![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#3501 closed defect (can't reproduce)
Problem saving map: No such file or directory
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
cannot save maps (maybe other file types too).
OSX 10.15.5
ChimeraX 1.0 (2020-06-04)
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/cryosparc_P2_J1010_003_volume_map.mrc"
> "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/cryosparc_P2_J1011_004_volume_map.mrc"
> "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/cryosparc_P2_J1013_001_volume_map.mrc"
> "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/cryosparc_P2_J1014_002_volume_map.mrc"
> "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/cryosparc_P2_J1016_002_volume_map.mrc"
> "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/cryosparc_P2_J1017_003_volume_map.mrc"
Opened cryosparc_P2_J1010_003_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.118, step 1, values float32
Opened cryosparc_P2_J1011_004_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.116, step 1, values float32
Opened cryosparc_P2_J1013_001_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.094, step 1, values float32
Opened cryosparc_P2_J1014_002_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.0924, step 1, values float32
Opened cryosparc_P2_J1016_002_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.109, step 1, values float32
Opened cryosparc_P2_J1017_003_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.103, step 1, values float32
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!2 models
> volume #1 level 0.06359
> volume #1 level 0.06586
> show #!3 models
> volume #3 level 0.03478
> show #!5 models
> volume #5 level 0.03602
> hide #!5 models
> hide #!3 models
> hide #1.1 models
> volume #1 level 0.1101
> show #!2 models
> hide #!1 models
> volume #2 level 0.07445
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!6 models
> show #!4 models
> show #!2 models
> hide #!4 models
> hide #!6 models
> open /Users/gil/Downloads/k5/cryosparc_P2_J1009_006_volume_map.mrc
Opened cryosparc_P2_J1009_006_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.0648, step 1, values float32
> open /Users/gil/Downloads/k5/cryosparc_P2_J998_007_volume_map.mrc
Opened cryosparc_P2_J998_007_volume_map.mrc, grid size 256,256,256, pixel
1.45, shown at level 0.102, step 1, values float32
> hide #!7 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #7
> volume #8 level 0.1043
> volume #8 level 0.07793
> open "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/model-2/K5C3_C5.pdb"
Chain information for K5C3_C5.pdb #7
---
Chain | Description
A B C D E | No description available
F G H I J | No description available
> hide surfaces
> hide surfaces
> hide surfaces
> hide surfaces
> show cartoons
> show cartoons
> show cartoons
> hide #!8 models
Drag select of 10563 atoms, 2 pseudobonds, 2124 residues, 99 bonds
Drag select of 13215 atoms, 10 pseudobonds, 2680 residues, 135 bonds
> hide sel surfaces
> hide sel surfaces
> ~select #7.1
21330 atoms, 135 bonds, 1 model selected
> select #7.1
10 pseudobonds, 1 model selected
> select #7
21330 atoms, 21665 bonds, 10 pseudobonds, 2 models selected
> ~select #7
Nothing selected
> select #7
21330 atoms, 21665 bonds, 10 pseudobonds, 2 models selected
> ~select #7.1
21330 atoms, 21665 bonds, 1 model selected
> hide #7.1 models
> hide sel surfaces
> show sel cartoons
> show sel cartoons
> view #!7 clip false
> hide sel surfaces
> hide sel surfaces
> color sel byhetero
> hide #* target a
> show sel target ab
> cartoon sel
> hide sel target a
> select clear
> show #!8 models
> hide #!8 models
> ui mousemode right select
> select clear
> select clear
Drag select of 2671 residues
> select clear
Drag select of 2680 residues
> show #!8 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui tool show "Fit in Map"
Fit molecule K5C3_C5.pdb (#7) to map cryosparc_P2_J998_007_volume_map.mrc (#8)
