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Opened 5 years ago
Closed 5 years ago
#4074 closed defect (can't reproduce)
ValueError after closing one session and opening another
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Thanks for the swift reply to my last report! I couldn't figure out how to reply to you, so I am re-reporting the issue after having the same results in ChimeraX 1.1 as in ChimeraX 0.93 and not 1.1. I'm getting these error messages when I try to File->Close Session and then re-open a new session (.cxs file) without closing ChimeraX 1.1 and they seem to relate to the alignment.py file in the seqalign folder. I did recently try some "align" commands, but I am not sure what I might have messed up. Oddly, when I restart ChimeraX 1.1, I have no trouble opening these same .cxs files. The error I get when I close a session is:
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
The error I get when I try to reopen a new session is:
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py", line 649, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session
Log from Sat Dec 12 22:38:48 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\ProgramData\ChimeraX\cpSRP43_NMR.cxs format session
Log from Sat Dec 12 13:41:49 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_PRE.cxs" format session
Log from Sun Nov 15 22:59:07 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session
Log from Fri Sep 18 14:58:13 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session
Log from Sun Aug 30 16:37:13 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43 structures\200812 cpSRP43
> FL CD2 labels.cxs" format session
Log from Wed Aug 12 13:28:02 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812 cpSRP43
> FL CD2 labels.cxs"
Log from Wed Aug 12 11:30:26 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\Alex\Desktop\Zoom call.cxs" format session
File not found: C:\Users\Alex\Desktop\Zoom call.cxs
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_composite.pdb"
Summary of feedback from opening C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
structures/cpSRP43_composite.pdb
---
warning | Ignored bad PDB record found on line 2610
END
Chain information for cpSRP43_composite.pdb #1
---
Chain | Description
A | No description available
B | No description available
F | No description available
G | No description available
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_BTFA.py"
ChimeraX cannot open a regular Chimera session.
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_alone.pdb"
Summary of feedback from opening C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
structures/cpSRP43_alone.pdb
---
warnings | Ignored bad PDB record found on line 2938
END
Start residue of secondary structure not found: HELIX 1 1 SER A 117 TYR A 119
1 3
Start residue of secondary structure not found: HELIX 2 2 ALA A 122 LYS A 138
1 17
Start residue of secondary structure not found: HELIX 3 3 GLU A 141 GLN A 146
1 6
Start residue of secondary structure not found: HELIX 4 4 ALA A 163 LEU A 170
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP A 173 GLU A 181
1 9
47 messages similar to the above omitted
cpSRP43_alone.pdb title:
Crystal structure of the CPSRP54 tail bound to CPSRP43 [more info...]
Chain information for cpSRP43_alone.pdb
---
Chain | Description
2.1/A | signal recognition particle 43 kda protein, chloroplastic
2.4/B | signal recognition particle 54 kda protein, chloroplastic
2.5/B | signal recognition particle 54 kda protein, chloroplastic
2.2/C | No description available
2.3/E | No description available
> close session
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_alone.pdb"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_alone.pdb
---
warnings | Ignored bad PDB record found on line 2938
END
Start residue of secondary structure not found: HELIX 1 1 SER A 117 TYR A 119
1 3
Start residue of secondary structure not found: HELIX 2 2 ALA A 122 LYS A 138
1 17
Start residue of secondary structure not found: HELIX 3 3 GLU A 141 GLN A 146
1 6
Start residue of secondary structure not found: HELIX 4 4 ALA A 163 LEU A 170
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP A 173 GLU A 181
1 9
47 messages similar to the above omitted
cpSRP43_alone.pdb title:
Crystal structure of the CPSRP54 tail bound to CPSRP43 [more info...]
