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Opened 8 days ago
Closed 7 days ago
#19421 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.11.dev202508300055 (2025-08-30 00:55:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d
Current thread 0x00006670 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open "D:\桌面\BLB4 and BLB21\my_session.cxs" format session
> view name session-start
opened ChimeraX session
> open "D:/桌面/BLB4 and BLB21/my_session.cxs"
> view name session-start
opened ChimeraX session
> open C:/Users/1/Desktop/my_session.cxs
> view name session-start
opened ChimeraX session
> hide #!1 models
> hide #!11 models
> hide #!8 models
> coulombic #10#!2,9
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
BLB21_9.pdb #9/A VAL -25
BLB21_9.pdb #9/A ARG -20
BLB21_9.pdb #9/A MET -17
BLB21_9.pdb #9/A ARG -13
BLB21_9.pdb #9/C ARG 3
BLB21_9.pdb #9/C GLU 17
BLB21_9.pdb #9/C LYS 21
BLB21_9.pdb #9/C LEU 35
BLB21_9.pdb #9/C GLN 44
BLB21_9.pdb #9/C GLU 51
BLB21_9.pdb #9/C GLU 59
BLB21_9.pdb #9/C SER 79
BLB21_9.pdb #9/C PHE 88
BLB21_9.pdb #9/C GLU 99
BLB21_9.pdb #9/C ARG 170
BLB21_9.pdb #9/C TRP 172
BLB21_9.pdb #9/D GLU 21
BLB21_9.pdb #9/D ARG 22
BLB21_9.pdb #9/D LYS 45
BLB21_9.pdb #9/D GLU 127
BLB21_9.pdb #9/D LYS 129
BLB21_9.pdb #9/D ARG 135
BLB21_9.pdb #9/D ARG 165
BLB21_9.pdb #9/D ARG 166
BLB21_9.pdb #9/D ARG 180
BLB21_10.pdb #10/A ARG 3
BLB21_10.pdb #10/A GLU 175
BLB21_10.pdb #10/B LYS 10
BLB21_10.pdb #10/B LEU 17
BLB21_10.pdb #10/B ASN 18
BLB21_10.pdb #10/B GLU 21
BLB21_10.pdb #10/B ARG 22
BLB21_10.pdb #10/B LYS 45
BLB21_10.pdb #10/B ARG 166
BLB21_10.pdb #10/B ARG 180
BLB21_10.pdb #10/B GLN 181
BLB21_10.pdb #10/B GLU 188
BLB21_10.pdb #10/C ARG -20
BLB21_10.pdb #10/C ARG -13
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BLB21_10.pdb_A SES surface #10.1: minimum, -24.44, mean
-2.75, maximum 9.60
Coulombic values for BLB21_10.pdb_B SES surface #10.2: minimum, -15.26, mean
-3.28, maximum 9.49
Coulombic values for BLB21_10.pdb_C SES surface #10.3: minimum, -10.44, mean
-0.77, maximum 7.65
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
Coulombic values for BLB21_9.pdb_A SES surface #9.2: minimum, -10.02, mean
-0.25, maximum 8.12
Coulombic values for BLB21_9.pdb_C SES surface #9.3: minimum, -16.55, mean
-2.29, maximum 11.12
Coulombic values for BLB21_9.pdb_D SES surface #9.4: minimum, -14.57, mean
-3.67, maximum 8.47
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #10.3 models
> show #10.3 models
> hide #!10 models
> hide #!9 models
> hide #!2 models
> hide #2.3 models
> show #2.1 models
> show #2.3 models
> hide #2.2 models
> show #!9 models
> hide #9.2 models
> show #!10 models
> hide #!10.1 models
> show #10.1 models
> hide #!10.2 models
> show #10.2 models
> hide #10.3 models
> hide #!10 models
> hide #!9 models
> hide #!2.3 models
> hide #!2.4 models
> hide #2.1 models
> show #2.4 models
> hide #!2.4 models
> show #2.3 models
> hide #!2.3 models
> show #2.2 models
> hide #2.2 models
> select add #2.2
104 atoms, 14 residues, 1 model selected
> show sel atoms
> hide #9.1 models
> show #!9 models
> hide #!9.4 models
> hide #!9.3 models
> select add #9.2
202 atoms, 29 residues, 3 models selected
> show sel atoms
> color sel byhetero
> select add #10.3
314 atoms, 45 residues, 5 models selected
> show #!10 models
> hide #!10.2 models
> hide #!10.1 models
> show sel atoms
Drag select of 24 atoms, 8 residues, 20 bonds
> hide sel atoms
> save my_session.cxs
> cd "D:/桌面/BLB4 and BLB21"
Current working directory is: D:\桌面\BLB4 and BLB21
> save my_session.cxs
Drag select of 18 atoms, 9 residues, 16 bonds
> hide sel atoms
> ui tool show "Side View"
> save my_session.cxs
> open E:/xwechat_files/wxid_idejr78pt1sr22_f116/msg/file/2025-11/21-9.pdb
21-9.pdb title:
\--- [more info...]
