The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505290006 (2025-05-29 00:06:37 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x80010012
Thread 0x0000d77c (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x80010012
Thread 0x0000d77c (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x80010012
Thread 0x0000d77c (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x80010012
Thread 0x0000d77c (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505290006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10rc202505290006 (2025-05-29)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/leena/Downloads/fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30/fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif
Chain information for
fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif
#1
---
Chain | Description
A | .
B C | .
D | .
E | .
> show cartoons
Computing secondary structure
> hide atoms
> color bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> C:/Users/leena/Downloads/fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30\\\fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_full_data_0.json
> color bfactor #1 palette alphafold
30858 atoms, 4042 residues, atom bfactor range 12.3 to 92.4
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 1/D
Alignment identifier is 1/E
> color bychain
> select /A:867
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:867
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel cartoons
> show sel atoms
> hide sel surfaces
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 9 atom styles
> ui mousemode right select
> select clear
> select /E:75
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> style sel stick
Changed 5 atom styles
> select /E:75
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /E:75
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> C:/Users/leena/Downloads/fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30\\\fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_full_data_0.json
> select clear
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> C:/Users/leena/Downloads/fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30\\\fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_full_data_0.json
> color bfactor #1 palette alphafold
30858 atoms, 4042 residues, 1 surfaces, atom bfactor range 12.3 to 92.4
> color bychain
> select /A:490
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:490
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color (#!1 & sel) red
> select /A:1162
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:1162
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color (#!1 & sel) red
> select clear
> color bfactor #1 palette alphafold
30858 atoms, 4042 residues, 1 surfaces, atom bfactor range 12.3 to 92.4
> color bychain
> select /E:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /D:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color bfactor #1 palette alphafold
30858 atoms, 4042 residues, 1 surfaces, atom bfactor range 12.3 to 92.4
> select /A:1291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1121-1291
1327 atoms, 1350 bonds, 171 residues, 1 model selected
> select clear
> select /A:1291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1206-1291
688 atoms, 704 bonds, 86 residues, 1 model selected
> select clear
> select /A:1291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1121-1291
1327 atoms, 1350 bonds, 171 residues, 1 model selected
> select clear
> open
> C:/Users/leena/Downloads/fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30/fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif
Chain information for
fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif #2
---
Chain | Description
A | .
B C | .
D | .
E | .
> hide #!1 models
> select add #2
30852 atoms, 31466 bonds, 4042 residues, 1 model selected
> style sel stick
Changed 30852 atom styles
> show sel cartoons
Computing secondary structure
> hide sel atoms
> select clear
> color #2 bychain
> select add #2
30852 atoms, 31466 bonds, 4042 residues, 1 model selected
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> C:/Users/leena/Downloads/fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30\\\fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_full_data_0.json
> color bfactor #2 palette alphafold
30852 atoms, 4042 residues, atom bfactor range 16.6 to 94.2
> select clear
> show #!1 models
> ui tool show Matchmaker
> matchmaker #2 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
fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif,
chain A (#1) with
fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif, chain A
(#2), sequence alignment score = 6160.2
RMSD between 360 pruned atom pairs is 0.517 angstroms; (across all 1291 pairs:
44.436)
> matchmaker #2 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
fold_automethylated_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif,
chain A (#1) with
fold_setdb1_ubiquitin_2x_atf7ip_h3k9me2_2025_05_29_11_30_model_0.cif, chain A
(#2), sequence alignment score = 6160.2
RMSD between 360 pruned atom pairs is 0.517 angstroms; (across all 1291 pairs:
44.436)
> select add #2
30852 atoms, 31466 bonds, 4042 residues, 1 model selected
> select add #1
61710 atoms, 62938 bonds, 8084 residues, 2 models selected
> color sel bychain
> select clear
> select #1/D:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/D:2-50
368 atoms, 373 bonds, 49 residues, 1 model selected
> select #1/D:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:1-108
858 atoms, 870 bonds, 108 residues, 1 model selected
> select clear
> select #1/D:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/D:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2
30863 atoms, 31476 bonds, 4043 residues, 2 models selected
Alignment identifier is 2
Alignment identifier is 2/A
Alignment identifier is 3
Alignment identifier is 2/E
QWindowsWindow::setGeometry: Unable to set geometry 1920x1087+0+23 (frame:
1936x1126-8-8) on QWidgetWindow/"MainWindowClassWindow" on "LEN-A540-B".
