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Opened 4 years ago
Closed 4 years ago
#4673 closed defect (duplicate)
Error in toolshed error message
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "P:/PhD/RNase P Paper/session files/NSMB_revised/4a.cxs"
Log from Wed Apr 28 18:49:38 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "P:\PhD\RNase P Paper\session files\NSMB\4a.cxs" format session
Log from Tue Mar 9 15:48:29 2021UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "P:\PhD\RNase P Paper\Models\newMRPPapo-active.cxs" format session
Log from Fri Jan 8 13:03:21 2021UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "W:\abhatta1\PhD\RNase P Paper\Models\apo-MRPP3-tRNA-clashes.cxs"
> format session
Log from Wed Nov 11 16:27:09 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "P:\PhD\RNase P Paper\Models\apo-MRPP3-tRNA-clashes.cxs" format session
Log from Wed Oct 28 14:12:17 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "P:/PhD/RNase P Paper/Models/apo-MRPP3-tRNA-clashes.cxs"
Log from Mon Oct 26 11:38:39 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "P:/PhD/RNase P Paper/Models/apo-MRPP3-tRNA-clashes.cxs"
Log from Wed Oct 21 14:36:04 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "P:/PhD/RNase P Paper/Models/apo_MRPP3_w_tRNA.pdb"
Chain information for apo_MRPP3_w_tRNA.pdb #1
---
Chain | Description
A | No description available
T | No description available
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> color /A:114-134 #6B8E23
> color /A:135-329 #228B22
> color /A:330-360 #9ACD32
> color /A:542-583 #9ACD32
> color /A:361-541 #3CB371
> color /T #B22222
> show /T atoms
> nucleotides /T stubs
> turn y 90
> turn x 90
> turn x -90
> turn z -90
> turn z 90
> turn y 40
> turn y -40
> turn y 60
> turn y -60
> turn x -90
> turn x 90
> turn x -50
> turn x 50
> view /A
> view clip false
> view /A
> ui tool show "Side View"
> lighting full
> lighting simple
> lighting shadows true
> lighting soft
> lighting soft
> save C:\Users\abhatta1\Desktop\image6.png supersample 3
> save "P:/PhD/RNase P Paper/Models/apo-MRPP3-tRNA-clashes.cxs"
opened ChimeraX session
> open "P:/PhD/RNase P
> Paper/RNAseP_HH_20200924_real_space_refined_nohydrogens_MRPP3-tRNA.pdb"
Chain information for
RNAseP_HH_20200924_real_space_refined_nohydrogens_MRPP3-tRNA.pdb #2
---
Chain | Description
E | No description available
T | No description available
> hide #2 all
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!2
> hide #2
> hide #2 atoms
> hide #2 ribbons
> show #2/E ribbons
> graphics selection color #ff006a width 2
> select /E
3812 atoms, 3897 bonds, 1 model selected
> color sel #000000
> color sel #ffffff
> transparency sel 100
> transparency sel 100 ribbons
> save C:\Users\abhatta1\Desktop\image31.png supersample 3
> select down
3812 atoms, 3897 bonds, 1 model selected
> graphics selection color #000000 width 3
> graphics selection color #000000 width 1
> transparency sel 900 ribbons
> transparency sel 90 ribbons
> save C:\Users\abhatta1\Desktop\image32.png supersample 3
> graphics silhouettes false
> save C:\Users\abhatta1\Desktop\image33.png supersample 3
> graphics selection color #3bc464
> save C:\Users\abhatta1\Desktop\image34.png supersample 3
> turn x 40
> save C:\Users\abhatta1\Desktop\image35.png supersample 3
> turn x 40
> save C:\Users\abhatta1\Desktop\image36.png supersample 3
> save "P:/PhD/RNase P Paper/Models/apo-MRPP3-tRNA-clashes.cxs"
opened ChimeraX session
> select clear
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T atoms
> hide /T ribbons
> color /T byhetero
> hide #1 ribbons
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #3bc464
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> transparency #2 0
> transparency #2 0 ribbons
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show/T ribbon
Unknown command: show/T ribbon
> color /T byhetero