Chain information for 21-9.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> color #5 #b3e1f3ff
> mmaker #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 BL4R.pdb, chain A (#1) with 21-9.pdb, chain A (#5), sequence
alignment score = 982.6
RMSD between 183 pruned atom pairs is 0.651 angstroms; (across all 184 pairs:
0.668)
> select #5/A
1496 atoms, 1546 bonds, 184 residues, 1 model selected
> color sel lightgray
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 21-9.pdb_A SES surface #5.2: minimum, -12.72, mean -1.82,
maximum 11.17
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #5.1 models
> select clear
> select add #5
3509 atoms, 3248 bonds, 1 pseudobond, 739 residues, 3 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 21-9.pdb_A SES surface #5.2: minimum, -12.72, mean -1.82,
maximum 11.17
Coulombic values for 21-9.pdb_B SES surface #5.3: minimum, -14.55, mean -1.56,
maximum 11.34
Coulombic values for 21-9.pdb_C SES surface #5.4: minimum, -10.06, mean -0.10,
maximum 14.64
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> hide sel atoms
> coulombic sel
Coulombic values for 21-9.pdb_A SES surface #5.2: minimum, -12.72, mean -1.82,
maximum 11.17
Coulombic values for 21-9.pdb_B SES surface #5.3: minimum, -14.55, mean -1.56,
maximum 11.34
Coulombic values for 21-9.pdb_C SES surface #5.4: minimum, -10.06, mean -0.10,
maximum 14.64
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #5.4 models
> hide sel surfaces
> select clear
> select add #5.4
116 atoms, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel cyan
> color sel deep sky blue
> select subtract #5.4
1 model selected
> select add #9.4
1481 atoms, 187 residues, 1 model selected
> select subtract #9.4
1 model selected
> select add #9.3
1452 atoms, 184 residues, 1 model selected
> select subtract #9.3
1 model selected
> select add #9.2
98 atoms, 15 residues, 1 model selected
> color sel powder blue
> color sel light sea green
> color sel medium turquoise
> select subtract #9.2
1 model selected
> select add #10.3
112 atoms, 16 residues, 1 model selected
> color sel light cyan
> color sel powder blue
> color sel byhetero
> show #!8 models
> select subtract #10.3
1 model selected
> hide #!10 models
> show #!1 models
> hide #!1-2,5,8-9 atoms
> show #!11 models
> show #!10 models
> hide atoms
> save "D:/桌面/BLB4 and BLB21/BLB_comparison_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
> save my_session.cxs
> hide #!1 models
> hide #!11 models
> hide #!8 models
> show #2.2 models
> hide #2.2 models
> select add #2.2
104 atoms, 14 residues, 1 model selected
> select add #5.4
220 atoms, 29 residues, 3 models selected
> select add #9.4
1701 atoms, 216 residues, 5 models selected
> select subtract #9.4
220 atoms, 29 residues, 5 models selected
> select add #9.2
318 atoms, 44 residues, 5 models selected
> select add #10.1
1835 atoms, 231 residues, 7 models selected
> select subtract #10.1
318 atoms, 44 residues, 7 models selected
> select add #10.3
430 atoms, 60 residues, 7 models selected
> show sel atoms
Drag select of 28 atoms, 36 residues, 18 bonds
Drag select of 26 atoms, 38 residues, 21 bonds
> hide sel atoms
Drag select of 27 atoms, 36 residues, 23 bonds
> hide sel atoms
> save "D:/桌面/BLB4 and BLB21/BLB21_comparison.png" width 1979 height 1169
> supersample 3 transparentBackground true
> show #!11 models
> hide #11.1 models
> select add #11
3289 atoms, 3134 bonds, 2 pseudobonds, 415 residues, 18 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
BLB2.pdb #11/A GLU 176
BLB2.pdb #11/B LEU 139
BLB2.pdb #11/B GLN 140
BLB2.pdb #11/B GLU 146
BLB2.pdb #11/B ARG 149
BLB2.pdb #11/B ARG 176
BLB2.pdb #11/B GLU 197
BLB2.pdb #11/B THR 198
BLB2.pdb #11/B VAL 199
BLB2.pdb #11/B GLU 224
BLB2.pdb #11/C ILE 6
BLB2.pdb #11/C GLU 7
BLB2.pdb #11/C LYS 22
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
Coulombic values for BLB21_9.pdb_A SES surface #9.2: minimum, -10.02, mean
-0.25, maximum 8.12
Coulombic values for BLB21_9.pdb_C SES surface #9.3: minimum, -16.55, mean
-2.29, maximum 11.12
Coulombic values for BLB21_9.pdb_D SES surface #9.4: minimum, -14.57, mean
-3.67, maximum 8.47
Coulombic values for BLB21_10.pdb_A SES surface #10.1: minimum, -24.44, mean
-2.75, maximum 9.60
Coulombic values for BLB21_10.pdb_B SES surface #10.2: minimum, -15.26, mean
-3.28, maximum 9.49
Coulombic values for BLB21_10.pdb_C SES surface #10.3: minimum, -10.44, mean
-0.77, maximum 7.65
Coulombic values for BLB2.pdb_A SES surface #11.2: minimum, -18.91, mean
-2.79, maximum 7.94
Coulombic values for BLB2.pdb_B SES surface #11.3: minimum, -15.68, mean
-2.67, maximum 9.18
Coulombic values for BLB2.pdb_C SES surface #11.4: minimum, -4.56, mean 0.18,
maximum 8.96
Coulombic values for 21-9.pdb_A SES surface #5.2: minimum, -12.72, mean -1.82,
maximum 11.17
Coulombic values for 21-9.pdb_B SES surface #5.3: minimum, -14.55, mean -1.56,
maximum 11.34
Coulombic values for 21-9.pdb_C SES surface #5.4: minimum, -10.06, mean -0.10,
maximum 14.64
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> hide #11.4 models
> show #11.4 models
> color sel bychain
> undo
> show sel surfaces
> hide sel surfaces
> hide #11.4 models
> hide #!11.3 models
> hide #!11.2 models
> show sel surfaces
> select add #11.3
3289 atoms, 3134 bonds, 2 pseudobonds, 415 residues, 23 models selected
> select add #11.2
3289 atoms, 3134 bonds, 2 pseudobonds, 415 residues, 24 models selected
> hide #!11.2 models
