The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\Users\LocalAdmin\Desktop\ChimeraX\NLRP3_iNEXT_202101\segmentatio.cxs
> format session
Showing run_class001_j154_C1.seg - 21 regions, 21 surfaces
Log from Fri Mar 19 20:35:51 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/postprocess_j138.mrc
Opened postprocess_j138.mrc, grid size 240,240,240, pixel 1.29, shown at level
0.0216, step 1, values float32
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/Decamer_mmcif.cif
Summary of feedback from opening
C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/Decamer_mmcif.cif
---
warnings | Atom H5' is not in the residue template for ADP /A:1101
Atom H5' is not in the residue template for ADP /A:1101
Chain information for Decamer_mmcif.cif
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A | NACHT, LRR and
PYD domains-containing protein 3
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/decamer_1CIF.cif
Summary of feedback from opening
C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/decamer_1CIF.cif
---
warnings | Atom H5' is not in the residue template for ADP /A:1101
Unknown polymer entity '2' near line 97300
Unknown polymer entity '3' near line 97655
Unknown polymer entity '4' near line 97936
Unknown polymer entity '5' near line 101849
Unknown polymer entity '6' near line 103061
3 messages similar to the above omitted
Atom H5' is not in the residue template for ADP /A:1101
Atom H is not in the residue template for ILE /B:133
Atom H5' is not in the residue template for ADP /B:1101
Atom H is not in the residue template for SER /B:161
Atom H is not in the residue template for ILE /B:201
Atom H is not in the residue template for GLY /B:459
Atom H is not in the residue template for ASN /B:543
Atom H is not in the residue template for GLU /B:561
2 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Atom H5' is not in the residue template for ADP /A:1101
Chain information for decamer_1CIF.cif
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A
3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A | NACHT, LRR and PYD
domains-containing protein 3
> close #3
> hide #!2 models
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j146_134_Cl3.mrc
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j145_134_Cl2.mrc
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j144_134_Cl1.mrc
Opened run_class001_j146_134_Cl3.mrc, grid size 240,240,240, pixel 1.29, shown
at level 0.0161, step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 458x198+1566+426 (frame:
476x245+1557+388) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x249+1567+433 (frame:
593x296+1558+395) margins: 9, 38, 9, 9 minimum size: 89x51 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,98
maxtrack=524305,524334)
> volume #3.3 level 0.01278
> volume #3.2 level 0.009362
> close #3.2
> volume #3.1 level 0.0122
> volume #3.3 level 0.0149
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j148_133_Cl2.mrc
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j147_133_Cl1.mrc
Opened run_class001_j148_133_Cl2.mrc, grid size 240,240,240, pixel 1.29, shown
at level 0.0161, step 1, values float32
> hide #!4.1 models
> hide #!3.3 models
> hide #!3 models
> close #4.2
> volume #4.1 level 0.01221
> volume #4.1 level 0.01206
> volume #4.1 level 0.01
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/postprocess_j156.mrc
Opened postprocess_j156.mrc, grid size 240,240,240, pixel 1.29, shown at level
0.0203, step 1, values float32
> hide #!4.1 models
> hide #!4 models
> lighting soft
> volume #5 level 0.02523
> volume #5 level 0.01807
> save C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/NLRP3.cxs
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j153_.mrc
Opened run_class001_j153_.mrc, grid size 240,240,240, pixel 1.29, shown at
level 0.0161, step 1, values float32
> hide #!5 models
> volume #6 level 0.01393
> volume #6 level 0.01172
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/run_class001_j154_C1.mrc
Opened run_class001_j154_C1.mrc, grid size 240,240,240, pixel 1.29, shown at
level 0.0167, step 1, values float32
> hide #!6 models
> volume #7 level 0.01
> open
> C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/postprocess_j158.mrc
Opened postprocess_j158.mrc, grid size 240,240,240, pixel 1.29, shown at level
0.0199, step 1, values float32