using 21330 atoms
average map value = 0.1006, steps = 372
shifted from previous position = 13.8
rotated from previous position = 39.5 degrees
atoms outside contour = 10767, contour level = 0.077928
Position of K5C3_C5.pdb (#7) relative to cryosparc_P2_J998_007_volume_map.mrc
(#8) coordinates:
Matrix rotation and translation
0.00734655 0.95187359 -0.30640283 114.32815661
-0.59453917 0.25052914 0.76404079 126.54434082
0.80403309 0.17655542 0.56776666 7.52577904
Axis -0.29486533 -0.55733993 -0.77616148
Axis point 94.21621447 12.24418689 -0.00000000
Rotation angle (degrees) 95.00132759
Shift along axis -110.08084359
> volume #8 style mesh
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecule K5C3_C5.pdb (#7) to map cryosparc_P2_J998_007_volume_map.mrc (#8)
using 21330 atoms
average map value = 0.098, steps = 168
shifted from previous position = 14.2
rotated from previous position = 16 degrees
atoms outside contour = 11195, contour level = 0.077928
Position of K5C3_C5.pdb (#7) relative to cryosparc_P2_J998_007_volume_map.mrc
(#8) coordinates:
Matrix rotation and translation
0.70654230 0.70764525 0.00601464 21.61835389
-0.70603111 0.70545799 -0.06204098 194.00569774
-0.04814608 0.03958806 0.99805548 65.11413958
Axis 0.07165254 0.03818547 -0.99669844
Axis point 249.71541132 67.34189682 0.00000000
Rotation angle (degrees) 45.16820303
Shift along axis -55.94195200
> select clear
> volume #8 level 0.1238
> volume #8 level 0.2635
> volume #8 level 0.3368
> hide #!7 models
> show #!7 models
> select #8
2 models selected
> ~select #8
Nothing selected
> hide #!8 models
> show #!8 models
> volume #8 level 0.1203
> hide #!8 models
> show #!8 models
> volume #8 level -0.1123
> volume #8 level 0.02752
> show #!1 models
> volume #1 style mesh
> volume #1 level -0.007925
> volume #8 level -0.1237
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.05224
> volume #1 level 0.0863
> volume #8 level 0.05731
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> show #!1 models
> hide #!8 models
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui tool show "Fit in Map"
> help flip map
No help found for 'flip map'
> help invert
No help found for 'invert'
> help hand
No help found for 'hand'
> help vop
> vop volume gaussian #1 invert
> volume volumes gaussian #1 invert
Invalid "volumes" argument: invalid density maps specifier
> vop volume gaussian #1 invert true
> volume volumes gaussian #1 invert true
Invalid "volumes" argument: invalid density maps specifier
> volume gaussian #1 invert true
> show #!1 models
> hide #!1 models
> show #!1 models
> ui mousemode right "translate selected models"
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!1 models
> ~select #1
Nothing selected
> hide #1.1 models
> select #9
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> hide #!9 models
> show #!9 models
> ui tool show Log
> volume flip #1
> close #9
> hide #!7 models
> show #!7 models
> hide #!10 models
> show #!10 models
> select #10
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ~select #10
Nothing selected
> show #!8 models
> select #10
2 models selected
> hide #!7 models
> ~select #10
Nothing selected
> select #10
2 models selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> show #!8 models
Fit map cryosparc_P2_J1010_003_volume_map.mrc z flip in map
cryosparc_P2_J998_007_volume_map.mrc using 227211 points
correlation = 0.8579, correlation about mean = 0.5543, overlap = 5818
steps = 240, shift = 17.9, angle = 30.3 degrees
Position of cryosparc_P2_J1010_003_volume_map.mrc z flip (#10) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.10219469 -0.46250207 0.88070885 118.51805703
-0.20092337 0.87669365 0.43707898 -19.49107601
-0.97426179 -0.13228784 -0.18252091 419.21447401
Axis -0.29079933 0.94741069 0.13359913
Axis point 235.98110142 0.00000000 159.74025888
Rotation angle (degrees) 101.77160864
Shift along axis 3.07566310
> ~select #10
