EMalign: AssertionError: Downsample must be less than input volume size

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26120
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  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_series

Expected a density maps specifier or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_series file-pattern: map_###.mrc

Expected a density maps specifier or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_.mrc

Expected a density maps specifier or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_#.mrc

Expected a density maps specifier or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume.mrc

Expected a density maps specifier or a keyword  

> volume series open folder-name: E:\analysis\cryosparc_P1_J444_00859_volume
> *.mrc

Expected a density maps specifier or a keyword  

> volume series

Expected a density maps specifier or a keyword  

> toolshed show

> ui tool show "Volume Viewer"

> view # clip false

Expected an objects specifier or a view name or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_series>

Expected a density maps specifier or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_series>*.mrc

Expected a density maps specifier or a keyword  

> volume series open folder-name:
> E:\analysis\cryosparc_P1_J444_00859_volume_series ###.mrc

Expected a density maps specifier or a keyword  

> volume series open folder-name: E:\analysis\ ###.mrc

Expected a density maps specifier or a keyword  

> open
> E:/analysis/cryosparc_P1_J429_01433_volume_series/J429_class_00_01433_volume.mrc

Opened J429_class_00_01433_volume.mrc as #1, grid size 56,56,56, pixel 5.53,
shown at level 0.399, step 1, values float32  

> volume #1 step 16

> volume #1 step 8

> volume #1 step 1

> volume #1 level 0.06087

> volume #1 level 0.04693

> select add #1

2 models selected  

> ui tool show "Volume Viewer"

> volume #1 style image

> view clip false

[Repeated 1 time(s)]

> volume #1 style surface

> volume #1 change image level -0.03091,0 level 0.3992,0.8 level 0.7676,1

> open
> E:/analysis/cryosparc_P1_J429_01433_volume_series/J429_class_01_01433_volume.mrc
> E:/analysis/cryosparc_P1_J429_01433_volume_series/J429_class_02_01433_volume.mrc

Opened J429_class_01_01433_volume.mrc as #2.1, grid size 56,56,56, pixel 5.53,
shown at level 0.457, step 1, values float32  
Opened J429_class_02_01433_volume.mrc as #2.2, grid size 56,56,56, pixel 5.53,
shown at level 0.396, step 1, values float32  

> volume #2.1 level 0.08347

> volume #2.2 level 0.07955

> volume #2.1 level 0.1463

> volume #2.2 level 0.1484

> volume #1 level 0.1027

> ui tool show "Measure Volume and Area"

> select add #2

7 models selected  

> close #1

> close

> open
> E:/analysis/cryosparc_P1_J429_01433_volume_series/J429_class_00_01433_volume.mrc
> E:/analysis/cryosparc_P1_J429_01433_volume_series/J429_class_01_01433_volume.mrc
> E:/analysis/cryosparc_P1_J429_01433_volume_series/J429_class_02_01433_volume.mrc

Opened J429_class_00_01433_volume.mrc as #1.1, grid size 56,56,56, pixel 5.53,
shown at level 0.399, step 1, values float32  
Opened J429_class_01_01433_volume.mrc as #1.2, grid size 56,56,56, pixel 5.53,
shown at level 0.457, step 1, values float32  
Opened J429_class_02_01433_volume.mrc as #1.3, grid size 56,56,56, pixel 5.53,
shown at level 0.396, step 1, values float32  

> volume step 1

> volume step 2

> volume step 1

> ui mousemode right "contour level"

> volume #1.1 level 0.1642

> volume #1.2 level 0.245

> volume #1.3 level 0.1564

> volume #1.3 level 0.197

> volume #1.3 level 0.1519

> lighting full

> lighting soft

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting simple

> lighting soft

> volume #1.3 level 0.1478

> set bgColor white

> volume #1.1 color #55aaff

> volume #1.2 color #ff55ff

> volume #1.3 color #00aaff

> volume #1.3 color #aaaaff

> volume #1.3 color cyan

> volume #1.3 color #aaffff

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series.tif" width
> 12700 height 8230 supersample 3 transparentBackground true

> volume #1.2 level 0.164

> volume #1.1 level 0.25

> volume #1.2 level 0.25

> volume #1.3 level 0.25

> volume #1.3 level 0.18

> volume #1.1 level 0.18

> volume #1.2 level 0.1799

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series2.tif" width
> 12700 height 8230 supersample 3 transparentBackground true

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series23.tif" width
> 12700 height 8230 supersample 3 transparentBackground true

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series3.tif" width
> 12700 height 8230 supersample 3 transparentBackground true

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting full

> lighting soft

[Repeated 1 time(s)]

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series31.tif" width
> 12700 height 8230 supersample 3 transparentBackground true

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series2.tif" width
> 964 height 823 supersample 3 transparentBackground true

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series12.tif" width
> 9640 height 8230 supersample 3 transparentBackground true

> save "D:/AIIMS/PCOX/figures and chimera sessions/volume series2.tif" width
> 9640 height 8230 supersample 3 transparentBackground true

> volume #1.2 level 0.1422

> volume #1.2 level 0.1638

> volume #1.1 level 0.1621

> lighting full

> lighting soft

> lighting full

> volume #1.1 level 0.2158

> volume #1.2 level 0.2105

> volume #1.3 level 0.2307

> ui tool show EMalign

Traceback (most recent call last):  
File "C:\Users\dipik\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\emalign\emalign_gui.py", line 161, in _emalign  
self._run_emalign(ref_map, query_map, downsample, projections, show_log,
use_masking)  
File "C:\Users\dipik\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\emalign\emalign_gui.py", line 164, in _run_emalign  
emalign(self.session, ref_map, query_map, downsample=downsample,
projections=projections, show_log=show_log, refine=self._use_fit_map.value,
mask=use_masking)  
File "C:\Users\dipik\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\emalign\emalign_cmd.py", line 176, in emalign  
bestR, bestdx, reflect, query_vol_aligned =
align_volumes_3d.align_volumes(ref_vol_copy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\dipik\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\emalign\align_volumes_3d.py", line 57, in align_volumes  
vol1_ds, vol2_ds = downsample_volumes(downsample, log, n_1, n_2, show_log,
starting_t, vol1, vol2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\dipik\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\emalign\align_volumes_3d.py", line 376, in
downsample_volumes  
assert downsample <= n, "Downsample must be less than input volume size"  
^^^^^^^^^^^^^^^  
AssertionError: Downsample must be less than input volume size  
  
AssertionError: Downsample must be less than input volume size  
  
File "C:\Users\dipik\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\emalign\align_volumes_3d.py", line 376, in
downsample_volumes  
assert downsample <= n, "Downsample must be less than input volume size"  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 555.99
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: GF63 Thin 11UC
OS: Microsoft Windows 11 Home Single Language (Build 26120)
Memory: 8,276,946,944
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-US

Installed Packages:
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    aiohappyeyeballs: 2.6.1
    aiohttp: 3.12.9
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    aiosignal: 1.3.2
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    biopython: 1.83
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    build: 1.2.1
    certifi: 2024.8.30
    cffi: 1.17.1
    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
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    ChimeraX-CageBuilder: 1.0.1
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    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
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    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
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    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-EMalign: 0.1.3
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
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    ChimeraX-Graphics: 1.4.1
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    ChimeraX-IHM: 1.1
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    ChimeraX-LigandRecognizer: 0.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
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    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
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    ChimeraX-vrml: 1.0
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    ChimeraX-WavefrontOBJ: 1.0
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    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    wrapt: 1.17.2
    yarl: 1.20.0
    zarr: 2.18.7
    zipp: 3.22.0