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Opened 5 years ago
Closed 5 years ago
#3164 closed defect (duplicate)
Nucleotides trying to save dead structure
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2 C:/Users/Murayama/Documents/200505/708BeC_200505.cxs
Log from Tue May 5 17:43:59 2020 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open2
> P:/yuko-m/Arctica/SerialEM/data/191025/PostProcess/job571/postprocess.mrc
Opened postprocess.mrc, grid size 240,240,240, pixel 1.47, shown at level
0.0131, step 1, values float32
> volume style image
> volume #1 level -0.002074,0 level 0.01311,0.8 level 0.05476,1
> volume #1 level -0.002074,0 level 0.005291,0.8864 level 0.05476,1
> volume #1 level -0.002074,0 level 0.005291,0.8864 level 0.04105,0.08642
> volume #1 level -0.002074,0 level 0.002985,0.8494 level 0.04105,0.08642
> volume style surface
> transparency 50
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 176.4 tiltedSlabSpacing 1.47 tiltedSlabPlaneCount 10
> mousemode right "rotate slab"
> volume style surface
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 176.4 tiltedSlabSpacing 1.47 tiltedSlabPlaneCount 10
> mousemode right "rotate slab"
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 176.4 tiltedSlabSpacing 1.47 tiltedSlabPlaneCount 10
> mousemode right "rotate slab"
> volume style surface
> volume #1 tiltedSlabAxis 0.05336,-0.9211,-0.3856 tiltedSlabOffset -229.6
> volume planes z style image imageMode "full region"
> mousemode right "move planes"
> volume #1 orthoplanes xyz positionPlanes 120,120,120 style image region all
> mousemode right "move planes"
> volume region all imageMode "full region"
> mousemode right "crop volume"
> volume #1 region 0,0,0,239,239,152
> volume #1 orthoplanes xyz positionPlanes 120,120,120 style image region all
> mousemode right "move planes"
> volume #1 orthoplanes xyz positionPlanes 120,120,109
> volume planes z style image imageMode "full region"
> mousemode right "move planes"
Missing or invalid "percent" argument: Expected a number
Missing or invalid "percent" argument: Expected a number
> volume style surface
> volume planes z style image imageMode "full region"
> mousemode right "move planes"
> volume planes z style image imageMode "full region"
> mousemode right "move planes"
> volume region all imageMode "full region"
> mousemode right "crop volume"
> volume style surface
> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 176.4 tiltedSlabSpacing 1.47 tiltedSlabPlaneCount 10
> mousemode right "rotate slab"
> volume #1 orthoplanes xyz positionPlanes 120,120,120 style image region all
> mousemode right "move planes"
> volume style surface
> volume #1 region 0,0,0,239,239,239
> volume projectionMode 2d-xyz
> volume projectionMode 2d-xyz
> volume projectionMode 3d
> volume appearance initial
> volume style surface
> volume style surface
> volume region all imageMode "full region"
> mousemode right "crop volume"
> volume style surface
> volume showOutlineBox false
> volume #1 region 0,0,0,239,239,239
> volume style surface
> volume style image
> volume style surface
> open2
> N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/RealSpaceRefine_21/191210_pp178_real_space_refined.pdb
Chain information for 191210_pp178_real_space_refined.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
F G I J K | No description available
H | No description available
N | No description available
R | No description available
T | No description available
> select /A:1-229
1806 atoms, 1838 bonds, 1 model selected
> select /A:1-229
1806 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select /B:1-229
1806 atoms, 1838 bonds, 1 model selected
> select /C:1-1119
8829 atoms, 8997 bonds, 1 model selected
> color bfactor sel
8829 atoms, 1119 residues, atom bfactor range 9.91 to 505
> select clear
> hide target a
> show cartoons
> close #2
> open2
> N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/ECRho_onRef200_2.pdb
Summary of feedback from opening <_io.textiowrapper
name="N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/ECRho_onRef200_2.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 43573
END
Chain information for ECRho_onRef200_2.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
F G H I J K | No description available
L | No description available
N | No description available
R | No description available
T | No description available
> select /A:1-229
1806 atoms, 1838 bonds, 1 model selected
> select /B:1-229
1806 atoms, 1838 bonds, 1 model selected
> select /A:1-229
