Opened 5 years ago

Closed 5 years ago

#3513 closed defect (duplicate)

show_surface_clip_caps: Array argument has non-numeric values

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version: 0.91
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        Linux-5.4.0-40-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 0.91 (2019-07-30)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-07-30)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/giovanni/Pramod/E_SMA/Publication_figure/CDL-A map contour.cxs"
format session

opened ChimeraX session  

Invalid "subdivisionLevels" argument: Expected an integer  

> volume #2 subdivideSurface true subdivisionLevels 1

> select #1/A:261-285

192 atoms, 196 bonds, 1 model selected  

> show sel atoms

> show sel ribbons

> hide sel atoms

> surface zone #2 nearAtoms #1/A:261-285

> select down

192 atoms, 196 bonds, 1 model selected  

> select up

2666 atoms, 2732 bonds, 1 model selected  

> select up

13330 atoms, 13660 bonds, 1 model selected  

> select up

13330 atoms, 13660 bonds, 3 models selected  

> select up

13330 atoms, 13660 bonds, 3 models selected  

> select down

13330 atoms, 13660 bonds, 1 model selected  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style selAtoms stick

Changed 13330 atom styles  

> style selAtoms stick

Changed 13330 atom styles  

> hide selAtoms ribbons

> show selAtoms

> hide selAtoms

> style selAtoms stick

Changed 13330 atom styles  

> select #1/A:261-285

192 atoms, 196 bonds, 1 model selected  

> style selAtoms stick

Changed 192 atom styles  

> style selAtoms sphere

Changed 192 atom styles  

> style selAtoms ball

Changed 192 atom styles  

> show sel atoms

> style selAtoms stick

Changed 192 atom styles  

Unknown command: cocor byhetero  

> color byhetero

> color cyan

> color byhetero

> lighting simple

> lighting soft

> lighting full

> lighting simple

> color byhetero

> save image
/home/giovanni/Pramod/E_SMA/Publication_figure/M3_261285_L0.741.png width 1920
height 1080

> save image
/home/giovanni/Pramod/E_SMA/Publication_figure/M3_261285_L0.741b.png width
1760 height 1939

> select clear

> lighting simple

> lighting soft

> lighting full

> lighting simple

> save image
/home/giovanni/Pramod/E_SMA/Publication_figure/M3_261285_L0.741.png width 985
height 1085

> save image
/home/giovanni/Pramod/E_SMA/Publication_figure/M3_261285_L1.89.png width 985
height 1085

> color byhetero

> open /home/giovanni/Pramod/E_SMA/Publication_figure/M4-Mesh-.cxs

opened ChimeraX session  

> close session

> open "/home/giovanni/Pramod/E_SMA/Publication_figure/CDL-A map contour.cxs"
format session

opened ChimeraX session  

> select #1/A:261-285

192 atoms, 196 bonds, 1 model selected  

> select ~sel

13138 atoms, 13464 bonds, 3 models selected  

> hide sel

> select #1/A:261-285

192 atoms, 196 bonds, 1 model selected  

> show sel atoms

> style selAtoms stick

Changed 192 atom styles  

> surface zone #2 nearAtoms #1/A:261-285

> volume #2 subdivideSurface true subdivisionLevels 1

> select clear

> save image
/home/giovanni/Pramod/E_SMA/Publication_figure/M3_261-285_L1.2.png width 1760
height 1939

> preset "overall look" publication

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 998, in <lambda>  
run(ses, "preset %s%s" % (cat, quote_if_necessary(name.lower()))))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/preset_mgr/cmd.py", line 43, in preset_cmd  
matches = text_match(preset_text, preset_map[cat])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/preset_mgr/cmd.py", line 74, in text_match  
if l_query == l_target:  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/utils.py", line 178, in __eq__  
if not other_sort:  
NameError: name 'other_sort' is not defined  
  
NameError: name 'other_sort' is not defined  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/utils.py", line 178, in __eq__  
if not other_sort:  
  
See log for complete Python traceback.  
  

> save image
/home/giovanni/Pramod/E_SMA/Publication_figure/M3_261-285_L1.2b.png width 1760
height 1939

> toolshed show Toolbar

> save /home/giovanni/Desktop/image1.png supersample 3

> toolshed show "Side View"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
  
See log for complete Python traceback.  
  

[lots of these deleted]

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
if not self.draw_new_frame():  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 38, in show_surface_clip_caps  
varray, tarray = refine_mesh(varray, tarray, subdivision)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.100
OpenGL renderer: GeForce GT 730/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Surface
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → show_surface_clip_caps: Array argument has non-numeric values
Version: → 0.91

An old version (0.91). The first error (involving a NameError for 'other_sort') was corrected on the same date as this version. The "Array argument has non-numeric values" error might also be long ago fixed.

comment:2 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Yeah, the clip cap error was also fixed the day after it was introduced 12 months ago, #2277. This user knows how to pick a winning version!

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