> show #1/T atoms
> nucleotides #1/T stubs
> show /T ribbons
> color /T byhetero
> color #1/T #B22222
> hide #2/T
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show /T ribbons
> color /T byhetero
> hide #1 ribbons
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #3bc464
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> turn x 40
> hide /T
> hide #2/T ribbons
> show #1/T ribbons
> show #1/T atoms
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> hide all ribbons
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show /T ribbons
> color /T byhetero
> hide #1 ribbons
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #3bc464
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> turn x 40
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> hide all ribbons
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> show #2/E ribbons
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show #1/T ribbons
> color #1/T byhetero
> hide #1 ribbons
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #3bc464
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> turn x 40
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> hide all ribbons
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> show #2/E ribbons
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show #1/T ribbons
> color #1/T byhetero
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #3bc464
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> turn x 40
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> hide all ribbons
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> show #2/E ribbons
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show #1/T ribbons
> color #1/T byhetero
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #000000 width 2
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> save C:\Users\abhatta1\Desktop\image42.png supersample 3
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> hide all ribbons
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> show #2/E ribbons
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show #1/T ribbons
> color #1/T byhetero
> show #1/A ribbons
> color #1/A #ffffff ribbons
> transparency #1/A 90 ribbons
> graphics silhouettes false
> graphics selection color #df03fc width 1.5
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> save C:\Users\abhatta1\Desktop\image43.png supersample 3
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> hide all ribbons
> color #2/E:114-134 #6B8E23
> color #2/E:135-329 #228B22
> color #2/E:330-360 #9ACD32
> color #2/E:542-583 #9ACD32
> color #2/E:361-541 #3CB371
> show #2/E ribbons
> color #1/T #B22222
> show #1/T atoms
> nucleotides #1/T stubs
> show #1/T ribbons
> color #1/T byhetero
> show #1/A ribbons
> color #1/A #b5b5b5 ribbons
> transparency #1/A 80 ribbons
> graphics silhouettes false
> graphics selection color #000000 width 1
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> view #1/A
> save C:\Users\abhatta1\Desktop\image44.png supersample 3
> view #1/A
> save C:\Users\abhatta1\Desktop\image45.png supersample 3
> turn y 40
> turn y -40
> turn x 40
> save C:\Users\abhatta1\Desktop\image46.png supersample 3
> save "P:/PhD/RNase P Paper/Models/apo-MRPP3-tRNA-clashes.cxs"
opened ChimeraX session
> transparency #1 50
> transparency #1 30
> transparency #1 50 ribbons
> transparency #1 30 ribbons
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting soft
> transparency #1 0 ribbons
> transparency #1 30 ribbons
> transparency #1 20 ribbons
> save C:\Users\abhatta1\Desktop\image29.png supersample 3
> cartoon style protein modeHelix tube
> cartoon style protein modeHelix tube radius 2 sides 24
> cartoon style protein modeHelix tube radius 1 sides 10
> select clear
> cartoon style protein modeHelix tube radius 1 sides 15
Invalid "sides" argument: Expected an even integer