Chain information for cpSRP43_alone.pdb
---
Chain | Description
1.1/A | signal recognition particle 43 kda protein, chloroplastic
1.4/B | signal recognition particle 54 kda protein, chloroplastic
1.5/B | signal recognition particle 54 kda protein, chloroplastic
1.2/C | No description available
1.3/E | No description available
> set bgColor white
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"
> select clear
> close session
> open "C:\Users\Alex\Desktop\Zoom call.cxs" format session
File not found: C:\Users\Alex\Desktop\Zoom call.cxs
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_NMRnum.pdb"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_NMRnum.pdb
---
warning | Ignored bad PDB record found on line 2498
END
Chain information for cpSRP43_NMRnum.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Alignment identifier is 1.A
Alignment identifier is 1.B
Alignment identifier is 1.C
Alignment identifier is 1.D
> select clear
> color lightgray
> select clear
> select clear
> select clear
> select clear
> show sel cartoons
> hide sel atoms
> color sel green
> show sel cartoons
> hide sel atoms
> color sel purple
> color sel red
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"
> select clear
> select /A:267
9 atoms, 8 bonds, 1 model selected
> select up
67 atoms, 67 bonds, 1 model selected
> select up
2227 atoms, 2266 bonds, 1 model selected
> hide sel atoms
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"
> select clear
> select clear
> show sel atoms
> color sel black
> style sel ball
Changed 64 atom styles
> style sel sphere
Changed 64 atom styles
> style sel sphere
Changed 70 atom styles
> show sel atoms
> color sel black
> hbonds sel
9 hydrogen bonds found
> hbonds sel
9 hydrogen bonds found
> select clear
> toolshed show H-Bonds
> hbonds
249 hydrogen bonds found
> style sel stick
Changed 70 atom styles
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
> style sel stick
Changed 8 atom styles
> color sel black
> show sel atoms
> :145
Unknown command: :145
> select :145
11 atoms, 10 bonds, 1 model selected
> select :145,146
19 atoms, 18 bonds, 1 model selected
> select :145,146+2
Expected an objects specifier or a keyword
> select :145,146
19 atoms, 18 bonds, 1 model selected
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel ladder
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select clear
> toolshed show "Blast Protein"
> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service1597256347514386636114
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1597256347514386636114
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
> style stick
Changed 2494 atom styles
> color bynucleotide
> graphics silhouettes true
> toolshed show "Side View"
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> graphics silhouettes true
> lighting flat
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> ui mousemode rightMode "mark maximum"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode select
> ui mousemode rightMode select
Drag select of 2 residues, 1 pseudobonds
Drag select of 10 residues
> select clear
> ui mousemode rightMode pivot
> ui mousemode rightMode pivot
> ui mousemode rightMode "translate selected atoms"
> ui mousemode rightMode "translate selected atoms"
> ui mousemode rightMode translate
> ui mousemode rightMode rotate
> ui mousemode rightMode select
> select clear
> select /A:44
9 atoms, 8 bonds, 1 model selected
> select /A:43
8 atoms, 7 bonds, 1 model selected
> select /A:61
9 atoms, 8 bonds, 1 model selected
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
> toolshed show Toolbar
> toolshed show "Basic Actions"
> hide /A target abp
> hide /A target abp
> show /A target abp
> hide /A target abp
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> show sel atoms
> style sel stick
Changed 78 atom styles
> style sel stick
Changed 78 atom styles
> hide sel atoms
> style sel stick
Changed 78 atom styles
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 78 atom styles
> style sel sphere
Changed 78 atom styles
> style sel stick
Changed 78 atom styles
> show /A target abp
> hide sel atoms
> show sel atoms
> select clear
> hide atoms
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> show sel atoms
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
opened ChimeraX session
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color /A #ff11b8 target abp
> color /A #58fffa target abp
> color /A #cf3cff target abp
> show /A target c
> color /A #ffffff target c
> ui mousemode rightMode select
> ui mousemode rightMode pivot
> ui mousemode rightMode select
> ~hbonds
> hbonds
249 hydrogen bonds found
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> name frozen "single cys" sel
registering illegal selector name "single cys"
> select clear
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete
self.session.tools.remove([self])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
KeyError: 7
KeyError: 7
