ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\WT.pdb format pdb

Chain information for WT.pdb #1  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\WT_inclusion.pdb format pdb

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M1.pdb format pdb

Chain information for M1.pdb #3  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M1_inclusion.pdb format pdb

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M2.pdb format pdb

Chain information for M2.pdb #5  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M2_inclusion.pdb format pdb

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M3.pdb format pdb

Chain information for M3.pdb #7  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M3_inclusion.pdb format pdb

> matchmaker #3 to #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 WT.pdb, chain (blank) (#1) with M1.pdb, chain (blank) (#3),
sequence alignment score = 1298.6  
RMSD between 250 pruned atom pairs is 0.005 angstroms; (across all 250 pairs:
0.005)  
  

> matchmaker #5 to #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 WT.pdb, chain (blank) (#1) with M2.pdb, chain (blank) (#5),
sequence alignment score = 1300.2  
RMSD between 250 pruned atom pairs is 0.004 angstroms; (across all 250 pairs:
0.004)  
  

> matchmaker #7 to #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 WT.pdb, chain (blank) (#1) with M3.pdb, chain (blank) (#7),
sequence alignment score = 1298.8  
RMSD between 250 pruned atom pairs is 0.004 angstroms; (across all 250 pairs:
0.004)  
  

> setattr #2,4,6,8 atoms occupancy 1.0

Assigning occupancy attribute to 16716 items  

> setattr #2,4,6,8 atoms radius 1.5

Assigning radius attribute to 16716 items  

> molmap #2 3

Opened WT_inclusion.pdb map 3 as #9, grid size 36,37,37, pixel 1, shown at
level -1, step 1, values float32  

> molmap #4 3

Opened M1_inclusion.pdb map 3 as #10, grid size 36,37,37, pixel 1, shown at
level -1, step 1, values float32  

> molmap #6 3

Opened M2_inclusion.pdb map 3 as #11, grid size 37,37,37, pixel 1, shown at
level -1, step 1, values float32  

> molmap #8 3

Opened M3_inclusion.pdb map 3 as #12, grid size 36,37,37, pixel 1, shown at
level -1, step 1, values float32  

> hide #2,4,6,8 models

> volume #9 level 0.1 style surface color #3498db transparency 0.15

> volume #10 level 0.1 style surface color #2ecc71 transparency 0.15

> volume #11 level 0.1 style surface color #e67e22 transparency 0.15

> volume #12 level 0.1 style surface color #e74c3c transparency 0.15

> preset publication 1

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> color #1,3,5,7 gray

> hide #1,3,5,7 atoms

> show #1,3,5,7 cartoons

> show #1,3,5,7:88,110 atoms

> style #1,3,5,7:88,110 stick

Changed 88 atom styles  

> color #1:88,110 #3498db

> color #3:88,110 #2ecc71

> color #5:88,110 #e67e22

> color #7:88,110 #e74c3c

> volume #9 level 0.1

> volume #9 level -0.202

> volume #9 style mesh

> volume #9 style image

> volume #9 level 0.0001,0 level 9.001e-05,0.8 level 0,1

> volume #9 level 1,0 level 9.001e-05,0.8 level 0,1

> volume #9 level 3,0 level 9.001e-05,0.8 level 0,1

> volume #9 maximumIntensityProjection true

> volume #9 region 0,0,18,35,36,18 step 1 maximumIntensityProjection false
> showOutlineBox true

> volume #9 region 0,0,0,35,36,36 step 1

> volume #9 region 0,0,0,35,36,36 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 17,18,18 imageMode orthoplanes

> volume #9 style surface

> volume #9 style mesh

> volume #9 style image colorMode auto8 imageMode "full region"

> volume #9 style surface

> volume #9 level 0.03738

> volume #9 level 0.1

> volume #9

> volume #12 level -0.3088

> volume #11 level -0.2499

> volume #10 level -0.2978

> volume #9 level -0.3383

> close session

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\WT.pdb format pdb

Chain information for WT.pdb #1  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\WT_inclusion.pdb format pdb

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M1.pdb format pdb

Chain information for M1.pdb #3  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M1_inclusion.pdb format pdb

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M2.pdb format pdb

Chain information for M2.pdb #5  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M2_inclusion.pdb format pdb

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M3.pdb format pdb

Chain information for M3.pdb #7  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open E:\桌面\何琴\酶催化腔计算材料—何琴\Dm-dNK\M3_inclusion.pdb format pdb

