Opened 5 months ago

Closed 5 months ago

#17828 closed defect (not a bug)

Segger: invalid literal for int

Reported by: chimerax-bug-report@… 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:        macOS-13.7.3-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nino/Downloads/cryosparc_P16_J67_009_volume_mask_refine.mrc

Opened cryosparc_P16_J67_009_volume_mask_refine.mrc as #1, grid size
360,360,360, pixel 0.862, shown at level 1, step 2, values float32  

> volume #1 level 0.05566

> open /Users/nino/Downloads/cryosparc_P16_J67_009_volume_map.mrc

Opened cryosparc_P16_J67_009_volume_map.mrc as #2, grid size 360,360,360,
pixel 0.862, shown at level 0.156, step 2, values float32  

> volume #1 level 0.7522

> volume #1 level 1

> close #1

> open
> "/Users/nino/Documents/Doctoral_projects/Actin/CARP_actin_titin_processing
> /fold_cp_u_g_actin_6mer/fold_cp_u_g_actin_6mer_model_0.cif"

Chain information for fold_cp_u_g_actin_6mer_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C D E F G H | .  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  
Computing secondary structure  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /C /D /E /F /G /H

Alignment identifier is 1  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1-64

526 atoms, 531 bonds, 64 residues, 1 model selected  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1-90

750 atoms, 757 bonds, 90 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> molmap #1 5

Opened fold_cp_u_g_actin_6mer_model_0.cif map 5 as #3, grid size 134,79,110,
pixel 1.67, shown at level 0.105, step 1, values float32  

> hide #1 models

> ui tool show "Segment Map"

Segmenting fold_cp_u_g_actin_6mer_model_0.cif map 5, density threshold
0.105494  
Showing 15 region surfaces  
2154 watershed regions, grouped to 15 regions  
Showing fold_cp_u_g_actin_6mer_model_0 map 5.seg - 15 regions, 15 surfaces  

> select add #4.8

1 model selected  

> select add #4.1

2 models selected  

> select add #4.9

3 models selected  

> select add #4.12

4 models selected  

> select add #4.3

5 models selected  

> select add #4.10

6 models selected  

> select add #4.14

7 models selected  

> select add #4.15

8 models selected  

> select add #4.5

9 models selected  

> select add #4.4

10 models selected  

> select add #4.11

11 models selected  

> select add #4.2

12 models selected  

> select add #4.13

13 models selected  
Grouped 13 regions  

> select add #4.7

2 models selected  
Grouped 2 regions  

> select add #4.6

2 models selected  
Grouped 2 regions  
Saving 1 regions to mrc file...  
Opened fold_cp_u_g_actin_6mer_model_0_region_2712.mrc as #5, grid size
122,67,98, pixel 1.67, shown at step 1, values float32  
Wrote fold_cp_u_g_actin_6mer_model_0_region_2712.mrc  

> volume mask #5 map #2 sameGrid true

Expected a keyword  

> volume mask #5 byMap #2 sameGrid true

Expected a keyword  

> volume mask map #2 mask #5 sameGrid true

Missing or invalid "volumes" argument: invalid density maps specifier  

> volume resample #5 onGrid #2

Opened fold_cp_u_g_actin_6mer_model_0_region_2712.mrc resampled as #6, grid
size 360,360,360, pixel 0.862, shown at step 1, values float32  

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!5 models

> select clear

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!5 models

> volume pad #2 pad 10

Expected a density maps specifier or a keyword  

> volume pad #5 pad 10

Expected a density maps specifier or a keyword  

> volume pad #2 size 10

Expected a density maps specifier or a keyword  

> bounds #2

Unknown command: measure bounds #2  

> hide #!5 models

> show #!6 models

> volume #6 level 0

> show #!5 models

> show #!2 models

> volume #2 level -0.1683

> hide #!2 models

> hide #!6 models

> ui tool show "Volume Viewer"

> volume #2 step 16

> vop extract #5 region 0,360,0,360,0,360

> volume extract #5 region 0,360,0,360,0,360

Expected a density maps specifier or a keyword  

> 2dlabels

> vop box #1 size 360

> volume boxes #1 size 360

Missing required "centers" argument  

> vop box #5 size 360

> volume boxes #5 size 360

Missing required "centers" argument  

> measure center #5

Center of mass grid index for fold_cp_u_g_actin_6mer_model_0_region_2712.mrc =
(61.81, 31.68, 40.57)  
Center of mass xyz scene coordinates for
fold_cp_u_g_actin_6mer_model_0_region_2712.mrc = (0.71, 0.01, -0.57)  

