Opened 6 years ago

Closed 6 years ago

#2277 closed defect (fixed)

Clipping error when plane does not intersect surface

Reported by: yazan.abbas@… Owned by: Tom Goddard
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:        Linux-4.15.0-55-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-07-31)
Description
was trying to adjust front clip in side view when error popped up.

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  
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
yazan.abbas@gmail.com is subscribed to the ChimeraX announcements list  

> open maps_and_models/state1_composite_190730.cif name State1

Summary of feedback from opening maps_and_models/state1_composite_190730.cif  
---  
warnings | skipping chem_comp category: Missing column 'type' near line 297  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
skipping chem_comp category: Missing column 'type' near line 70025  
skipping chem_comp category: Missing column 'type' near line 70052  
  
Chain information for State1 #1  
---  
Chain | Description  
A1 A2 A3 | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
C | No description available  
D | No description available  
E1 E2 E3 | No description available  
F | No description available  
G1 G2 G3 | No description available  
K1 | No description available  
K2 | No description available  
K3 | No description available  
a | No description available  
b | No description available  
c1 c2 c3 c4 c5 c6 c7 c8 c9 | No description available  
d | No description available  
e | No description available  
f | No description available  
p | No description available  
s1 | No description available  
  

> open maps_and_models/composite_state1_vopmax_190730a.mrc

File not found: maps_and_models/composite_state1_vopmax_190730a.mrc  

> set bgColor white

> set silhouettes true

> camera ortho

Expected true or false or a keyword  

> lighting soft shadows true intensity 0.3

> set selectionWidth 2

> set silhouetteWidth 2.5

> lighting soft shadows true intensity 0.2 depthCue true direction 1,-1,-1
qualityOfShadows normal

> zoom pixelSize 0.101

> close #1.1

> split #1 chains

Chain information for State1 A1 #1.1  
---  
Chain | Description  
A1 | No description available  
  
Chain information for State1 A2 #1.2  
---  
Chain | Description  
A2 | No description available  
  
Chain information for State1 A3 #1.3  
---  
Chain | Description  
A3 | No description available  
  
Chain information for State1 B1 #1.4  
---  
Chain | Description  
B1 | No description available  
  
Chain information for State1 B2 #1.5  
---  
Chain | Description  
B2 | No description available  
  
Chain information for State1 B3 #1.6  
---  
Chain | Description  
B3 | No description available  
  
Chain information for State1 C #1.7  
---  
Chain | Description  
C | No description available  
  
Chain information for State1 D #1.8  
---  
Chain | Description  
D | No description available  
  
Chain information for State1 E1 #1.9  
---  
Chain | Description  
E1 | No description available  
  
Chain information for State1 E2 #1.10  
---  
Chain | Description  
E2 | No description available  
  
Chain information for State1 E3 #1.11  
---  
Chain | Description  
E3 | No description available  
  
Chain information for State1 F #1.12  
---  
Chain | Description  
F | No description available  
  
Chain information for State1 G1 #1.13  
---  
Chain | Description  
G1 | No description available  
  
Chain information for State1 G2 #1.14  
---  
Chain | Description  
G2 | No description available  
  
Chain information for State1 G3 #1.15  
---  
Chain | Description  
G3 | No description available  
  
Chain information for State1 K1 #1.16  
---  
Chain | Description  
K1 | No description available  
  
Chain information for State1 K2 #1.17  
---  
Chain | Description  
K2 | No description available  
  
Chain information for State1 K3 #1.18  
---  
Chain | Description  
K3 | No description available  
  
Chain information for State1 a #1.19  
---  
Chain | Description  
a | No description available  
  
Chain information for State1 b #1.20  
---  
Chain | Description  
b | No description available  
  
Chain information for State1 c1 #1.21  
---  
Chain | Description  
c1 | No description available  
  
Chain information for State1 c2 #1.22  
---  
Chain | Description  
c2 | No description available  
  
Chain information for State1 c3 #1.23  
---  
Chain | Description  
c3 | No description available  
  
Chain information for State1 c4 #1.24  
---  
Chain | Description  
c4 | No description available  
  
Chain information for State1 c5 #1.25  
---  
Chain | Description  
c5 | No description available  
  
Chain information for State1 c6 #1.26  
---  
Chain | Description  
c6 | No description available  
  
Chain information for State1 c7 #1.27  
---  
Chain | Description  
c7 | No description available  
  
Chain information for State1 c8 #1.28  
---  
Chain | Description  
c8 | No description available  
  
Chain information for State1 c9 #1.29  
---  
Chain | Description  
c9 | No description available  
  
Chain information for State1 d #1.30  
---  
Chain | Description  
d | No description available  
  
Chain information for State1 e #1.31  
---  
Chain | Description  
e | No description available  
  
Chain information for State1 f #1.32  
---  
Chain | Description  
f | No description available  
  
Chain information for State1 p #1.33  
---  
Chain | Description  
p | No description available  
  
Chain information for State1 s1 #1.34  
---  
Chain | Description  
s1 | No description available  
  
