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Opened 4 years ago
Closed 4 years ago
#4822 closed defect (duplicate)
Nucleotides: object of type 'NoneType' has no len(
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: [Errno 60] Operation timed out
> open2
> /Users/eduljeea/Documents/Backtracked/backtrack_40_inprogress_build_AE-
> coot-0.pdb
> /Users/eduljeea/Documents/Backtracked/backtrack_60_inprogress_build_AE-
> coot-0.pdb
Chain information for backtrack_40_inprogress_build_AE-coot-0.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
Chain information for backtrack_60_inprogress_build_AE-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open2
> /Users/eduljeea/Documents/GreA/U_EMBL/builds/U_EcRNAP_GreA_20-0723_real_space_refined-
> coot-build-AE.pdb
Chain information for U_EcRNAP_GreA_20-0723_real_space_refined-coot-build-
AE.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
N | No description available
R | No description available
T | No description available
> lighting simple
> preset cartoons/nucleotides ribbons/slabs
Changed 79782 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> set bgColor white
> close
> open2 "/Users/eduljeea/Documents/Manuscripts/chimerax
> 2/figure9_greAgreB_swiv_CORE-ALIGN.cxc"
> open ./pdb-mrc-for-figs/GreA-pc.pdb
Chain information for GreA-pc.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/GreB-pc.pdb
GreB-pc.pdb title:
Cryo-em structure of E. Coli RNA polymerase backtracked elongation complex
bound to greb transcription factor [more info...]
Chain information for GreB-pc.pdb #2
---
Chain | Description
A B | DNA-directed RNA polymerase subunit α
C | DNA-directed RNA polymerase subunit β
D | DNA-directed RNA polymerase subunit β'
E | DNA-directed RNA polymerase subunit ω
F | transcript cleavage factor GREB
N | non-template DNA
R | RNA
T | template DNA
Non-standard residues in GreB-pc.pdb #2
---
MG — magnesium ion
ZN — zinc ion
> open ./pdb-mrc-for-figs/bt140.pdb
Chain information for bt140.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/bt160.pdb
Chain information for bt160.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/bt340.pdb
bt340.pdb title:
Cryo-em structure of E. Coli RNA polymerase backtracked elongation complex In
non-swiveled state [more info...]
Chain information for bt340.pdb #5
---
Chain | Description
A B | DNA-directed RNA polymerase subunit α
C | DNA-directed RNA polymerase subunit β
D | DNA-directed RNA polymerase subunit β'
E | DNA-directed RNA polymerase subunit ω
N | non-template DNA
R | RNA
T | template DNA
Non-standard residues in bt340.pdb #5
---
MG — magnesium ion
ZN — zinc ion
> open ./pdb-mrc-for-figs/bt360.pdb
bt360.pdb title:
Cryo-em structure of E. Coli RNA polymerase backtracked elongation complex In
swiveled state [more info...]
Chain information for bt360.pdb #6
---
Chain | Description
A B | DNA-directed RNA polymerase subunit α
C | DNA-directed RNA polymerase subunit β
D | DNA-directed RNA polymerase subunit β'
E | DNA-directed RNA polymerase subunit ω
N | non-template DNA
R | RNA
T | template DNA
Non-standard residues in bt360.pdb #6
---
MG — magnesium ion
ZN — zinc ion
> name greA #1
> name greB #2
> name bt140 #3
> name bt160 #4
> name bt340 #5
> name bt360 #6
> name Asi3 #1/d:945-1130
> name Bsi3 #2/d:945-1130
> name Acore #1/a/b/c:10-26:514-828:1071-1235/d:504-771
> name Bcore #2/a/b/c:10-26:514-828:1071-1235/d:504-771
> name Aclamp #1/c:1299-1342/d:1-329:1321-1344
> name Bclamp #2/c:1299-1342/d:1-329:1321-1344
> name Ashelf #1/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name Bshelf #2/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name Aswimod Aclamp | Ashelf
> name Bswimod Bclamp | Bshelf
> name Aswi-nosi3 Aclamp | Ashelf & ~Asi3
> name Bswi-nosi3 Bclamp | Bshelf & ~Bsi3
> name bt140-si3 #3/d:945-1130
> name bt140-core #3/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt140-clamp #3/c:1299-1342/d:1-329:1321-1344
> name bt140-shelf #3/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt140-swimod bt140-clamp | bt140-shelf
> name bt140swi-nosi3 bt140-clamp | bt140-shelf & ~bt140-si3
> name bt160-si3 #4/d:945-1130
> name bt160-core #4/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt160-clamp #4/c:1299-1342/d:1-329:1321-1344