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete
self.session.tools.remove([self])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
KeyError: 8
KeyError: 8
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete
self.session.tools.remove([self])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
KeyError: 9
KeyError: 9
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> name frozen "single cys" sel
registering illegal selector name "single cys"
> name frozen "single cys" sel
registering illegal selector name "single cys"
> name frozen "single cys" sel
registering illegal selector name "single cys"
> name frozen singlecys sel
> name frozen singlecys sel
> color singlecys #ff3030 target abp
> color singlecys #00ff3b target abp
> select clear
> select /A:274
9 atoms, 8 bonds, 1 model selected
> select clear
Drag select of 1 atoms, 5 residues, 1 bonds
> select clear
> select /A:246
11 atoms, 10 bonds, 1 model selected
> select /A:253
6 atoms, 5 bonds, 1 model selected
> select /A:234
9 atoms, 8 bonds, 1 model selected
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\200812 cpSRP43 FL CD2 labels.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs
> select /A:213
9 atoms, 8 bonds, 1 model selected
> select up
142 atoms, 142 bonds, 1 model selected
> select up
2227 atoms, 2266 bonds, 1 model selected
> hide sel atoms
> ~hbonds
> select clear
> select :209,216,234,239,253,267
49 atoms, 43 bonds, 1 model selected
> show sel atoms
> select clear
> save C:\Users\Alex\Desktop\image2.png supersample 3
> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs
Summary of feedback from opening C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> save C:\Users\Alex\Desktop\image4.png supersample 3
> select :260,257,239,219,212,188,192
64 atoms, 58 bonds, 1 model selected
> select clear
> select :209,216,234,239,253,267
49 atoms, 43 bonds, 1 model selected
> label sel residues
> label sel residues size 96
> label sel residues font-size 96
Expected a keyword
> label sel residues 96
Expected a keyword
> label sel residues
> label sel residues 10
Expected a keyword
> label sel residues height 10
> label sel residues height 2
> select clear
> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs
Summary of feedback from opening C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> close #1.1
> select /A:213
9 atoms, 8 bonds, 1 model selected
> select up
142 atoms, 142 bonds, 1 model selected
> select up
2227 atoms, 2266 bonds, 1 model selected
> hide sel atoms
> select clear
> :90
Unknown command: :90
> select :46
8 atoms, 7 bonds, 1 model selected
> select :46,60,71,76,131,148,161,209,222
81 atoms, 72 bonds, 1 model selected
> style sel sphere
Changed 81 atom styles
> show sel cartoons
> show sel atoms
> style sel stick
Changed 81 atom styles
> select :46.CA,60,71,76,131,148,161,209,222
Expected an objects specifier or a keyword
> select :46@CA,60,71,76,131,148,161,209,222
1 atom, 1 model selected
> select :46@CA,60@CA,71@CA,76@CA,131@CA,148@CA,161@CA,20@CA9,222@CA
1 atom, 1 model selected
> hide sel atoms
> select CA :46,60,71,76,131,148,161,209,222
Expected an objects specifier or a keyword
> select @CA :46,60,71,76,131,148,161,209,222
390 atoms, 72 bonds, 1 model selected
> select :46,60,71,76,131,148,161,209,222@CA
10 atoms, 1 model selected
> style sel sphere
Changed 10 atom styles
> show sel atoms
> show sel atoms
> style sel sphere
Changed 10 atom styles
> select :46,60,71,76,131,148,161,209,222
81 atoms, 72 bonds, 1 model selected
> select :46,60,71,76,131,148,161,209,222@CA
10 atoms, 1 model selected
> show sel atoms
> style sel sphere
Changed 10 atom styles
> show sel atoms
> show sel cartoons
> style sel sphere
Changed 10 atom styles
> style sel stick
Changed 10 atom styles
> select #1:46,60,71,76,131,148,161,209,222@CA
10 atoms, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel black
> select #1.A:46,60,71,76,131,148,161,209,222@CA
Expected an objects specifier or a keyword
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> hide sel cartoons
> select clear
> color lightgray,a;~display;color #A1FF00,a :90@CA1;display :90@CA1;color
> #1BFF00,a :104@CA1;display :104@CA1;color #FF0000,a :115@CA1;display
> :115@CA1;color #FF4600,a :120@CA1;display :120@CA1;color #FFCA00,a
> :175@CA1;display :175@CA1;color #00FF00,a :192@CA1;display :192@CA1;color
> #94FF00,a :205@CA1;display :205@CA1;color #44FF00,a :253@CA1;display
> :253@CA1;color #45FF00,a :266@CA1;display :266@CA1;~display
> #4.2;~ribbackbone;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color lightgray,a; ~display;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #A1FF00,a :90@CA1; display :90@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1BFF00,a :104@CA1; display :104@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #FF0000,a :115@CA1; display :115@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #FF4600,a :120@CA1; display :120@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #FFCA00,a :175@CA1; display :175@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #00FF00,a :192@CA1; display :192@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #94FF00,a :205@CA1; display :205@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #44FF00,a :253@CA1; display :253@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #45FF00,a :266@CA1; display :266@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #A1FF00,a :90@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> hide sel cartoons
