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Opened 3 years ago
Closed 3 years ago
#8185 closed defect (not a bug)
Unable to open file for writing
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: Windows-10-10.0.22000
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\sonom\\\Dropbox\\\0. Thesis\\\ChimeraX\\\Fig.4-3.cxs"
Opened cryosparc_P104_J52_005_volume_map.mrc as #1, grid size 300,300,300,
pixel 1.66, shown at level 0.446, step 1, values float32
Log from Fri Dec 2 21:31:43 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\sonom\Dropbox\0. Thesis\ChimeraX\overall_2.cxs" format
> session
Opened cryosparc_P104_J52_005_volume_map.mrc as #1, grid size 300,300,300,
pixel 1.66, shown at level 0.446, step 1, values float32
Log from Fri Nov 25 09:39:56 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/sonom/Dropbox/0. Thesis/4comp/a.cxs"
Opened cryosparc_P104_J52_005_volume_map.mrc as #1, grid size 300,300,300,
pixel 1.66, shown at level 0.446, step 1, values float32
Log from Fri Nov 25 09:09:12 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\sonom\\\Pictures\\\cryosparc_P104_J52_005_volume_map.mrc
Opened cryosparc_P104_J52_005_volume_map.mrc as #1, grid size 300,300,300,
pixel 1.66, shown at level 0.0241, step 2, values float32
> volume #1 step 1
> volume #1 level 0.4464
> open 7w0d
Summary of feedback from opening 7w0d fetched from pdb
---
note | Fetching compressed mmCIF 7w0d from
http://files.rcsb.org/download/7w0d.cif
7w0d title:
Dicer2-LoqsPD-dsRNA complex at mid-translocation state [more info...]
Chain information for 7w0d #2
---
Chain | Description
A F | Dicer-2, isoform A
B G | Loquacious, isoform D
C D | dsRNA
Non-standard residues in 7w0d #2
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> select #2/F
5340 atoms, 5440 bonds, 3 pseudobonds, 662 residues, 2 models selected
> delete #2/F
> delete #2/G
> hide cartoons
> hide atoms
> show cartoons
> ui mousemode right select
Drag select of 1664 residues, 2 pseudobonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,120.61,0,1,0,121.55,0,0,1,78.811
> view matrix models #2,1,0,0,120.01,0,1,0,122.57,0,0,1,103.18
> fitmap #2 inMap #1
Fit molecule 7w0d (#2) to map cryosparc_P104_J52_005_volume_map.mrc (#1) using
14865 atoms
average map value = 0.7528, steps = 224
shifted from previous position = 4.82
rotated from previous position = 56.4 degrees
atoms outside contour = 3802, contour level = 0.44642
Position of 7w0d (#2) relative to cryosparc_P104_J52_005_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.55469382 -0.82957605 -0.06417433 302.30786813
0.83188368 0.55449094 0.02256867 65.07028178
0.01686166 -0.06590428 0.99768347 114.54037193
Axis -0.05311184 -0.04864730 0.99740291
Axis point 89.04209017 322.69932257 0.00000000
Rotation angle (degrees) 56.39707194
Shift along axis 95.02128103
> fitmap #2 inMap #1
Fit molecule 7w0d (#2) to map cryosparc_P104_J52_005_volume_map.mrc (#1) using
14865 atoms
average map value = 0.7527, steps = 44
shifted from previous position = 0.0236
rotated from previous position = 0.0125 degrees
atoms outside contour = 3805, contour level = 0.44642
Position of 7w0d (#2) relative to cryosparc_P104_J52_005_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.55464853 -0.82960239 -0.06422527 302.32967764
0.83190982 0.55446016 0.02236014 65.12002937
0.01706033 -0.06583166 0.99768489 114.49000129
Axis -0.05294148 -0.04879569 0.99740472
Axis point 88.98633846 322.72017175 0.00000000
Rotation angle (degrees) 56.39963949
Shift along axis 95.00950974
> select #2
14865 atoms, 15393 bonds, 122 pseudobonds, 1666 residues, 4 models selected
> ~select #2
Nothing selected
> open 7V6B
7v6b title:
Structure of the Dicer-2-R2D2 heterodimer [more info...]