> hide #!11.3 models
> hide #11.4 models
> hide #!11 models
> hide #!9 models
> hide #!5 models
> hide #!10 models
> hide #!2 models
> select subtract #11
262 atoms, 23 bonds, 36 residues, 19 models selected
> show #!11 models
> show #11.2 models
> show #11.4 models
> hide #11.4 models
> show #11.3 models
> select add #11.4
379 atoms, 23 bonds, 53 residues, 17 models selected
> show sel & #!11 atoms
> select subtract #11.4
262 atoms, 23 bonds, 36 residues, 17 models selected
> show #!10 models
> hide #!11 models
> coulombic sel & #!10
Coulombic values for BLB21_10.pdb_A SES surface #10.1: minimum, -24.44, mean
-2.75, maximum 9.60
Coulombic values for BLB21_10.pdb_B SES surface #10.2: minimum, -15.26, mean
-3.28, maximum 9.49
Coulombic values for BLB21_10.pdb_C SES surface #10.3: minimum, -10.44, mean
-0.77, maximum 7.65
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #10
3304 atoms, 3223 bonds, 417 residues, 16 models selected
> coulombic sel & #!10
Coulombic values for BLB21_10.pdb_A SES surface #10.1: minimum, -24.44, mean
-2.75, maximum 9.60
Coulombic values for BLB21_10.pdb_B SES surface #10.2: minimum, -15.26, mean
-3.28, maximum 9.49
Coulombic values for BLB21_10.pdb_C SES surface #10.3: minimum, -10.44, mean
-0.77, maximum 7.65
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #10.3 models
> hide #11.3 models
> hide #11.2 models
> select add #2
6286 atoms, 6358 bonds, 62 pseudobonds, 783 residues, 19 models selected
> select subtract #2
3235 atoms, 3218 bonds, 408 residues, 15 models selected
> select add #3
3235 atoms, 3218 bonds, 45 pseudobonds, 408 residues, 13 models selected
> select subtract #3
3235 atoms, 3218 bonds, 408 residues, 12 models selected
> select add #5
6678 atoms, 6457 bonds, 1 pseudobond, 1138 residues, 13 models selected
> select subtract #5
3169 atoms, 3209 bonds, 399 residues, 11 models selected
> select add #9
6146 atoms, 6321 bonds, 1 pseudobond, 777 residues, 9 models selected
> select subtract #9
3115 atoms, 3205 bonds, 391 residues, 7 models selected
> select add #10
3115 atoms, 3205 bonds, 391 residues, 6 models selected
> select subtract #10
3 models selected
> show #!11 models
> hide #!11 models
> hide #!10 models
> show #!11 models
> show #11.2 models
> show #11.3 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> select add #9.4
1481 atoms, 187 residues, 1 model selected
> select subtract #9.4
1 model selected
> hide #9.4 models
> show #9.4 models
> select add #9
3031 atoms, 3116 bonds, 1 pseudobond, 386 residues, 2 models selected
> coulombic sel
Coulombic values for BLB21_9.pdb_A SES surface #9.2: minimum, -10.02, mean
-0.25, maximum 8.12
Coulombic values for BLB21_9.pdb_C SES surface #9.3: minimum, -16.55, mean
-2.29, maximum 11.12
Coulombic values for BLB21_9.pdb_D SES surface #9.4: minimum, -14.57, mean
-3.67, maximum 8.47
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #9
3031 atoms, 3116 bonds, 1 pseudobond, 386 residues, 7 models selected
> select subtract #9
3 models selected
> hide #!9.4 models
> show #9.4 models
> hide #9.2 models
> select add #9.2
98 atoms, 15 residues, 1 model selected
> color sel byhetero
> hide #!9 models
> show #!5 models
> select add #5
3607 atoms, 3248 bonds, 1 pseudobond, 754 residues, 4 models selected
> coulombic sel & #!5
Coulombic values for 21-9.pdb_A SES surface #5.2: minimum, -12.72, mean -1.82,
maximum 11.17
Coulombic values for 21-9.pdb_B SES surface #5.3: minimum, -14.55, mean -1.56,
maximum 11.34
Coulombic values for 21-9.pdb_C SES surface #5.4: minimum, -10.06, mean -0.10,
maximum 14.64
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #5.4 models
> select subtract #5.1
3607 atoms, 3248 bonds, 754 residues, 6 models selected
> select add #5.3
3607 atoms, 3248 bonds, 754 residues, 7 models selected
> select add #5.2
3607 atoms, 3248 bonds, 754 residues, 8 models selected
> select subtract #5.4
3491 atoms, 3132 bonds, 739 residues, 8 models selected
> select subtract #5.3
1946 atoms, 1546 bonds, 551 residues, 6 models selected
> select subtract #5.2
450 atoms, 367 residues, 4 models selected
> select add #5.4
566 atoms, 382 residues, 3 models selected
> color sel & #!5 byhetero
> hide #!5 models
> select add #2.4
2034 atoms, 561 residues, 5 models selected
> select subtract #2.4
566 atoms, 382 residues, 5 models selected
> show #2.1 models
> select add #2.1
566 atoms, 2 pseudobonds, 382 residues, 5 models selected
> coulombic #!2
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.4 models
> show #2.4 models
> hide #2.2 models
> hide #!2 models
> save my_session.cxs
> show #!1 models
> select add #1
3665 atoms, 3190 bonds, 3 pseudobonds, 760 residues, 7 models selected
> coulombic sel & #!1
Coulombic values for BL4R.pdb_A SES surface #1.2: minimum, -13.30, mean -2.41,
maximum 9.55
Coulombic values for BL4R.pdb_B SES surface #1.3: minimum, -14.87, mean -1.87,
maximum 11.23
Coulombic values for BL4R.pdb_C SES surface #1.4: minimum, -8.31, mean 2.68,
maximum 12.11
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.4 models
> select subtract #1.1
3665 atoms, 3190 bonds, 2 pseudobonds, 760 residues, 9 models selected
> select subtract #1.4
3549 atoms, 3075 bonds, 2 pseudobonds, 745 residues, 9 models selected
> select add #1.4
3665 atoms, 3075 bonds, 2 pseudobonds, 760 residues, 8 models selected
> select subtract #1.4
3549 atoms, 3075 bonds, 2 pseudobonds, 745 residues, 9 models selected
> select add #1.3