> color #A1FF00 /A:90@CA1;
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #A1FF00 :90@CA;
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select /A:46
8 atoms, 7 bonds, 1 model selected
> color #A1FF00,a :46@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #A1FF00,a :46@CA;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select :46@CA
1 atom, 1 model selected
> color sel #A1FF00
> color lightgray,a;sel /A:46@CA;color sel #A1FF00,a :46@CA;sel /A:60@CA;color
> sel #1BFF00,a :60@CA;sel /A:71@CA;color sel #FF0000,a :71@CA;sel
> /A:76@CA;color sel #FF4600,a :76@CA;sel /A:131@CA;color sel #FFCA00,a
> :131@CA;sel /A:148@CA;color sel #00FF00,a :148@CA;sel /A:161@CA;color sel
> #94FF00,a :161@CA;sel /A:209@CA;color sel #44FF00,a :209@CA;sel
> /A:222@CA;color sel #45FF00,a :222@CA;~display #4.2;~ribbackbone;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select /A:46@CA
1 atom, 1 model selected
> color sel #A1FF00,a :46@CA;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color lightgray,a;sel /A:46@CA;color sel #A1FF00;sel /A:60@CA;color sel
> #1BFF00;sel /A:71@CA;color sel #FF0000;sel /A:76@CA;color sel #FF4600;sel
> /A:131@CA;color sel #FFCA00;sel /A:148@CA;color sel #00FF00;sel
> /A:161@CA;color sel #94FF00;sel /A:209@CA;color sel #44FF00;sel
> /A:222@CA;color sel #45FF00;~display #4.2;~ribbackbone;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel #A1FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #1BFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:76@CA
1 atom, 1 model selected
> color sel #FF4600
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFCA00
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #94FF00
> select /A:209@CA
1 atom, 1 model selected
> color sel #44FF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #45FF00
> select clear
> select /A:46@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #8AFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #94FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFA000
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FFDC00
> select /A:209@CA
1 atom, 1 model selected
> color sel #CAFF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #FFBC00
> vdwdefine 2.0
Unknown command: vdwdefine 2.0
> vdw 2.0
Unknown command: vdw 2.0
> ballScale 0.5
Unknown command: ballScale 0.5
> ballScale
Unknown command: ballScale
> size ballScale 0.5
Changed 1 ball scales
> size ballScale 1
Changed 1 ball scales
> select clear
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> size ballScale 1
Changed 1 ball scales
> size atomRadius 1
Changed 2494 atom radii
> size atomRadius 5
Changed 2494 atom radii
> size atomRadius 2
Changed 2494 atom radii
> size atomRadius 3
Changed 2494 atom radii
> select clear
> save C:\Users\Alex\Desktop\image9.png supersample 3
> save C:\Users\Alex\Desktop\image10.png supersample 3
> select /A:46@CA
1 atom, 1 model selected
> color sel #99FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #5EFF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #5AFF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFD700
> select /A:148@CA
1 atom, 1 model selected
> color sel #3DFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF2100
> select /A:209@CA
1 atom, 1 model selected
> color sel #FFB500
> select /A:222@CA
1 atom, 1 model selected
> color sel #FFE400
> select /A:46@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #5CFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #62FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #EAFF00
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #C2FF00
> select /A:209@CA
1 atom, 1 model selected
> color sel #86FF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #D7FF00
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select clear
> save C:\Users\Alex\Desktop\image10.png supersample 3
> select /A:46,60,71,75,131,148,161,209,222@CA
9 atoms, 1 model selected
> hide sel cartoons
> style sel sphere
Changed 9 atom styles
> show sel atoms
> select /A:76@CA
1 atom, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select /A:76
8 atoms, 7 bonds, 1 model selected
> color sel lightgray
> select clear
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:75@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select clear
> save C:\Users\Alex\Desktop\image11.png supersample 3
> select /A:46@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #8AFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:75@CA
1 atom, 1 model selected