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!10 models
> show #!8 models
> volume #8 level 0.1078
> show #!10 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume flip #2
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
Fit map cryosparc_P2_J1011_004_volume_map.mrc z flip in map
cryosparc_P2_J998_007_volume_map.mrc using 263659 points
correlation = 0.8779, correlation about mean = 0.726, overlap = 5947
steps = 104, shift = 1.28, angle = 8.97 degrees
Position of cryosparc_P2_J1011_004_volume_map.mrc z flip (#9) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.98776623 -0.15594179 0.00020212 31.17912176
0.15594186 0.98776618 -0.00034318 -26.62993981
-0.00014613 0.00037050 0.99999992 1.23354781
Axis 0.00228831 0.00111659 0.99999676
Axis point 185.32107310 185.38345009 0.00000000
Rotation angle (degrees) 8.97145237
Shift along axis 1.27515657
> hide #!8 models
> hide #!9 models
> show #!3 models
> select #3
2 models selected
> hide #!3 models
> show #!3 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ~select #3
Nothing selected
Fit map cryosparc_P2_J1013_001_volume_map.mrc in map
cryosparc_P2_J998_007_volume_map.mrc using 349645 points
correlation = 0.8717, correlation about mean = 0.7139, overlap = 6181
steps = 200, shift = 24.2, angle = 15 degrees
Position of cryosparc_P2_J1013_001_volume_map.mrc (#3) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.08359893 0.40876203 0.90880406 -37.45085791
-0.03355958 0.91032432 -0.41253289 103.15027229
-0.99593422 -0.06498639 -0.06238426 386.84391479
Axis 0.17499227 0.95905003 -0.22271225
Axis point 151.67024627 0.00000000 223.24794460
Rotation angle (degrees) 96.76684959
Shift along axis 6.21778037
> hide #!3 models
> show #!3 models
> volume #3 level 0.1006
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
Fit map cryosparc_P2_J1014_002_volume_map.mrc in map
cryosparc_P2_J998_007_volume_map.mrc using 167718 points
correlation = 0.8435, correlation about mean = 0.3473, overlap = 4171
steps = 128, shift = 24.3, angle = 1.38 degrees
Position of cryosparc_P2_J1014_002_volume_map.mrc (#4) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99970875 -0.02413281 -0.00016181 4.55880920
0.02413282 0.99970876 0.00003044 -4.44071073
0.00016103 -0.00003433 0.99999999 -24.36137628
Axis -0.00134188 -0.00668875 0.99997673
Axis point 192.99199816 185.22260641 0.00000000
Rotation angle (degrees) 1.38287481
Shift along axis -24.33722396
> hide #!4 models
> show #!4 models
> select #4
2 models selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit map cryosparc_P2_J1014_002_volume_map.mrc in map
cryosparc_P2_J998_007_volume_map.mrc using 167718 points
correlation = 0.9357, correlation about mean = 0.5964, overlap = 5939
steps = 92, shift = 4.29, angle = 6.92 degrees
Position of cryosparc_P2_J1014_002_volume_map.mrc (#4) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.68154722 -0.73177414 0.00003280 447.90793721
-0.73177414 0.68154722 -0.00006637 194.94689857
0.00002622 -0.00006924 -1.00000000 363.50471130
Axis -0.39901272 0.91694539 -0.00008969
Axis point 266.37031383 0.00000000 181.76145151
Rotation angle (degrees) 179.99979439
Shift along axis 0.00209355
> hide #!4 models
> ~select #4
Nothing selected
> hide #!8 models
> show #!8 models
> show #!5 models
> select #5
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> volume #5 level 0.1128
Fit map cryosparc_P2_J1016_002_volume_map.mrc in map
cryosparc_P2_J998_007_volume_map.mrc using 160789 points
correlation = 0.9385, correlation about mean = 0.6787, overlap = 5838
steps = 196, shift = 25.9, angle = 27.7 degrees
Position of cryosparc_P2_J1016_002_volume_map.mrc (#5) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.18843167 0.92511386 0.32963291 -87.50452861
-0.20053410 -0.29232965 0.93505585 106.35149668
0.96139460 -0.24229678 0.13043271 26.52283375
Axis -0.67388889 -0.36160550 -0.64429436
Axis point 0.00000000 89.17696271 8.18874073
Rotation angle (degrees) 119.12605233