3549 atoms, 3075 bonds, 2 pseudobonds, 745 residues, 9 models selected
> select add #1.2
3549 atoms, 3075 bonds, 2 pseudobonds, 745 residues, 10 models selected
> select add #1
3665 atoms, 3190 bonds, 3 pseudobonds, 760 residues, 11 models selected
> select subtract #1
566 atoms, 2 pseudobonds, 382 residues, 8 models selected
> select add #1.4
682 atoms, 2 pseudobonds, 397 residues, 6 models selected
> color sel & #!1 byhetero
> show sel & #!1 atoms
> show #!11 models
> hide #!1 models
> show #!1 models
> hide #!11 models
> hide #!1.3 models
> hide #!1.2 models
> show #1.2 models
> show #1.3 models
> select subtract #1.4
566 atoms, 2 pseudobonds, 382 residues, 6 models selected
> save "D:/桌面/BLB4 and BLB21/BLB4_electr_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
Drag select of BL4R.pdb_A SES surface, 9411 of 196572 triangles, cap far, 80
of 5143 triangles, BL4R.pdb_B SES surface, 2620 of 193984 triangles, cap far,
275 of 1717 triangles, 9 atoms, 14 residues, 8 bonds
Drag select of BL4R.pdb_B SES surface, 8 of 193984 triangles
Drag select of BL4R.pdb_B SES surface, 100 of 193984 triangles, cap far, 23 of
1717 triangles, 3 residues
> select clear
Drag select of BL4R.pdb_A SES surface, 9674 of 196572 triangles, cap far, 80
of 5143 triangles, BL4R.pdb_B SES surface, 3679 of 193984 triangles, cap far,
393 of 1717 triangles, 9 atoms, 18 residues, 8 bonds
Drag select of BL4R.pdb_A SES surface, 9201 of 196572 triangles, cap far, 33
of 5143 triangles, BL4R.pdb_B SES surface, 2516 of 193984 triangles, cap far,
248 of 1717 triangles, 9 atoms, 17 residues, 7 bonds
> hide sel atoms
Drag select of BL4R.pdb_A SES surface, 8859 of 196572 triangles, cap far, 39
of 5143 triangles, BL4R.pdb_B SES surface, 3665 of 193984 triangles, 13 atoms,
14 residues, 11 bonds
> select clear
Drag select of BL4R.pdb_A SES surface, 7595 of 196572 triangles, cap far, 46
of 5143 triangles, BL4R.pdb_B SES surface, 4142 of 193984 triangles, 13 atoms,
15 residues, 11 bonds
> hide sel atoms
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB4_electr_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_2.png" width 1979 height 1169
> supersample 3
> hide #!2 models
> show #!5 models
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_3.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!5 models
> show #!8 models
> select add #8
3317 atoms, 3198 bonds, 1 pseudobond, 591 residues, 3 models selected
> select subtract #8
3 models selected
> hide #!8 models
> show #!9 models
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_4.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!9 models
> show #!10 models
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_5.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!10 models
> show #!11 models
Drag select of BLB2.pdb_A SES surface, 8070 of 192918 triangles, cap far, 62
of 4919 triangles, BLB2.pdb_B SES surface, 2324 of 185962 triangles, cap far,
195 of 1350 triangles, 4 atoms, 12 residues, 2 bonds
> hide sel atoms
Drag select of BLB2.pdb_A SES surface, 4692 of 192918 triangles, cap far, 67
of 4919 triangles, BLB2.pdb_B SES surface, 3133 of 185962 triangles, 10 atoms,
16 residues, 8 bonds
Drag select of BLB2.pdb_A SES surface, 2447 of 192918 triangles, BLB2.pdb_B
SES surface, 1591 of 185962 triangles, 7 atoms, 10 residues, 6 bonds
> hide sel atoms
Drag select of BLB2.pdb_A SES surface, 372 of 192918 triangles, BLB2.pdb_B SES
surface, 1057 of 185962 triangles, 1 atoms, 2 residues, 2 bonds
> hide sel atoms
> save "D:/桌面/BLB4 and BLB21/BLB2_electr.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!11 models
> show #!8 models
> select add #8
3331 atoms, 3200 bonds, 1 pseudobond, 593 residues, 5 models selected
> coulombic sel & #!8
Coulombic values for 6kvm_A SES surface #8.2: minimum, -14.93, mean -2.22,
maximum 11.36
Coulombic values for 6kvm_B SES surface #8.3: minimum, -14.93, mean -1.92,
maximum 8.37
Coulombic values for 6kvm_C SES surface #8.4: minimum, -10.45, mean -2.08,
maximum 7.02
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #8.4
3201 atoms, 3069 bonds, 1 pseudobond, 576 residues, 8 models selected
> hide #8.4 models
> select subtract #8.1
3201 atoms, 3069 bonds, 576 residues, 5 models selected
> select add #8.3
3201 atoms, 3069 bonds, 576 residues, 6 models selected
> select add #8.2
3201 atoms, 3069 bonds, 576 residues, 7 models selected
> select subtract #8.3
1726 atoms, 1553 bonds, 397 residues, 6 models selected
> select subtract #8.2
230 atoms, 7 bonds, 213 residues, 4 models selected
> select add #8.4
360 atoms, 7 bonds, 230 residues, 3 models selected
> show sel & #!8 atoms
> color sel & #!8 byhetero
> delete water
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #8.4
230 atoms, 7 bonds, 213 residues, 4 models selected
> hide sel
> select add #8.4
360 atoms, 7 bonds, 230 residues, 3 models selected
Drag select of 6kvm_A SES surface, 10114 of 196386 triangles, cap far, 133 of
4802 triangles, 6kvm_B SES surface, 6126 of 190828 triangles, cap far, 535 of
1662 triangles, 15 atoms, 24 residues, 12 bonds
> hide sel atoms
Drag select of 6kvm_A SES surface, 5650 of 196386 triangles, cap far, 57 of
4802 triangles, 6kvm_B SES surface, 3659 of 190828 triangles, 13 atoms, 16
residues, 11 bonds
> hide sel atoms
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB19_electr.png" width 1979 height 1169
> supersample 3 transparentBackground true
> save my_session.cxs
> hide #!8.3 models