1806 atoms, 1838 bonds, 1 model selected
> toolshed show "Fit in Map"
Fit molecule ECRho_onRef200_2.pdb (#2) to map postprocess.mrc (#1) using 43108
atoms
average map value = 0.01278, steps = 148
shifted from previous position = 4.06
rotated from previous position = 10.2 degrees
atoms outside contour = 22633, contour level = 0.013109
Position of ECRho_onRef200_2.pdb (#2) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.99351508 -0.04884384 0.10267454 -9.05083888
0.03446540 0.98991342 0.13741747 -24.19196741
-0.10835091 -0.13298761 0.98517733 44.84622227
Axis -0.76607515 0.59784880 0.23602050
Axis point 0.00000000 308.17422593 211.95912725
Rotation angle (degrees) 10.16522184
Shift along axis 3.05511188
> hide #!2 models
> show sel cartoons
> show #!2 models
> style sel sphere
Changed 1806 atom styles
> style sel sphere
Changed 1806 atom styles
> hide sel atoms
> hide sel atoms
> select clear
> hide atoms
> show cartoons
> hide #!1 models
Drag select of 1333 residues
> select clear
Drag select of 2108 residues
> select sel :< 5
17895 atoms, 18138 bonds, 1 model selected
Fit molecule ECRho_onRef200_2.pdb (#2) to map postprocess.mrc (#1) using 17895
atoms
average map value = 0.01005, steps = 104
shifted from previous position = 3.38
rotated from previous position = 7.74 degrees
atoms outside contour = 12613, contour level = 0.013109
Position of ECRho_onRef200_2.pdb (#2) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.98874773 -0.13253198 0.06937730 14.38599909
0.11206577 0.96344465 0.24334270 -50.09441224
-0.09909187 -0.23282972 0.96745601 68.45451684
Axis -0.84848343 0.30019231 0.43584452
Axis point 0.00000000 254.59350836 247.30165118
Rotation angle (degrees) 16.29614155
Shift along axis 2.59128645
> show #!1 models
Fit molecule ECRho_onRef200_2.pdb (#2) to map postprocess.mrc (#1) using 17895
atoms
average map value = 0.01005, steps = 104
shifted from previous position = 3.38
rotated from previous position = 7.74 degrees
atoms outside contour = 12613, contour level = 0.013109
Position of ECRho_onRef200_2.pdb (#2) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.98874773 -0.13253198 0.06937730 14.38599909
0.11206577 0.96344465 0.24334270 -50.09441224
-0.09909187 -0.23282972 0.96745601 68.45451684
Axis -0.84848343 0.30019231 0.43584452
Axis point 0.00000000 254.59350836 247.30165118
Rotation angle (degrees) 16.29614155
Shift along axis 2.59128645
> select /F
2843 atoms, 2887 bonds, 1 model selected
> select /F
2843 atoms, 2887 bonds, 1 model selected
Unknown command: select/F:K
Unknown command: select/F,G,H
> open2
> N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/3ice_dN59_onRef200.pdb
Summary of feedback from opening <_io.textiowrapper
name="N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/3ice_dN59_onRef200.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 17625
END
3ice_dN59_onRef200.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) test3 [more info...]
Chain information for 3ice_dN59_onRef200.pdb #3
---
Chain | Description
A B C D E F | No description available
G | No description available
> select clear
> hide atoms
> show cartoons
Fit molecule 3ice_dN59_onRef200.pdb (#3) to map postprocess.mrc (#1) using
17179 atoms
average map value = 0.01002, steps = 108
shifted from previous position = 10.3
rotated from previous position = 14.8 degrees
atoms outside contour = 12545, contour level = 0.013109
Position of 3ice_dN59_onRef200.pdb (#3) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.99453972 -0.09565829 0.04171620 4.26058100
0.08322325 0.96817954 0.23601327 -41.56261656
-0.06296539 -0.23125281 0.97085400 58.13850002
Axis -0.91411152 0.20478834 0.34994553
Axis point 0.00000000 212.71473696 211.67088127
Rotation angle (degrees) 14.80824203
Shift along axis 7.93912250
> hide #!2 models
> open2
> N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/191126_Ec_DNARNA_zn.pdb
Summary of feedback from opening <_io.textiowrapper
name="N:/yuko-m/Arctica/SerialEM/data/191025/1_F4_3/phenix/191126_Ec_DNARNA_zn.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 25940
END
Chain information for 191126_Ec_DNARNA_zn.pdb #4
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> hide #!4 models
> hide #3 models
> open2
> P:/yuko-m/Arctica/SerialEM/data/191025/phenix/RealSpaceRefine_3/pp478_test_real_space_refined.pdb
Chain information for pp478_test_real_space_refined.pdb #5
---
Chain | Description
A B C D E F | No description available
G H | No description available
I | No description available
J | No description available
K | No description available