> cartoon style protein modeHelix tube radius 1 sides 16
> cartoon style protein modeHelix tube radius 1 sides 8
> cartoon style protein modeHelix tube radius 1 sides 24
> cartoon style protein modeHelix tube radius 1.5 sides 24
> select #1
4399 atoms, 4441 bonds, 18 pseudobonds, 3 models selected
> save C:\Users\abhatta1\Desktop\image30.png supersample 3
> select #1/A
2985 atoms, 2859 bonds, 16 pseudobonds, 3 models selected
> save C:\Users\abhatta1\Desktop\image31.png supersample 3
> save "W:/abhatta1/PhD/RNase P Paper/Models/apo-MRPP3-tRNA-clashes.cxs"
opened ChimeraX session
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select clear
> graphics silhouettes true
> color #1/A grey
> transparency #1/A 0
> transparency #1/A 0 cartoons
> color #1/A:114-134 #6B8E23
> color #1/A:135-329 #228B22
> color #1/A:330-360 #9ACD32
> color #1/A:542-583 #9ACD32
> color #1/A:361-541 #3CB371
> select clear
> transparency #1/T 50
> transparency #1/T 70
> transparency #1/T 70 cartoons
> transparency #1/T 80 cartoons
> color #1/T white
> color #1/T grey
> color #1/T #eeeeee
> hide #!1 models
> show #!2 models
> show #2/T
> hide #2/T atoms
> show #2/T cartoons
> show #2/T atoms
> nucleotides style stubs
Missing or invalid "representation" argument: Should be one of 'atoms',
'fill', 'ladder', 'slab', 'stubs', or 'tube/slab'
> nucleotides stubs
> color #2/T #B22222
> show #2/A-D
> show #2/A-D ribbons
> ui tool show "Side View"
> show #2/A ribbons
> open "P:/PhD/RNase P
> Paper/Models/RNAseP_HH_20200924_real_space_refined_nohydrogens.pdb"
Chain information for RNAseP_HH_20200924_real_space_refined_nohydrogens.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
E | No description available
F | No description available
T | No description available
> hide #3 atoms
> show #3 ribbons
> hide #!2 models
> color #3/E:114-134 #6B8E23
> color #3/E:135-329 #228B22
> color #3/E:330-360 #9ACD32
> color #3/E:542-583 #9ACD32
> color #3/E:361-541 #3CB371
> show #3/E ribbons
> color #3/T #B22222
> show #3/T atoms
> nucleotides #3/T stubs
> show #3/T ribbons
> color #3/F:39-174 #00CED1
> color #3/F:175-202 #87CEFA
> color #3/F:203-385 #1E90FF
> transparency #3/F 90
> transparency #3/F 90 ribbons
> color #3/A #D3D3D3
> color #3/B #A9A9A9
> color #3/C #808080
> color #3/D #778899
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> cartoon style protein modeHelix tube radius 2 sides 24
> cartoon style protein modeHelix tube radius 1 sides 24
> cartoon style protein modeHelix tube radius 1.5 sides 24
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> save C:\Users\abhatta1\Desktop\image13.png supersample 3
> hide #!1 models
> show #!3 models
> save C:\Users\abhatta1\Desktop\image14.png supersample 3
> save "P:/PhD/RNase P Paper/Models/newMRPPapo-active.cxs"
opened ChimeraX session
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> open "P:/PhD/RNase P Paper/Models/RNAseP_withMg.pdb"
Summary of feedback from opening P:/PhD/RNase P Paper/Models/RNAseP_withMg.pdb
---
warning | Ignored bad PDB record found on line 17451
END
Chain information for RNAseP_withMg.pdb #4
---
Chain | Description
A B D | No description available
C | No description available
E | No description available
F | No description available
T | No description available
> hide #4 atoms
> hide #!4 models
> show #!1 models
> hide #!1 models
> color #4 magenta
> show #!4 models
> hide #!4 models
> show #4/E:1001-1101 atoms
> show #!4 models
> hide #!4 models
> open "P:/PhD/RNase P Paper/Models/RNAseP_wMg_resampledto4xgl.pdb"
Chain information for RNAseP_wMg_resampledto4xgl.pdb #5
---
Chain | Description
A | No description available
B D | No description available
C | No description available
E | No description available
F | No description available
T | No description available
> select up
Nothing selected
> select up
Nothing selected
> hide #5 atoms
> color #5 magenta
