Opened 4 years ago

Closed 4 years ago

#4945 closed defect (fixed)

Volume mesh: masked_edges(): edge mask array size does not equal triangle array

Reported by: marco.salamina@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-22)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Updating list of available bundles failed: Internal Server Error  
  
UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /Users/marcosalamina/Downloads/cryosparc_P14_J161_003_volume_map_sharp.mrc
> /Users/marcosalamina/Downloads/cryosparc_P14_J159_004_volume_map_sharp.mrc

Opened cryosparc_P14_J161_003_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.07, shown at level 0.126, step 1, values float32  
Opened cryosparc_P14_J159_004_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.07, shown at level 0.133, step 1, values float32  

> volume #1 level 0.2612

> volume #2 level 0.436

> set bgColor white

> select #2

2 models selected  

> ui mousemode rightMode "translate selected models"

> undo

> undo

> volume #2 level 0.3223

> volume #1 level 0.4374

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> volume #2 level 0.3792

> volume #1 level 0.5458

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ~select #2

Nothing selected  

> volume #2 level 0.436

> volume #1 level 0.4916

> rock y 3 136 cycle 68

Unknown command: rock y 3 136 cycle 68  

> rock y 3 136 cycle 68

Unknown command: rock y 3 136 cycle 68  

> rock y 3 136

Unknown command: rock y 3 136  

> help help:user

> roll y 3 136

> roll y 3 120

> lighting soft

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> roll y 3 120

> roll y 3 120

> roll x 3 120

> rock y 3 120

Unknown command: rock y 3 120  

> wobble y 3 120

Unknown command: wobble y 3 120  

> rock

Unknown command: rock  

> volume #1 level 0.6001

> volume #2 level 0.4171

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> roll x 3 120

> cd /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos

Current working directory is:
/Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos  

> windowsize 400 300

> movie record supersample 3

> roll x 3 120

> movie stop

> movie encode 2A_cdc25.mp4 quality higher

Movie saved to 2A_cdc25.mp4  
  

> close #1-2

> open2
> /Users/marcosalamina/Downloads/cryosparc_P14_J163_005_volume_map_sharp_local.mrc
> /Users/marcosalamina/Downloads/cryosparc_P14_J162_005_volume_map_sharp_local.mrc

Opened cryosparc_P14_J163_005_volume_map_sharp_local.mrc, grid size
256,256,256, pixel 1.07, shown at level 0.0776, step 1, values float32  
Opened cryosparc_P14_J162_005_volume_map_sharp_local.mrc, grid size
256,256,256, pixel 1.07, shown at level 0.0832, step 1, values float32  

> volume #1 level 0.1345

> volume #2 level 0.1791

> volume #1 level 0.2554

> volume #2 level 0.2856

> toolshed show "Fit in Map"

Fit map cryosparc_P14_J163_005_volume_map_sharp_local.mrc in map
cryosparc_P14_J162_005_volume_map_sharp_local.mrc using 79140 points  
correlation = 0.7141, correlation about mean = 0.3767, overlap = 1.481e+04  
steps = 568, shift = 4.36, angle = 38.6 degrees  
  
Position of cryosparc_P14_J163_005_volume_map_sharp_local.mrc (#1) relative to
cryosparc_P14_J162_005_volume_map_sharp_local.mrc (#2) coordinates:  
Matrix rotation and translation  
0.78519979 -0.61028361 -0.10495329 129.10613582  
0.59913788 0.79155256 -0.12032602 -36.54390143  
0.15650904 0.03159847 0.98717094 -20.09351460  
Axis 0.12186589 -0.20973143 0.97013475  
Axis point 118.45230145 169.07994025 0.00000000  
Rotation angle (degrees) 38.55946591  
Shift along axis 3.90462171  
  
Fit map cryosparc_P14_J163_005_volume_map_sharp_local.mrc in map
cryosparc_P14_J162_005_volume_map_sharp_local.mrc using 79140 points  
correlation = 0.7141, correlation about mean = 0.3768, overlap = 1.481e+04  
steps = 48, shift = 0.0228, angle = 0.166 degrees  
  
Position of cryosparc_P14_J163_005_volume_map_sharp_local.mrc (#1) relative to
cryosparc_P14_J162_005_volume_map_sharp_local.mrc (#2) coordinates:  
Matrix rotation and translation  
0.78342199 -0.61243073 -0.10572885 129.76475939  
0.60127345 0.78992729 -0.12035414 -36.59429967  
0.15722667 0.03071613 0.98708474 -20.05561236  
Axis 0.12075788 -0.21019326 0.97017335  
Axis point 118.60193397 169.17289571 0.00000000  
Rotation angle (degrees) 38.71955118  
Shift along axis 3.90457194  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #2 level 0.3623