N | No description available
R | No description available
T | No description available
> hide #!5 atoms
> show #!5 cartoons
> volume #1 region 0,0,0,239,239,239
> volume #1 region 6,0,0,239,239,239
> ui mousemode rightMode zoom
> toolshed show "Side View"
> volume #1 level 0.01247
> open2
> S:/yuko-m/Arctica/SerialEM/data/191025/phenix/RealSpaceRefine_5/ref474_test2_real_space_refined.pdb
Chain information for ref474_test2_real_space_refined.pdb #6
---
Chain | Description
A B C D E F | No description available
G H | No description available
I | No description available
J | No description available
K | No description available
N | No description available
R | No description available
T | No description available
> hide #!5 models
> hide #!6 atoms
> show #!6 cartoons
> toolshed show "Segment Map"
Segmenting postprocess.mrc, density threshold 0.012474
Showing postprocess.seg - 0 regions, 0 surfaces
Showing 33 region surfaces
3411 watershed regions, grouped to 33 regions
> hide #!1 models
Showing 33 region surfaces
Showing 33 region surfaces
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> open2
> S:/yuko-m/Arctica/SerialEM/data/191025/phenix/RealSpaceRefine_12/ref493_subRho_all_real_space_refined.pdb
Chain information for ref493_subRho_all_real_space_refined.pdb #8
---
Chain | Description
A B C D E F | No description available
> hide #!8 atoms
> show #!8 cartoons
> open2
> S:/yuko-m/Arctica/SerialEM/data/191025/PostProcess/job541/postprocess.mrc
Opened postprocess.mrc, grid size 240,240,240, pixel 1.47, shown at level
0.00897, step 1, values float32
> close #9
> open2
> S:/yuko-m/Arctica/SerialEM/data/191025/PostProcess/job516/postprocess.mrc
Opened postprocess.mrc, grid size 240,240,240, pixel 1.47, shown at level
0.00731, step 1, values float32
> volume #9 level 0.01572
> rename #9 pp516
> open2
> S:/yuko-m/Arctica/SerialEM/data/191025/PostProcess/job515/postprocess.mrc
Opened postprocess.mrc, grid size 240,240,240, pixel 1.47, shown at level
0.00784, step 1, values float32
> volume #10 level 0.0144
> close #10
> open2 S:/yuko-m/Arctica/SerialEM/data/191025/postprocess.mrc format mrc
Opened postprocess.mrc, grid size 240,240,240, pixel 1.47, shown at level
0.00626, step 1, values float32
> hide #!8 models
> rename #10 708BeC
> volume #10 level 0.01355
> volume #10 level 0.02157
> volume #10 level 0.02303
> vop gaussian #10 sdev 4.41
> vop gaussian #11 sdev 4.41
> close #12
> show #!11 models
> show #!10 models
> hide #!11 models
> transparency sel 0
> volume #!10 style surface
> open2 S:/yuko-m/Arctica/SerialEM/data/191025/tthRho_c6.pdb format pdb
Summary of feedback from opening <_io.textiowrapper
name="S:/yuko-m/Arctica/SerialEM/data/191025/tthRho_c6.pdb" mode="rt"
encoding="utf-8">
---
warning | Ignored bad PDB record found on line 17625
END
tthRho_c6.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) test3 [more info...]
Chain information for tthRho_c6.pdb #12
---
Chain | Description
A B C D E F | No description available
G | No description available
> hide #12 atoms
> show #12 cartoons
> transparency sel 50
> transparency sel 0
> select #12/G
121 atoms, 132 bonds, 1 model selected
> hide sel cartoons
> close #11
> transparency #10.1 50
> toolshed show "Side View"
> toolshed show "Segment Map"
Segmenting 708BeC, density threshold 0.023033
Showing 708BeC.seg - 0 regions, 0 surfaces
Showing 18 region surfaces
1328 watershed regions, grouped to 18 regions
> hide #!10 models
Ungrouped to 6 regions
Ungrouped to 5 regions
Showing 27 region surfaces
Ungrouped to 17 regions
Drag select of 1830, 25758 of 36860 triangles, 1829, 4717 of 36004 triangles,
1834, 8144 of 35148 triangles, 1811, 2057 of 8352 triangles, 1837, 493 of 6736
triangles, 1821, 884 of 6832 triangles, 1836, 5711 of 6996 triangles, 1810,
574 of 6844 triangles, 356 residues
> select clear
> hide #12 cartoons
> select #12/F
2843 atoms, 2887 bonds, 1 model selected
> show sel cartoons
> select clear
Drag select of 1809, 1124 of 8336 triangles, 1835, 2532 of 6980 triangles,
1798, 158 of 16812 triangles, 1804, 2391 of 6720 triangles, 1786, 2131 of 2180
triangles, 1812, 1699 of 2648 triangles, 1827, 5389 of 7756 triangles, 1712,
2196 of 3316 triangles, 1691, 426 of 2836 triangles, 1641, 281 of 608
triangles, 1781, 796 of 1072 triangles, 1764, 1444 of 2208 triangles, 1790,
107 of 1688 triangles, 1755, 963 of 1308 triangles, 1473, 1065 of 1092
triangles, 1741, 1542 of 4496 triangles, 1730, 3474 of 4316 triangles, 1727,
1396 of 2644 triangles, 191 residues
Grouped 17 regions
Region has 11 adjacent regions
