Opened 6 years ago

Closed 6 years ago

#2691 closed defect (duplicate)

Error with nucleotide/ring graphics after session restore

Reported by: nicholas.sofos@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
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: 0.91 (2019-08-24)
Description
Executing the same command multiple times using different values suddently started triggering the problem.

Log:
UCSF ChimeraX version: 0.91 (2019-08-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/hqj603/Desktop/Postdoc_Montoya_lab/CmrB_ChimeraX_sessions/ANP1_CTRdensity_stalk_overview.cxs
format session

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2664, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 314, in
_update_graphics_if_needed  
self._create_ring_graphics()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 500, in _create_ring_graphics  
atoms = ring.ordered_atoms  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 161, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 93, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'Ring' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "graphics update":  
AttributeError: 'Ring' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 93, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> cartoon style helix width 1.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
ZeroDivisionError: float division by zero  
  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
  
See log for complete Python traceback.  
  

Expected a keyword  

> cartoon style #1 width 1.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
ZeroDivisionError: float division by zero  
  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
  
See log for complete Python traceback.  
  

> cartoon style #1 thickness 1.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
ZeroDivisionError: float division by zero  
  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
  
See log for complete Python traceback.  
  

> cartoon style thickness 1.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
ZeroDivisionError: float division by zero  
  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 298, in cartoon_style  
old_arrow_scale = aw / w  
  
See log for complete Python traceback.  
  

> cartoon style strand thickness 1.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 406, in cartoon_style  
old_arrow_scale = aw / w  
ZeroDivisionError: float division by zero  
  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 406, in cartoon_style  
old_arrow_scale = aw / w  
  
See log for complete Python traceback.  
  

> cartoon style strand thickness 1.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 406, in cartoon_style  
old_arrow_scale = aw / w  
ZeroDivisionError: float division by zero  
  
ZeroDivisionError: float division by zero  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/cartoon.py", line 406, in cartoon_style  
old_arrow_scale = aw / w  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Error with nucleotide/ring graphics after session restore

comment:2 by pett, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Hi Nicholas,

This problem was fixed about two months after you downloaded your version of ChimeraX, so if you get the current daily build you should be able to restore that session. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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