Resulting geometry: 1920x1057+0+23 (frame: 1936x1096-8-8) margins: 8, 31, 8, 8
minimum size: 674x1087 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=690, y=1126)))
QWindowsWindow::setGeometry: Unable to set geometry 1920x1153+0+23 (frame:
1936x1192-8-8) on QWidgetWindow/"MainWindowClassWindow" on "LEN-A540-B".
Resulting geometry: 1920x1057+0+23 (frame: 1936x1096-8-8) margins: 8, 31, 8, 8
minimum size: 674x1153 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=690, y=1192)))
Alignment identifier is 1
Alignment identifier is 2/A
Alignment identifier is 2
Alignment identifier is 2/E
> select #1/D:1 #2/D:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/D:1-10 #2/D:1-10
166 atoms, 164 bonds, 20 residues, 2 models selected
. [ID: 1] region 2 chains [1-10] RMSD: 8.353
> select clear
> select #1/D:10 #2/D:10
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/D:10 #2/D:10
22 atoms, 20 bonds, 2 residues, 2 models selected
. [ID: 1] region 2 chains [10] RMSD: 0.219
> hide #2 models
> hide #!1 models
> show #2 models
Alignment identifier is 1
> select #1/D:10 #2/D:10
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/D:10 #2/D:10
22 atoms, 20 bonds, 2 residues, 2 models selected
. [ID: 1] region 2 chains [10] RMSD: 0.219
> show sel & #2 atoms
> select clear
> show #!1 models
> color bfactor #2 palette alphafold
30852 atoms, 4042 residues, atom bfactor range 16.6 to 94.2
> select #1/D:1 #2/D:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/D:1-10 #2/D:1-10
166 atoms, 164 bonds, 20 residues, 2 models selected
. [ID: 1] region 2 chains [1-10] RMSD: 8.353
> select clear
> select #1/D:10 #2/D:10
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/D:10 #2/D:10
22 atoms, 20 bonds, 2 residues, 2 models selected
. [ID: 1] region 2 chains [10] RMSD: 0.219
Alignment identifier is 2
> select clear
> color bfactor #2 palette alphafold
30852 atoms, 4042 residues, atom bfactor range 16.6 to 94.2
> color bfactor #1 palette alphafold
30858 atoms, 4042 residues, 1 surfaces, atom bfactor range 12.3 to 92.4
> select add #1
30858 atoms, 31472 bonds, 4042 residues, 1 model selected
> select subtract #1
1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #2
30852 atoms, 31466 bonds, 4042 residues, 1 model selected
Alignment identifier is 2/A
Alignment identifier is 1
Alignment identifier is 2/D
Alignment identifier is 2/E
> select clear
> hide #2 models
> open C:/Users/leena/Downloads/fold_setdb2_atf7ip_2025_06_01_22_34.zip
Unrecognized file suffix '.zip'
> open
> C:/Users/leena/Downloads/fold_setdb2_atf7ip_2025_06_01_22_34/fold_setdb2_atf7ip_2025_06_01_22_34_model_0.cif
Chain information for fold_setdb2_atf7ip_2025_06_01_22_34_model_0.cif #3
---
Chain | Description
A | .
B C | .