Ungrouped to 13 regions
Grouped 2 regions
Grouped 2 regions
> select clear
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> hide #!7 models
> show #!7 models
Expected a density maps specifier or a keyword
> transparency #7.5#!7 0
> transparency #7.5#!7 50
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> transparency #7.5#!7 0
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> transparency #7.5#!7 50
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> transparency #7.5#!7 0
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> hide #12 models
> show #12 models
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> transparency #7.5#!7 50
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
Expected a density maps specifier or a keyword
> nucleotides #12 atoms
> style nucleic & #12 stick
Changed 121 atom styles
> show #12 atoms
> nucleotides #12 atoms
> style nucleic & #12 stick
Changed 121 atom styles
> hide #12 atoms
> nucleotides #12 fill
> style nucleic & #12 stick
Changed 121 atom styles
> nucleotides #12 fill
> style nucleic & #12 stick
Changed 121 atom styles
> nucleotides #12 atoms
> style nucleic & #12 stick
Changed 121 atom styles
> show target ab
> style ball
Changed 224954 atom styles
> nucleotides #12 atoms
> style nucleic & #12 stick
Changed 121 atom styles
> nucleotides #12 atoms
> style nucleic & #12 stick
Changed 121 atom styles
> style #12 stick
Changed 17179 atom styles
> nucleotides #12 atoms
> style nucleic & #12 stick
Changed 121 atom styles
> hide #12 atoms
> hide #!7 models
> show #!10 models
> surface zone #10 nearAtoms #12/A
> hide #12 cartoons
> select #12/A
2843 atoms, 2887 bonds, 1 model selected
> show sel cartoons
> select clear
> volume #10 level 0.02121
> open2
> S:/yuko-m/Arctica/SerialEM/data/191025/phenix/RealSpaceRefine_15/708BeC_Rho_real_space_refined.pdb
Chain information for 708BeC_Rho_real_space_refined.pdb #11
---
Chain | Description
A B C D E F | No description available
> hide #12#!11 atoms
> show #12#!11 cartoons
> hide #12 models
> hide #!11 models
> show #!11 models
> surface zone #10 nearAtoms #12/A
Invalid "nearAtoms" argument: only initial part "#11/A" of atom specifier
valid
> surface zone #10 nearAtoms #11/A,B
> volume #!10 style mesh
> hide #!11 cartoons
> select #12/A
2843 atoms, 2887 bonds, 1 model selected
> show sel cartoons
> select #11/A
5808 atoms, 5849 bonds, 2 pseudobonds, 2 models selected
> select #11/A
5808 atoms, 5849 bonds, 2 pseudobonds, 2 models selected
> show sel cartoons
> select #11/B
5807 atoms, 5848 bonds, 1 pseudobond, 2 models selected
> show sel cartoons
> volume #10 color #0055ff80
> select #11/A
5808 atoms, 5849 bonds, 2 pseudobonds, 2 models selected
> surface zone #10 nearAtoms #11/A,B distance 6
> volume #!10 style surface
> volume #!10 style mesh
> color sel bychain
> color sel bychain
> color sel bychain
> color sel byhetero
> color sel bychain
> surface zone #10 nearAtoms #11/A,B distance 5.5
> surface zone #10 nearAtoms #11/A,B distance 5
> color sel pink
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel red
> color sel #ff00ff
> color sel #ff55ff
> color sel #ff99ff
> select clear
> select ::name="ADP"
792 atoms, 840 bonds, 4 models selected
> select #11/A:1000:1002
43 atoms, 41 bonds, 1 pseudobond, 2 models selected
> show sel atoms
> color sel byhetero
> close #7
> save2 S:/yuko-m/Arctica/SerialEM/data/191025/phenix/708BeC_1.cxs
> select #11/A:1002
4 atoms, 1 model selected
> hide sel atoms
> select #11/A:1000
39 atoms, 41 bonds, 1 model selected
> volume #10 color #00007f80
> select clear
> volume #!10 style surface
> volume #!10 style mesh
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
QFileSystemWatcher::removePaths: list is empty
> save2 C:/Users/Murayama/Documents/200505/708BeC_chainAB_ADP.png width 929
> height 754 supersample 3
> set bgColor white
> volume #!10 style surface
> volume #10 color #aaaaff80
> volume #10 color #00aaff80
> volume #10 color #00ffff80
> volume #10 color #aaffff80
> volume #10 color #ffffff80
> volume #10 color #fefefe80
> volume #10 color #fdfdfd80
> volume #10 color #f7f7f780
> volume #10 color #e7e7e780
> volume #10 color #d9d9d980
> volume #10 color #d3d3d380
> volume #10 color #cecece80
> volume #10 color #c7c7c780
> volume #10 color #c2c2c280
> volume #10 color #bcbcbc80
> volume #10 color #b4b4b480
> volume #10 color #acacac80
> volume #10 color #a8a8a880
> volume #10 color #a5a5a580
> volume #10 color #9f9f9f80
> volume #10 color #9d9d9d80
> volume #10 color #99999980
> volume #10 color #98989880
> volume #10 color #95959580