> volume #1 level 0.2895

> volume #1 level 0.2937

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> select #1

2 models selected  

> ui mousemode rightMode "translate selected atoms"

> ui mousemode rightMode "translate selected models"

> volume #2 level 0.3239

> ui mousemode rightMode "rotate selected models"

> select clear

> select #2

2 models selected  

> ui mousemode rightMode "translate selected models"

> select clear

> graphics silhouettes false

> graphics silhouettes true

> view

> view

> view orient

> view orient

> view orient

> toolshed show "Side View"

Empty filename passed to function  

> volume #1 level 0.5199

> volume #2 level 0.3303

> cd /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos

Current working directory is:
/Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos  

> save 2A_CDC25Session includeMaps true compress gzip

Invalid "compress" argument: Expected true or false (or 1 or 0)  

> save 2A_CDC25Session includeMaps true compress

Missing "compress" keyword's argument  

> save 2ACdc25_VideoSession

Missing filename suffix 2ACdc25_VideoSession  

> save 2ACdc25_VideoSession.csx

Unrecognized file suffix '.csx'  

> save 2ACdc25_VideoSession.cxs

> roll x 3 120

> movie record supersample 3

> roll x 3 120

> movie stop

> movie encode 2Acdc25.mp4 quality higher

Movie saved to 2Acdc25.mp4  
  

> movie record supersample 3

> roll x 3 120

> movie stop

> movie encode 2Acdc25.mp4 quality higher

Movie saved to 2Acdc25.mp4  
  

> save2
> /Volumes/FastSSD/WorkSSD/CryoEM_paper_SSD/Figures/chimeraVideos/2ACdc25_VideoSession.cxs

> close session

> open2 /Users/marcosalamina/Downloads/postprocess_pentamer_153.mrc

Opened postprocess_pentamer_153.mrc, grid size 256,256,256, pixel 0.86, shown
at level 0.0101, step 1, values float32  

> open2 /Users/marcosalamina/Desktop/pentamer.pdb

Summary of feedback from opening /Users/marcosalamina/Desktop/pentamer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP C 18
TYR C 32 1 15  
Start residue of secondary structure not found: HELIX 2 2 ALA C 38 CYS C 53 1
16  
Start residue of secondary structure not found: HELIX 3 3 GLY C 85 ASP C 106 1
22  
Start residue of secondary structure not found: HELIX 4 4 SER C 114 CYS C 137
1 24  
Start residue of secondary structure not found: HELIX 5 5 TYR C 139 TRP C 144
1 6  
12 messages similar to the above omitted  
Cannot find LINK/SSBOND residue GLN (186 )  
Cannot find LINK/SSBOND residue TPO (187 )  
  
pentamer.pdb title:  
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-
assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-cyclin A-CDK2-P27 [more info...]  
  
Chain information for pentamer.pdb #2  
---  
Chain | Description  
K | CKS-1  
L | cyclin-dependent kinase 2  
S | S-phase kinase-associated protein 1  
T | S-phase kinase-associated protein 2  
Y | cyclin-A2  
  

> hide surfaces

> show cartoons

> hide surfaces

> hide atoms

> toolshed show "Fit in Map"

Fit molecule pentamer.pdb (#2) to map postprocess_pentamer_153.mrc (#1) using
8556 atoms  
average map value = 0.007106, steps = 252  
shifted from previous position = 4.1  
rotated from previous position = 34.7 degrees  
atoms outside contour = 5690, contour level = 0.010138  
  
Position of pentamer.pdb (#2) relative to postprocess_pentamer_153.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.91854713 0.29885921 -0.25875537 3.45449576  
-0.15555822 0.87501541 0.45842085 -23.49645645  
0.36341823 -0.38082964 0.85023290 19.02963528  
Axis -0.73665624 -0.54611593 -0.39886712  
Axis point 0.00000000 30.61706410 56.39009916  
Rotation angle (degrees) 34.72478380  
Shift along axis 2.69671742  
  

> select #2

8556 atoms, 8747 bonds, 12 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> ~select #2

Nothing selected  
Fit molecule pentamer.pdb (#2) to map postprocess_pentamer_153.mrc (#1) using
8556 atoms  
average map value = 0.01212, steps = 216  
shifted from previous position = 14.3  
rotated from previous position = 30.8 degrees  
atoms outside contour = 3093, contour level = 0.010138  
  