> color sel #94FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFA000
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FFDC00
> select /A:209@CA
1 atom, 1 model selected
> color sel #CAFF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #FFBC00
> save C:\Users\Alex\Desktop\image12.png supersample 3
> select clear
> save C:\Users\Alex\Desktop\image13.png supersample 3
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:75@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:220@CA
1 atom, 1 model selected
> color sel #FF5600
> select /A:220@CA
1 atom, 1 model selected
> hide sel cartoons
> select /A:220@CA
1 atom, 1 model selected
> select /A:220@CA
1 atom, 1 model selected
> hide sel cartoons
> style sel sphere
Changed 1 atom style
> select clear
> save C:\Users\Alex\Desktop\image14.png supersample 3
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select clear
> save C:\Users\Alex\Desktop\image15.png supersample 3
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select /A:220@CA
1 atom, 1 model selected
> show sel atoms
> select /A:222@CA
1 atom, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> color sel lightgray
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_EPR.cxs"
> select clear
> select :240
8 atoms, 7 bonds, 1 model selected
> select :240,242
17 atoms, 15 bonds, 1 model selected
> select clear
> hide atoms
> show cartoons
> color lightgray
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> color sel lightgray
> select /A:220
4 atoms, 3 bonds, 1 model selected
> color sel lightgray
> select clear
> select /A:75
12 atoms, 12 bonds, 1 model selected
> color sel lightgray
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_PRE.cxs"
> select clear
> select :240,242
17 atoms, 15 bonds, 1 model selected
> show sel atoms
> color sel lightgray
> select clear
> select /A:242@OE2
1 atom, 1 model selected
> select /A:242
9 atoms, 8 bonds, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 model selected
> select clear
> toolshed show "Build Structure"
> swapaa :240 CYS
Using Dunbrack library
/A ASP 240: phi -80.0, psi 25.3 trans
Applying CYS rotamer (chi angles: -177.4) to /A CYS 240
> swapaa :242 CYS
Using Dunbrack library
/A GLU 242: phi -114.6, psi 124.4 trans
Applying CYS rotamer (chi angles: -61.6) to /A CYS 242
> select /A:242@SG
1 atom, 1 model selected
> style sel sphere
Changed 2 atom styles
> color sel red
> select /A:242@SG
1 atom, 1 model selected
> color :240@S red
> color :240@CS red
> color :240@SH red
> color :240@SG red
> color :242@SG red
> select clear
> select /A:242@SG
1 atom, 1 model selected
> select /A:213
9 atoms, 8 bonds, 1 model selected
> select clear
> select /A:242
6 atoms, 5 bonds, 1 model selected
> color :242@CA lightgray
> color :240@CA lightgray
> select clear
> select :ile
88 atoms, 78 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 88 atom styles
> color sel lightgray
> select :ile@CG
Nothing selected
> select :ile@CD
Nothing selected
> select :ile@CG1
11 atoms, 1 model selected
> style sel sphere
Changed 11 atom styles
> select down
11 atoms, 1 model selected
> select up
88 atoms, 78 bonds, 1 model selected
> select up
559 atoms, 558 bonds, 1 model selected
> select up
2222 atoms, 2261 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select down
2222 atoms, 2261 bonds, 1 model selected
> select down
559 atoms, 558 bonds, 1 model selected
> select down
88 atoms, 78 bonds, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> size sphereRadius 2
Expected a keyword
> size sphereRadius
Expected a keyword
> size radius 2
Expected a keyword
> size atomRadius 2
Changed 2489 atom radii
> select clear
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select :ile@CG1
11 atoms, 1 model selected
> color sel black
> select :ile@CA
11 atoms, 1 model selected
> color sel lightgray
> select clear
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select :leu@CD1
28 atoms, 1 model selected
> select clear
> select /A:242@SG
1 atom, 1 model selected
> toolshed show Distances
> distance /A:209@CG1 /A:242@SG
Distance between /A ILE 209 CG1 and CYS 242 SG: 28.782Å
> distance style color red
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style decimalPlaces 1
> distance style decimalPlaces 0
> distance style decimalPlaces 0
> distance style radius 0.11
> distance style radius 0.11
> distance style radius 0.12
> distance style radius 0.12
> distance style radius 0.13
> distance style radius 0.13
> distance style radius 0.14
> distance style radius 0.14
> distance style radius 0.15
> distance style radius 0.15
> distance style radius 0.16
> distance style radius 0.16
> distance style radius 0.17
> distance style radius 0.17
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.19
> distance style radius 0.19
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.17
> distance style radius 0.17
> distance style radius 0.16
> distance style radius 0.16
> distance style radius 0.15
> distance style radius 0.15