Split State1 (#1) into 34 models  

> dssp

> name subunitA #1.1-3 & ~#1.3:701,702

> name subunitB #1.4-6

> name subunitC #1.7

> name subunitD #1.8

> name subunitE #1.9-11

> name subunitF #1.12

> name subunitG #1.13-15

> name SidK #1.16-18

> name V0a #1.19

> name V0b #1.21

> name V0cring #1.22-30

> name V0d #1.31

> name V0e #1.32

> name V0RNAseK #1.33

> name V0Ac45 #1.20

> name V0PRR #1.34

> surface cap true

> open maps_and_models/composite_state1_vopmax_190730.mrc

Opened composite_state1_vopmax_190730.mrc, grid size 340,340,340, pixel 1.06,
shown at level 1.16, step 2, values float32  

> hide #!1 models

> show #!1 models

> hide #!2 models

> name subunitA #1.1-3 & ~#1.3:701,702

> name subunitB #1.4-6

> name subunitC #1.7

> name subunitD #1.8

> name subunitE #1.9-11

> name subunitF #1.12

> name subunitG #1.13-15

> name SidK #1.16-18

> name V0a #1.19

> name V0b #1.20

> name V0cring #1.21-29

> name V0d #1.30

> name V0e #1.31

> name V0RNAseK #1.32

> name V0Ac45 #1.34

> name V0PRR #1.33

> name adp #1.3:701

> name magnesium #1.3:702

> select subunitA

13953 atoms, 14238 bonds, 3 models selected  

> select clear

> color subunitA #F2EA42

> color subunitB #D01F26

> color subunitC #996633

> color subunitD #3A53A3

> color subunitE #804F9F

> color subunitF #B9529E

> color subunitG #fce94f

> color SidK #D2D2D2

> color V0a #8ef826

> color V0b #9d42bf

> color V0cring #f4b0ef

> color V0d #96cff7

> color V0e #3465a4

> color V0RNAseK #CC0000

> color V0Ac45 #B2B2FF

> color V0PRR #edd400

> color adp #8ae234

> color magnesium #75507b

> lighting flat

> set silhouettes false

> set silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting simple

> lighting soft

> lighting soft shadows true intensity 0.2 depthCue true direction 1,-1,-1
qualityOfShadows normal

> color subunitC #e9b96e target abp

> color subunitC #e9b96e

> color subunitG #edd400 target abp

> color subunitG #c4a000 target abp

> color subunitA #fce94f target abp

> color subunitA #edd400 target abp

> color subunitA #fce94f target abp

> color subunitA #F2EA42

> color subunitA #fce94f target abp

> color subunitA #fff845 target abp

> color subunitA #fff845

> color subunitG #f7c618 target abp

> lighting flat

> color subunitG #d9ad10 target abp

> color subunitG #d9ad10

> lighting soft shadows true intensity 0.2 depthCue true direction 1,-1,-1
qualityOfShadows normal

> hide atoms

> show cartoons

> show #!2 models

> volume #2 step 1 level 1 color #eeeeec surfaceSmoothing false
subdivideSurface false smoothingIterations 4

> surface dust #2 size 10

> volume #2 step 1 level 1 color #B2B2FF surfaceSmoothing false
subdivideSurface false smoothingIterations 4

> volume zone #2 nearAtoms #1 range 2 invert true minimalBounds true modelId
#3

> volume #3 level 1 color #B2B2FF

> hide #!1 models

> surface dust #3 size 10

> surface dust #3 size 20

> surface dust #3 size 40

> surface dust #3 size 30

> surface dust #3 size 35

> surface dust #3 size 36

> surface dust #3 size 37

> surface dust #3 size 38

> surface dust #3 size 40

> show #!2 models

> hide #!3 models

> color zone #2 near #1 distance 3 update false

> color zone #2 near #1 distance 4 update false

> color zone #2 near #1 distance 5 update false

> color zone #2 near #1 distance 6 update false

> color zone #2 near #1 distance 7 update false

> color zone #2 near #1 distance 8 update false

> color zone #2 near #1 distance 10 update false

> show #!3 models

> hide #!3 models

> show #!3 models

> lighting gentle shadows true intensity 0.1 qualityOfShadows normal

> lighting gentle shadows true intensity 0.1 qualityOfShadows normal direction
0,0,-1 multiShadow 1024

> lighting gentle shadows true intensity 0.1 qualityOfShadows normal direction
0,0,-1 multiShadow 128

> lighting gentle shadows true intensity 0.1 qualityOfShadows normal direction
0,0,-1 multiShadow 64

> lighting soft shadows true intensity 0.1 qualityOfShadows normal direction
0,0,-1 multiShadow 64

> lighting soft shadows true intensity 0.1 qualityOfShadows normal direction
0,0,-1 multiShadow 512

> lighting soft shadows true intensity 0.1 qualityOfShadows normal direction
0,0,-1 multiShadow 1024

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 127, in _redraw_timer_callback  
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 418.56
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Tom Goddard, 6 years ago

Component: Unassigned → Depiction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipping error when plane does not intersect surface

comment:2 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Code added yesterday to refine clip cap meshes did not handle empty caps correctly.

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