Position of pentamer.pdb (#2) relative to postprocess_pentamer_153.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.96574800 0.15771731 -0.20604850 10.41716658  
0.02949344 -0.85565103 -0.51671212 259.92682703  
-0.25780008 0.49293663 -0.83099492 182.01230240  
Axis 0.99075194 0.05078298 -0.12582401  
Axis point 0.00000000 104.52840339 127.58969549  
Rotation angle (degrees) 149.36703213  
Shift along axis 0.61917040  
  

> hide #!1 models

> select /T:354

8 atoms, 7 bonds, 1 model selected  

> select up

77 atoms, 77 bonds, 1 model selected  

> select up

2536 atoms, 2585 bonds, 1 model selected  

> color sel orange

> select /K:69

11 atoms, 11 bonds, 1 model selected  

> select up

64 atoms, 65 bonds, 1 model selected  

> select up

598 atoms, 618 bonds, 1 model selected  

> color sel red

> select /S:28

9 atoms, 8 bonds, 1 model selected  

> select up

74 atoms, 73 bonds, 1 model selected  

> select up

1097 atoms, 1114 bonds, 1 model selected  

> color sel gray

> select /Y:293

11 atoms, 10 bonds, 1 model selected  

> select up

141 atoms, 141 bonds, 1 model selected  

> select up

2046 atoms, 2093 bonds, 1 model selected  

> color sel cornflowerblue

> select /L:141

8 atoms, 7 bonds, 1 model selected  

> select up

17 atoms, 16 bonds, 1 model selected  

> select up

2279 atoms, 2337 bonds, 1 model selected  

> color sel forestgreen

> select clear

> show #!1 models

> color zone #1 near #3 distance 8 sharpEdges true update true

> color zone #1 near #2 distance 8 sharpEdges true update true

> volume #1 level 0.01072

> volume #1 level 0.009026

> volume #1 level 0.01745

> volume #1 level 0.01458

> volume #1 style mesh

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings +
transparent_drawings, camera)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 559, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, drawings,
self._shadow_bounds)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1329, in use_shadow_map  
draw_depth(r, sdrawings, opaque_only = not
r.material.transparent_cast_shadows)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1439, in draw_depth  
draw_opaque(r, drawings)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1420, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1431, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 716, in draw  
self.draw_self(renderer, draw_pass)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 723, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 747, in _draw_geometry  
self._update_buffers()  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 864, in _update_buffers  
ds.update_element_buffer(ta, style, tm, em)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1640, in update_element_buffer  
self.elements = e = self.masked_elements(triangles, style, triangle_mask,
edge_mask)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1674, in masked_elements  
self.masked_edges = me = masked_edges(ta, **kw)  
TypeError: masked_edges(): edge mask array size does not equal triangle array
size  
  

> volume #1 level 0.01265

> volume #1 level 0.01183

> graphics restart

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings +
transparent_drawings, camera)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 559, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, drawings,
self._shadow_bounds)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1329, in use_shadow_map  
draw_depth(r, sdrawings, opaque_only = not
r.material.transparent_cast_shadows)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1439, in draw_depth  
draw_opaque(r, drawings)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1420, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1431, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 716, in draw  
self.draw_self(renderer, draw_pass)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 723, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 747, in _draw_geometry  
self._update_buffers()  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 864, in _update_buffers  
ds.update_element_buffer(ta, style, tm, em)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1640, in update_element_buffer  
self.elements = e = self.masked_elements(triangles, style, triangle_mask,
edge_mask)  
File
"/private/var/folders/1_/n2g7d7n91pd16d71x59w7vt00000gn/T/AppTranslocation/2116C91C-0CE5-4238-8206-3FB99898236F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1674, in masked_elements  
self.masked_edges = me = masked_edges(ta, **kw)  
TypeError: masked_edges(): edge mask array size does not equal triangle array
size  
  




OpenGL version: 4.1 INTEL-14.7.13
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume mesh: masked_edges(): edge mask array size does not equal triangle array

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tonight's daily build.

This error was caused by using the color zone command "sharpEdges true" option with a volume mesh. When the volume gets set to mesh style it resets the surface triangulation and the sharp edges option automatically adds new mesh lines to make the sharp edges, and after that the volume mesh code tries to hide the diagonal mesh edges of the original mesh (so the mesh appears composed of squares instead of triangles) and that produces the error because the edge mask was not computed for the sharp edges mesh. My fix sets the edge mask before the sharp edges adds new mesh lines. Adding the mesh lines removes the edge mask so all triangles are displayed -- not ideal, but using sharpEdges in combination with mesh style is not particularly useful, so seems an ok compromise.

Note: See TracTickets for help on using tickets.