Chain information for 7v6b #3
---
Chain | Description
A | Dicer-2, isoform A
B | R2D2
> ui mousemode right select
Drag select of 1678 residues, 17 pseudobonds
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,129.24,0,1,0,14.532,0,0,1,178.45
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.64982,-0.64315,0.40507,339.4,-0.73022,0.38033,-0.56756,220.85,0.21097,-0.66461,-0.71679,404.15
> view matrix models
> #3,-0.89827,-0.31762,-0.3037,417.36,-0.099797,0.82047,-0.56291,105.08,0.42797,-0.47533,-0.7687,366.75
> view matrix models
> #3,-0.90441,0.0074647,-0.42659,401.83,0.26493,0.79356,-0.54779,62.569,0.33444,-0.60845,-0.71968,384.66
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.90441,0.0074647,-0.42659,413.32,0.26493,0.79356,-0.54779,101.14,0.33444,-0.60845,-0.71968,381.92
> view matrix models
> #3,-0.90441,0.0074647,-0.42659,392.38,0.26493,0.79356,-0.54779,108.31,0.33444,-0.60845,-0.71968,390.74
> view matrix models
> #3,-0.90441,0.0074647,-0.42659,385.51,0.26493,0.79356,-0.54779,132.23,0.33444,-0.60845,-0.71968,375.26
> view matrix models
> #3,-0.90441,0.0074647,-0.42659,390.15,0.26493,0.79356,-0.54779,117.19,0.33444,-0.60845,-0.71968,386.42
> select #3/A:548-2000
8168 atoms, 8367 bonds, 10 pseudobonds, 1001 residues, 2 models selected
> hide #3/A:548-2000
> hide #3/A:548-2000 target c
> hide #3/B:1-548 target c
> fitmap #3 inMap #1
Fit molecule 7v6b (#3) to map cryosparc_P104_J52_005_volume_map.mrc (#1) using
13633 atoms
average map value = 0.1782, steps = 236
shifted from previous position = 21.1
rotated from previous position = 17.4 degrees
atoms outside contour = 11551, contour level = 0.44642
Position of 7v6b (#3) relative to cryosparc_P104_J52_005_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.98921566 -0.00367767 -0.14642015 375.82554907
0.07672957 0.83851641 -0.53944675 145.16096648
0.12475960 -0.54486393 -0.82919138 403.24215251
Axis -0.01914864 -0.95856676 0.28422366
Axis point 171.17723626 0.00000000 237.05401539
Rotation angle (degrees) 171.86820302
Shift along axis -31.73206514
> save "C:/Users/sonom/Dropbox/0. Thesis/4comp/a.cxs"
> transparency #1 50 target s
> show #3 target c
> select #3
13633 atoms, 13918 bonds, 17 pseudobonds, 1678 residues, 2 models selected
> ~select #3
Nothing selected
> hide target p
> set bgColor white
> lighting full
> lighting full
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> color #2,#3 lightgray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> ui tool show "Side View"
> save "C:/Users/sonom/Dropbox/0. Thesis/4comp/a.cxs"
——— End of log from Fri Nov 25 09:09:12 2022 ———
opened ChimeraX session
> color #2/A:1656-2000 #FF9999
> color #2/A:1017-1190 #F2DAA9
> color #2/B:1-500 #241CE8
> color #2/A:1191-1259,1363-1409 #CCFF99
> color #2/A:1410-1655 #99FF33
> color #2/A:1-218 #99DDFF
> color #2/A:346-508,219-232 #33BBFF
> color #2/A:233-345 #CCEEFF
> color #2/A:508-548 #667FFF
> color #2/A:720-855 #BB99FF
> color #2/A:855-982 #EE99FF
> color #2/A:983-1017 #FF66CC
> color #2/A:657-719 #E6E6E6
> color #2/A:554-656 #999999
> color #2/A:1260-1362 #E6FFCC
> select #2/B
144 atoms, 146 bonds, 16 residues, 1 model selected
> delete #2/B
> color #3/A:1656-2000 #FF9999
> color #3/B:165-330 #E68A5C
> color #3/B:69-164 #FFAA00
> color #3/A:1017-1190 #F2DAA9
> color #3/B:1-69 #FFD500
> color #3/A:1191-1259,1363-1409 #CCFF99
> color #3/A:1410-1655 #99FF33
> color #3/A:1-218 #99DDFF
> color #3/A:346-508,219-232 #33BBFF
