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#5595 closed defect (fixed)

cartoon undo: 'list' object has no attribute 'ribbon_tether_opacities'

Reported by:	ed.luk@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Undo/Redo	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005180441 (2020-05-18 04:41:25 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Updating list of available bundles failed: Internal Server Error  
  
UCSF ChimeraX version: 1.0rc202005180441 (2020-05-18)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> close

> device snav true

> open 7O4I

Summary of feedback from opening 7O4I fetched from pdb  
---  
notes | Fetching compressed mmCIF 7o4i from
http://files.rcsb.org/download/7o4i.cif  
Fetching CCD SF4 from http://ligand-expo.rcsb.org/reports/S/SF4/SF4.cif  
Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif  
  
7o4i title:  
Yeast RNA polymerase II transcription pre-initiation complex with initial
transcription bubble [more info...]  
  
Chain information for 7o4i #1  
---  
Chain | Description  
0 | General transcription and DNA repair factor IIH helicase subunit XPD  
1 | General transcription and DNA repair factor IIH subunit TFB1  
2 | General transcription and DNA repair factor IIH subunit TFB2  
3 | RNA polymerase II transcription factor B subunit 3  
4 | General transcription and DNA repair factor IIH subunit TFB4  
5 | General transcription and DNA repair factor IIH subunit TFB5  
6 | General transcription and DNA repair factor IIH subunit SSL1  
7 | General transcription and DNA repair factor IIH helicase subunit XPB  
A | DNA-directed RNA polymerase II subunit RPB1  
B | DNA-directed RNA polymerase II subunit RPB2  
C | DNA-directed RNA polymerase II subunit RPB3  
D | DNA-directed RNA polymerase II subunit RPB4  
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1  
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2  
G | DNA-directed RNA polymerase II subunit RPB7  
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3  
I | DNA-directed RNA polymerase II subunit RPB9  
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5  
K | DNA-directed RNA polymerase II subunit RPB11  
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4  
M | Transcription initiation factor IIB  
N | Non-template DNA  
O | TATA-box-binding protein  
Q | Transcription initiation factor IIF subunit α  
R | Transcription initiation factor IIF subunit β  
T | Template DNA  
U | Transcription initiation factor IIA large subunit,Transcription initiation
factor IIA large subunit  
V | Transcription initiation factor IIA subunit 2  
W | Transcription initiation factor IIE subunit α  
X | Transcription initiation factor IIE subunit β  
  
Non-standard residues in 7o4i #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> close

> device snav true

> open 7O4I

7o4i title:  
Yeast RNA polymerase II transcription pre-initiation complex with initial
transcription bubble [more info...]  
  
Chain information for 7o4i #1  
---  
Chain | Description  
0 | General transcription and DNA repair factor IIH helicase subunit XPD  
1 | General transcription and DNA repair factor IIH subunit TFB1  
2 | General transcription and DNA repair factor IIH subunit TFB2  
3 | RNA polymerase II transcription factor B subunit 3  
4 | General transcription and DNA repair factor IIH subunit TFB4  
5 | General transcription and DNA repair factor IIH subunit TFB5  
6 | General transcription and DNA repair factor IIH subunit SSL1  
7 | General transcription and DNA repair factor IIH helicase subunit XPB  
A | DNA-directed RNA polymerase II subunit RPB1  
B | DNA-directed RNA polymerase II subunit RPB2  
C | DNA-directed RNA polymerase II subunit RPB3  
D | DNA-directed RNA polymerase II subunit RPB4  
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1  
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2  
G | DNA-directed RNA polymerase II subunit RPB7  
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3  
I | DNA-directed RNA polymerase II subunit RPB9  
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5  
K | DNA-directed RNA polymerase II subunit RPB11  
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4  
M | Transcription initiation factor IIB  
N | Non-template DNA  
O | TATA-box-binding protein  
Q | Transcription initiation factor IIF subunit α  
R | Transcription initiation factor IIF subunit β  
T | Template DNA  
U | Transcription initiation factor IIA large subunit,Transcription initiation
factor IIA large subunit  
V | Transcription initiation factor IIA subunit 2  
W | Transcription initiation factor IIE subunit α  
X | Transcription initiation factor IIE subunit β  
  
Non-standard residues in 7o4i #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> hide atoms

> show surfaces

> color /A,B,C,D,E,F,G,H,I,J,K,L gray

> color /A,B,C,D,E,F,G,H,I,J,K,L rgb(150,150,150)