> center of #5 = 100, 150, 200

Unknown command: center of #5 = 100, 150, 200  

> vop box #5 center 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> vop box #5 center 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> vop box #5 centers 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> vop box #5 centers 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> vop box #5 centers 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> vop box #5 centers 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> vop box #5 centers 61.81,31.68,40.57 size 360

> volume boxes #5 centers 61.81,31.68,40.57 size 360

Invalid "centers" argument: invalid atoms specifier  

> view position #5

Missing required "same_as_models" argument  

> view position #5 sameAsModels #2

> hide #!5 models

> show #!5 models

> volume #2 level 0.01891

> volume #2 level 0.205

> volume #2 level 0.05255

> hide #!2 models

> open /Users/nino/Downloads/cryosparc_P16_J67_009_volume_map.mrc

Opened cryosparc_P16_J67_009_volume_map.mrc as #7, grid size 360,360,360,
pixel 0.862, shown at level 0.156, step 2, values float32  

> volume #7 level 0.1397

> show #!6 models

> volume #6 level 0.2071

Please select one ore more regions to save to .mrc file  

> volume #7 level 0.1412

> volume #7 level 0.3181

> close #6

> view position #5 sameAsModels #5

[Repeated 1 time(s)]

> volume gaussian #5 sDev 2

Opened fold_cp_u_g_actin_6mer_model_0_region_2712.mrc gaussian as #6, grid
size 122,67,98, pixel 1.67, shown at step 1, values float32  

> volume #6 level 0.1775

> volume resample #5 onGrid #2

Opened fold_cp_u_g_actin_6mer_model_0_region_2712.mrc resampled as #8, grid
size 360,360,360, pixel 0.862, shown at step 1, values float32  

> volume #8 level 0.6156

> close #8

Segmenting fold_cp_u_g_actin_6mer_model_0_region_2712.mrc gaussian, density
threshold 0.177540  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1968, in RegsDispUpdate  
maxnr = self.MaximumRegionsToDisplay()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1987, in
MaximumRegionsToDisplay  
maxnr = self._max_num_regions.value  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing fold_cp_u_g_actin_6mer_model_0_region_2712 gaussian.seg - 14 regions,
0 surfaces  
Segmenting fold_cp_u_g_actin_6mer_model_0_region_2712.mrc gaussian, density
threshold 0.177540  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1968, in RegsDispUpdate  
maxnr = self.MaximumRegionsToDisplay()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1987, in
MaximumRegionsToDisplay  
maxnr = self._max_num_regions.value  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing fold_cp_u_g_actin_6mer_model_0_region_2712 gaussian.seg - 14 regions,
0 surfaces  

> ui tool show "Segment Map"

Segmenting fold_cp_u_g_actin_6mer_model_0_region_2712.mrc gaussian, density
threshold 0.177540  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1968, in RegsDispUpdate  
maxnr = self.MaximumRegionsToDisplay()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1987, in
MaximumRegionsToDisplay  
maxnr = self._max_num_regions.value  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing fold_cp_u_g_actin_6mer_model_0_region_2712 gaussian.seg - 14 regions,
0 surfaces  

> select #6

2 models selected  
Please select one ore more regions to save to .mrc file  
Must include '%d' in map file name for region number  
Please select one ore more regions to save to .mrc file  
[Repeated 1 time(s)]No map chosen to save  
Segmenting fold_cp_u_g_actin_6mer_model_0_region_2712.mrc gaussian, density
threshold 0.177540  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1968, in RegsDispUpdate  
maxnr = self.MaximumRegionsToDisplay()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1987, in
MaximumRegionsToDisplay  
maxnr = self._max_num_regions.value  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing fold_cp_u_g_actin_6mer_model_0_region_2712 gaussian.seg - 14 regions,
0 surfaces  

> close #4

Segmenting fold_cp_u_g_actin_6mer_model_0_region_2712.mrc, density threshold
0.634321  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1968, in RegsDispUpdate  
maxnr = self.MaximumRegionsToDisplay()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1987, in
MaximumRegionsToDisplay  
maxnr = self._max_num_regions.value  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
ValueError: invalid literal for int() with base 10: '6vop extract #1 region
0,360,0,360,0,360\n'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing fold_cp_u_g_actin_6mer_model_0_region_2712.seg - 15 regions, 0
surfaces  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 8 GB
      System Firmware Version: 529.140.2.0.0
      OS Loader Version: 577.140.2~30
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.7.3 (22H417)
      Kernel Version: Darwin 22.6.0
      Time since boot: 71 days, 17 hours, 37 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 5 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger: invalid literal for int

comment:2 by Tom Goddard, 5 months ago

Resolution: → not a bug
Status: assigned → closed

User apparently pasted "6vop extract #1 region 0,360,0,360,0,360\n" into the Segger maximum number of regions field. Could make the error message better but not worth the time for such a rare error.

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