Computing secondary structure
> color #3 bychain
> select add #3
24869 atoms, 25350 bonds, 3259 residues, 1 model selected
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> C:/Users/leena/Downloads/fold_setdb2_atf7ip_2025_06_01_22_34\\\fold_setdb2_atf7ip_2025_06_01_22_34_full_data_0.json
> color bfactor #3 palette alphafold
24869 atoms, 3259 residues, atom bfactor range 20.3 to 86.7
> select clear
> color #3/A:258-650 lime
> color #3/B:937-1009 magenta
> color bfactor #3 palette alphafold
24869 atoms, 3259 residues, atom bfactor range 20.3 to 86.7
> color #3/A:209-432 lime
> color #3/B:944-983 magenta
> color bfactor #3 palette alphafold
24869 atoms, 3259 residues, atom bfactor range 20.3 to 86.7
> select add #3
24869 atoms, 25350 bonds, 3259 residues, 1 model selected
Alignment identifier is 3/A
Alignment identifier is 1
> select clear
> select #3/A:406-448
337 atoms, 339 bonds, 43 residues, 1 model selected
> select #3/A:406-543
1096 atoms, 1116 bonds, 138 residues, 1 model selected
> select #3/A:574
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:574-702
1030 atoms, 1048 bonds, 129 residues, 1 model selected
Drag select of 20 residues
> select #3/A:241
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:241-389
1186 atoms, 1206 bonds, 149 residues, 1 model selected
> hide #3 models
> open
> C:/Users/leena/Downloads/fold_setdb2_atf7ip_574_666_2025_06_01_22_36/fold_setdb2_atf7ip_574_666_2025_06_01_22_36_model_0.cif
Chain information for fold_setdb2_atf7ip_574_666_2025_06_01_22_36_model_0.cif
#4
---
Chain | Description
A | .
B C | .
Computing secondary structure
> select add #4
8467 atoms, 8606 bonds, 1054 residues, 2 models selected
> select clear
> select add #4
7281 atoms, 7400 bonds, 905 residues, 1 model selected
> color sel bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #4 file
> C:/Users/leena/Downloads/fold_setdb2_atf7ip_574_666_2025_06_01_22_36\\\fold_setdb2_atf7ip_574_666_2025_06_01_22_36_full_data_0.json
> color bfactor #4 palette alphafold
7281 atoms, 905 residues, atom bfactor range 12.5 to 94.9
> select clear
> show #3 models
> hide #4 models
> color #3 bychain
> close
> open C:/Users/leena/Downloads/8hfp.cif
Summary of feedback from opening C:/Users/leena/Downloads/8hfp.cif
---
note | Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
8hfp.cif title:
Crystal structure of the methyl-CpG-binding domain of SETDB2 in complex with
the cysteine-rich domain of C11orf46 protein [more info...]
Chain information for 8hfp.cif #1
---
Chain | Description | UniProt
A B | ARL14 effector protein | AL14E_HUMAN 3-77
C D | Histone-lysine N-methyltransferase SETDB2 | SETB2_HUMAN 2-108
Non-standard residues in 8hfp.cif #1
---
SO4 — sulfate ion
ZN — zinc ion
8hfp.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select /D:33
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> color bychain
Alignment identifier is 1
Alignment identifier is 2
> select clear
> select /C-D:9-87
1131 atoms, 1157 bonds, 2 pseudobonds, 140 residues, 2 models selected
> select clear
> select /A-B:9-46
552 atoms, 560 bonds, 76 residues, 1 model selected
> select clear
> select /A-B:9-76
1042 atoms, 1060 bonds, 136 residues, 1 model selected
> color sel cornflower blue
> color sel purple
> ui tool show "Color Actions"
> color sel medium slate blue
> select clear
> select /C:9-103/D:9-101
1380 atoms, 1412 bonds, 2 pseudobonds, 170 residues, 2 models selected
> color sel salmon
> color sel tomato
> select clear
> select /C:203@S
1 atom, 1 residue, 1 model selected
> select clear
> color bychain
> select /C/D
1453 atoms, 1424 bonds, 10 pseudobonds, 231 residues, 3 models selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel medium slate blue
> select /A/B
1115 atoms, 1072 bonds, 16 pseudobonds, 197 residues, 2 models selected
> color sel tomato
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
> select /C:9-103/D:9-101
1380 atoms, 1412 bonds, 2 pseudobonds, 170 residues, 2 models selected
> select clear
> select /B
559 atoms, 538 bonds, 8 pseudobonds, 98 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select /C
742 atoms, 727 bonds, 5 pseudobonds, 118 residues, 3 models selected
> select /D
711 atoms, 697 bonds, 5 pseudobonds, 113 residues, 3 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select clear
> select /A-B:9-76
1042 atoms, 1060 bonds, 136 residues, 1 model selected
> select clear
> save C:/Users/leena/Downloads/8HFP_setdb2_c11orf46_crystal.cxs
> save C:/Users/leena/Downloads/8HFP_setdb2_c110rf46_crystal.png width 1246
> height 826 supersample 3 transparentBackground true
> open
> C:/Users/leena/Downloads/fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49/fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49_model_0.cif
Chain information for
fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49_model_0.cif #2
---
Chain | Description
A | .