> hide #!8.2 models
> undo
> redo
> show #!8.1 models
> hide #!8.2 models
> hide #!8.3 models
> hide #!8.1 models
> hide #!8 models
> show #8.3 models
> select add #8.3
1705 atoms, 7 bonds, 392 residues, 4 models selected
> select subtract #8.3
230 atoms, 7 bonds, 213 residues, 4 models selected
> select add #8.3
1705 atoms, 7 bonds, 392 residues, 4 models selected
> sequence chain #8/B
Alignment identifier is 8/B
> sequence chain #11/C
Alignment identifier is 11/C
> show #!8.1 models
> show #8.2 models
> sequence chain #8/B
Alignment identifier is 8/B
> sequence chain #11/C
Alignment identifier is 11/C
> select #8/B:77
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:77
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:77
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:76-77
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #8/B:77
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:76-77
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #8/B:77
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:76-77
19 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select #8/B:78
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/B:78-80
28 atoms, 28 bonds, 3 residues, 1 model selected
> hide sel surfaces
> select #8/B:80
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:75-80
54 atoms, 54 bonds, 6 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select #8/B:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/B:72-74
25 atoms, 24 bonds, 3 residues, 1 model selected
> hide sel surfaces
> show sel atoms
> hide sel atoms
> show sel surfaces
> select clear
Drag select of 6kvm_A SES surface, 5617 of 196386 triangles, cap far, 89 of
4802 triangles, 6kvm_B SES surface, 5538 of 190828 triangles, 15 atoms, 19
residues, 12 bonds
> undo
Drag select of 6kvm_A SES surface, 3932 of 196386 triangles, cap far, 34 of
4564 triangles, 6kvm_B SES surface, 4142 of 190828 triangles, 13 atoms, 17
residues, 10 bonds
Drag select of 6kvm_A SES surface, 3550 of 196386 triangles, cap far, 44 of
4564 triangles, 6kvm_B SES surface, 3057 of 190828 triangles, 11 atoms, 13
residues, 10 bonds
> hide sel atoms
Drag select of 6kvm_A SES surface, 5173 of 196386 triangles, cap far, 53 of
4564 triangles, 6kvm_B SES surface, 5793 of 190828 triangles, cap far, 501 of
1649 triangles, 13 atoms, 22 residues, 10 bonds
> hide sel atoms
> select clear
> save my_session.cxs
> hide #!8 models
> show #1.4 models
> hide #1.4 models
> select add #1.4
116 atoms, 15 residues, 1 model selected
> hide #!1.3 models
> hide #!1.2 models
QDxgiVSyncService: DXGI Factory is no longer Current
> color #1.2 #f3f3f3ff
> color #1.2 #f0f0f0ff
> show #1.2 models
> show #1.3 models
> color #1.3 #e5ccacff
> hide #!1 models
> hide #1.3 models
> hide #1.2 models
> show #!8 models
> hide #!8.1 models
> hide #!8.2 models
> hide #!8.3 models
> show #!5 models
> hide #!5 models
> select add #8
3433 atoms, 3198 bonds, 1 pseudobond, 606 residues, 5 models selected
> mlp sel & #!8
Map values for surface "6kvm_A SES surface": minimum -25.19, mean -3.996,
maximum 22.29
Map values for surface "6kvm_B SES surface": minimum -27.41, mean -4.337,
maximum 23.15
Map values for surface "6kvm_C SES surface": minimum -27.99, mean -7.224,
maximum 19.15
To also show corresponding color key, enter the above mlp command and add key
true
> style sel & #!8 sphere
Changed 3317 atom styles
> select add #8
3433 atoms, 3198 bonds, 1 pseudobond, 606 residues, 10 models selected
> style sel & #!8 sphere
Changed 3317 atom styles
> style sel & #!8 stick
Changed 3317 atom styles
> select subtract #8
116 atoms, 15 residues, 5 models selected
> select add #8.2
1612 atoms, 199 residues, 4 models selected
> select subtract #8.2
116 atoms, 15 residues, 3 models selected
> hide #!8.2 models
> show #8.2 models
> select add #8.2
1612 atoms, 199 residues, 4 models selected
> color #8.2 #f7f7f7ff
> color #8.2 #f4f4f4ff
> hide #8.4 models
> color #8.3 white
> color #8.3 #f3edb3ff
> select subtract #8.2
116 atoms, 15 residues, 3 models selected
> select add #8.3
1591 atoms, 194 residues, 4 models selected
> show sel & #!8 atoms
> hide sel & #!8 surfaces
> show sel & #!8 surfaces
> select subtract #8.3
116 atoms, 15 residues, 3 models selected
> select subtract #1.4
1 model selected
> hide #!8.3 models
> hide #!8.2 models
> hide #!8 models
> show #!2 models
> hide #!2.3 models
> show #2.3 models
> color #2.3 #f3f3f3ff
> color #2.4 #b8e5f6ff
> color #2.4 #b3e1f3ff
> color #2.4 #b0dff1ff
> hide #!2 models
> hide #5.2 models
> show #5.2 models
> show #5.1 models
> hide #5.1 models
> color #5.2 white
> color #5.2 #f0f0f0ff
> color #5.2 #f7f7f7ff
> color #5.3 #ceeaf4ff
> color #5.3 #adddf0ff
> hide #!5 models
> show #!9 models
> color #9.3 whitesmoke
> color #9.4 #b3e1f3ff
> show #!10 models
> color #10.1 #fafafaff
> color #10.2 white
> color #10.2 #b3e1f3ff
> hide #!10.2 models
> hide #!10.1 models
> hide #!10 models
> hide #!9.4 models
> hide #!9.3 models
> show #!11 models
> color #11.2 #f7f7f7ff
> color #11.3 #b8d7baff
> hide #!11 models
> hide #!9 models
> hide #2.4 models
> hide #2.3 models
> hide #2.1 models
> save my_session_2.cxs
> show #!1 models
> show #!2 models
> show #3 models
> hide #3 models
> show #1.1 models
> hide #!2 models
> hide #1.1 models
> show #1.2 models
> show #1.3 models
> color #1.3 #e8cfafff
> color #1.3 #e2caaaff
> save "D:/桌面/BLB4 and BLB21/BLB4_surface.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!1.3 models