Shift along axis 3.42253194
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> ~select #5
Nothing selected
> show #!6 models
> select #6
2 models selected
> hide #!8 models
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!6 models
> ~select #6
Nothing selected
> show #!6 models
Fit map cryosparc_P2_J1017_003_volume_map.mrc in map
cryosparc_P2_J998_007_volume_map.mrc using 167739 points
correlation = 0.9823, correlation about mean = 0.8709, overlap = 6213
steps = 48, shift = 0.564, angle = 0.091 degrees
Position of cryosparc_P2_J1017_003_volume_map.mrc (#6) relative to
cryosparc_P2_J998_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99999874 -0.00157890 -0.00016417 0.32173105
0.00157891 0.99999875 0.00002144 -0.30333899
0.00016414 -0.00002170 0.99999999 0.53776811
Axis -0.01358638 -0.10339898 0.99454716
Axis point 155.49146458 208.47932467 0.00000000
Rotation angle (degrees) 0.09096054
Shift along axis 0.56182954
> show #!7 models
> hide #!8 models
> hide #!6 models
> show #!10 models
> volume #10 style mesh
> volume #10 level 0.1966
> volume #10 level 0.2854
> hide #!7 models
> volume #9 level 0.076
> volume #10 level 0.2431
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> volume #9 level 0.2216
> volume #9 style mesh
> volume #9 level 0.282
> volume #9 level 0.2456
> volume #9 level 0.1054
> volume #9 level 0.2216
> show #!7 models
> hide #!7 models
> volume #9 level 0.2208
Drag select of 9 cryosparc_P2_J1011_004_volume_map.mrc z flip
> select clear
> volume #8 level 0.3234
> volume #8 level 0.333
> show #!9 models
> volume #8 level 0.3278
> hide #!9 models
> volume #8 level 0.1947
> volume #8 level 0.2417
> volume #8 level 0.2991
> volume #8 level 0.09905
> volume #8 level 0.3034
> show #!4 models
> volume #3 style mesh
> volume #4 level 0.1969
> volume #4 level 0.09707
> volume #4 level 0.1367
> volume #4 level 0.265
> volume #4 level 0.09707
> volume #4 level 0.06268
> hide #!4 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.1304
> volume #8 level 0.1217
> show #!2 models
> volume #2 level 0.1697
> volume #2 level 0.292
> volume #2 level 0.05277
> ui mousemode right "rotate selected models"
> volume #8 level 0.2078
> volume #8 level 0.306
> volume #8 level 0.133
> volume #8 level 0.1756
> volume #8 level 0.306
> volume #8 level 0.2252
> volume #8 level 0.1112
> volume #8 level 0.1304
> volume #8 level 0.2626
> volume #8 level 0.3278
> volume #8 level 0.09905
> volume #8 level 0.106
> volume #8 level 0.1321
> show #!2 models
> show #!8 models
> hide #!2 models
> show #!2 models
> ui mousemode right "rotate selected models"
> select #2
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> volume #8 level 0.0947
> hide #!2 models
> show #!2 models
> hide #!2 models
> ~select #2
Nothing selected
> show #!9 models
> volume #8 level 0.3191
> volume #8 level 0.2095
> volume #8 level 0.2086
> volume #8 level 0.1843
> volume #8 level 0.3174
> volume #8 level 0.2713
> volume #8 level 0.3017
> volume #8 level 0.1373
> volume #8 level 0.2156
> volume #9 level 0.1751
> volume #9 level 0.2603
> volume #9 level 0.07909
> hide #!9 models
> show #!8 models
> show #!3 models
> volume #3 level 0.2038
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.2075
> volume #4 level 0.2617
> volume #4 level 0.09905
> volume #4 level 0.06996
> show #!6 models
> volume #6 level 0.3103
> volume #8 level 0.3182
> volume #6 level 0.1032
> volume #6 level 0.3069
> hide #!6 models
> show #!4 models
> volume #4 level 0.02169
> volume #4 level 0.03161
> volume #4 level 0.3305
> volume #4 level 0.2624
> show #!2 models
> hide #!2 models
> show #!9 models
> volume #9 style surface
> volume #9 level 0.1209
> volume #9 level 0.2371
> volume #9 level 0.2665
> hide #!9 models
> show #!8 models
> volume #8 style surface style image
Repeated keyword argument "style"
> volume #8 style surface
> volume #8 change image level -0.008343,0 level 0.102,0.8 level 0.4012,1
> volume #8 level 0.1008