> hide #!7 models
> transparency #7.1#8.1 50
> transparency #7.1#8.1 0
> transparency #7.1#8.1 50
> hide #!7 models
> transparency #8.1 0
> show #!7 models
> save C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/masks+.cxs
> color zone #7 near /a
> color zone #7 near /a 5
Expected a keyword
Must specify one map, got 0
Must specify one map, got 0
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #9
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #9
---
ADP — adenosine-5'-diphosphate
> color zone #7 near /a distance 5
> color zone #7 near /a distance 4
> delete /b
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #7.1 models
> show #7.1 models
> volume #!7 style surface
> volume #!7 style surface
> volume #!7 style mesh
> volume #!7 style image
> volume #!7 style surface
> transparency #7.1 0
> transparency #7.1 50
> select #2.10
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 2 models selected
> ~select #2.10
Nothing selected
> hide #7.1 models
> show #7.2 models
> hide #7.2 models
> close #7.2
> select #7.1
1 model selected
> show #7.1 models
> ~select #7.1
Nothing selected
> mmaker #9 to #2.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Decamer_mmcif.cif, chain A (#2.1) with 6npy, chain A (#9), sequence
alignment score = 4921.6
RMSD between 798 pruned atom pairs is 0.000 angstroms; (across all 798 pairs:
0.000)
> hide #!9 models
> hide #7.1 models
> volume #!7 style surface
> volume #7 change image level -0.001277,0 level 0.01671,0.8 level 0.0305,1
> volume #7 level 0.01492
> color zone #7 near #3.1/a distance 4
> volume #!7 style surface
> select #7
2 models selected
> transparency sel 0
> color zone #7 near #2.1/a distance 4
> volume #7 level 0.01463
> volume #7 level 0.015
> volume #7 level 0.012
> color zone #7 near #2.1/a distance 4
> color zone #7 near #2.2/a distance 4
> color zone #7 near #2.1-2/a distance 4
> volume splitbyzone
Missing or invalid "volumes" argument: empty atom specifier
> color zone #7 near #2.2/a distance 4 red
Expected a keyword
> volume splitbyzone #7
> hide #!10.7 models
> hide #!10.6 models
> hide #!10.5 models
> hide #!10.4 models
> hide #!10.3 models
> hide #!10.2 models
> show #!10.2 models
> show #!10.3 models
> close #10
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> color zone #7 near #2.1-2/a distance 4 S´sharpEdge true
Expected a keyword
> color zone #7 near #2.1-2/a distance 4 sharpEdges true
> color zone #7 near #2.1-2/a distance 4 sharpEdges true
> color zone #7 near #2.1-2/a distance 5
> color zone #7 near #2.1-2/a distance 7
> color zone #7 near #2.1-2/a distance 4
> color zone #7 near #2.1-2/a distance 4 red
Expected a keyword
> color zone #7 near #2.1-2/a distance 4 color red
Expected a keyword
> color zone #7 near #2.1-2/a distance 4 color red
Expected a keyword
> select #7 near '2.1
Expected a keyword
> select #2.1
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 2 models selected
> select sel @< 5
18689 atoms, 18902 bonds, 14 pseudobonds, 1626 residues, 8 models selected
> close #9
> ~select #2.1
137 atoms, 116 bonds, 28 residues, 4 models selected
> select #2.1
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 2 models selected
> select sel @< 5
12470 atoms, 12566 bonds, 7 pseudobonds, 827 residues, 6 models selected
> transparency #7.1 50
> show #!2 models
> color (#!2.1-2,6-7,10 & sel) red
> undo
> ui tool show "Color Actions"
> color sel yellow green
> color sel lawn green
> select #2
74418 atoms, 75588 bonds, 70 pseudobonds, 7990 residues, 21 models selected
> transparency #7.1 0
> hide #!2 models
> ui tool show "Segment Map"
No map selected
No segmentation chosen
No segmentation selected
> ~select #2.1
62085 atoms, 63138 bonds, 63 pseudobonds, 7191 residues, 19 models selected
> select #2.1
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 2 models selected
No segmentation chosen
No segmentation selected
No segmentation chosen
No segmentation selected
No segmentation chosen
Segmenting run_class001_j154_C1.mrc, density threshold 0.012000
Showing run_class001_j154_C1.seg - 0 regions, 0 surfaces
Only showing 60 of 77 regions.
Showing 60 of 77 region surfaces
801 watershed regions, grouped to 77 regions
Segmenting run_class001_j154_C1.mrc, density threshold 0.012000
Showing run_class001_j154_C1.seg - 0 regions, 0 surfaces
Only showing 20 of 77 regions.