> matchmaker #3 to #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 WT.pdb, chain (blank) (#1) with M1.pdb, chain (blank) (#3),
sequence alignment score = 1298.6  
RMSD between 250 pruned atom pairs is 0.005 angstroms; (across all 250 pairs:
0.005)  
  

> matchmaker #5 to #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 WT.pdb, chain (blank) (#1) with M2.pdb, chain (blank) (#5),
sequence alignment score = 1300.2  
RMSD between 250 pruned atom pairs is 0.004 angstroms; (across all 250 pairs:
0.004)  
  

> matchmaker #7 to #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 WT.pdb, chain (blank) (#1) with M3.pdb, chain (blank) (#7),
sequence alignment score = 1298.8  
RMSD between 250 pruned atom pairs is 0.004 angstroms; (across all 250 pairs:
0.004)  
  

> volume gaussian #2 sDev 1 gridSpacing 0.5

Expected a keyword  

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> lighting soft

> lighting full

> lighting simple

> show cartoons

> hide cartoons

> show cartoons

> show atoms

> hide atoms

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Public\Desktop\movie1.mp4

C:\Program Files\ChimeraX 1.11\bin\ffmpeg.exe -r 25 -i
C:\Users\Lenovo\AppData\Local\Temp\chimovie_mjwW-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\Public\Desktop\movie1.mp4  
stdout:  
  
stderr:  
ffmpeg version 6.1.1-essentials_build-www.gyan.dev Copyright (c) 2000-2023 the
FFmpeg developers  
built with gcc 12.2.0 (Rev10, Built by MSYS2 project)  
configuration: --enable-gpl --enable-version3 --enable-static --pkg-
config=pkgconf --disable-w32threads --disable-autodetect --enable-fontconfig
--enable-iconv --enable-gnutls --enable-libxml2 --enable-gmp --enable-bzlib
--enable-lzma --enable-zlib --enable-libsrt --enable-libssh --enable-libzmq
--enable-avisynth --enable-sdl2 --enable-libwebp --enable-libx264 --enable-
libx265 --enable-libxvid --enable-libaom --enable-libopenjpeg --enable-libvpx
--enable-mediafoundation --enable-libass --enable-libfreetype --enable-
libfribidi --enable-libharfbuzz --enable-libvidstab --enable-libvmaf --enable-
libzimg --enable-amf --enable-cuda-llvm --enable-cuvid --enable-ffnvcodec
--enable-nvdec --enable-nvenc --enable-dxva2 --enable-d3d11va --enable-libvpl
--enable-libgme --enable-libopenmpt --enable-libopencore-amrwb --enable-
libmp3lame --enable-libtheora --enable-libvo-amrwbenc --enable-libgsm
--enable-libopencore-amrnb --enable-libopus --enable-libspeex --enable-
libvorbis --enable-librubberband  
libavutil 58. 29.100 / 58. 29.100  
libavcodec 60. 31.102 / 60. 31.102  
libavformat 60. 16.100 / 60. 16.100  
libavdevice 60. 3.100 / 60. 3.100  
libavfilter 9. 12.100 / 9. 12.100  
libswscale 7. 5.100 / 7. 5.100  
libswresample 4. 12.100 / 4. 12.100  
libpostproc 57. 3.100 / 57. 3.100  
Input #0, image2, from
'C:\Users\Lenovo\AppData\Local\Temp\chimovie_mjwW-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1339x809, 25 fps, 25 tbr, 25 tbn  
[out#0/mp4 @ 0000019b268fd940] Error opening output
C:\Users\Public\Desktop\movie1.mp4: Permission denied  
Error opening output file C:\Users\Public\Desktop\movie1.mp4.  
Error opening output files: Permission denied  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 4294967283  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 6.1.1-essentials_build-www.gyan.dev Copyright (c) 2000-2023 the
FFmpeg developers  
built with gcc 12.2.0 (Rev10, Built by MSYS2 project)  
configuration: --enable-gpl --enable-version3 --enable-static --pkg-
config=pkgconf --disable-w32threads --disable-autodetect --enable-fontconfig
--enable-iconv --enable-gnutls --enable-libxml2 --enable-gmp --enable-bzlib
--enable-lzma --enable-zlib --enable-libsrt --enable-libssh --enable-libzmq
--enable-avisynth --enable-sdl2 --enable-libwebp --enable-libx264 --enable-
libx265 --enable-libxvid --enable-libaom --enable-libopenjpeg --enable-libvpx
--enable-mediafoundation --enable-libass --enable-libfreetype --enable-
libfribidi --enable-libharfbuzz --enable-libvidstab --enable-libvmaf --enable-
libzimg --enable-amf --enable-cuda-llvm --enable-cuvid --enable-ffnvcodec
--enable-nvdec --enable-nvenc --enable-dxva2 --enable-d3d11va --enable-libvpl
--enable-libgme --enable-libopenmpt --enable-libopencore-amrwb --enable-
libmp3lame --enable-libtheora --enable-libvo-amrwbenc --enable-libgsm
--enable-libopencore-amrnb --enable-libopus --enable-libspeex --enable-
libvorbis --enable-librubberband  
libavutil 58. 29.100 / 58. 29.100  
libavcodec 60. 31.102 / 60. 31.102  
libavformat 60. 16.100 / 60. 16.100  
libavdevice 60. 3.100 / 60. 3.100  
libavfilter 9. 12.100 / 9. 12.100  
libswscale 7. 5.100 / 7. 5.100  
libswresample 4. 12.100 / 4. 12.100  
libpostproc 57. 3.100 / 57. 3.100  
Input #0, image2, from
'C:\Users\Lenovo\AppData\Local\Temp\chimovie_mjwW-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1339x809, 25 fps, 25 tbr, 25 tbn  
[out#0/mp4 @ 0000019b268fd940] Error opening output
C:\Users\Public\Desktop\movie1.mp4: Permission denied  
Error opening output file C:\Users\Public\Desktop\movie1.mp4.  
Error opening output files: Permission denied  
  