> color #3/A:233-345 #CCEEFF
> color #3/A:508-548 #667FFF
> color #3/A:720-855 #BB99FF
> color #3/A:855-982 #EE99FF
> color #3/A:983-1017 #FF66CC
> color #3/A:657-719 #E6E6E6
> color #3/A:554-656 #999999
> color #3/A:1260-1362 #E6FFCC
> color #2/C,D dim gray
> select #2/C,D tar a
Expected a keyword
> show #2/C,D target a
> nucleotides atoms
> style nucleic stick
Changed 2203 atom styles
> nucleotides fill
> style nucleic stick
Changed 2203 atom styles
> nucleotides ladder
> hide #!1 models
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> show #!1 models
> graphics silhouettes true
> lighting shadows false
> save C:\Users\sonom\Dropbox\dimer_overall.png pixelSize 0.1
> hide #!1 models
> show #!1 models
> color #1 white target s
> transparancy #1 40 tar s
Unknown command: transparancy #1 40 tar s
> transparency #1 40 target s
> transparency #1 80 target s
> transparency #1 70 target s
> save C:\Users\sonom\Dropbox\dimer_overall.png pixelSize 0.1
> select #3/A:548-2000
8168 atoms, 8367 bonds, 10 pseudobonds, 1001 residues, 2 models selected
> select #3/A:548-1040, 1060-2000
8149 atoms, 8348 bonds, 9 pseudobonds, 999 residues, 2 models selected
> select #3/A:548-1094, 1120-2000
7960 atoms, 8152 bonds, 9 pseudobonds, 976 residues, 2 models selected
> hide #3/A:548-1094, 1120-2000
> hide #3/A:548-1094, 1120-2000 target c
> select #3/B:1-200
614 atoms, 616 bonds, 2 pseudobonds, 77 residues, 2 models selected
> select #3/B:1-215
705 atoms, 711 bonds, 2 pseudobonds, 87 residues, 2 models selected
> hide #3/B:1-200
> hide #3/B:1-200 target c
> hide sel
> hide sel target c
> open 7v6b
7v6b title:
Structure of the Dicer-2-R2D2 heterodimer [more info...]
Chain information for 7v6b #4
---
Chain | Description
A | Dicer-2, isoform A
B | R2D2
> color #4/A:1656-2000 #FF9999
> color #4/B:165-330 #E68A5C
> color #4/B:69-164 #FFAA00
> color #4/A:1017-1190 #F2DAA9
> color #4/B:1-69 #FFD500
> color #4/A:1191-1259,1363-1409 #CCFF99
> color #4/A:1410-1655 #99FF33
> color #4/A:1-218 #99DDFF
> color #4/A:346-508,219-232 #33BBFF
> color #4/A:233-345 #CCEEFF
> color #4/A:508-548 #667FFF
> color #4/A:720-855 #BB99FF
> color #4/A:855-982 #EE99FF
> color #4/A:983-1017 #FF66CC
> color #4/A:657-719 #E6E6E6
> color #4/A:554-656 #999999
> color #4/A:1260-1362 #E6FFCC
> matchmaker #4 ro #2/A:1-548
Expected a keyword
> matchmaker #4 to #2/A:1-548
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7w0d, chain A (#2) with 7v6b, chain A (#4), sequence alignment
score = 2528.9
RMSD between 241 pruned atom pairs is 1.003 angstroms; (across all 495 pairs:
9.444)
> delete #4/A
> delete #4/B:1:215
> delete #4/B:1:215 tar a
Expected a keyword
> select #4/B:1:215 t
Expected a keyword
> select #4/B:1:215
Nothing selected
> volume style mesh
> graphics silhouettes false
> set bgColor black
> select #4/B:1:215
Nothing selected
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> ui mousemode right select
Drag select of 1 cryosparc_P104_J52_005_volume_map.mrc , 44 residues
> select clear
> hide #!1 models
Drag select of 68 residues
Drag select of 54 residues, 1 pseudobonds
Drag select of 64 residues, 2 pseudobonds
> select #4/B:1:215
Nothing selected
> select #4/B:1:215
Nothing selected
> select #4/C:1:215
Nothing selected
> select #4/V:1:215
Nothing selected
Drag select of 79 residues, 2 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 2 residues
> delete atoms sel
> delete bonds sel
Drag select of 11 residues