Showing 20 of 77 region surfaces
801 watershed regions, grouped to 77 regions
QWindowsWindow::setGeometry: Unable to set geometry 458x108+3253+492 (frame:
474x147+3245+461) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 458x113+3253+492 (frame:
474x152+3245+461) margins: 8, 31, 8, 8 minimum size: 180x113 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=196,152
maxtrack=524303,524326)
QWindowsWindow::setGeometry: Unable to set geometry 458x113+1617+589 (frame:
476x160+1608+551) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x143+1618+596 (frame:
593x190+1609+558) margins: 9, 38, 9, 9 minimum size: 180x113 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=198,160
maxtrack=524305,524334)
> hide #9.20 models
> hide #9.18 models
> hide #9.19 models
> hide #9.17 models
> hide #9.16 models
> hide #9.15 models
> hide #9.14 models
> hide #9.13 models
> hide #9.12 models
> hide #9.10 models
> hide #9.9 models
> hide #9.8 models
> hide #9.7 models
> hide #9.6 models
> hide #9.5 models
> hide #9.11 models
> hide #9.4 models
> hide #9.3 models
> hide #9.2 models
> show #9.2 models
> hide #9.1 models
> show #9.1 models
> hide #7.1 models
> hide #9.2 models
> show #9.2 models
> hide #9.1 models
> show #9.1 models
> show #9.3 models
> show #9.4 models
> show #9.5 models
> show #9.6 models
> show #9.7 models
> show #9.8 models
> show #9.10 models
> show #9.9 models
> hide #9.9 models
> show #9.9 models
> hide #9.8 models
> show #9.11 models
> show #9.12 models
> show #9.13 models
> show #9.14 models
> show #9.16 models
> hide #9.16 models
> hide #9.14 models
> show #9.14 models
> hide #9.14 models
> hide #9.13 models
> hide #9.11 models
> hide #9.12 models
> show #9.13 models
> hide #9.13 models
> show #9.14 models
> show #9.16 models
> show #9.15 models
> hide #9.16 models
> hide #9.15 models
> hide #9.14 models
> show #9.20 models
> show #9.19 models
> show #9.18 models
> show #9.17 models
> show #9.16 models
> show #9.15 models
> show #9.13 models
> show #9.14 models
> show #9.12 models
> show #9.11 models
> show #9.8 models
Segmenting run_class001_j154_C1.mrc, density threshold 0.012000
Showing run_class001_j154_C1.seg - 0 regions, 0 surfaces
Only showing 50 of 799 regions.
Showing 50 of 799 region surfaces
Only showing 50 of 77 regions.
Showing 50 of 77 region surfaces
799 watershed regions, grouped to 77 regions
Segmenting run_class001_j154_C1.mrc, density threshold 0.012000
Showing run_class001_j154_C1.seg - 0 regions, 0 surfaces
Only showing 50 of 799 regions.
Showing 50 of 799 region surfaces
Only showing 50 of 77 regions.
Showing 50 of 77 region surfaces
799 watershed regions, grouped to 77 regions
Smoothing and grouping, standard deviation 5 voxels
Showing 44 region surfaces
Got 44 regions after smoothing 5 voxels.
> select #9.1
1 model selected
> select #9.2
1 model selected
> select #9.1
1 model selected
> ui mousemode right select
Grouped 3 regions
Grouped 3 regions
Grouped 4 regions
Grouped 2 regions
Grouped 4 regions
Grouped 3 regions
Grouped 2 regions
Grouped 4 regions
Grouped 3 regions
Grouped 4 regions
Grouped 2 regions
> save C:/Users/LocalAdmin/Desktop/ChimeraX/NLRP3_iNEXT_202101/segmentatio.cxs
opened ChimeraX session
Smoothing and grouping, standard deviation 6 voxels
No new groups smoothing 6 voxels
No new groups smoothing 7 voxels
No new groups smoothing 8 voxels
No new groups smoothing 9 voxels
Showing 18 region surfaces
Got 18 regions after smoothing 10 voxels.