> distance style radius 0.14
> distance style radius 0.14
> distance style radius 0.13
> distance style radius 0.13
> distance style radius 0.12
> distance style radius 0.12
> distance style radius 0.11
> distance style radius 0.11
> distance style radius 0.1
> distance style radius 0.1
> select /A:242@SG
1 atom, 1 model selected
> distance /A:215@CG1 /A:242@SG
Distance between /A ILE 215 CG1 and CYS 242 SG: 22Å
> select /A:242@SG
1 atom, 1 model selected
> select clear
> select /A:242@SG
1 atom, 1 model selected
> distance /A:176@CG1 /A:242@SG
Distance between /A ILE 176 CG1 and CYS 242 SG: 25Å
Must select one or more distances in the table
> ~distance /A:176@CG1 /A:242@SG
> ~distance /A:209@CG1 /A:242@SG
> ~distance /A:215@CG1 /A:242@SG
> select /A:240@SG
1 atom, 1 model selected
> distance /A:176@CG1 /A:240@SG
Distance between /A ILE 176 CG1 and CYS 240 SG: 27Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:215@CG1 /A:240@SG
Distance between /A ILE 215 CG1 and CYS 240 SG: 22Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:209@CG1 /A:240@SG
Distance between /A ILE 209 CG1 and CYS 240 SG: 27Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:193@CG1 /A:240@SG
Distance between /A ILE 193 CG1 and CYS 240 SG: 27Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:231@CG1 /A:240@SG
Distance between /A ILE 231 CG1 and CYS 240 SG: 15Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:293@CG1 /A:240@SG
Distance between /A ILE 293 CG1 and CYS 240 SG: 41Å
> select clear
> ~distance /A:215@CG1 /A:240@SG
> undo
> select /A:215@CG1
1 atom, 1 model selected
> distance /A:215@CG1 /A:240@SG
Distance between /A ILE 215 CG1 and CYS 240 SG: 22Å
> select clear
> ~distance /A:293@CG1 /A:240@SG
> select clear
> 2dlabels size 12
> 2dlabels size 24
> label size 24
> label size 48
> select clear
> save C:\Users\Alex\Desktop\image16.png supersample 3
> select clear
> select /D:536
11 atoms, 10 bonds, 1 model selected
> select up
43 atoms, 42 bonds, 1 model selected
> select up
104 atoms, 105 bonds, 1 model selected
> hide sel cartoons
> select clear
> select /A:225
12 atoms, 12 bonds, 1 model selected
> select /A:285
11 atoms, 10 bonds, 1 model selected
> select up
31 atoms, 30 bonds, 1 model selected
> select up
2222 atoms, 2261 bonds, 1 model selected
> select down
31 atoms, 30 bonds, 1 model selected
> select down
11 atoms, 10 bonds, 1 model selected
> select down
11 atoms, 10 bonds, 1 model selected
Destroying pre-existing alignment with identifier 1.A
Alignment identifier is 1.A
> select clear
> select /A:223
11 atoms, 11 bonds, 1 model selected
> hide sel cartoons
> show sel atoms
> toolshed show Rotamers
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_PRE.cxs"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_PRE.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs
> select clear
> hide target a
> select clear
> select /A:224
9 atoms, 8 bonds, 1 model selected
> select up
46 atoms, 47 bonds, 1 model selected
> select up
2222 atoms, 2261 bonds, 1 model selected
> show sel cartoons
> select clear
> show cartoons
> select clear
> select /A:240
6 atoms, 5 bonds, 1 model selected
> select :240@S
Nothing selected
> select :240.S
Expected an objects specifier or a keyword
> select :240@SH
Nothing selected
> select :240@sh
Nothing selected
> select :240@s
Nothing selected
> select :240@c
1 atom, 1 model selected
> select :240@ca
1 atom, 1 model selected
> select :240@cb
1 atom, 1 model selected
> select :240@sh
Nothing selected
> select /A:240
6 atoms, 5 bonds, 1 model selected
> show sel atoms
> select /A:240@SG
1 atom, 1 model selected
> color sel black
> select clear
> select clear
> select /A:240@SG
1 atom, 1 model selected
> color sel lightgray
> select :240@sg
1 atom, 1 model selected
> select clear
> select :240@sg
1 atom, 1 model selected
> color sel black
> ribbackbone
Unknown command: ribbackbone
> select clear
> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs
> select /A:240
6 atoms, 5 bonds, 1 model selected
> color sel lightgray
> color :240 at SG black
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black, :240 at SG
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black, :240@sg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black,a :240@sg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black,a :240.a@sg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black :240.a@sg
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color black :240@sg
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select /A:240@SG
1 atom, 1 model selected
> color black :240@sg
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
[had to nuke a large part of the log in order to fit in ticket]
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> ~display /B
> select /A:239@N
1 atom, 1 model selected
> hide sel atoms
> select clear
> view fron
Expected an objects specifier or a view name or a keyword
> view front
> select /A:44@N
1 atom, 1 model selected
> hide sel atoms