> delete atoms sel
> delete bonds sel
> show #!1 models
> show #!2 models
> show #!3 models
> select clear
> save C:\Users\sonom\Dropbox\dimer_overall_1.png pixelSize 0.1
> save C:\Users\sonom\Dropbox\dimer_overall_2.png pixelSize 0.1
> volume style image
> volume style mesh
> volume style surface
> ui tool show "Side View"
> save C:\Users\sonom\Dropbox\helicase.png pixelSize 0.1
> viewname hel
Unknown command: viewname hel
> view name hel
> save C:\Users\sonom\Dropbox\dimer_overall_1.png pixelSize 0.1
> save C:\Users\sonom\Dropbox\dimer_overall_2.png pixelSize 0.1
> save "C:/Users/sonom/Dropbox/0. Thesis/4comp/overall.cxs"
> show #2 target c
> select #2
14721 atoms, 15247 bonds, 122 pseudobonds, 1650 residues, 4 models selected
> select #3
13633 atoms, 13918 bonds, 17 pseudobonds, 1678 residues, 2 models selected
> select #2
14721 atoms, 15247 bonds, 122 pseudobonds, 1650 residues, 4 models selected
> ~select #2
Nothing selected
> select #3
13633 atoms, 13918 bonds, 17 pseudobonds, 1678 residues, 2 models selected
> show #2 target c
> select clear
> open 7v6b
7v6b title:
Structure of the Dicer-2-R2D2 heterodimer [more info...]
Chain information for 7v6b #5
---
Chain | Description
A | Dicer-2, isoform A
B | R2D2
> matchmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7v6b, chain A (#3) with 7v6b, chain A (#5), sequence alignment
score = 8614.9
RMSD between 1496 pruned atom pairs is 0.000 angstroms; (across all 1496
pairs: 0.000)
> hide target p
> color #5 target c
> color #5 white
> transparency #5 50
> transparency #5 50 target c
> hide #5/A:1-548
> hide #5/A:1-548 target c
> hide #5/B:215-548 target c
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> save "C:/Users/sonom/Dropbox/0. Thesis/4comp/overall_2.cxs"
——— End of log from Fri Nov 25 09:39:56 2022 ———
opened ChimeraX session
> set bgColor white
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> color #1 gray
> view
> ui tool show "Side View"
> select D:1-43
Expected an objects specifier or a keyword
> select #1/D:1-43
Nothing selected
> select #2/D:1-43
916 atoms, 1023 bonds, 43 residues, 1 model selected
> select #2/D:1-23,43-100
701 atoms, 781 bonds, 33 residues, 1 model selected
> hide sel #2/D:1-23,43-100 tar c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2/D:1-23,43-100 target c
> hide #2/D:1-23,43-100 target a
> hide #2/D:1-26,43-100 target a
> hide #2/C:1-26,43-100 target a
> hide #2/C:1-26,43-100 target a
> hide #2/C:26-43 target a
> undo
> hide #2/C:26-53, 1-10 target a
> hide #2/C:26-53, 1-10 target c
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> save "C:/Users/sonom/Dropbox/0. Thesis/ChimeraX/Fig.4-2.cxs"
> view sel
> ui mousemode right select
Drag select of 5 residues
> hide sel target c
Drag select of 3 residues
> hide sel target c
> save "C:/Users/sonom/Dropbox/0. Thesis/ChimeraX/Fig.4-2.cxs"
> view name front
> view name front
> save C:\Users\sonom\Dropbox\Fig4-3.png pixelSize 0.1
> save C:\Users\sonom\Dropbox\Fig4-3.png pixelSize 0.1
> view name 180
> view front
> save C:\Users\sonom\Dropbox\Fig4-3_1.png pixelSize 0.1
> select up
68 atoms, 70 bonds, 8 residues, 1 model selected
> select #3
13633 atoms, 13918 bonds, 17 pseudobonds, 1678 residues, 2 models selected
> ~select #3
Nothing selected
> view name up_interface1
> view name up_interface2
> view 180
> view front
> view name up_interface2
> view front
> view name up_interface2
> view name up_interface
> view name up_interface1