> hide #!9 models
> volume #7 level 0.01303
> ui tool show "Measure and Color Blobs"
> volume #7 level 0.01082
> volume #7 level 0.01119
> measure blob #!7.1 triangleNumber 354834 color #0000ccff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 1.0193e+06
area = 2.7368e+05
size = 189.91 188.23 145.82
> measure blob #!7.1 triangleNumber 240948 color #be4c98ff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 1.0193e+06
area = 2.7368e+05
size = 189.91 188.23 145.82
> measure blob #!7.1 triangleNumber 457171 color #ce527eff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 1.0193e+06
area = 2.7368e+05
size = 189.91 188.23 145.82
> volume #7 level 0.0134
> measure blob #!7.1 triangleNumber 153536 color #a6ab5aff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 70300
area = 26241
size = 99.042 64.781 50.617
> measure blob #!7.1 triangleNumber 359607 color #5c02eeff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 65759
area = 25021
size = 98.768 63.407 50.784
> measure blob #!7.1 triangleNumber 263611 color #5a78ceff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 60635
area = 23923
size = 97.14 60.51 49.697
> measure blob #!7.1 triangleNumber 159083 color #d88615ff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 60460
area = 23981
size = 97.325 62.297 49.167
> measure blob #!7.1 triangleNumber 86264 color #7674c2ff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 66112
area = 25012
size = 98.452 64.117 49.743
> measure blob #!7.1 triangleNumber 209889 color #0297cdff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 3.5347e+05
area = 1.3169e+05
size = 185.66 145.28 114.48
> measure blob #!7.1 triangleNumber 25314 color #ee5b01ff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 4326.8
area = 2308.9
size = 31.021 27.349 19.476
> measure blob #!7.1 triangleNumber 440391 color #67b296ff outline true
Surface run_class001_j154_C1.mrc #7.1 blob:
volume = 4734.5
area = 2564.3
size = 31.81 28.986 22.155
> volume splitbyzone #7
Volume run_class001_j154_C1.mrc #7 does not have zone coloring
QWindowsWindow::setGeometry: Unable to set geometry 458x108+3241+288 (frame:
474x147+3233+257) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 458x113+3241+288 (frame:
474x152+3233+257) margins: 8, 31, 8, 8 minimum size: 180x113 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=196,152
maxtrack=524303,524326)
> select #7.12
1 model selected
> select #7.9
1 model selected
> volume subtract #7 #7.9
volume subtract operation requires exactly two volumes
> color zone #7.9 red
Expected a keyword
> color zone #7.9
Missing required "near" argument
> color zone #7 near #7.9
> segmentation colors #9 map #7
No segmentations specified
> hide #9.19 models
> show #9.19 models
> hide #9.17 models
> show #9.17 models
> hide #9.7 models
> show #9.7 models
> segmentation colors #9.7 map #7
No segmentations specified
> select #9.7
1 model selected
> ~select #9.7
Nothing selected
> select #9.7
1 model selected
> ~select #9.7
Nothing selected
> select #9.7
1 model selected
> ~select #9.7
Nothing selected
> hide #9.7 models
> show #9.7 models
> segmentation colors 1283 map #7
Missing or invalid "segmentations" argument: invalid density maps specifier
> segmentation colors #9 #7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 41, in segmentation_colors
_color_segmentation(seg, by_attribute, color, outside_color)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 70, in _color_segmentation
ac = _attribute_colors(seg, attribute_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 160, in _attribute_colors
c = AttributeColors(seg, attribute_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 186, in __init__
self.attribute_rgba = _random_colors(nc, seed = (attribute_name or 'all'))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 234, in _random_colors
c = random.randint(cmin, high = cmax, size = (count, 4), dtype = uint8)
File "mtrand.pyx", line 755, in numpy.random.mtrand.RandomState.randint
File "_bounded_integers.pyx", line 1083, in
numpy.random._bounded_integers._rand_uint8
TypeError: 'numpy.float64' object cannot be interpreted as an integer
TypeError: 'numpy.float64' object cannot be interpreted as an integer
File "_bounded_integers.pyx", line 1083, in
numpy.random._bounded_integers._rand_uint8
See log for complete Python traceback.
> hide #!7 models
> show #!7 models
> hide #!9 models
> hide #!7 models
> show #!7 models
> segmentation colors #9 #7
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 41, in segmentation_colors
_color_segmentation(seg, by_attribute, color, outside_color)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 70, in _color_segmentation
ac = _attribute_colors(seg, attribute_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 160, in _attribute_colors
c = AttributeColors(seg, attribute_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 186, in __init__
self.attribute_rgba = _random_colors(nc, seed = (attribute_name or 'all'))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segment\segment.py", line 234, in _random_colors
c = random.randint(cmin, high = cmax, size = (count, 4), dtype = uint8)
File "mtrand.pyx", line 755, in numpy.random.mtrand.RandomState.randint
File "_bounded_integers.pyx", line 1083, in
numpy.random._bounded_integers._rand_uint8
TypeError: 'numpy.float64' object cannot be interpreted as an integer
TypeError: 'numpy.float64' object cannot be interpreted as an integer
File "_bounded_integers.pyx", line 1083, in
numpy.random._bounded_integers._rand_uint8
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 23.20.16.4973
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 850 G5
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 8,425,529,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed.
User gave a floating-point value map as the segmentation argument of the segmentation color command. Added code to make sure segmentations are integer valued and give an sensible error message if not.