B C | .
Computing secondary structure
> hide #!1 models
> color #2 bychain
> hide #2 models
> open "C:/Users/leena/Downloads/fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49
> (1)/fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49_model_0.cif"
Chain information for
fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> show #!1 models
> hide #!1 models
> show #2 models
> hide #2 models
> show #!1 models
> ui tool show Matchmaker
> 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 8hfp.cif, chain A (#1) with
fold_setdb1_mbd_c11orf46_crd_2025_06_01_23_49_model_0.cif, chain A (#3),
sequence alignment score = 385.9
RMSD between 67 pruned atom pairs is 0.581 angstroms; (across all 68 pairs:
0.631)
> hide #!1 models
> color #3 bychain
> select add #3
1511 atoms, 1546 bonds, 185 residues, 1 model selected
> select #3/A
571 atoms, 581 bonds, 75 residues, 1 model selected
> show #!1 models
> hide #3 models
> select clear
> select #1/A-B:9-76
1042 atoms, 1060 bonds, 136 residues, 1 model selected
> show #3 models
> hide #!1 models
> select #3/A
571 atoms, 581 bonds, 75 residues, 1 model selected
> show #!1 models
> hide #!1 models
> ui tool show "Color Actions"
> color sel tomato
> select #3/B
940 atoms, 965 bonds, 110 residues, 1 model selected
> color sel cornflower blue
> select clear
> save C:/Users/leena/Downloads/AF3_model_Setdb1_MBD_C11orf46_CRD.png width
> 1246 height 826 supersample 3
> save C:/Users/leena/Downloads/AF3_model_Setdb1_MBD_C11orf46_CRD.png width
> 1246 height 826 supersample 3 transparentBackground true
> close
> open
> C:/Users/leena/Downloads/fold_atf7ip_1_364_trimethylated_mpp8_50_120_2025_05_09_14_50/fold_atf7ip_1_364_trimethylated_mpp8_50_120_2025_05_09_14_50_model_0.cif
Chain information for
fold_atf7ip_1_364_trimethylated_mpp8_50_120_2025_05_09_14_50_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:1-56
458 atoms, 462 bonds, 56 residues, 1 model selected
> open
> C:/Users/leena/Downloads/fold_atf7ip_1_56_trimethylated_mpp8_50_120_2025_05_09_14_50/fold_atf7ip_1_56_trimethylated_mpp8_50_120_2025_05_09_14_50_model_0.cif
Chain information for
fold_atf7ip_1_56_trimethylated_mpp8_50_120_2025_05_09_14_50_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #1 models
> color #2 bychain
Alignment identifier is 1/B
> select add #2
1505 atoms, 1522 bonds, 183 residues, 2 models selected
> select add #1
4311 atoms, 4375 bonds, 562 residues, 2 models selected
> select subtract #1
1047 atoms, 1060 bonds, 127 residues, 1 model selected
Alignment identifier is 2/A
Alignment identifier is 2/B
> select clear
> select #2/B:16
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:16
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save C:/Users/leena/Downloads/atf7ip_1-56_mpp8_50-120_AF3model.png width
> 1246 height 826 supersample 3 transparentBackground true
> close
> open
> C:/Users/leena/Downloads/fold_atf7ip_kdm5b_2025_05_22_05_40/fold_atf7ip_kdm5b_2025_05_22_05_40_model_0.cif
Chain information for fold_atf7ip_kdm5b_2025_05_22_05_40_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> C:/Users/leena/Downloads/fold_atf7ip_kdm5b_2025_05_22_05_40\\\fold_atf7ip_kdm5b_2025_05_22_05_40_full_data_0.json
> color bfactor #1 palette alphafold
21879 atoms, 2814 residues, atom bfactor range 18.1 to 95
> open "C:/Users/leena/Downloads/fold_setdb1_kdm5b_2025_05_17_17_59
> (1)/fold_setdb1_kdm5b_2025_05_17_17_59_model_0.cif"
Chain information for fold_setdb1_kdm5b_2025_05_17_17_59_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #1 models
> color #2 bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> "C:/Users/leena/Downloads/fold_setdb1_kdm5b_2025_05_17_17_59
