Opened 6 years ago

Closed 6 years ago

#2116 closed defect (fixed)

Adjust surface geometry: not enough values to unpack

Reported by: yazan.abbas@… 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:        Linux-4.15.0-51-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-06-25)
Description
color zone #2 near #1 distance 5 sharpEdges true.

color zone repeatedly causes this error to occur. Often times the color zone function will not work, and in those cases what helps is to change the map level, and then repeat the command. Even though the error is produced, the color zone 9 command could still work

Log:
UCSF ChimeraX version: 0.91 (2019-06-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open maps_and_models/State1_composite.cif name State1

Summary of feedback from opening maps_and_models/State1_composite.cif  
---  
warnings | skipping chem_comp category: Missing column 'type' near line 297  
Unknown polymer entity '?' near line 342  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
skipping chem_comp category: Missing column 'type' near line 72840  
skipping chem_comp category: Missing column 'type' near line 72867  
  
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 | No description available  
G2 | No description available  
G3 | No description available  
K1 | No description available  
K2 | No description available  
K3 | No description available  
a | No description available  
ac | 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  
pr | No description available  
  

> open maps_and_models/J1509_state1_Vo.mrc name State1FocusedVo

Opened J1509_state1_Vo.mrc, grid size 340,340,340, pixel 1.06, shown at level
0.16, step 2, values float32  

> set bgColor white

> set silhouettes true

> camera ortho

> surface cap true

> lighting soft shadows true intensity 0.1

> 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 ac #1.20  
---  
Chain | Description  
ac | No description available  
  
Chain information for State1 b #1.21  
---  
Chain | Description  
b | No description available  
  
Chain information for State1 c1 #1.22  
---  
Chain | Description  
c1 | No description available  
  
Chain information for State1 c2 #1.23  
---  
Chain | Description  
c2 | No description available  
  
Chain information for State1 c3 #1.24  
---  
Chain | Description  
c3 | No description available  
  
Chain information for State1 c4 #1.25  
---  
Chain | Description  
c4 | No description available  
  
Chain information for State1 c5 #1.26  
---  
Chain | Description  
c5 | No description available  
  
Chain information for State1 c6 #1.27  
---  
Chain | Description  
c6 | No description available  
  
Chain information for State1 c7 #1.28  
---  
Chain | Description  
c7 | No description available  
  
Chain information for State1 c8 #1.29  
---  
Chain | Description  
c8 | No description available  
  
Chain information for State1 c9 #1.30  
---  
Chain | Description  
c9 | No description available  
  
Chain information for State1 d #1.31  
---  
Chain | Description  
d | No description available  
  
Chain information for State1 e #1.32  
---  
Chain | Description  
e | No description available  
  
Chain information for State1 f #1.33  
---  
Chain | Description  
f | No description available  
  
Chain information for State1 pr #1.34  
---  
Chain | Description  
pr | No description available  
  
Split State1 (#1) into 34 models  

> dssp

> select #1.1-3

13993 atoms, 14279 bonds, 3 models selected  

> name frozen subunitA sel

> select #1.4-6

10847 atoms, 11060 bonds, 3 models selected  

> name frozen subunitB sel

> select #1.7

2927 atoms, 2981 bonds, 1 model selected  

> name frozen subunitC sel

> select #1.8

1726 atoms, 1744 bonds, 1 model selected  

> name frozen subunitD sel

> select #1.9-11

5040 atoms, 5079 bonds, 3 models selected  

> name frozen subunitE sel

> select #1.12

876 atoms, 890 bonds, 1 model selected  

> name frozen subunitF sel

> select #1.13-15

2392 atoms, 2401 bonds, 3 models selected  

> name frozen subunitG sel

> select #1.16-18

5441 atoms, 5542 bonds, 3 models selected  

> name frozen SidK sel

> select #1.19

5615 atoms, 5754 bonds, 1 model selected  

> name frozen V0a sel

> select #1.21

1503 atoms, 1537 bonds, 1 model selected  

> name frozen V0b sel

> select #1.22-30

9612 atoms, 9747 bonds, 9 models selected  

> name frozen V0cring sel

> select #1.31

2833 atoms, 2899 bonds, 1 model selected  

> name frozen V0d sel

> select #1.32

628 atoms, 653 bonds, 1 model selected  

> name frozen V0e sel

> select #1.33

675 atoms, 691 bonds, 1 model selected  

> name frozen V0RNAseK sel

> select #1.20

337 atoms, 347 bonds, 1 model selected  

> name frozen V0Ac45 sel

> select #1.34

443 atoms, 456 bonds, 1 model selected  

> name frozen V0PRR sel

> hide SidK target c

> hide subunitG target c

> hide subunitF target c

> hide subunitE target c

> hide subunitC target c

> hide subunitA target c

> hide subunitB target c

> hide subunitD target c

> hide subunitF target c

> hide V0cring

> color subunitA #F2EA42 target cabp

> color subunitB #D01F26 target cabp

> color subunitC #996633 target cabp

> color subunitD #3A53A3 target cabp

> color subunitE #804F9F target cabp

> color subunitF #B9529E target cabp

> color subunitG #fce94f target cabp

> color SidK #D2D2D2 target cabp

> color V0a #8ae234 target cabp

> color V0b #9d42bf target cabp

> color V0cring #e182d9 target cabp

> color V0d #8ab7ff target cabp

> color V0e #3465a4 target cabp

> color V0RNAseK #cc0000 target cabp

> color V0Ac45 #EEEEEC target cabp

> color V0PRR #edd400 target cabp

> select clear

> hide atoms

> show cartoons

> surface dust #2 size 6

> volume #2 step 1 level 0.35 color #EEEEEC surfaceSmoothing true
subdivideSurface true smoothingIterations 4