> view name up_interface2
> view 180
> view name up_interface3
> save C:\Users\sonom\Dropbox\interface_3.png pixelSize 0.1
> view up_interface2
> save C:\Users\sonom\Dropbox\interface_2.png pixelSize 0.1
> view up_interface1
> save C:\Users\sonom\Dropbox\interface_1.png pixelSize 0.1
> hide #!1 models
> show #!1 models
> view list
Named views: 180, front, hel, up_interface, up_interface1, up_interface2,
up_interface3
> view 180
> hide #!1 models
> graphics silhouettes true
> save C:\Users\sonom\Dropbox\overall_180.png pixelSize 0.1
> view front
> save C:\Users\sonom\Dropbox\overall_180_front.png pixelSize 0.1
> show #!1 models
> save C:\Users\sonom\Dropbox\overall_den.png pixelSize 0.1
> view name up_interface2
> show #!1 models
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> save C:\Users\sonom\Dropbox\interface_1.png pixelSize 0.1
> save C:\Users\sonom\Dropbox\interface_2.png pixelSize 0.1
> save C:\Users\sonom\Dropbox\interface_3.png pixelSize 0.1
> save C:\Users\sonom\Dropbox\interface_3.png pixelSize 0.05
> lighting shadows true
> lighting shadows false
> save C:\Users\sonom\Dropbox\interface_1.png pixelSize 0.05
Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 1 maps.
> save C:\Users\sonom\Dropbox\interface_2.png pixelSize 0.05
> save "C:/Users/sonom/Dropbox/0. Thesis/ChimeraX/Fig.4-3.cxs"
——— End of log from Fri Dec 2 21:31:43 2022 ———
opened ChimeraX session
> open "C:/Users/sonom/Dropbox/0.
> Thesis/ChimeraX/cryosparc_P53_J141_008_volume_map.mrc"
Opened cryosparc_P53_J141_008_volume_map.mrc as #6, grid size 300,300,300,
pixel 1.33, shown at level 0.0704, step 2, values float32
> select #6
4 models selected
> ui mousemode right "translate selected models"
> view list
Named views: 180, front, hel, up_interface, up_interface1, up_interface2,
up_interface3
> view 180
> view matrix models #6,1,0,0,23.312,0,1,0,30.22,0,0,1,37.627
> view matrix models #6,1,0,0,35.952,0,1,0,46.781,0,0,1,56.165
> view matrix models #6,1,0,0,40.978,0,1,0,48.363,0,0,1,57.252
> hide #!3 models
> hide #!2 models
> hide #!4 models
> fitmap #6 inMap #1
Fit map cryosparc_P53_J141_008_volume_map.mrc in map
cryosparc_P104_J52_005_volume_map.mrc using 33733 points
correlation = 0.9152, correlation about mean = 0.8143, overlap = 6909
steps = 208, shift = 8.42, angle = 15.2 degrees
Position of cryosparc_P53_J141_008_volume_map.mrc (#6) relative to
cryosparc_P104_J52_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.97155126 0.23334827 -0.04045656 16.58573885
-0.23647040 0.96522155 -0.11148588 120.26333175
0.01303451 0.11788103 0.99294218 29.83743977
Axis 0.43643430 -0.10178163 -0.89396063
Axis point 505.05365968 -68.74649870 0.00000000
Rotation angle (degrees) 15.23470740
Shift along axis -31.67550927
> transparency #6 30
> color #6 gray
> volume #6 step 1
> volume #6 level 0.411
> show #!2 models
> show #!3 models
> color #6 lightgray
> show #!4 models
> select up
42713 atoms, 43822 bonds, 5096 residues, 10 models selected
> color #6 lgray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #6 gray
> color #6 dark gray
> transparency #6 70
> transparency #6 60
> ui mousemode right select
> select clear
> volume #6 level 0.4169
> view 180
> view front
> view front
> view 180
> view front
> save "C:/Users/sonom/Dropbox/0. Thesis/ChimeraX/Fig.4-4_new.cxs"
> view up_interface
> save C:\Users\sonom\Dropbox\Fig4-5_interface_1.png pixelSize 0.05
> view list
Named views: 180, front, hel, up_interface, up_interface1, up_interface2,