> show #5/E:1001-1101 atoms
> hide #!5 models
> hide #!2 models
> show #!1 models
> show #!5 models
> transparency #5 90 atoms
> hide #4-5:1101 atoms
> hide /T atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> graphics silhouettes width 1.5
> save "P:/PhD/RNase P Paper/session files/NSMB/4a.cxs"
> save 4a1.png pixelSize 0.03 supersample 3
> hide #!5 models
> hide #!1 models
> show #!4 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> graphics silhouettes width 1.5
> save 4a1.png pixelSize 0.03 supersample 3
> save 4a2.png pixelSize 0.03 supersample 3
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> save 4a2.png pixelSize 0.03 supersample 3
> graphics silhouettes width 2
> save 4a1.png pixelSize 0.03 supersample 3
> hide #!5 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #3/A-D
> hide #3/A-D ribbons
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save 4a1.png pixelSize 0.03 supersample 3
> hide #!1 models
> hide #!5 models
> show #!2 models
> show #!3 models
> show #!4 models
> save 4a2.png pixelSize 0.03 supersample 3
> save "P:/PhD/RNase P Paper/session files/NSMB/4a.cxs"
opened ChimeraX session
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> color #1/T #999999
> color #1/T #888888
> color #1/T #666666
> save 4a1.png pixelSize 0.03 supersample 3
> hide #!1 models
> hide #!5 models
> show #!2 models
> show #!3 models
> show #!4 models
> save 4a2.png pixelSize 0.03 supersample 3
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> save 4a1.png pixelSize 0.03 supersample 3
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> save 4a1.png pixelSize 0.03 supersample 3
> hide #!1 models
> hide #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> select down
Nothing selected
> save 4a2.png pixelSize 0.03 supersample 3
> save "P:/PhD/RNase P Paper/session files/NSMB_revised/4a.cxs"
opened ChimeraX session
> view name fig
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> transparency all 0 ribbons
> nucleotides atoms
> show #1/T atoms
> ui tool show "Side View"
> clashes #1/T:-2-7,58-66 restrict #1/A select true reveal true radius 1
401 clashes
> clashes #1/T:-2-7,58-66 restrict #1/A reveal true radius 1 intraModel true
> interModel false intraMol false intraRes false
401 clashes
> clashes #1/T:-2-7,58-66 restrict #1/A reveal true radius 0.5 intraModel true
> interModel false intraMol false intraRes false
401 clashes
> view fig
> save apo-clash.png supersample 3 pixelSize 0.01
> save apo-clash.png supersample 3 pixelSize 0.03
> turn y -90
> turn y 90
> turn x 90
> turn x -90
> turn z 90
> turn z -90
> turn x 9
> turn x -9
> turn y -45
> turn y 45
> turn y -4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y 4
> turn y -48
> turn y -4
> view fig
> view turn x 10
Expected an objects specifier or a view name or a keyword
> turn x 10
> turn x 10
> turn y -45
> turn y 45
> 45
Unknown command: 45
> turn y 45
> select clear
> view fig
> turn y 45
> turn y 15
> turn x -15
> turn x 15
> turn z 15
> turn z 15
> turn z 15
> turn y 10
> turn y -20
> turn y 10
> turn x 15
> turn x -15
> turn x -15
> select clear
> nucleotides #!1 tube/slab shape muffler
> nucleotides #!1 stubs
> nucleotides #!1 ladder
> save apo-clash2.png supersample 3 pixelSize 0.03
> save apo-clash2.png pixelSize 0.05 supersample 3
> view fig
> save apo-clash.png pixelSize 0.05 supersample 3
> save "P:/PhD/RNase P Paper/session files/NSMB_revised/S7.cxs"
> close session
> open "P:/PhD/RNase P Paper/mtRNaseP_refine51_final_noH_c.pdb"
Summary of feedback from opening P:/PhD/RNase P
Paper/mtRNaseP_refine51_final_noH_c.pdb
---
warning | Ignored bad PDB record found on line 15091
END
Chain information for mtRNaseP_refine51_final_noH_c.pdb #1
---
Chain | Description
A B C D | No description available
E | No description available
F | No description available
T | No description available