> (1)\\\fold_setdb1_kdm5b_2025_05_17_17_59_full_data_0.json"
> color bfactor #2 palette alphafold
22352 atoms, 2835 residues, atom bfactor range 15.7 to 94.8
> color #2/A:563-947 lime
> color #2/B:374-753 magenta
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 2/A
> select add #2
22352 atoms, 22838 bonds, 2835 residues, 1 model selected
Alignment identifier is 2/A
Alignment identifier is 2/B
> select clear
Drag select of 43 residues
> select #2/B:561
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:561-786
1820 atoms, 1858 bonds, 226 residues, 1 model selected
> select #2/B:601-602
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/B:601-777
1428 atoms, 1454 bonds, 177 residues, 1 model selected
> select #2/B:622
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:622-703
648 atoms, 654 bonds, 82 residues, 1 model selected
> select #2/B:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:619-700
656 atoms, 662 bonds, 82 residues, 1 model selected
Drag select of 14 residues
> select #2/B:753-754
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/B:567-754
1512 atoms, 1545 bonds, 188 residues, 1 model selected
> select #2/B:754
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:485-754
2194 atoms, 2256 bonds, 270 residues, 1 model selected
> select #2/B:754
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:401-754
2855 atoms, 2931 bonds, 354 residues, 1 model selected
> select #2/B:754-755
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/B:379-755
3048 atoms, 3131 bonds, 377 residues, 1 model selected
> select #2/B:354
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:354-755
3244 atoms, 3332 bonds, 402 residues, 1 model selected
> select #2/B:361
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:361-753
3173 atoms, 3259 bonds, 393 residues, 1 model selected
Drag select of 11 residues
> select #2/A:931-932
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:931-936
49 atoms, 48 bonds, 6 residues, 1 model selected
> select #2/A:943
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:939-943
37 atoms, 36 bonds, 5 residues, 1 model selected
> select #2/A:949
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:928-949
175 atoms, 176 bonds, 22 residues, 1 model selected
> select #2/A:951
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:841-951
865 atoms, 880 bonds, 111 residues, 1 model selected
> select #2/A:951-952
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:721-952
1795 atoms, 1826 bonds, 232 residues, 1 model selected
> select #2/A:952-953
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/A:521-953
3419 atoms, 3502 bonds, 433 residues, 1 model selected
> select #2/A:561
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:561-953
3138 atoms, 3209 bonds, 393 residues, 1 model selected
> open
> C:/Users/leena/Downloads/fold_setdb1_561_953_kdmb_361_753_2025_06_02_03_03/fold_setdb1_561_953_kdmb_361_753_2025_06_02_03_03_model_0.cif
Chain information for
fold_setdb1_561_953_kdmb_361_753_2025_06_02_03_03_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #2 models
> select add #2
22352 atoms, 22838 bonds, 2835 residues, 1 model selected
> select subtract #2
Nothing selected
> color #3 bychain
> select add #3
6320 atoms, 6478 bonds, 787 residues, 1 model selected
Alignment identifier is 3/A
Alignment identifier is 3/B
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> C:/Users/leena/Downloads/fold_setdb1_561_953_kdmb_361_753_2025_06_02_03_03\\\fold_setdb1_561_953_kdmb_361_753_2025_06_02_03_03_full_data_0.json
> color bfactor #3 palette alphafold
6320 atoms, 787 residues, atom bfactor range 9.61 to 98