> volume #10 color #93939380
> volume #10 color #91919180
> volume #10 color #90909080
> volume #10 color #8f8f8f80
> volume #10 color #90909080
> volume #10 color #91919180
> volume #10 color #93939380
> volume #10 color #94949480
> volume #10 color #96969680
> volume #10 color #98989880
Expected a keyword
> surface dust #10
> surface zone #10 nearAtoms #11/A,B distance 5
Expected a keyword
> surface zone #10 nearAtoms #11/A,B distance 5 maxComponents 10
> surface zone #10 nearAtoms #11/A,B distance 5 maxComponents 5
> surface zone #10 nearAtoms #11/A,B distance 5 maxComponents 1
> surface zone #10 nearAtoms #11/A,B distance 5 maxComponents 2
> surface zone #10 nearAtoms #11/A,B distance 6 maxComponents 2
> surface zone #10 nearAtoms #11/A,B distance 3 maxComponents 2
> surface zone #10 nearAtoms #11/A,B distance 2.8 maxComponents 2
> volume #10 level 0.02559
> volume #10 level 0.03033
> surface zone #10 nearAtoms #11/A,B distance 2.8 maxComponents 2
> surface zone #10 nearAtoms #11/A:142-1002,B distance 2.8 maxComponents 2
> surface zone #10 nearAtoms #11/A:142-1002,B:142-1002 distance 2.8
> maxComponents 2
> surface zone #10 nearAtoms #11/A,B:142-1002 distance 2.8 maxComponents 2
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 2
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 1
> volume #10 level 0.03106
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 1
> volume #10 level 0.03725
> volume #10 level 0.03251
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 1
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 2
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 3
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 4
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 3
Expected a keyword
> select #11/A,B:141-1002
9053 atoms, 9113 bonds, 3 pseudobonds, 2 models selected
> hide sel cartoons
> select clear
> hide #!11 cartoons
> select #11/A,B:141-1002
9053 atoms, 9113 bonds, 3 pseudobonds, 2 models selected
> show sel cartoons
> select clear
> volume #10 level 0.03033
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 3
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 1
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 2.8 maxComponents 2
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 3 maxComponents 2
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 3.2 maxComponents 2
> select up
Nothing selected
> select up
Nothing selected
> select #11/A:1001
1 atom, 1 model selected
> select #11/A:1000
39 atoms, 41 bonds, 1 model selected
> style sel sphere
Changed 39 atom styles
> style sel ball
Changed 39 atom styles
> select clear
> save C:\Users\Murayama\Desktop\image1.png supersample 3
> save test.png transparentBackground true
> save C:/Users/Murayama/Documents/200505/test.png transparentBackground true
> save C:/Users/Murayama/Documents/200505/test2.png
> surface dust #10
> volume #1 level 0.01184
> hide #!1 models
> volume #10 level 0.02741
> volume #10 level 0.01282
> show #12 models
> hide #12 models
> show #!11 cartoons
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select #11/A
5808 atoms, 5849 bonds, 2 pseudobonds, 2 models selected
> select #11/C,E
11613 atoms, 11695 bonds, 2 pseudobonds, 2 models selected
> color sel #ff99ff
> select #11/B,D,F
17426 atoms, 17549 bonds, 3 pseudobonds, 2 models selected
> color sel #ff9999
> select #11/500-1000
Nothing selected
> show #!11 atoms
> hide #!11 atoms
> select #11/C,D,E,F:1000
156 atoms, 164 bonds, 1 model selected
> show sel atoms
> style sel ball
Changed 156 atom styles
> style sel stick
Changed 156 atom styles
> color sel byhetero
> select #11/B:1000
Nothing selected
> select #11/B:500
Nothing selected
> select #11/B:501
39 atoms, 41 bonds, 1 model selected
> style sel stick
Changed 39 atom styles
> hide sel atoms
> show sel atoms
> style sel stick
Changed 39 atom styles
> color sel byhetero
> select clear
> volume #10 level 0.01975
> select up
Nothing selected
> select up
Nothing selected
> surface dust #10
> transparency #10 0.5
> transparency #10 30
> transparency #10 50
> transparency #10 30
> save C:/Users/Murayama/Documents/200505/708BeC_top.png transparentBackground
> true
> transparency #10 40
> save C:/Users/Murayama/Documents/200505/708BeC_top_t40.png
> transparentBackground true
> transparency #10 50
> save C:/Users/Murayama/Documents/200505/708BeC_top_t50.png
> transparentBackground true
> transparency #10 40
> save C:/Users/Murayama/Documents/200505/708BeC_top_t40_clip.png
> transparentBackground true
> save C:/Users/Murayama/Documents/200505/708BeC_top_t40_white.png
