Opened 6 years ago

Closed 6 years ago

#2360 closed defect (duplicate)

Show clipping caps: Array argument has non-numeric values

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
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:        Darwin-17.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-07-31)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-07-31)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd flycatcher/chimerax

Current working directory is: /Users/saotome/Desktop/flycatcher/chimerax  

> open flyc1.cxc

> close all

> open /Users/saotome/Desktop/flycatcher/chimerax/class6class34_composite.mrc

Opened class6class34_composite.mrc, grid size 256,256,256, pixel 1.03, shown
at level 2.87, step 1, values float32  

> open
/Users/saotome/Desktop/flycatcher/chimerax/up_rosetta_withlipid_withpeptides_heptamer.pdb

Chain information for up_rosetta_withlipid_withpeptides_heptamer.pdb #2  
---  
Chain | Description  
A B C D E F G | No description available  
  

> open /Users/saotome/Desktop/flycatcher/chimerax/cryosparc_C1.mrc

Opened cryosparc_C1.mrc, grid size 256,256,256, pixel 1.03, shown at level
0.24, step 1, values float32  

> color #2 yellow

> color #2/a #66c2a5

> color #2/b #fc8d62

> color #2/c #8da0cb

> color #2/d #e78ac3

> color #2/e #a6d854

> color #2/f #ffd92f

> color #2/g #e5c494

> color zone #1 near #2 distance 3

> set bgColor white

> lighting soft

> hide #2 models

> surface dust #3 size 7

> surface dust #1 size 7

> surface dust #4 size 7

No surfaces specified  

> volume selMaps planes z orthoplanes off style solid

> volume selMaps planes z orthoplanes off style solid

> volume selMaps region all orthoplanes off

> volume selMaps style surface

> volume selMaps style surface

> volume selMaps style mesh

> volume selMaps style surface

> open /Users/saotome/Desktop/flycatcher/combination/runC7masked_class001.mrc

Opened runC7masked_class001.mrc, grid size 256,256,256, pixel 1.03, shown at
level 0.00872, step 1, values float32  

> open /Users/saotome/Desktop/flycatcher/c7sharp_resampled.mrc

Opened c7sharp_resampled.mrc, grid size 256,256,256, pixel 1.03, shown at
level 0.0167, step 1, values float32  

> open flyc1.cxc

> close all

> open /Users/saotome/Desktop/flycatcher/chimerax/class6class34_composite.mrc

Opened class6class34_composite.mrc, grid size 256,256,256, pixel 1.03, shown
at level 2.87, step 1, values float32  

> open
/Users/saotome/Desktop/flycatcher/chimerax/up_rosetta_withlipid_withpeptides_heptamer.pdb

Chain information for up_rosetta_withlipid_withpeptides_heptamer.pdb #2  
---  
Chain | Description  
A B C D E F G | No description available  
  

> open /Users/saotome/Desktop/flycatcher/chimerax/cryosparc_C1.mrc

Opened cryosparc_C1.mrc, grid size 256,256,256, pixel 1.03, shown at level
0.24, step 1, values float32  

> color #2 gray

> color #2/a #66c2a5

> color #2/b #fc8d62

> color #2/c #8da0cb

> color #2/d #e78ac3

> color #2/e #a6d854

> color #2/f #ffd92f

> color #2/g #e5c494

> color zone #1 near #2 distance 3

> set bgColor white

> lighting soft

> hide #2 models

> surface dust #3 size 7

> surface dust #1 size 7

> surface dust #4 size 7

No surfaces specified  

> open flyc1.cxc

> close all

> open /Users/saotome/Desktop/flycatcher/chimerax/class6class34_composite.mrc

Opened class6class34_composite.mrc, grid size 256,256,256, pixel 1.03, shown
at level 2.87, step 1, values float32  

> open
/Users/saotome/Desktop/flycatcher/chimerax/up_rosetta_withlipid_withpeptides_heptamer.pdb

Chain information for up_rosetta_withlipid_withpeptides_heptamer.pdb #2  
---  
Chain | Description  
A B C D E F G | No description available  
  

> open /Users/saotome/Desktop/flycatcher/chimerax/cryosparc_C1.mrc

Opened cryosparc_C1.mrc, grid size 256,256,256, pixel 1.03, shown at level
0.24, step 1, values float32  

> color #2 gray

> color #2/a #66c2a5

> color #2/b #fc8d62

> color #2/c #8da0cb

> color #2/d #e78ac3

> color #2/e #a6d854

> color #2/f #ffd92f

> color #2/g #e5c494

> color zone #1 near #2 distance 4

> set bgColor white

> lighting soft

> hide #2 models

> surface dust #3 size 7

> surface dust #1 size 7

> surface dust #4 size 7

No surfaces specified  

> volume #1 orthoplanes xyz positionPlanes 128,128,128 style solid region all

> volume #3 orthoplanes xyz positionPlanes 128,128,128 style solid region all

> volume #1 orthoplanes xyz positionPlanes 128,128,128 style solid region all

> volume #3 orthoplanes xyz positionPlanes 128,128,128 style solid region all

> volume selMaps region all orthoplanes off

> volume selMaps style surface

> volume selMaps style surface

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting simple

> lighting simple

> lighting soft

> set silhouettes false

> lighting shadows true intensity 0.5

> toolshed show "Side View"

Traceback (most recent call last):  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 127, in _redraw_timer_callback  
self.draw_new_frame()  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 127, in _redraw_timer_callback  
self.draw_new_frame()  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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.  
  

[removed a bunch of these]

Traceback (most recent call last):  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 127, in _redraw_timer_callback  
self.draw_new_frame()  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 127, in _redraw_timer_callback  
self.draw_new_frame()  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 127, in _redraw_timer_callback  
self.draw_new_frame()  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 61, in draw_new_frame  
surface.update_clip_caps(view)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 27, in update_clip_caps  
subdivision = settings.clipping_cap_subdivision)  
File
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/private/var/folders/70/4whnfgn155bc2r4bzdj1_r88000twt/T/AppTranslocation/BB54134E-96FB-4745-BDA2-E10E22E926A9/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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: 4.1 NVIDIA-10.30.33 355.11.10.10.35.101
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 6 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 clipping caps: Array argument has non-numeric values

comment:2 by Tom Goddard, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #2277. Fixed a month ago.

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