No models specified by "#2.1"
Invalid "models" argument: No models specified by "#2.1"
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
executed chimeraX_desensitized_state_cartoon_view.cxc
> view matrix
camera position:
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
Missing "models" keyword's argument
Missing "models" keyword's argument
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
executed chimeraX_desensitized_state_cartoon_view.cxc
> toolshed show "Side View"
> clip list
Using 2 clip planes: far -24.678, near -110.61
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -111 far -25
executed chimeraX_desensitized_state_cartoon_view.cxc
> toolshed show "Side View"
> clip list
Using 2 clip planes: near -111, far 25
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -111 far -75
executed chimeraX_desensitized_state_cartoon_view.cxc
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -111
executed chimeraX_desensitized_state_cartoon_view.cxc
> clip list
Using 1 clip planes: near -111
> clip far -25
> clip far 25
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -111
executed chimeraX_desensitized_state_cartoon_view.cxc
> clip far 25
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_desensitized_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/desensitized/cryosparc_P23_J149_010_volume_map_sharp_local.mrc"
Opened cryosparc_P23_J149_010_volume_map_sharp_local.mrc, grid size
360,360,360, pixel 1.1, shown at level 0.128, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/desensitized/refine-11-fit-to-map_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-sma/models/desensitized/refine-11-fit-to-
map_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.076 10962
Ignored bad PDB record found on line 24
ANGLE : 0.801 12.442 14883
18 messages similar to the above omitted
Chain information for refine-11-fit-to-map_real_space_refined.pdb #2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
-0.99859,0.052689,-0.0058495,202.95,-0.0042014,0.031337,0.9995,440.94,0.052846,0.99812,-0.031072,180.79
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -111 far 25
executed chimeraX_desensitized_state_cartoon_view.cxc
> save image "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/images/desensitized-ss-overview.png" width 800 height 800 supersample 3
transparentBackground true
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
executed chimeraX_resting_state_cartoon_view.cxc
> view matrix
camera position:
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip list
Clipping is off
> toolshed show "Side View"
> clip list
Using 2 clip planes: far -34.626, near -84.46
> clip list
Using 2 clip planes: far -36.366, near -84.46
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -35 far 85
executed chimeraX_resting_state_cartoon_view.cxc
> clip list
Using 2 clip planes: near -35, far -85
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -35 far -85
clip far plane is in front of near plane
executed chimeraX_resting_state_cartoon_view.cxc
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -35 far 45
executed chimeraX_resting_state_cartoon_view.cxc
> toolshed show "Side View"
> clip far 45
> lighting shadows true
> lighting shadows false
Expected a keyword
> clip list
Using 2 clip planes: near -75.369, far -40.496
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
executed chimeraX_resting_state_cartoon_view.cxc
> clip near -35
> toolshed show "Side View"
> clip far -85
clip far plane is in front of near plane
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
executed chimeraX_resting_state_cartoon_view.cxc
> clip near -45
> clip far -90
clip far plane is in front of near plane
> clip far 90
> clip far 90
> close session
> open "C:/Users/Nate Yoder/Documents/manuscripts/asic-
sma/scripts/chimeraX_resting_state_cartoon_view.cxc"
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/maps/resting/cryosparc_P18_J62_010_volume_map_sharp_local.mrc"
Opened cryosparc_P18_J62_010_volume_map_sharp_local.mrc, grid size
408,408,408, pixel 0.648, shown at level 0.101, step 2, values float32
> open "C:\\\Users\\\Nate Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb"
Summary of feedback from opening C:\Users\Nate
Yoder/Documents/manuscripts/asic-
sma/models/resting/5WKU_real_space_refined5-coot-1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.004 0.054 10509
Ignored bad PDB record found on line 24
ANGLE : 0.765 10.354 14316
18 messages similar to the above omitted
Chain information for 5WKU_real_space_refined5-coot-1_real_space_refined.pdb
#2
---
Chain | Description
A B C | No description available
> volume #1 level 0.4 step 1
> volume #1 color #55aaff
> lighting full
> set silhouettes true
> lighting shadows false
> surface dust #1 size 10
> transparency #1 75
> set bgColor white
> cartoon style strand xsection oval width 1.75
> cartoon style helix width 1.5 thickness 0.3
> cartoon style modeHelix tube sides 24
> transparency #2/a,b 100 target c
> color #2:74-88,171-181,205-224,268-283,366-380,404-423 yellow cartoons
> color #2:89-95,182-204,246-267 orange cartoons
> color #2:284-365 green cartoons
> color #2:96-170,225-245 purple cartoons
> color #2:381-403 cyan cartoons
> color #2: 40-73,424-462 red cartoons
> color #2:17-39 blue cartoons
> hide #1
> hide atoms
> view matrix camera
0.91505,-0.0030502,-0.40333,35.883,-0.40333,-0.00071263,-0.91505,-79.199,0.0025037,1,-0.0018823,138.88
models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> clip near -35 far 115
executed chimeraX_resting_state_cartoon_view.cxc
> toolshed show "Side View"
> clip list
Using 2 clip planes: near -98.777, far -42.806
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 116, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 411.95
OpenGL renderer: Quadro M1200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Sorry to take so long to get back to you. Do you still have these problematic sessions? There are many weird errors in the log that I can't explain. The first one being the "close session" followed by "incomplete quoted text". How reproducible is this for you?