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

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

> volume splitbyzone #2

Volume J1509_state1_Vo.mrc #2 does not have zone coloring  

> color zone #2 near #1 distance 5 sharpEdges true

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 1248, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,
auto_update = update)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 14, in color_zone  
zc.set_vertex_colors()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 84, in set_vertex_colors  
replace = True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 123, in color_zone_sharp_edges  
ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 147, in _edge_cuts  
f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
ValueError: Cut fraction 1.8061 is out of range (0,1)  
  
ValueError: Cut fraction 1.8061 is out of range (0,1)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
  
See log for complete Python traceback.  
  

> color zone #2 near #1 distance 5 sharpEdges true

> volume splitbyzone #2

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3557, in _update_drawings  
v.update_drawings()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 701, in update_drawings  
self._update_surfaces()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 724, in _update_surfaces  
s.update_surface(ro)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1953, in update_surface  
va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, level,
rendering_options)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 2048, in _calculate_contour_surface  
rendering_options, level)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 2071, in _adjust_surface_geometry  
varray, tarray, narray = subdivide_triangles(varray, tarray, narray)  
ValueError: not enough values to unpack (expected 3, got 2)  
  
Error processing trigger "graphics update": not enough values to unpack
(expected 3, got 2):  
ValueError: not enough values to unpack (expected 3, got 2)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 2071, in _adjust_surface_geometry  
varray, tarray, narray = subdivide_triangles(varray, tarray, narray)  
  
See log for complete Python traceback.  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3.17 models

> show #!3.17 models

> hide #!3.11 models

> show #!3.11 models

> hide #!3.11 models

> show #!3.11 models

> hide #!3.10 models

> show #!3.10 models

> hide #!3.17 models

> show #!3.17 models

> hide #!3.16 models

> show #!3.16 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3.3 models

> show #!3.3 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3.17 models

> hide #!3.16 models

> hide #!3.15 models

> hide #!3.14 models

> hide #!3.13 models

> hide #!3.12 models

> hide #!3.11 models

> hide #!3.10 models

> hide #!3.9 models

> hide #!3.7 models

> hide #!3.8 models

> hide #!3.6 models

> hide #!3.5 models

> hide #!3.4 models

> hide #!3.3 models

> hide #!3.2 models

> hide #!3.1 models

> show #!3.1 models

> ui mousemode rightMode "pick blobs"

> measure blob #!3.1.1 triangleNumber 129990 color #0000ccff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> measure blob #!3.1.1 triangleNumber 142990 color #78cb62ff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> measure blob #!3.1.1 triangleNumber 134319 color #d5128bff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> measure blob #!3.1.1 triangleNumber 143192 color #a3b44dff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> measure blob #!3.1.1 triangleNumber 143183 color #658ebbff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> show #!2 models

> hide #!2 models

> show #!1 models

> hide SidK target c

> hide subunitG target c

> hide subunitF target c

> hide subunitE target c

> hide subunitC target c

> hide subunitA target c

> hide subunitB target c

> hide subunitD target c

> hide subunitF target c

> cartoon style V0cring modeHelix tube

> measure blob #!3.1.1 triangleNumber 190427 color #a7b938ff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> measure blob #!3.1.1 triangleNumber 125607 color #0ad290ff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> measure blob #!3.1.1 triangleNumber 150877 color #d8357cff outline true

Surface J1509_state1_Vo.mrc 0 #3.1.1 blob:  
volume = 9913.8  
area = 8265  
size = 50.018 49.658 35.516  
  

> hide #!3.1 models

> show #!3.1 models

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> close #3

> show #!2 models

> color zone #2 near #1 distance 4 sharpEdges true

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 1248, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,
auto_update = update)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 14, in color_zone  
zc.set_vertex_colors()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 84, in set_vertex_colors  
replace = True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 123, in color_zone_sharp_edges  
ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 147, in _edge_cuts  
f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
ValueError: Cut fraction -0.35032 is out of range (0,1)  
  
ValueError: Cut fraction -0.35032 is out of range (0,1)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
  
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 (4)

comment:1 by pett, 6 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Adjust surface geometry: not enough values to unpack

comment:2 by Tom Goddard, 6 years ago

There are two bugs here.

One is that using color zone command "sharpEdges true" option repeatedly on the same surface causes numerical errors ("Cut fraction is out of range") because it keeps trying to subdivide the triangles of the same surface at the same position, except for floating point rounding errors.

The second is that using volume command "subdivideSurface true" and then increasing the volume threshold above the highest density map value causes a unpack tuple error.

A third issue that is confusing but not a bug is that if color zone is used with "update false" then a subsequent volume splitbyzone command reports that "Volume does not have zone coloring". If color zone updating is turned off then the zone coloring is not remembered so splitbyzone does nothing.

comment:3 by Tom Goddard, 6 years ago

Fixed subdivideSurface unpack error.

comment:4 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

The subdivideSurface unpack error is fixed and the Cut fraction error is the subject of another ticket #2118, so closing this one.

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