> volume #10 level 0.02923
> surface dust #10
Invalid "nearAtoms" argument: invalid atoms specifier
> surface zone #10 nearAtoms #11 distance 3.2 maxComponents 12
> surface zone #10 nearAtoms #11 distance 3.2 maxComponents 18
> surface zone #10 nearAtoms #11 distance 3.2 maxComponents 24
> surface zone #10 nearAtoms #11 distance 3.2 maxComponents 36
> surface zone #10 nearAtoms #11 distance 3.2 maxComponents 60
> surface zone #10 nearAtoms #11 distance 3.5 maxComponents 60
> save C:/Users/Murayama/Documents/200505/708BeC_top_t40_white2.png
> save C:/Users/Murayama/Documents/200505/708BeC_top_t40_white2.png
> save C:/Users/Murayama/Documents/200505/708BeC_side_t40.png
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 3.2 maxComponents 2
> surface zone #10 nearAtoms #11/A,B:141-1002 distance 3.2 maxComponents 4
> select up
Nothing selected
> select #11/A,B:141-1002
9053 atoms, 9113 bonds, 3 pseudobonds, 2 models selected
> select clear
> hide #!11 cartoons
> select #11/A,B:141-1002
9053 atoms, 9113 bonds, 3 pseudobonds, 2 models selected
> show sel cartoons
> select #11/A:1000
39 atoms, 41 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 39 atom styles
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 3.2 maxComponents 5
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 3 maxComponents 5
> volume #10 level 0.02996
> volume #10 level 0.03944
> volume #10 level 0.04054
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 5
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 10
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 12
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 16
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 14
> volume #10 level 0.03762
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 14
> volume #10 level 0.03397
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 14
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 12
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 10
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 4 maxComponents 6
> hide sel cartoons
> hide sel atoms
> select clear
> hide #!11 cartoons
> hide #!11 atoms
> select up
Nothing selected
> select #11/A:1000
39 atoms, 41 bonds, 1 model selected
> style sel stick
Changed 39 atom styles
> show sel atoms
> style sel stick
Changed 39 atom styles
> select #11/A,B:141-420
8965 atoms, 9031 bonds, 1 model selected
> show sel cartoons
> select clear
> volume #!10 style mesh
> surface zone #10 nearAtoms #11/A,B:141-1000 distance 3 maxComponents 6
> volume #1 color #00550080
> volume #1 color #aaffff80
> volume #10 color #00550099
> volume #10 color #00aa0099
> volume #10 color #00550099
> volume #10 color #00557f99
> volume #10 color #00550099
> volume #10 color #00557f99
> volume #10 color #00598399
> volume #10 color #00598299
> volume #10 color #00598399
> volume #10 color #005b8699
> volume #10 color #005c8799
> volume #10 color #005d8899
> volume #10 color #005e8a99
> volume #10 color #005f8b99
> volume #10 color #00608c99
> volume #10 color #00608d99
> volume #10 color #00629099
> volume #10 color #00628f99
> volume #10 color #00608d99
> volume #10 color #00608c99
> volume #10 color #005e8a99
> volume #10 color #005d8899
> volume #10 color #005c8799
> volume #10 color #005b8699
> volume #10 color #005a8499
> select up
Nothing selected
> save C:/Users/Murayama/Documents/200505/708BeC_zoom_mesh.png
> save2 C:/Users/Murayama/Documents/200505/708BeC_200505.cxs includeMaps true
opened ChimeraX session
> close #1
> close #2
> close #3
> close #4
> show #!5 models
> hide #!5 models
> close #5
> close #6
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> close #9
> close #8
> smoothlines #10
Surface model surface does not consist of lines
> volume style surface
> smoothlines #10
Surface model surface does not consist of lines
> lighting flat
> smoothlines #10
Surface model surface does not consist of lines
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> volume style mesh
> transparency #10 0
> volume gaussian #10 sDev 1
> surface zone #10 nearAtoms #11/A:142-420/B142-420
> surface zone #1 nearAtoms #11/A:142-420/B142-420
> surface zone #1 nearAtoms #11/A:142-420/B:142-420
> volume #1 level 0.0341
> volume #1 level 0.033
> volume #1 level 0.03
> surface zone #1 nearAtoms #11/A:142-420/B:142-420 distance 3 maxComponents
> 10
> surface zone #1 nearAtoms #11/A:142-420/B:142-420 distance 3 maxComponents 9
> volume #1 color #00557f
> volume #1 color #005b86
> volume #1 color #00628f
> volume #1 color #006696