> select clear
> select add #3
6320 atoms, 6478 bonds, 787 residues, 1 model selected
> color sel bychain
> select #3/A
3174 atoms, 3260 bonds, 393 residues, 1 model selected
> color sel forest green
> select #3/B
3146 atoms, 3218 bonds, 394 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> color sel dark red
> select clear
> select #3/B
3146 atoms, 3218 bonds, 394 residues, 1 model selected
> ui tool show "Color Actions"
> color sel coral
> color sel sienna
> select clear
> select #3/B
3146 atoms, 3218 bonds, 394 residues, 1 model selected
> color sel spring green
> color sel light slate gray
> color sel cornflower blue
> color sel saddle brown
> color sel yellow
> color sel orange
> color sel medium purple
> color sel khaki
> color sel pale goldenrod
> color sel violet
> color sel medium slate blue
> color sel pale green
> color sel plum
> color sel olive drab
> color sel sea green
> color sel crimson
> color sel fire brick
> select clear
> color bfactor #3 palette alphafold
6320 atoms, 787 residues, atom bfactor range 9.61 to 98
> undo
> save C:/Users/leena/Downloads/setdb1_561-953_kdm5b_361-753_AF3model.png
> width 1246 height 826 supersample 3 transparentBackground true
> close
> open
> C:/Users/leena/Downloads/fold_mettl3_setdb1_2025_06_02_03_44/fold_mettl3_setdb1_2025_06_02_03_44_model_0.cif
Chain information for fold_mettl3_setdb1_2025_06_02_03_44_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> C:/Users/leena/Downloads/fold_mettl3_setdb1_2025_06_02_03_44\\\fold_mettl3_setdb1_2025_06_02_03_44_full_data_0.json
> color bfactor #1 palette alphafold
14564 atoms, 1871 residues, atom bfactor range 15.9 to 96
> color bfactor #1 palette alphafold
14564 atoms, 1871 residues, atom bfactor range 15.9 to 96
Alignment identifier is 1/A
Alignment identifier is 1/B
> color /B:517-853 lime
> color /A:120-169 magenta
> color /B:537-847 lime
> color /A:55-167 magenta
> color bfactor #1 palette alphafold
14564 atoms, 1871 residues, atom bfactor range 15.9 to 96
> color /B:175-416 lime
> color /B:545-859 lime
> color /A:74-148 magenta
Drag select of 23 residues
> select /A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:96-186
666 atoms, 673 bonds, 91 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-94
726 atoms, 742 bonds, 94 residues, 1 model selected
> select /A:14
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:14-145
998 atoms, 1016 bonds, 132 residues, 1 model selected
> select clear
> select /A:51
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:51-134
608 atoms, 620 bonds, 84 residues, 1 model selected
> select /A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:96-137
310 atoms, 312 bonds, 42 residues, 1 model selected
Drag select of 7 residues
> select /A:70
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:70-149
605 atoms, 615 bonds, 80 residues, 1 model selected
> select /A:70
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:70-160
681 atoms, 692 bonds, 91 residues, 1 model selected
> select /A:70
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:70-153
638 atoms, 649 bonds, 84 residues, 1 model selected
> select /B:545
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:545-625
674 atoms, 696 bonds, 81 residues, 1 model selected
> select /B:545
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:545-704
1332 atoms, 1375 bonds, 160 residues, 1 model selected
> select /B:545
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:545-756
1713 atoms, 1763 bonds, 212 residues, 1 model selected
> select /B:545
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:545-796
2032 atoms, 2088 bonds, 252 residues, 1 model selected
> select /B:545