> select clear
> view back
> save C:\Users\Alex\Desktop\image26.png supersample 3
> view front
> save C:\Users\Alex\Desktop\image27.png supersample 3
> select clear
> view back
> save C:\Users\Alex\Desktop\image28.png supersample 3
> color /A lightgray
> cartoon suppressBackboneDisplay false
> ~display
> color :240@n,a black target a
> display :240@n
> color :15@CG1,a #00FF00 target a
> display :15@CG1
> color :26@CG1,a #B3FF00 target a
> display :26@CG1
> color :26@CG2,a #00FF00 target a
> display :26@CG2
> color :42@CG1,a #00FF00 target a
> display :42@CG1
> color :42@CG2,a #FF0000 target a
> display :42@CG2
> color :45@CD1,a #00FF00 target a
> display :45@CD1
> color :59@CD1,a #00FF00 target a
> display :59@CD1
> color :59@CD2,a #FF1F00 target a
> display :59@CD2
> color :60@CD1,a #61FF00 target a
> display :60@CD1
> color :71@CG1,a #FFBC00 target a
> display :71@CG1
> color :80@CG1,a #17FF00 target a
> display :80@CG1
> color :81@CG1,a #FF0000 target a
> display :81@CG1
> color :109@CG1,a #FF0000 target a
> display :109@CG1
> color :112@CG1,a #FF0000 target a
> display :112@CG1
> color :134@CD1,a #FF0000 target a
> display :134@CD1
> color :142@CD1,a #00FF00 target a
> display :142@CD1
> color :142@CD2,a #FF0000 target a
> display :142@CD2
> color :209@CD1,a #FF0000 target a
> display :209@CD1
> color :211@CD1,a #FF0000 target a
> display :211@CD1
> color :215@CD1,a #FF0000 target a
> display :215@CD1
> color :217@CG1,a #FF0000 target a
> display :217@CG1
> color :277@CG1,a #FFD600 target a
> display :277@CG1
> color :281@CG1,a #00FF00 target a
> display :281@CG1
> color :281@CG2,a #00FF00 target a
> display :281@CG2
> color :282@CD1,a #00FF00 target a
> display :282@CD1
> color :286@CG1,a #00FF00 target a
> display :286@CG1
> color :286@CG2,a #00FF00 target a
> display :286@CG2
> color :293@CD1,a #00FF00 target a
> display :293@CD1
> color :296@CD1,a #00FF00 target a
> display :296@CD1
> color :297@CG1,a #00FF00 target a
> display :297@CG1
> color :297@CG2,a #00FF00 target a
> display :297@CG2
> color :313@CG1,a #00FF00 target a
> display :313@CG1
> color :317@CD1,a #FFD700 target a
> display :317@CD1
> color :317@CD2,a #CBFF00 target a
> display :317@CD2
> color :318@CG1,a #00FF00 target a
> display :318@CG1
> color :319@CD1,a #FF0000 target a
> display :319@CD1
> color :319@CD2,a #FF0000 target a
> display :319@CD2
> color :320@CD1,a #FF1B00 target a
> display :320@CD1
> color :0@1,a #FF0000 target a
> display :0@1
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> ~display /B
> hide sel atoms
> select clear
> view back
> view front
> save C:\Users\Alex\Desktop\image25.png supersample 3
> view front
> view front
> color :3@N,a #FF4900 target a
> display :3@N
> color :4@N,a #FF0000 target a
> display :4@N
> color :12@N,a #FFAA00 target a
> display :12@N
> color :13@N,a #FFB500 target a
> display :13@N
> color :14@N,a #FF9D00 target a
> display :14@N
> color :17@N,a #FFFA00 target a
> display :17@N
> color :19@N,a #FFB500 target a
> display :19@N
> color :20@N,a #FFF600 target a
> display :20@N
> color :22@N,a #A2FF00 target a
> display :22@N
> color :23@N,a #6AFF00 target a
> display :23@N
> color :26@N,a #42FF00 target a
> display :26@N
> color :27@N,a #00FF00 target a
> display :27@N
> color :28@N,a #E9FF00 target a
> display :28@N
> color :29@N,a #00FF00 target a
> display :29@N
> color :30@N,a #25FF00 target a
> display :30@N
> color :31@N,a #2DFF00 target a
> display :31@N
> color :32@N,a #87FF00 target a
> display :32@N
> color :33@N,a #44FF00 target a
> display :33@N
> color :34@N,a #52FF00 target a
> display :34@N
> color :36@N,a #8CFF00 target a
> display :36@N
> color :37@N,a #FF0000 target a
> display :37@N
> color :39@N,a #FF7000 target a
> display :39@N
> color :44@N,a #FF0000 target a
> display :44@N
> color :54@N,a #FFBB00 target a
> display :54@N
> color :74@N,a #FFB800 target a
> display :74@N
> color :128@N,a #FF6F00 target a
> display :128@N
> color :140@N,a #FF3C00 target a
> display :140@N
> color :150@N,a #FFF800 target a
> display :150@N
> color :156@N,a #FF6700 target a
> display :156@N
> color :157@N,a #FF4C00 target a
> display :157@N
> color :169@N,a #FFED00 target a
> display :169@N
> color :177@N,a #FFC700 target a
> display :177@N
> color :188@N,a #FFA400 target a
> display :188@N
> color :189@N,a #FF0000 target a
> display :189@N
> color :190@N,a #FFBA00 target a
> display :190@N
> color :191@N,a #FF3C00 target a
> display :191@N
> color :192@N,a #FF0000 target a
> display :192@N
> color :239@N,a #FFF300 target a
> display :239@N
> color :274@N,a #FF7400 target a
> display :274@N
> color :281@N,a #FFA900 target a
> display :281@N
> color :282@N,a #4CFF00 target a
> display :282@N
> color :283@N,a #5AFF00 target a
> display :283@N
> color :284@N,a #D8FF00 target a
> display :284@N
> color :285@N,a #05FF00 target a
> display :285@N
> color :286@N,a #AFFF00 target a
> display :286@N
> color :287@N,a #0EFF00 target a
> display :287@N