> volume #1 color #0071a6
> volume #1 color #0078b0
> volume #1 color #007bb4
> volume #1 color #007fba
> volume #1 color #0081bd
> volume #1 color #0082be
> volume #1 color #0083bf
> volume #1 color #0087c5
> volume #1 color #0085c3
> volume #1 color #0084c1
> volume #1 color #0080bc
> volume #1 color #5896bc
> volume #1 color #5998bf
> volume #1 color #5997be
> volume #1 color #5794ba
> volume #1 color #5693b9
> volume #1 color #528cb0
> volume #1 color #5089ac
> volume #1 color #4f87aa
> volume #1 color #4e85a7
> volume #1 color #4d84a6
> volume #1 color #4c82a3
> volume #1 color #4b81a2
> volume #1 color #4c82a3
> volume #1 color #4d83a5
> volume #1 color #4e85a7
> volume #1 color #4e86a8
> volume #1 color #4f87aa
> volume #1 color #5088ab
> surface zone #1 nearAtoms #11/A:142-1002/B:142-420 distance 3 maxComponents
> 9
> surface zone #1 nearAtoms #11/A:142-1002/B:142-420 distance 3.5
> maxComponents 9
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting full
> lighting shadows false
> volume #1 color #518aad
> volume #1 color #5c9dc5
> volume #1 color #5ea1ca
> volume #1 color #61a6d0
> volume #1 color #4199d0
> volume #1 color #3896d0
> volume #1 color #4498d0
> volume #1 color #459bd3
> volume #1 color #4599d1
> volume #1 color #4395cc
> volume #1 color #408fc3
> volume #1 color #3f8cbf
> color #11/B,D,F #FF8877
> color #11/A,C,E #ff66bb
> color #11/A,C,E #ff66cc
> color #11/A,C,E #ff55cc
> color #11/A,C,E #ff77dd
> select #11/A:1000
39 atoms, 41 bonds, 1 model selected
> style sel ball
Changed 39 atom styles
> color sel byhetero
> select clear
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> save2 C:/Users/Murayama/Documents/200505/708BeC_zoom_3.png width 960 height
> 790 supersample 3
> save2 C:/Users/Murayama/Documents/200505/708BeC_200505.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1373, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 90, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 101, in show_save_file_dialog
_dlg.display(session, session.ui.main_window)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 31, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
> save2 C:/Users/Murayama/Documents/200505/708BeC_200508.cxs includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1373, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 90, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 101, in show_save_file_dialog
_dlg.display(session, session.ui.main_window)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 31, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
> save2 C:/Users/Murayama/Documents/200505/708BeC_200508.cxs includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1373, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 90, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 101, in show_save_file_dialog
_dlg.display(session, session.ui.main_window)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 31, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
> close session
> open2 C:/Users/Murayama/Documents/200505/pp478_rsr3_edit.pdb
Summary of feedback from opening <_io.textiowrapper
name="C:/Users/Murayama/Documents/200505/pp478_rsr3_edit.pdb" mode="rt"
encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 116 116 ASN A
415 PHE A 419 1 5
Start residue of secondary structure not found: HELIX 130 130 ASN B 415 PHE B
419 1 5
Start residue of secondary structure not found: HELIX 144 144 ASN C 415 PHE C
419 1 5
Start residue of secondary structure not found: HELIX 158 158 ASN D 415 PHE D
419 1 5
Start residue of secondary structure not found: HELIX 172 172 ASN E 415 PHE E
419 1 5
1 messages similar to the above omitted
Chain information for pp478_rsr3_edit.pdb #1
---
Chain | Description
A B C D E F | No description available
G H | No description available
I | No description available
J | No description available
K | No description available
N | No description available
R | No description available
T | No description available
> hide atoms
> show cartoons
> hide atoms
> hide cartoons
> hide cartoons
> show cartoons
> hide atoms
> hide cartoons
> show #1/A-E:150-206/A-E:349-420 cartoons
> show #1/A-F:150-206/A-E:349-420 cartoons
> show #1/A-F:150-206/A-F:349-420 cartoons
> hide cartoons
> show #1/A-F:150-206/A-F:349-412 cartoons
> color #1/A,C,E #ff55cc
> color #1/B,D,F #FF8877
> show #1/R cartoons
> show #1/R:7-19 surfaces
> show #1/R:6-19 surfaces
> color #1/R gold
> show #1/I:701-832 cartoons
> color #1/I:701-832 #55ddff
> lighting shadows false