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:545-840
2379 atoms, 2441 bonds, 296 residues, 1 model selected
> select /B:544-545
12 atoms, 12 bonds, 2 residues, 1 model selected
> select /B:544-873
2653 atoms, 2721 bonds, 330 residues, 1 model selected
> select /B:544
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:544-865
2585 atoms, 2651 bonds, 322 residues, 1 model selected
> open
> C:/Users/leena/Downloads/fold_mettl3_70_153_setdb1_544_865_2025_06_02_03_44/fold_mettl3_70_153_setdb1_544_865_2025_06_02_03_44_model_0.cif
Chain information for
fold_mettl3_70_153_setdb1_544_865_2025_06_02_03_44_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #1 models
> select add #1
14564 atoms, 14871 bonds, 1871 residues, 1 model selected
> select subtract #1
Nothing selected
> color #2 bychain
> select add #2
3225 atoms, 3302 bonds, 406 residues, 1 model selected
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> C:/Users/leena/Downloads/fold_mettl3_70_153_setdb1_544_865_2025_06_02_03_44\\\fold_mettl3_70_153_setdb1_544_865_2025_06_02_03_44_full_data_0.json
> color #2/A:7-84/B:1-6 lime
> color #2/B:15-287 magenta
> select clear
> hide #2 models
> show #1 models
> select add #1
14564 atoms, 14871 bonds, 1871 residues, 1 model selected
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> C:/Users/leena/Downloads/fold_mettl3_setdb1_2025_06_02_03_44\\\fold_mettl3_setdb1_2025_06_02_03_44_full_data_0.json
> color bfactor #1 palette alphafold
14564 atoms, 1871 residues, atom bfactor range 15.9 to 96
> select clear
> color #1/A:112-146 lime
> color #1/B:554-868 magenta
> color #1/B:548-861 lime
> color #1/A:123-140 magenta
> color bfactor #1 palette alphafold
14564 atoms, 1871 residues, atom bfactor range 15.9 to 96
> show #2 models
> hide #1 models
> color bfactor #2 palette alphafold
3225 atoms, 406 residues, atom bfactor range 15.8 to 93.4
> open C:/Users/leena/Downloads/fold_mettl3_setdb1_trim28_2025_06_02_03_44.zip
Unrecognized file suffix '.zip'
> open
> C:/Users/leena/Downloads/fold_mettl3_setdb1_trim28_2025_06_02_03_44/fold_mettl3_setdb1_trim28_2025_06_02_03_44_model_0.cif
Chain information for fold_mettl3_setdb1_trim28_2025_06_02_03_44_model_0.cif
#3
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #2 models
> select add #3
20755 atoms, 21185 bonds, 2706 residues, 1 model selected
> color sel bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> C:/Users/leena/Downloads/fold_mettl3_setdb1_trim28_2025_06_02_03_44\\\fold_mettl3_setdb1_trim28_2025_06_02_03_44_full_data_0.json
> color bfactor #3 palette alphafold
20755 atoms, 2706 residues, atom bfactor range 16.9 to 94.6
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505290006 (2025-05-29)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 - Build 30.0.101.1371
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: LENOVO
Model: F0EL000UUS
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 17,044,664,320
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700T CPU @ 2.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.4
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505290006
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: 2.5.1
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: 1.6.2
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: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
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: 1.19.1
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: 1.45.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.8.2
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.1
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