up_interface3
> view up_interface2
> view up_interface
> view up_interface1
> view up_interface3
> ui tool show "Side View"
> save C:\Users\sonom\Dropbox\Fig4-5_interface_3.png pixelSize 0.05
> view up_interface1
> view up_interface
> view up_interface2
> view up_interface1
Drag select of 56 residues, 6 cryosparc_P53_J141_008_volume_map.mrc
> select clear
> ui mousemode right translate
> volume #1 change image level -0.01693,0 level 0.02374,0.8 level 2.909,1
> volume #1 level 0.7
> select #3/A:1-218
1665 atoms, 1695 bonds, 211 residues, 1 model selected
> hide #3/A:1-218 target c
> volume #1 level 0.6431
> select #3/A:500-548 tar c
Expected a keyword
> select #3/A:500-548
337 atoms, 342 bonds, 39 residues, 1 model selected
> select #3/A:530-548
81 atoms, 81 bonds, 9 residues, 1 model selected
> select #3/A:510-548
257 atoms, 260 bonds, 29 residues, 1 model selected
> select #3/A:508-548
274 atoms, 277 bonds, 31 residues, 1 model selected
> hide #3/A:508-548 target c
> save "C:/Users/sonom/Dropbox/0. Thesis/ChimeraX/Fig.4-4_new.cxs"
Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 2 maps.
> hide #!4 models
> hide #!3 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> color zone #6 near #2 distance 7.97
> hide #!2 models
> show #!4 models
> color zone #6 near #4 distance 7.97
> show #!2 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> hide #!4 models
> color zone #6 near #2 distance 7.97
> save #2 initial.pdb
Cannot determine format for '#2'
> save initial.pdb #2,4
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'initial.pdb' for writing
OSError: Unable to open file 'initial.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> save initial.pdb #2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'initial.pdb' for writing
OSError: Unable to open file 'initial.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> select #3
13633 atoms, 13918 bonds, 17 pseudobonds, 1678 residues, 2 models selected
> ~select #3
Nothing selected
> save initial.pdb #2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'initial.pdb' for writing
OSError: Unable to open file 'initial.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> save heterodimer-1.pdb #2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'heterodimer-1.pdb' for writing
OSError: Unable to open file 'heterodimer-1.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> select #2
14721 atoms, 15247 bonds, 122 pseudobonds, 1650 residues, 4 models selected
> save heterodimer-1.pdb #2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'heterodimer-1.pdb' for writing
OSError: Unable to open file 'heterodimer-1.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> hide #!6 models
> show #!6 models
> hide #!2 models
> ~select #2
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> save heterodimer-1.pdb #2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'heterodimer-1.pdb' for writing
OSError: Unable to open file 'heterodimer-1.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 Pro (Build 22000)
Memory: 17,081,131,008
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5600X 6-Core Processor
OSLanguage: ja-JP
Locale: ('ja_JP', 'cp932')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unable to open file for writing |
comment:2 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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User probably in non-writable folder