> toolshed show
> help slab
No help found for 'slab'
> ui mousemode right clip
> help resample
No help found for 'resample'
> help volume resample
> volume #8 level -0.2001
> volume #8 style mesh
> volume #8 step 8
> volume #8
> volume #8 level 0.009097
> volume #8 level 0.009922
> volume #8 style surface
> volume #8 level 0.01322
> volume #8 step 2
> select #8
4 models selected
> select #8
4 models selected
> hide #!8 models
> select #8
4 models selected
> show #!8 models
> volume #8 style image
> volume #8 level -0.008343,0 level 0.0289,0.2923 level 0.4012,1
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> help volume
> help write
No help found for 'write'
> show #!8 target m
> select #10
2 models selected
> show #!10 target m
> show #!10 target m
> ~select #10
Nothing selected
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right "translate selected models"
> hide #!8 models
> show #!8 models
> hide #!10 models
> volume #8 style mesh
> volume #8 level -0.1955
> volume #8 style surface style image colorMode opaque8 showOutlineBox True
> imageMode "box faces"
Repeated keyword argument "style"
> volume #10 style surface style image
Repeated keyword argument "style"
> volume #8 style mesh region 0,0,0,255,255,255 step 1
> volume #8 level 0.01409
> volume #8 level 0.06801
> ui mousemode right clip
> ui mousemode right "translate selected models"
> volume #10 style mesh
> volume #10 change image level -0.01137,0 level 0.1181,0.8 level 0.4793,1
> volume #10 level 0.08544
> volume #8 level 0.1011
> volume #10 level -0.0921
> volume #10 level 0.01821
> volume #10 level 0.1259
> volume resample #10 onGrid #8
> hide #!11 models
> show #!11 models
> volume #11 level -0.05633
> volume #11 step 8
> volume #11 level -0.01313
> volume #11 step 4
> volume #11 step 1
> volume #11 level 0.07246
> volume #11 level 0.08787
> volume #11 level 0.02624
> save "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/J1010_resampled.mrc"
> models #11
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 38, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 157, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3910, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 296, in save_grid_data
if matching_grid_path(glist, path):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 338, in matching_grid_path
if realpath(gp) == rp:
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 396, in realpath
return abspath(path)
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
See log for complete Python traceback.
> save "/Users/gil/OneDrive -
> UHN/Work/RIS_AUFS/projects/BTB/KCTD/KCTD_G_protein_interactions/KCTD9_Cul3_em_rubinstein/cryoSPARC/12July2020_analysis/J1010_resampled.mrc"
> models #11
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 38, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 157, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3910, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 296, in save_grid_data
if matching_grid_path(glist, path):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 338, in matching_grid_path
if realpath(gp) == rp:
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 396, in realpath
return abspath(path)
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
See log for complete Python traceback.
> save /Users/gil/J1010_resampled.mrc models #11
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 38, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 157, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3910, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 296, in save_grid_data
if matching_grid_path(glist, path):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 338, in matching_grid_path
if realpath(gp) == rp:
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 396, in realpath
return abspath(path)
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
See log for complete Python traceback.