> hide #!1.2 models
> hide #!1 models
> show #2.1 models
> show #2.3 models
> show #2.4 models
> save "D:/桌面/BLB4 and BLB21/BLB21_surface1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!2 models
> show #!5 models
> hide #!5.3 models
> show #5.3 models
> save "D:/桌面/BLB4 and BLB21/BLB21_surface2.png" width 1979 height 1169
> supersample 3
> hide #!5 models
> show #!8 models
> color #8.3 #f6f0b9ff
> color #8.3 #f7f1bcff
> show #8.3 models
> show #8.2 models
> save "D:/桌面/BLB4 and BLB21/BLB19_surface.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!8 models
> show #!9 models
> show #9.4 models
> show #9.3 models
> save "D:/桌面/BLB4 and BLB21/BLB21_surface3.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!9 models
> show #!10 models
> show #10.3 models
> hide #10.3 models
> show #10.2 models
> show #10.1 models
> save "D:/桌面/BLB4 and BLB21/BLB21_surface4.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!10 models
> show #!11 models
> save "D:/桌面/BLB4 and BLB21/BLB2_surface.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!11 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> show #1.3 models
> hide #1.1 models
> show #!2 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> hide #1.3 models
> hide #1.2 models
> show #!1 models
> hide #!1 atoms
> save "D:/桌面/BLB4 and BLB21/BLB4_cartoon.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> hide #!2 surfaces
> hide #!2 atoms
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!2 models
> show #!5 models
> hide #!5 surfaces
> hide #!5 atoms
> show #1.4 models
> hide #1.4 models
> hide #!1 models
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_2.png" width 1979 height 1169
> supersample 3
QDxgiVSyncService: DXGI Factory is no longer Current
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!5 models
> show #!2 models
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> show #!5 models
> show #!1 models
QDxgiVSyncService: DXGI Factory is no longer Current
> color #5 #aaffffff
> color #5 #82c8a9ff
> color #5 #79b9d3ff
> hide #!2 models
> show #!2 models
> hide #2.1 models
> color #5 #90d8f5ff
> color #5 #a2f7ffff
> color #5 #a0f5ffff
> color #5 #a1f6ffff
> color #5 #a1f5ffff
> color #5 #517c8eff
> color #5 #82c6e2ff
> color #5 #85cae6ff
> color #5 #85cbe7ff
> show #1.4 models
> hide #1.4 models
> select add #5.3
1545 atoms, 188 residues, 1 model selected
> select subtract #5.3
1 model selected
> color #5.3 #cbf5f5ff
> color #5.3 white
> color #5.3 #f0f0f0ff
> color #5.3 white
> color #5.3 #f0f0f0ff
> color #5.3 white
> color #5.3 #f3f3f3ff
> color #5.3 #f0f0f0ff
> color #5.3 #efefefff
> color #5.3 #b5b6b6ff
> color #5.3 white
> color #5.3 #cbf5f5ff
> show #5.4 models
> hide #5.4 models
QDxgiVSyncService: DXGI Factory is no longer Current
> select #5/C
116 atoms, 116 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel deep sky blue
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel deep sky blue
> select clear
QDxgiVSyncService: DXGI Factory is no longer Current
> save "D:/桌面/BLB4 and BLB21/BLB21_comparison_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!2 models
> hide #!5 models
> save "D:/桌面/BLB4 and BLB21/BLB4_cartoon_1.png" width 1979 height 1169
> supersample 3
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!1 models
> show #2.1 models
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_1.png" width 1979 height 1169
> supersample 3
> hide #!2 models
> show #!5 models
> color #5.2 #f4f4f4ff
> select add #5.2
1496 atoms, 184 residues, 1 model selected
> hide #5.2 models
> show #5.2 models
> color #5.2 white
> color #5.2 #f4f4f4ff
> color (#!5 & sel) light gray
> select subtract #5.2
1 model selected
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_2.png" width 1979 height 1169
> supersample 3
QDxgiVSyncService: DXGI Factory is no longer Current
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!5 models
> show #!2 models
> save "D:/桌面/BLB4 and BLB21/BLB21_cartoon_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> show #!5 models
> hide #!5 models
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!2 models
> show #!1 models
> save "D:/桌面/BLB4 and BLB21/BLB4_cartoon_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> mmaker #2/B to #1/B showAlignment true
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 BL4R.pdb, chain B (#1) with BLB21_ABC.cif, chain B (#2), sequence
alignment score = 863.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: BL4R.pdb #1/B, BLB21_ABC.cif
#2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 176 pruned atom pairs is 0.815 angstroms; (across all 179 pairs:
0.876)
> show #!2 models
> mmaker #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 BL4R.pdb, chain A (#1) with BLB21_ABC.cif, chain A (#2), sequence
alignment score = 954.1
RMSD between 182 pruned atom pairs is 0.547 angstroms; (across all 182 pairs:
0.547)
> select #1/B:2-165,167-188 #2/B:2-165,167-188
2907 atoms, 2984 bonds, 3 pseudobonds, 352 residues, 4 models selected
> select ::seq_identity color sel
> color (#!1-2 & sel) hot pink
> select clear
> show #!5 models
> mmaker #5/B to #1/B showAlignment true
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 BL4R.pdb, chain B (#1) with 21-9.pdb, chain B (#5), sequence
alignment score = 864.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: BL4R.pdb #1/B, 21-9.pdb #5/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 175 pruned atom pairs is 0.740 angstroms; (across all 179 pairs:
0.821)
> mmaker #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 BL4R.pdb, chain A (#1) with 21-9.pdb, chain A (#5), sequence
alignment score = 982.6
RMSD between 183 pruned atom pairs is 0.651 angstroms; (across all 184 pairs:
0.668)
> select #1/B:2-133,135-167,170-188,190 #5/B:2-103,114-133,135-167,170-188,190
2909 atoms, 2984 bonds, 1 pseudobond, 350 residues, 3 models selected
> sequence refreshAttrs 2
> select ::seq_identity color (#!1,5 & sel) hot pink
> mmaker #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 BL4R.pdb, chain A (#1) with 21-9.pdb, chain A (#5), sequence
alignment score = 982.6
RMSD between 183 pruned atom pairs is 0.651 angstroms; (across all 184 pairs:
0.668)
> save my_session_3.cxs
> select clear
> select #5/B:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:104-113
58 atoms, 57 bonds, 1 pseudobond, 8 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB4_BLB21_comparison.png" width 1979 height 1169
> supersample 3 transparentBackground true
> save "D:/桌面/BLB4 and BLB21/BLB4_BLB21_comparison_1.png" width 1979 height
> 1169 supersample 3 transparentBackground true
> select #1/B:14 #2/B:14
18 atoms, 16 bonds, 2 residues, 2 models selected
> sequence refreshAttrs 1
> select ::seq_identity select #1/B:2-165,167-188 #2/B:2-165,167-188
2907 atoms, 2984 bonds, 3 pseudobonds, 352 residues, 4 models selected
> sequence header 1 consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> sequence header 1 conservation show
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
> sequence refreshAttrs 1
> select ::seq_identity undo
> redo
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!1 models
> hide #!2 models
> hide #2.1 models
> hide #5.2 models
> hide #2.4 models
> hide #2.3 models
> hide #5.3 models
> hide #!5 models
> show #!1 models
> show sel & #!1 surfaces
> show #1.1 models
> show #1.2 models
> select subtract #2.4
143 atoms, 136 bonds, 17 residues, 3 models selected
> select add #1.3
1487 atoms, 136 bonds, 179 residues, 4 models selected
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 6 models selected
> select subtract #1
3 models selected
> select add #1.4
116 atoms, 15 residues, 1 model selected
> show sel atoms
Drag select of BL4R.pdb_A SES surface, 8356 of 196572 triangles, BL4R.pdb_B
SES surface, 2277 of 193984 triangles, cap far, 153 of 1545 triangles, 10
atoms, 15 residues, 9 bonds
> hide sel atoms
Drag select of BL4R.pdb_A SES surface, 2995 of 196572 triangles, BL4R.pdb_B
SES surface, 4379 of 193984 triangles, 8 atoms, 13 residues, 7 bonds
> hide sel atoms
> select subtract #1.4
70 atoms, 10 residues, 4 models selected
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 7 models selected
> select subtract #1.4
2983 atoms, 3075 bonds, 1 pseudobond, 363 residues, 8 models selected
> show sel atoms
> hide sel atoms
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 7 models selected
> select subtract #1
3 models selected
> select add #1.4
116 atoms, 15 residues, 1 model selected
> show sel atoms
> select subtract #1.4
1 model selected
> save "D:/桌面/BLB4 and BLB21/BLB4_groove_1.png" width 1979 height 1169
> supersample 3
> hide #!1 models
> show #!2 models
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #2.4 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #!2 models
> show #!2 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 4 models selected
> select subtract #4
3051 atoms, 3140 bonds, 24 pseudobonds, 375 residues, 6 models selected
> select add #3
3051 atoms, 3140 bonds, 47 pseudobonds, 375 residues, 6 models selected
> show sel surfaces
> hide #2.2 models
> select add #2
3051 atoms, 3140 bonds, 85 pseudobonds, 375 residues, 9 models selected
> select subtract #2
3 models selected
> select add #2.1
2 pseudobonds, 1 model selected
> select subtract #2.1
Nothing selected
> select add #2.1
2 pseudobonds, 1 model selected
> show #!2 atoms
> save "D:/桌面/BLB4 and BLB21/BLB21_groove_1.png" width 1979 height 1169
> supersample 3
> hide #!2 models
> show #4 models
> hide #4 models
> show #!5 models
> show #!5 surfaces
> hide #5.4 models
> select add #5.4
116 atoms, 2 pseudobonds, 15 residues, 2 models selected
> show sel atoms
> color sel byhetero
> hide #2.1 models
> hide #2.3 models
> hide #2.4 models
> hide #!5 models
> show #!5 models
> select subtract #5.4
2 pseudobonds, 2 models selected
> select subtract #2.1
Nothing selected
> hide #!5 models
> show #!5 models
> show #5.1 models
> select add #5.1
1 pseudobond, 1 model selected
> select subtract #5.1
Nothing selected
> hide #5.1 models
> show #5.4 models
> hide #5.4 models
> color #5.3 white
> color #5.3 #57d2fbff
> color #5.3 #adddf0ff
> select #1/B:2-133,135-167,170-188,190 #5/B:2-103,114-133,135-167,170-188,190
2909 atoms, 2984 bonds, 1 pseudobond, 350 residues, 3 models selected
> select ::seq_identity color (#!5 & sel) hot pink
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB21_groove_2.png" width 1979 height 1169
> supersample 3
> save my_session_4.cxs
> save "D:/桌面/BLB4 and BLB21/BLB21_groove_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!5 models
> show #!2 models
> hide #!2 atoms
> show #2.1 models
> show #2.2 models
> show #2.3 models
> hide #2.1 models
> show #2.4 models
> hide #!2 models
> show #!2 models
> hide #2.2 models
> select add #2.2
104 atoms, 14 residues, 1 model selected