> color :288@N,a #FFEA00 target a
> display :288@N
> color :289@N,a #E4FF00 target a
> display :289@N
> color :290@N,a #35FF00 target a
> display :290@N
> color :292@N,a #5FFF00 target a
> display :292@N
> color :293@N,a #22FF00 target a
> display :293@N
> color :294@N,a #2FFF00 target a
> display :294@N
> color :295@N,a #00FF00 target a
> display :295@N
> color :296@N,a #14FF00 target a
> display :296@N
> color :297@N,a #18FF00 target a
> display :297@N
> color :298@N,a #6AFF00 target a
> display :298@N
> color :304@N,a #FFD000 target a
> display :304@N
> color :305@N,a #FF0000 target a
> display :305@N
> color :306@N,a #AAFF00 target a
> display :306@N
> color :307@N,a #FF9E00 target a
> display :307@N
> color :310@N,a #65FF00 target a
> display :310@N
> color :313@N,a #FFCB00 target a
> display :313@N
> color :314@N,a #FF9E00 target a
> display :314@N
> color :315@N,a #FF6600 target a
> display :315@N
> color :316@N,a #FFDB00 target a
> display :316@N
> color :317@N,a #E3FF00 target a
> display :317@N
> color :318@N,a #5AFF00 target a
> display :318@N
> color :319@N,a #C6FF00 target a
> display :319@N
> color :320@N,a #9CFF00 target a
> display :320@N
> color :321@N,a #3DFF00 target a
> display :321@N
> color :323@N,a #61FF00 target a
> display :323@N
> color :324@N,a #00FF00 target a
> display :324@N
> color :325@N,a #35FF00 target a
> display :325@N
> color :327@N,a #77FF00 target a
> display :327@N
> color :328@N,a #38FF00 target a
> display :328@N
> color :329@N,a #00FF00 target a
> display :329@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
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> display :0@N
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> ~display /B
> hide sel atoms
> select clear
> save C:\Users\Alex\Desktop\image25.png supersample 3
> color /A lightgray
> cartoon suppressBackboneDisplay false
> ~display
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> ~display /B
> hide sel atoms
> color /A lightgray
> cartoon suppressBackboneDisplay false
> ~display
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> ~display /B
> select clear
> hide sel atoms
> view back
> hide sel atoms
> save C:\Users\Alex\Desktop\image25.png supersample 3
> view front
> save C:\Users\Alex\Desktop\image26.png supersample 3
> select clear
> select clear
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> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> ~display /B
> hide sel atoms
> hide sel atoms
> view front
> view back
> hide sel atoms
> hide sel atoms
> select clear
> hide sel atoms
> select clear
> save C:\Users\Alex\Desktop\image27.png supersample 3
> view front
> save C:\Users\Alex\Desktop\image28.png supersample 3
> hide sel atoms
> save C:\Users\Alex\Desktop\image29.png supersample 3
> select /A:209@CD1
1 atom, 1 model selected
> toolshed show Distances
> distance /A:142@N /A:209@CD1
Distance between /A LEU 142 N and ILE 209 CD1: 30.140Å
> view back
> select clear
> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs
opened ChimeraX session
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 914, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 633, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 373, in detach_viewer
self.session.alignments.destroy_alignment(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment
del self._alignments[alignment.ident]
KeyError: '1.A'
KeyError: '1.A'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment
del self._alignments[alignment.ident]
See log for complete Python traceback.
> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 649, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 649, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 629, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 440, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 456, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 691, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 24.20.100.6293
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Book
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 17,101,541,376
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-6600U CPU @ 2.60GHz"
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: 2.1.1
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: 1.0
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
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 (3)
comment:1 by , 5 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → ValueError after closing one session and opening another |
comment:2 by , 5 years ago
| Status: | accepted → feedback |
|---|
comment:3 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | feedback → closed |
Unfortunately the problem (Sequence Viewer showing alignment not tracked by alignments manager) happened before the problematic session file was saved and is therefore not really reproducible per se. It may well be fixed (for future session files).
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Hi Alex,
--Eric