> name bt160-shelf #4/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt160-swimod bt160-clamp | bt160-shelf
> name bt160swi-nosi3 bt160-clamp | bt160-shelf & ~bt160-si3
> name bt340-si3 #5/d:945-1130
> name bt340-core #5/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt340-clamp #5/c:1299-1342/d:1-329:1321-1344
> name bt340-shelf #5/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt340-swimod bt340-clamp | bt340-shelf
> name bt340swi-nosi3 bt340-clamp | bt340-shelf & ~bt340-si3
> name bt360-si3 #6/d:945-1130
> name bt360-core #6/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt360-clamp #6/c:1299-1342/d:1-329:1321-1344
> name bt360-shelf #6/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt360-swimod bt360-clamp | bt360-shelf
> name bt360swi-nosi3 bt360-clamp | bt360-shelf & ~bt360-si3
> color greA powderblue
> color Aswimod dodgerblue
> color #1/f skyblue
> color greB lightpink
> color Bswimod tomato
> color #2/f plum
> color bt140 peachpuff
> color bt140-swimod darkorange
> color bt160-swimod gold
> color bt340 lightgreen
> color bt340-swimod forestgreen
> color bt360-swimod yellowgreen
> align Bcore toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.750 angstroms
> align bt140-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.281 angstroms
> align bt160-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.310 angstroms
> align bt340-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.619 angstroms
> align bt360-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.542 angstroms
> set bgColor white
> lighting simple
> preset cartoons/nucleotides licorice/ovals
Changed 159967 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide all
> hide all cartoons
> transparency #1 & ~ (Aswimod | #1/f) 50 target c
> transparency #2 & ~ (Bswimod | #2/f) 50 target c
> transparency #3 & ~ (bt140-swimod) 50 target c
> transparency #5 & ~ (bt340-swimod) 50 target c
> show #1#2#3#5 cartoons
executed figure9_greAgreB_swiv_CORE-ALIGN.cxc
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Changed 159967 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!6 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> nucleotides #!1 ladder
Expected ',' or a keyword
> hide #1 cartoons
> show #1/r/n/t
> show #1/r/n/t cartoons
> open2 "/Users/eduljeea/Documents/Manuscripts/chimerax 2/pdb-mrc-for-
> figs/maps/GreA-pc.mrc"
Opened GreA-pc.mrc, grid size 400,400,400, pixel 0.8, shown at level 2.89,
step 2, values float32
> volume #7 step 1
> volume #7 color #b2b2b2fe
> volume #7 color #b2b2b2f1
> volume #7 color #b2b2b2e1
> volume #7 color #b2b2b2d4
> volume #7 color #b2b2b2cc
> volume #7 color #b2b2b2c6
> volume #7 color #b2b2b2c5
> volume #7 color #b2b2b2c3
> volume #7 color #b2b2b2ab
> volume #7 color #b2b2b2a0
> volume #7 color #b2b2b29a
> volume #7 color #b2b2b290
> volume #7 color #b2b2b284
> volume #7 color #b2b2b278
> volume #7 color #b2b2b26d
> volume #7 color #b2b2b257
> volume #7 color #b2b2b24b
> volume #7 color #b2b2b240
> volume #7 color #b2b2b23d
> volume #7 color #b2b2b23c
> volume #7 color #b2b2b230
> volume #7 color #b2b2b222
> volume #7 color #b2b2b21f
> volume #7 color #b2b2b21b
> volume #7 color #b2b2b20f
> volume #7 color #b2b2b200
> volume #7 color #b2b2b209
> volume #7 color #b2b2b20c
> volume #7 color #b2b2b213
> volume #7 color #b2b2b21b
> volume #7 color #b2b2b221
> volume #7 color #b2b2b227
> volume #7 color #b2b2b22c
> volume #7 color #b2b2b22e
> volume #7 color #b2b2b22f
> volume #7 color #b2b2b231
> volume #7 level 6.515
> hide #!7 models
> show #1/d:770-804:931-936 cartoons
> show #1/d:770-804:914-936 cartoons
> show #1/d:770-804:914-936/f cartoons
> color #1/n blue
> lighting full
> lighting soft
> 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 #1/n navy
> color #1/t olive
> color #1/r darkorange
> color #1/f dodgerblue
> show #!7 models
> close
> open2 "/Users/eduljeea/Documents/Manuscripts/chimerax
> 2/fig11_nucac_gre_bh_tl_highlight.cxc"
> open ./pdb-mrc-for-figs/GreA-pc.pdb
Chain information for GreA-pc.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/bt140.pdb
Chain information for bt140.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/bt160.pdb
Chain information for bt160.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/maps/GreA-pc.mrc
Opened GreA-pc.mrc, grid size 400,400,400, pixel 0.8, shown at level 2.89,