\-----------------------------  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Public\Desktop\movie1.mp4

C:\Program Files\ChimeraX 1.11\bin\ffmpeg.exe -r 25 -i
C:\Users\Lenovo\AppData\Local\Temp\chimovie_mjwW-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\Public\Desktop\movie1.mp4  
stdout:  
  
stderr:  
ffmpeg version 6.1.1-essentials_build-www.gyan.dev Copyright (c) 2000-2023 the
FFmpeg developers  
built with gcc 12.2.0 (Rev10, Built by MSYS2 project)  
configuration: --enable-gpl --enable-version3 --enable-static --pkg-
config=pkgconf --disable-w32threads --disable-autodetect --enable-fontconfig
--enable-iconv --enable-gnutls --enable-libxml2 --enable-gmp --enable-bzlib
--enable-lzma --enable-zlib --enable-libsrt --enable-libssh --enable-libzmq
--enable-avisynth --enable-sdl2 --enable-libwebp --enable-libx264 --enable-
libx265 --enable-libxvid --enable-libaom --enable-libopenjpeg --enable-libvpx
--enable-mediafoundation --enable-libass --enable-libfreetype --enable-
libfribidi --enable-libharfbuzz --enable-libvidstab --enable-libvmaf --enable-
libzimg --enable-amf --enable-cuda-llvm --enable-cuvid --enable-ffnvcodec
--enable-nvdec --enable-nvenc --enable-dxva2 --enable-d3d11va --enable-libvpl
--enable-libgme --enable-libopenmpt --enable-libopencore-amrwb --enable-
libmp3lame --enable-libtheora --enable-libvo-amrwbenc --enable-libgsm
--enable-libopencore-amrnb --enable-libopus --enable-libspeex --enable-
libvorbis --enable-librubberband  
libavutil 58. 29.100 / 58. 29.100  
libavcodec 60. 31.102 / 60. 31.102  
libavformat 60. 16.100 / 60. 16.100  
libavdevice 60. 3.100 / 60. 3.100  
libavfilter 9. 12.100 / 9. 12.100  
libswscale 7. 5.100 / 7. 5.100  
libswresample 4. 12.100 / 4. 12.100  
libpostproc 57. 3.100 / 57. 3.100  
Input #0, image2, from
'C:\Users\Lenovo\AppData\Local\Temp\chimovie_mjwW-%05d.ppm':  
Duration: 00:00:14.40, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1339x809, 25 fps, 25 tbr, 25 tbn  
[out#0/mp4 @ 000001b85be2d940] Error opening output
C:\Users\Public\Desktop\movie1.mp4: Permission denied  
Error opening output file C:\Users\Public\Desktop\movie1.mp4.  
Error opening output files: Permission denied  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 4294967283  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 6.1.1-essentials_build-www.gyan.dev Copyright (c) 2000-2023 the
FFmpeg developers  
built with gcc 12.2.0 (Rev10, Built by MSYS2 project)  
configuration: --enable-gpl --enable-version3 --enable-static --pkg-
config=pkgconf --disable-w32threads --disable-autodetect --enable-fontconfig
--enable-iconv --enable-gnutls --enable-libxml2 --enable-gmp --enable-bzlib
--enable-lzma --enable-zlib --enable-libsrt --enable-libssh --enable-libzmq
--enable-avisynth --enable-sdl2 --enable-libwebp --enable-libx264 --enable-
libx265 --enable-libxvid --enable-libaom --enable-libopenjpeg --enable-libvpx
--enable-mediafoundation --enable-libass --enable-libfreetype --enable-
libfribidi --enable-libharfbuzz --enable-libvidstab --enable-libvmaf --enable-
libzimg --enable-amf --enable-cuda-llvm --enable-cuvid --enable-ffnvcodec
--enable-nvdec --enable-nvenc --enable-dxva2 --enable-d3d11va --enable-libvpl
--enable-libgme --enable-libopenmpt --enable-libopencore-amrwb --enable-
libmp3lame --enable-libtheora --enable-libvo-amrwbenc --enable-libgsm
--enable-libopencore-amrnb --enable-libopus --enable-libspeex --enable-
libvorbis --enable-librubberband  
libavutil 58. 29.100 / 58. 29.100  
libavcodec 60. 31.102 / 60. 31.102  
libavformat 60. 16.100 / 60. 16.100  
libavdevice 60. 3.100 / 60. 3.100  
libavfilter 9. 12.100 / 9. 12.100  
