The following bug report has been submitted:
Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0rc202005242323 (2020-05-24 23:23:37 UTC)
Description
cartoon style modeHelix wrap broke redraw
Log:
UCSF ChimeraX version: 1.0rc202005242323 (2020-05-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /home/tic20/structure_dump/pu_qian/new_2020_05/visualisation.cxs
Log from Tue May 26 14:10:30 2020 Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 1.0rc202005242323 (2020-05-24)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open final.cif
Summary of feedback from opening final.cif
---
warnings | Unknown polymer entity '1' near line 599
Unknown polymer entity '2' near line 10916
Unknown polymer entity '3' near line 11350
Unknown polymer entity '4' near line 21311
Unknown polymer entity '5' near line 23726
8 messages similar to the above omitted
Atom C1 is not in the residue template for GPC /AV:101
Atom C1 is not in the residue template for GPC /BA:101
Atom C1 is not in the residue template for GPC /BB:101
Atom C1 is not in the residue template for GPC /BC:101
Atom C1 is not in the residue template for GPC /BD:101
36 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for final.cif #1
---
Chain | Description
AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?
BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg bh
bi bj bk bl bm bo bp | ?
BB BD BE BI BV BW bn | ?
C | ?
H1 | ?
H2 | ?
L | ?
M | ?
UA | ?
UB | ?
UC | ?
aa | ?
ab ac ad ae af ag ah ai aj ak al am an ao ap | ?
> select protein
38226 atoms, 39573 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> set bgColor white
> select clear
> 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* palegreen
> color /B* powderblue
> color /a* limegreen
> color /a* mediumturquoise
> color /a* limegreen
> color /b* mediumturquoise
> color /H1,H2 lightgrey
> select HEM
Expected an objects specifier or a keyword
> select :HEC
172 atoms, 184 bonds, 16 pseudobonds, 2 models selected
> style sel sphere
Changed 172 atom styles
> seattr sel a displayradii 0.5
Unknown command: seattr sel a displayradii 0.5
> setattr sel a displayradii 0.5
Assigning displayradii attribute to 172 items
Not creating attribute 'displayradii'; use 'create true' to override
> setattr sel a displayradius 05
Assigning displayradius attribute to 172 items
Not creating attribute 'displayradius'; use 'create true' to override
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> select :BCL
5544 atoms, 5880 bonds, 336 pseudobonds, 2 models selected
> color sel tan
> color sel byhetero
> style sel sphere
Changed 5544 atom styles
> select clear
> select /L,M
5280 atoms, 5490 bonds, 16 pseudobonds, 2 models selected
> color sel thistle
> select :HEM
Nothing selected
> select :HEC
172 atoms, 184 bonds, 16 pseudobonds, 2 models selected
> select :HEC
172 atoms, 184 bonds, 16 pseudobonds, 2 models selected
> select :BCL
5544 atoms, 5880 bonds, 336 pseudobonds, 2 models selected
> color sel tan
> color sel byhetero
> select clear
> select prot
Expected an objects specifier or a keyword
> select protein
38226 atoms, 39573 bonds, 1 model selected
> usage trans
transparency [objects] percent [what] [target characters from 'abcfprs']
— change object transparency
objects: an objects specifier or nothing
percent: a number
what: a collection of one of All, atoms, bonds, cartoons, labels, pseudobonds,
ribbons, rings, or surfaces
> transparency sel 90
> transparency sel 90 target r
> transparency sel 70 target r
> transparency sel 40 target r
> transparency sel 60 target r
> select clear
> select ~prot
Expected an objects specifier or a keyword
> select ~protein
7750 atoms, 8075 bonds, 352 pseudobonds, 2 models selected
> style sel stick
Changed 7750 atom styles
> select /AB:44
5 atoms, 4 bonds, 1 model selected
> select :HEC&FE
Expected an objects specifier or a keyword
> select :HEC@FE
4 atoms, 1 model selected
> style sel sphere
Changed 4 atom styles
> select :BCL@MG
84 atoms, 1 model selected
> style sel sphere
Changed 84 atom styles
> select clear
> select :BCL,HEC
5716 atoms, 6064 bonds, 352 pseudobonds, 2 models selected
> setattr sel b radii 0.3
Assigning radii attribute to 6064 items
Not creating attribute 'radii'; use 'create true' to override
> setattr sel b radius 0.3
Assigning radius attribute to 6064 items
> select clear
> select :BCL@MG|:HEC@FE
88 atoms, 1 model selected
> setattr sel a radius 2
Assigning radius attribute to 88 items
> setattr sel a radius 1.5
Assigning radius attribute to 88 items
> select clear
> select :GPC
1800 atoms, 1760 bonds, 1 model selected
> color sel purple
Drag select of
> lighting full
> select clear
> lighting soft
> lighting full
> graphics silhouettes true
> select clear
> graphics silhouettes false
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting full
> set bgColor gray
> set bgColor black
> set bgColor white
> save /run/media/tic20/storage/structure_dump/pu_qian/new_2020_05/scene.obj
> transparency 0
> transparency 0 target r
> transparency 50 target r
> lighting soft
> transparency 0 target r
> select /A*,B*,a*,b*
36116 atoms, 37444 bonds, 320 pseudobonds, 2 models selected
> usage cartoo style
cartoon style [atoms] [width a number] [thickness a number] [arrows true or