step 2, values float32
> name greA #1
> name bt140 #2
> name bt160 #3
> name Amap #4
> name Asi3 #1/d:945-1130
> name Acore #1/a/b/c:10-26:514-828:1071-1235/d:504-771
> name Aclamp #1/c:1299-1342/d:1-329:1321-1344
> name Ashelf #1/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name Aswimod Aclamp | Ashelf
> name Aswi-nosi3 Aclamp | Ashelf & ~Asi3
> name bt140-si3 #2/d:945-1130
> name bt140-core #2/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt140-clamp #2/c:1299-1342/d:1-329:1321-1344
> name bt140-shelf #2/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt140-swimod bt140-clamp | bt140-shelf
> name bt140swi-nosi3 bt140-clamp | bt140-shelf & ~bt140-si3
> name bt160-si3 #3/d:945-1130
> name bt160-core #3/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt160-clamp #3/c:1299-1342/d:1-329:1321-1344
> name bt160-shelf #3/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt160-swimod bt160-clamp | bt160-shelf
> name bt160swi-nosi3 bt160-clamp | bt160-shelf & ~bt160-si3
> align bt140-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.281 angstroms
> align bt160-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.310 angstroms
> set bgColor white
> lighting simple
> transparency #4 25 target s
> show #*/r/n/t
> show #*/r/n/t cartoons
> show #*/d:770-804:914-936/f cartoons
> color #*/n navy
> color #*/t olive
> color #*/r darkorange
> color #*/f dodgerblue
executed fig11_nucac_gre_bh_tl_highlight.cxc
> close
> open "/Users/eduljeea/Documents/Manuscripts/chimerax
> 2/fig11_nucac_gre_bh_tl_highlight.cxc" format cmd
> open ./pdb-mrc-for-figs/GreA-pc.pdb
Chain information for GreA-pc.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/bt140.pdb
Chain information for bt140.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/bt160.pdb
Chain information for bt160.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open ./pdb-mrc-for-figs/maps/GreA-pc.mrc
Opened GreA-pc.mrc, grid size 400,400,400, pixel 0.8, shown at level 2.89,
step 2, values float32
> name greA #1
> name bt140 #2
> name bt160 #3
> name Amap #4
> name Asi3 #1/d:945-1130
> name Acore #1/a/b/c:10-26:514-828:1071-1235/d:504-771
> name Aclamp #1/c:1299-1342/d:1-329:1321-1344
> name Ashelf #1/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name Aswimod Aclamp | Ashelf
> name Aswi-nosi3 Aclamp | Ashelf & ~Asi3
> name bt140-si3 #2/d:945-1130
> name bt140-core #2/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt140-clamp #2/c:1299-1342/d:1-329:1321-1344
> name bt140-shelf #2/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt140-swimod bt140-clamp | bt140-shelf
> name bt140swi-nosi3 bt140-clamp | bt140-shelf & ~bt140-si3
> name bt160-si3 #3/d:945-1130
> name bt160-core #3/a/b/c:10-26:514-828:1071-1235/d:504-771
> name bt160-clamp #3/c:1299-1342/d:1-329:1321-1344
> name bt160-shelf #3/c:1244-1309/d:346-499:805-1317:1358-1407/e
> name bt160-swimod bt160-clamp | bt160-shelf
> name bt160swi-nosi3 bt160-clamp | bt160-shelf & ~bt160-si3
> align bt140-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.281 angstroms
> align bt160-core toAtoms Acore matchNumbering true
RMSD between 9462 atom pairs is 1.310 angstroms
> set bgColor white
> lighting simple
> transparency #4 25 target s
> preset cartoons/nucleotides ribbons/slabs
Changed 79782 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> nucleotides #* ladder
> show #*/r/n/t
> show #*/r/n/t cartoons
> show #*/d:770-804:914-936/f cartoons
> color #*/n navy
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> color #*/t olive
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> color #*/r darkorange
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> color #*/f dodgerblue
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
executed fig11_nucac_gre_bh_tl_highlight.cxc
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild
_rebuild_molecule('internal', mol)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "new frame":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.30
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Depiction |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Nucleotides: object of type 'NoneType' has no len( |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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