> save J1010_resampled_.mrc #11
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 157, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3910, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 296, in save_grid_data
if matching_grid_path(glist, path):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 338, in matching_grid_path
if realpath(gp) == rp:
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 396, in realpath
return abspath(path)
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
See log for complete Python traceback.
> ui tool show Log
> save /Users/gil/aaa.mrc models #11
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 38, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 157, in save
save_map(session, path, _name, **kw)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3910, in save_map
save_grid_data(grids, path, session, format_name, options)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 296, in save_grid_data
if matching_grid_path(glist, path):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 338, in matching_grid_path
if realpath(gp) == rp:
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 396, in realpath
return abspath(path)
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.0.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath
cwd = os.getcwd()
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.6.18
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro13,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
Boot ROM Version: 267.0.0.0.0
SMC Version (system): 2.37f24
Software:
System Software Overview:
System Version: macOS 10.15.5 (19F101)
Kernel Version: Darwin 19.5.0
Time since boot: 1 day 11:41
Graphics/Displays:
Intel Iris Graphics 550:
Chipset Model: Intel Iris Graphics 550
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1927
Revision ID: 0x000a
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (5)
comment:1 by , 5 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem saving map: No such file or directory |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
This error
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
says ChimeraX cannot find your current working directory which is set to your Desktop if you start ChimeraX by clicking its icon. Not sure why it can't find your Desktop, but probably related to macOS Catalina security. Check if macOS system preferences to allow Desktop access to ChimeraX is enabled, Security & Privacy / Files and Folders / UCSF ChimeraX / Desktop -> checked. Still I don't think that setting should cause this problem, and I tried unckecking it and restarting ChimeraX and it had no effect, ChimeraX could still read and write Desktop files. macOS Catalina security is just flakey.
One way to produce this error is start ChimeraX from a Terminal then delete the directory you started in. I doubt you did that.
The reason Python is trying to get the current directory is it is trying to expand "~" in some path. Not sure why Python does that when there is no "~" at the start of the path.
follow-up: 4 comment:4 by , 5 years ago
Thanks Tom - I'll try this.
Much appreciated.
Gil
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, July 13, 2020 1:22 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Prive, Gil - UHN Research <prive@uhnres.utoronto.ca>
Subject: [External] Re: [ChimeraX] #3501: Problem saving map: No such file or directory
#3501: Problem saving map: No such file or directory
-----------------------------------+-------------------------
Reporter: prive@… | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------+-------------------------
Comment (by Tom Goddard):
This error
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
says ChimeraX cannot find your current working directory which is set to
your Desktop if you start ChimeraX by clicking its icon. Not sure why it
can't find your Desktop, but probably related to macOS Catalina security.
Check if macOS system preferences to allow Desktop access to ChimeraX is
enabled, Security & Privacy / Files and Folders / UCSF ChimeraX / Desktop
-> checked. Still I don't think that setting should cause this problem,
and I tried unckecking it and restarting ChimeraX and it had no effect,
ChimeraX could still read and write Desktop files. macOS Catalina
security is just flakey.
One way to produce this error is start ChimeraX from a Terminal then
delete the directory you started in. I doubt you did that.
The reason Python is trying to get the current directory is it is trying
to expand "~" in some path. Not sure why Python does that when there is
no "~" at the start of the path.
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3501#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.
If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.
comment:5 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
If this os.getcwd() error is reported again I'll add some code on macOS after ChimeraX switches the current directory to ~/Desktop at startup to make sure os.getcwd() works, and if it fails issue a warning and revert the working directory to "/" or whatever the value was before switching to ~/Desktop.
I haven't been able to reproduce this error (except by deleting the directory ChimeraX starts in), so I don't want to add checking code with no ability to test.
Note:
See TracTickets
for help on using tickets.
Reported by Gil Privé