Opened 3 years ago

Closed 3 years ago

#7279 closed defect (duplicate)

Attempt to draw dead arrow

Reported by: apadavannil@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_73/Open_Refine73.cif

Summary of feedback from opening
/Users/apadavan/Desktop/Drosophila_processing/Model_Building/Refinement_Drosophila_Model/RealSpaceRefine_73/Open_Refine73.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom C27 has no neighbors to form bonds with according to residue template for
CDL /2:404  
Atom OXT is not in the residue template for ASN /3:117  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Open_Refine73.cif #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
4L | No description available  
5 | No description available  
6 | No description available  
A1 | No description available  
A3 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
AB | No description available  
AC | No description available  
AL | No description available  
AM | No description available  
AN | No description available  
AO | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BL | No description available  
BM | No description available  
C2 | No description available  
S1 | No description available  
S2 | No description available  
S3 | No description available  
S4 | No description available  
S5 | No description available  
S6 | No description available  
S7 | No description available  
S8 | No description available  
V1 | No description available  
V2 | No description available  
V3 | No description available  
  

> hide atoms

> show cartoons

> set bgColor white

> view

> view

> view

> view matrix

camera position:
-0.2743,-0.16326,-0.94768,-735.34,-0.50089,-0.81699,0.28573,522.49,-0.8209,0.55306,0.14232,372.86  
model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix

camera position:
0.0232,-0.14544,-0.9891,-777.44,-0.57241,-0.81307,0.10613,339.93,-0.81964,0.56371,-0.10211,124.38  
model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> turn y 180

> color #1/V1 #DC050C

> color #1/V2 #E8601C

> color #1/S1 #F1932D

> color #1/S2 #F6C141

> color #1/S3 #F7F056

> color #1/S7 #CAE0AB

> color #1/S8 #90C987

> color #1/1 #7BAFDE

> color #1/2 #D1BBD7

> color #1/3 #4EB265

> color #1/4 #AE76A3

> color #1/4L #1965B0

> color #1/5 #882E72

> color #1/6 #5289C7

> color #1/A1 #B8221E

> color #1/A3 #69B190

> color #1/A5 #95211b

> color #1/A6 #DF4828

> color #1/A7 #4D8AC6

> color #1/A8 #C3A8D1

> color #1/A9 #6F4C9B

> color #1/AL #59A5A9

> color #1/AM #FEDA8B

> color #1/AN #D1B541

> color #1/AO #BEBC48

> color #1/AB #B58FC2

> color #1/AC #B58FC2

> color #1/B1 #DA2222

> color #1/B2 #E78C35

> color #1/B3 #77B77D

> color #1/B4 #D1B541

> color #1/B5 #4A7BB7

> color #1/B6 #D1B541

> color #1/B7 #DDAA3C

> color #1/B8 #E67932

> color #1/B9 #E49C39

> color #1/BL #95211B

> color #1/BM #E4632D

> color #1/C2 #8CBC68

> color #1/S4 #8C4E99

> color #1/S5 #60AB9E

> color #1/S6 #721E17

> color #1/V3 #A778B4

> show surfaces

> color #1/V1 #DC050C

> color #1/V2 #E8601C

> color #1/S1 #F1932D

> color #1/S2 #F6C141

> color #1/S3 #F7F056

> color #1/S7 #CAE0AB

> color #1/S8 #90C987

> color #1/1 #7BAFDE

> color #1/2 #D1BBD7

> color #1/3 #4EB265

> color #1/4 #AE76A3

> color #1/4L #1965B0

> color #1/5 #882E72

> color #1/6 #5289C7

> color #1/A1 #B8221E

> color #1/A3 #69B190

> color #1/A5 #95211b

> color #1/A6 #DF4828

> color #1/A7 #4D8AC6

> color #1/A8 #C3A8D1

> color #1/A9 #6F4C9B

> color #1/AL #59A5A9

> color #1/AM #FEDA8B

> color #1/AN #D1B541

> color #1/AO #BEBC48

> color #1/AB #B58FC2

> color #1/AC #B58FC2

> color #1/B1 #DA2222

> color #1/B2 #E78C35

> color #1/B3 #77B77D

> color #1/B4 #D1B541

> color #1/B5 #4A7BB7

> color #1/B6 #D1B541

> color #1/B7 #DDAA3C

> color #1/B8 #E67932

> color #1/B9 #E49C39

> color #1/BL #95211B

> color #1/BM #E4632D

> color #1/C2 #8CBC68

> color #1/S4 #8C4E99

> color #1/S5 #60AB9E

> color #1/S6 #721E17

> color #1/V3 #A778B4

> lighting soft

> select
> ::name="3PE"::name="C14"::name="CDL"::name="D12"::name="DGT"::name="FES"::name="FMN"::name="NDP"::name="OCT"::name="PC1"::name="SF4"::name="U10"::name="ZMP"::name="ZN"

2393 atoms, 2368 bonds, 68 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 2393 atom styles  

> setattr sel a radius 1.2

Assigning radius attribute to 2393 items  

> color sel byelement

> select clear

> movie record supersample 3

> 2dlabels arrow start .5, .075 end .9, .2 color #FEDA8B

> ui mousemode right "move label"

> 2dlabels arrow #2.1 end 0.900,0.200

> 2dlabels arrow #2.1 end 0.830,0.250

> 2dlabels arrow #2.1 end 0.616,0.365

> 2dlabels arrow #2.1 end 0.422,0.371

> 2dlabels arrow #2.1 end 0.454,0.381

> 2dlabels arrow delete

Expected an arrow models specifier or a keyword  

> 2dlabels arrow #2.1 start .5, .075 end .454, .381, color #FEDA8B, weight 0.1

Invalid "end" argument: Expected a number  

> 2dlabels arrow #2.1 start .5, .075 end 0.454, 0.381, color #FEDA8B, weight
> 0.1

Invalid "end" argument: Expected a number  

> close #2.1

> hide #2 models

> show #2 models

> 2dlabels arrow start .5, .075 end .9, .2 color #FEDA8B, weight 0.5

Invalid "color" argument: Expected 'default' or a color  

> 2dlabels arrow start .5, .075 end .9, .2 color #FEDA8B , weight 0.5

Expected a keyword  

> 2dlabels arrow start .5, .075 end .9, .2 color #FEDA8B weight 0.5

> turn #2.1 y 120

Expected an axis vector or a keyword  

> 2dlabels arrow #2.1 end 0.477,0.246

Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/label/arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 368, in set_display  
dp = self.display_positions  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Users/apadavan/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  

> 2dlabels arrow # start 0.506,0.070

Expected an arrow models specifier or a keyword  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 432.60.3.0.0
      SMC Version (system): 2.17f7

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1615)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1 day 23:33

Graphics/Displays:

    NVIDIA GeForce GT 750M:

      Chipset Model: NVIDIA GeForce GT 750M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fe9
      Revision ID: 0x00a2
      ROM Revision: 3762
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        HP VH240a:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 6CM1160B4N  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
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    ChimeraX-PubChem: 2.0.1
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    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
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    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-SDF: 2.0
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    ChimeraX-Segment: 1.0
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    ChimeraX-Storm: 1.0
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    ChimeraX-SwapRes: 2.1
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    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
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    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
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    ChimeraX-Zone: 1.0
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    comtypes: 1.1.7
    cxservices: 1.0
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    distlib: 0.3.1
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    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
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    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Depiction
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Attempt to draw dead arrow

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Abhilash,

Thanks for reporting this problem. It was fixed about 4 months ago, so if you get the 1.4 production release you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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