> bgcolor white

Unknown command: bgcolor white  

> set bgColor white

> color /N cyan

> color /T blue

> color /0,1,2,4,5,6,7 pink

> hide /W,X target s

> show /W,X atoms

> style /W,X cartoon

Expected a keyword  

> hide /W,X target s

> show /W,X cartoons

> hide /W,X target a

> cartoon style /W,X protein model tube rad 2 sides 24

Expected a keyword  

> cartoon style /W,X tube

Expected a keyword  

> cartoon style /W,X protein tube

Expected a keyword  

> cartoon style /W,X

7o4i #1  
\- helix mode=default xsection=round width=2 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 /W,X modeHelix

Missing "modeHelix" keyword's argument  

> cartoon style /W,X tube

Expected a keyword  

> cartoon style /W,X tube rad 2

Expected a keyword  

> cartoon style /W,X helix tube rad 2

Expected a keyword  

> preset cylinder

Changed 73891 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

  

> close

> device snav true

> open 7O4I

7o4i title:  
Yeast RNA polymerase II transcription pre-initiation complex with initial
transcription bubble [more info...]  
  
Chain information for 7o4i #1  
---  
Chain | Description  
0 | General transcription and DNA repair factor IIH helicase subunit XPD  
1 | General transcription and DNA repair factor IIH subunit TFB1  
2 | General transcription and DNA repair factor IIH subunit TFB2  
3 | RNA polymerase II transcription factor B subunit 3  
4 | General transcription and DNA repair factor IIH subunit TFB4  
5 | General transcription and DNA repair factor IIH subunit TFB5  
6 | General transcription and DNA repair factor IIH subunit SSL1  
7 | General transcription and DNA repair factor IIH helicase subunit XPB  
A | DNA-directed RNA polymerase II subunit RPB1  
B | DNA-directed RNA polymerase II subunit RPB2  
C | DNA-directed RNA polymerase II subunit RPB3  
D | DNA-directed RNA polymerase II subunit RPB4  
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1  
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2  
G | DNA-directed RNA polymerase II subunit RPB7  
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3  
I | DNA-directed RNA polymerase II subunit RPB9  
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5  
K | DNA-directed RNA polymerase II subunit RPB11  
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4  
M | Transcription initiation factor IIB  
N | Non-template DNA  
O | TATA-box-binding protein  
Q | Transcription initiation factor IIF subunit α  
R | Transcription initiation factor IIF subunit β  
T | Template DNA  
U | Transcription initiation factor IIA large subunit,Transcription initiation
factor IIA large subunit  
V | Transcription initiation factor IIA subunit 2  
W | Transcription initiation factor IIE subunit α  
X | Transcription initiation factor IIE subunit β  
  
Non-standard residues in 7o4i #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> hide atoms

> show surfaces

> set bgColor white

> color /A,B,C,D,E,F,G,H,I,J,K,L rgb(150,150,150)

> color /N cyan

> color /T blue

> color /0,1,2,4,5,6,7 pink

> hide /W,X target s

> present /W,X cylinders

Unknown command: present /W,X cylinders  

> alias /W,X cylinders cartoon style protein modeh tube rad 2 sides 24

> alias cylinders /W,X cartoon style protein modeh tube rad 2 sides 24

> show /W,X cartoons

> alias cylinders /W,X cartoon style protein modeh tube rad 2 sides 24

> cartoon style /W,X modeHelix tube

> cartoon style /W,X modeHelix tube radius 3

> cartoon style /W,X modeHelix tube radius 2

> cartoon style /W,X modeHelix tube width 1.5

> cartoon style /W,X modeHelix tube width 3

> cartoon style /W,X modeHelix tube width 2

> cartoon style /W,X strand xsection rect width 2

Expected a keyword  

> cartoon style /W,X strand width 2

Expected a keyword  

> cartoon style /W,X width 2

> cartoon style /W,X width 5

> cartoon style /W,X width 2 thickness 2

> cartoon style /W,X width 2 thickness 1

> color /W,X hot pink

> cartoon tether opacity 0

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 151, in cartoon_tether  
undo_state.add(structures, "ribbon_tether_opacities",
structures.ribbon_tether_opacities, opacity)  
AttributeError: 'list' object has no attribute 'ribbon_tether_opacities'  
  
AttributeError: 'list' object has no attribute 'ribbon_tether_opacities'  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 151, in cartoon_tether  
undo_state.add(structures, "ribbon_tether_opacities",
structures.ribbon_tether_opacities, opacity)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.22
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1419)
      Kernel Version: Darwin 19.6.0
      Time since boot: 25 days 32 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR DQHD:
          Resolution: 7680 x 2160
          UI Looks like: 3840 x 1080 @ 30 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by pett, 4 years ago

Component:	Unassigned → Undo/Redo
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → cartoon undo: 'list' object has no attribute 'ribbon_tether_opacities'

comment:2 by Tom Goddard, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

This bug in the cartoon tether command was fixed more than a year ago. Update ChimeraX if you want this to work. There have been a few new ChimeraX versions since your pre 1.0 release version.

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