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> color /A #D3D3D3
> color /B #A9A9A9
> color /C #808080
> color /D #778899
> color /F:39-174 #00CED1
> color /F:175-202 #87CEFA
> color /F:203-385 #1E90FF
> color /E:114-134 #6B8E23
> color /E:135-329 #228B22
> color /E:330-360 #9ACD32
> color /E:542-583 #9ACD32
> color /E:361-541 #3CB371
> color /T #B22222
> show /T atoms
> style stick
Changed 15083 atom styles
> color all byhetero
> nucleotides stubs
> nucleotides tube/slab shape muffler
> lighting simple
> lighting shadows true
> lighting flat
> lighting soft
> nucleotides stubs
> hide /A-E ribbons, atoms, pbonds
> coulombic /F
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /F LEU 385 OXT
> coulombic /F:175-400
> hide /F:1-170 ribbons
> hide /T atoms
> turn y 90
> turn y -90
> turn y -90
> turn y 90
> coulombic /F:175-400 range -5,5
> coulombic /F:175-400 range -7,7
> coulombic /F:175-400 range -20,20
> coulombic /F:175-400 range -5,5
> coulombic /F:175-400 range -10,10
> coulombic /F:175-400 range -8,8
> show /T atoms
> coulombic /F:175-400 range -9,9
> coulombic /F:175-400 range -10,10
> coulombic /F:175-400 range -5,5
> coulombic /F:175-400 range -1,1
> coulombic /F:175-400 range -5,5
> coulombic /F:175-400 range -10,10
> transparency all 60 surfaces
> coulombic /F:175-400 range -5,5
> transparency all 60 surfaces
> coulombic /F:175-400 range -10,10
> save mtase_surfacecharge.png pixelSize 0.03 supersample 3
> save mtase_surfacecharge.png pixelSize 0.05 supersample 3
> turn y -45
> turn y 45
> turn y 45
> turn y 5
> turn y -5
> turn y -45
> turn x -45
> turn x 45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x -45
> turn x 90
> turn x -90
> turn x 45
> turn y 45
> save mtase_surfacecharge_side.png pixelSize 0.05 supersample 3
> turn y 45
> save "P:/PhD/RNase P Paper/session files/NSMB_revised/s5newa.cxs"
> close session
> open "P:/PhD/RNase P Paper/test.pdb"
Summary of feedback from opening P:/PhD/RNase P Paper/test.pdb
---
warning | Ignored bad PDB record found on line 15091
END
Chain information for test.pdb #1
---
Chain | Description
A B C D | No description available
E | No description available
F | No description available
T | No description available
> set bgColor white
> show all cartoons
> lighting soft
> graphics silhouettes true
> hide all atoms
> color /A #D3D3D3
> color /B #A9A9A9
> color /C #808080
> color /D #778899
> color /F:39-174 #00CED1
> color /F:175-202 #87CEFA
> color /F:203-385 #1E90FF
> color /E:114-134 #6B8E23
> color /E:135-329 #228B22
> color /E:330-360 #9ACD32
> color /E:542-583 #9ACD32
> color /E:361-541 #3CB371
> color /T #B22222
> show /T atoms
> style stick
Changed 15083 atom styles
> color all byhetero
> nucleotides stubs
> hbonds /C:107 restrict /T
0 hydrogen bonds found
> hbonds /C:107 restrict /T relax true distSlop 0.5 angleSlop 45
0 hydrogen bonds found
> addH
Unknown command: addH
> toolshed show
Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished
session=self.session)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
AttributeError: 'str' object has no attribute 'name'
AttributeError: 'str' object has no attribute 'name'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 391.25
OpenGL renderer: GeForce GTX 645/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 17,119,182,848
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4570 CPU @ 3.20GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
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: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
Send2Trash: 1.5.0
SEQCROW: 0.25.2
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
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: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Error in toolshed error message |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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