libswscale 7. 5.100 / 7. 5.100  
libswresample 4. 12.100 / 4. 12.100  
libpostproc 57. 3.100 / 57. 3.100  
Input #0, image2, from
'C:\Users\Lenovo\AppData\Local\Temp\chimovie_mjwW-%05d.ppm':  
Duration: 00:00:14.40, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1339x809, 25 fps, 25 tbr, 25 tbn  
[out#0/mp4 @ 000001b85be2d940] Error opening output
C:\Users\Public\Desktop\movie1.mp4: Permission denied  
Error opening output file C:\Users\Public\Desktop\movie1.mp4.  
Error opening output files: Permission denied  
  
\-----------------------------  
  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> show atoms

> hide atoms

> show cartoons

> hide cartoons

> show cartoons

> hide surfaces

> show surfaces

> hide surfaces

> style stick

Changed 33012 atom styles  

> style sphere

Changed 33012 atom styles  

> style ball

Changed 33012 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> color byhetero

> color bychain

> color bypolymer

> rainbow

> coulombic

Residue M3_inclusion.pdb #8/X C 1832 changed CSL→C  
Computing secondary structure  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 143, in simple_add_hydrogens  
_prep_add(session, structures, unknowns_info, template, **prot_schemes)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 540, in _prep_add  
for atom in struct.atoms:  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 179, in get_prop  
vcount = getattr(self, value_count)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 84, in cmd_addh  
structure.alt_loc_change_notify = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 130, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1393, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 594, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 101, in assign_charges  
charged_struct.delete()  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 137, in delete  
t = self.session.triggers  
^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 137, in delete  
t = self.session.triggers  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> coulombic

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 143, in simple_add_hydrogens  
_prep_add(session, structures, unknowns_info, template, **prot_schemes)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 540, in _prep_add  
for atom in struct.atoms:  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 179, in get_prop  
vcount = getattr(self, value_count)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 84, in cmd_addh  
structure.alt_loc_change_notify = True  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 130, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1393, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 594, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 101, in assign_charges  
charged_struct.delete()  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 137, in delete  
t = self.session.triggers  
^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 137, in delete  
t = self.session.triggers  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 577.00
OpenGL renderer: NVIDIA GeForce GTX 1660 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: LENOVO
Model: 90NK0001CP
OS: Microsoft Windows 11 家庭中文版 (Build 26200)
Memory: 16,909,565,952
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: zh-CN

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.11.12
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-maskChains: 1.4
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.0.0
    roman-numerals-py: 4.0.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0