false] [arrowsHelix true or false] [arrowScale arrowScale] [xsection xsection]
[sides sides] [divisions divisions] [barScale a number] [barSides barSides]
[modeHelix modeHelix] [radius radius]
— set cartoon style for secondary structures in specified models
arrowScale: a number ≥ 1.0 and ≤ 5.0
xsection: one of barbell, oval, piping, rectangle, round, or square
sides: an even integer ≥ 3 and ≤ 24
divisions: an integer ≥ 2 and ≤ 40
barSides: an even integer ≥ 3 and ≤ 24
modeHelix: one of default, tube, or wrap
radius: a number or auto
> cartoon style sel width 0.5
> cartoon style sel width 0.5 modeHelix tube
> select clear
> cartoon style
final.cif #1
\- helix mode=tube xsection=round width=0.5 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> cartoon style #1
final.cif #1
\- helix mode=tube xsection=round width=0.5 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> preset cartoons/nucleotides licorice/ovals
Changed 38226 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
> preset cartoons/nucleotides cylinders/stubs
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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> transparency 0.5 target r
> transparency 0.5 target s
> transparency 0.5 target r
> lighting full
> lighting soft
> transparency 50 target r
> transparency 0 target r
> transparency 70 target r
> transparency 30 target r
> lighting full
> lighting soft
> graphics silhouettes true
> select :HEM&~@FE
Nothing selected
> select :HEC&~@FE
168 atoms, 184 bonds, 16 pseudobonds, 2 models selected
[had to truncate the log to make it acceptable length for Trac]
> select #2
119808 atoms, 117504 bonds, 1 model selected
> lighting simple
> ui mousemode right translate
> ui mousemode right "translate selected models"
> select #1
45976 atoms, 47648 bonds, 352 pseudobonds, 2 models selected
> ui mousemode right "rotate selected models"
> select #2
119808 atoms, 117504 bonds, 1 model selected
> ui mousemode right "translate selected models"
> select clear
> surface #2
> hide #!2 models
> show #!2 models
> color #2 cyan target s
> transparency #2 90
> hide #2
> surface close
> show #2
> ui tool show Shell
> select #2
119808 atoms, 117504 bonds, 1 model selected
> ui mousemode right "translate selected models"
> select clear
> select #1
45976 atoms, 47648 bonds, 352 pseudobonds, 2 models selected
> select #2
119808 atoms, 117504 bonds, 1 model selected
> select #1
45976 atoms, 47648 bonds, 352 pseudobonds, 2 models selected
> select #2
119808 atoms, 117504 bonds, 1 model selected
> select clear
> select up
36556 atoms, 35853 bonds, 1 model selected
> hide sel
> select #2&~sel
83252 atoms, 81651 bonds, 1 model selected
> surface sel
> color #2 cyan target s
> transparency #2 90 target s
> hide #2
> select clear
> transparency #1 0 target r
> ui tool show "Side View"
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> 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 #2 light steel blue target s
> transparency #2 90
> transparency #2 80
> transparency #2 70
> usage cartoon style
cartoon style [atoms] [width a number] [thickness a number] [arrows true or
false] [arrowsHelix true or false] [arrowScale arrowScale] [xsection xsection]
[sides sides] [divisions divisions] [barScale a number] [barSides barSides]
[modeHelix modeHelix] [radius radius]
— set cartoon style for secondary structures in specified models
arrowScale: a number ≥ 1.0 and ≤ 5.0
xsection: one of barbell, oval, piping, rectangle, round, or square
sides: an even integer ≥ 3 and ≤ 24
divisions: an integer ≥ 2 and ≤ 40
barSides: an even integer ≥ 3 and ≤ 24
modeHelix: one of default, tube, or wrap
radius: a number or auto
> cartoon style #1&~/a*,A*,B*,b* modeHelix default
> cartoon style #1&~/a*,A*,B*,b* modeHelix wrap
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1562, in
_update_graphics_if_needed
s[i]._update_graphics_if_needed()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 300, in
_update_graphics_if_needed
self._create_ribbon_graphics()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 553, in _create_ribbon_graphics
ribbons_drawing.compute_ribbons(self)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 586, in compute_ribbons
_make_ribbon_graphics(structure, self)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 117, in _make_ribbon_graphics
structure.ribbon_mode_helix, structure.ribbon_mode_strand)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 909, in _smooth_ribbon
_wrap_helix(rlist, coords, guides, start, end)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 999, in _wrap_helix
guides[start:end] = coords[start:end] + directions
TypeError: 'NoneType' object does not support item assignment
Error processing trigger "graphics update":
TypeError: 'NoneType' object does not support item assignment
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 999, in _wrap_helix
guides[start:end] = coords[start:end] + directions
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62G 12G 18G 355M 31G 49G
Swap: 4.9G 0B 4.9G
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed in ChimeraX 1.1.
Cartoon helix mode wrap assumed guide atoms (O for amino acids, C1' for nucleic acids) all existed. Made it handle the case where they do not all exist.