> lighting simple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1/I:763-783 #00BFFF
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> color #1/I:701-832 #55ddff
> color #1/I:701-832 #33ddff
> color #1/I:701-832 #33ccff
> color #1/I:701-832 #33bbff
> show #1/I:1083-1119/J:1-131,455-607,1443-1468 cartoons
> color #1/I:1083-1119/J:1-131,455-607,1443-1468 #88FF22
> color #1/I:1083-1119/J:1-131,455-607,1443-1468 #80FF22
> color #1/I:1083-1119/J:1-131,455-607,1443-1468 #80FF33
> color #1/J:55-81 #33FF33
> color #1/J:55-81 #33bb55
> color #1/J:55-81 #33aa55
> color #1/J:55-81 seagreen
> show #1/J:4058 atoms
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1/J:4058 seagreen
> show #1/J:55-81 atoms
> style stick
Changed 42548 atom styles
> color byhetero
> color #1/R gold
> hide #1/J:55-81 atoms
Unknown command: shoe #1/J:58,60,73,75 atoms
Unknown command: shoe #1/J:58/J:60/J:73/J:75 atoms
> show #1/J:58,60,73,75 atoms
> show #1/J:58,60,73,76 atoms
> hide #1/J:75 atoms
> toolshed show Rotamers
> select #1/J:60
6 atoms, 5 bonds, 1 model selected
> toolshed show Rotamers
> swapaa interactive sel CYH lib Dunbrack
/J CYS 60: phi -98.5, psi -40.9 trans
Changed 9 bond radii
> swapaa #1/J:60 CYH criteria 3
Using Dunbrack library
pp478_rsr3_edit.pdb #1/J CYS 60: phi -98.5, psi -40.9 trans
Applying CYS rotamer (chi angles: 66.5) to pp478_rsr3_edit.pdb #1/J CYS 60
> swapaa interactive sel CYH lib Dunbrack
/J CYS 60: phi -98.5, psi -40.9 trans
Changed 9 bond radii
> select clear
> select /J:4058@ZN
1 atom, 1 model selected
> style sel ball
Changed 1 atom style
> style sel sphere
Changed 1 atom style
> select clear
> show #1/J:663-672 cartoons
> show #1/J:649-690 cartoons
> hide #1/J:649-690 cartoons
> color #1/J:649-690 #aaaaaa
Unknown command: show#1/J:653-679 cartoons
> show #1/J:653-679 cartoons
> color #1/I:1006:1072/J:621-778,1103-1432,1473-1520/K #aaaaaa
> show #1/I:1006:1072/J:621-778,1103-1432,1473-1520/K cartoons
> hide #1/J:1255-1432 cartoons
> hide #1/J:1103-1432 cartoons
> color #1/K:84-96 #7733FF
> show #1/I:1006-1072 cartoons
> color #1/I:1006-1072 #aaaaaa
> select up
Nothing selected
> color #1/K:1083 #aa99FF
> color #1/K:1-83 #aa99FF
> color #1/I:763-783 #0099ff
> color #1/I:763-783 #0099dd
> color #1/I:763-783 #0099bb
> color #1/I:763-783 #0077bb
> show #1/R:6-21 surfaces
> hide #1/R cartoons
> hide #1/R:6 surfaces
> show #1/N:35-50/T:1-20 cartoons
> hide #1/N:35-50/T:1-20 cartoons
> hide #1/T:35-50/N:1-20 cartoons
> show #1/T:35-50/N:1-20 cartoons
> show #1/T:35-50/N:1-16 cartoons
> hide #1/T,N cartoons
> show #1/T:35-50/N:1-16 cartoons
> show #1/T:35-50/N:1-16 surfaces
> hide #1/T,N cartoons
> hide #1/T,N surfaces
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> toolshed show "Side View"
> save C:/Users/Murayama/Documents/200505/fig3_cartoon_1.png
> transparentBackground true
> lighting full
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> save C:/Users/Murayama/Documents/200505/fig3_cartoon_2.png
> transparentBackground true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save C:/Users/Murayama/Documents/200505/fig3_cartoon_3.png
> transparentBackground true
> show #1/I:763-783/J:51-89 surfaces
> color #1/I:763-783 #55ddff
> color #1/J:51-89 seagreen
> lighting shadows false
> transparency #1/I,J 50 surfaces
> lighting full
> transparency #1/I,J 40 surfaces
> save C:/Users/Murayama/Documents/200505/fig3_cartoon_4.png
> transparentBackground true
> save2 C:/Users/Murayama/Documents/200505/fig3_200508.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1373, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 90, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 101, in show_save_file_dialog
_dlg.display(session, session.ui.main_window)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 31, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 564, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x00000293B4410908> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000029317EA1A88> 'ref474_test2_real_space_refined.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'ref474_test2_real_space_refined.pdb'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 25.20.100.6577
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: LG Electronics
Model: 14Z980-GA55J
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 8,415,170,560
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz"
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Nucleotides trying to save dead structure |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #2955. Finally able to reproduce and fix.