> show sel atoms
> select subtract #2.2
1 model selected
> save "D:/桌面/BLB4 and BLB21/BLB21_groove_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> show #1.3 models
> save "D:/桌面/BLB4 and BLB21/BLB4_groove_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!1 models
> show #!2 models
> show #!5 models
> hide #!2 models
> show #!1 models
> hide #!5 models
QDxgiVSyncService: DXGI Factory is no longer Current
> interfaces #!1 & ~solvent
3 buried areas: A B 2689, B C 723, A C 701
> hide #!1.3 models
> hide #!1.2 models
> show sel atoms
> ui tool show Contacts
> contacts sel overlapCutoff -0.1 ignoreHiddenModels true
110 contacts
Restriction atom specifier must not be blank
> select subtract #1.4
263 atoms, 29 residues, 4 models selected
> select subtract #1.3
119 atoms, 14 residues, 3 models selected
> select subtract #1.2
1 model selected
> select add #1.4
116 atoms, 15 residues, 1 model selected
> contacts sel overlapCutoff -0.1 ignoreHiddenModels true
49 contacts
> contacts sel overlapCutoff -0.1 ignoreHiddenModels true
49 contacts
> show #4 models
> show #3 models
> hide #3 models
> ui tool show Contacts
Restriction atom specifier must not be blank
> contacts sel restrict both overlapCutoff -0.1 ignoreHiddenModels true
63 contacts
> select add #1
3099 atoms, 3190 bonds, 113 pseudobonds, 378 residues, 7 models selected
> color sel byhetero
> hide #1.5 models
> show #1.5 models
> hide #1.5 models
> hide #4 models
> show #1.5 models
> select subtract #4
3099 atoms, 3190 bonds, 64 pseudobonds, 378 residues, 6 models selected
> hide #1.5 models
> show #1.5 models
> hide #1.5 models
> select subtract #1
3 models selected
> select add #1.4
116 atoms, 15 residues, 1 model selected
> ui tool show Contacts
> contacts sel overlapCutoff -0.1 ignoreHiddenModels true
49 contacts
> show #1.5 models
> select add #1
3099 atoms, 3190 bonds, 113 pseudobonds, 378 residues, 5 models selected
> show sel cartoons
> select subtract #1
3 models selected
> select add #1
3099 atoms, 3190 bonds, 113 pseudobonds, 378 residues, 4 models selected
> color sel byhetero
> select ::seq_identity hide sel & #!1 atoms
> select add #1
3300 atoms, 3380 bonds, 114 pseudobonds, 404 residues, 8 models selected
> hide sel & #!1 atoms
> select subtract #1
201 atoms, 190 bonds, 1 pseudobond, 26 residues, 6 models selected
> select add #1.4
317 atoms, 190 bonds, 1 pseudobond, 41 residues, 4 models selected
> show sel & #!1 atoms
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.1 ignoreHiddenModels true
49 contacts
> hide #1.5 models
> show #1.5 models
> contacts sel overlapCutoff -0.1 ignoreHiddenModels true
49 contacts
> contacts sel distanceOnly 4.0 ignoreHiddenModels true
255 distances
> hide #1.5 models
> show #1.5 models
> contacts sel overlapCutoff -0.1 ignoreHiddenModels true
49 contacts
> contacts ignoreHiddenModels true
2164 contacts
> close #3
> close #4
> select add #1.5
116 atoms, 63 pseudobonds, 15 residues, 3 models selected
> select subtract #1.5
116 atoms, 15 residues, 2 models selected
> view #1.5 clip false
No displayed objects specified.
> hide sel atoms
> select clear
> ui tool show Contacts
> contacts ignoreHiddenModels true
2164 contacts
> select add #1.4
116 atoms, 15 residues, 1 model selected
> contacts ignoreHiddenModels true
2164 contacts
> hide #3 models
> hide #1.5 models
> show #1.5 models
> hide #1.5 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> contacts ignoreHiddenModels true
2164 contacts
> close #3
> contacts sel restrict cross distanceOnly 4.0 ignoreHiddenModels true
229 distances
> hide #3 models
> show #1.5 models
> hide #1.5 models
> show #3 models
> contacts sel restrict cross ignoreHiddenModels true
140 contacts
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB4_contacts_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> hide #!2.3 models
> hide #!2.4 models
> hide #3 models
> show #3 models
> select add #3
140 pseudobonds, 1 model selected
> select subtract #3
Nothing selected
> hide #3 models
> select add #2
3051 atoms, 3140 bonds, 2 pseudobonds, 375 residues, 2 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select add #2.4
1584 atoms, 194 residues, 3 models selected
> select add #2
3167 atoms, 3140 bonds, 2 pseudobonds, 390 residues, 5 models selected
> select subtract #2
116 atoms, 15 residues, 5 models selected
> select add #2.4
1584 atoms, 194 residues, 3 models selected
> select subtract #2.4
116 atoms, 15 residues, 3 models selected
> select add #2.3
1595 atoms, 197 residues, 3 models selected
> select subtract #2.3
116 atoms, 15 residues, 3 models selected
> select add #2.2
220 atoms, 29 residues, 3 models selected
> ui tool show Contacts
> contacts sel restrict cross ignoreHiddenModels true
115 contacts
> show #3 models
> select add #2
3167 atoms, 3140 bonds, 117 pseudobonds, 390 residues, 6 models selected
> hide #3 models
> select subtract #3
3167 atoms, 3140 bonds, 2 pseudobonds, 390 residues, 7 models selected
> close #3
> select subtract #2
116 atoms, 15 residues, 5 models selected
> select add #2
3167 atoms, 3140 bonds, 2 pseudobonds, 390 residues, 4 models selected
> interfaces select & #!2 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #2
116 atoms, 15 residues, 5 models selected
> select add #2
3167 atoms, 3140 bonds, 2 pseudobonds, 390 residues, 4 models selected
> show #!5 models
> select add #5
6676 atoms, 6388 bonds, 3 pseudobonds, 1129 residues, 12 models selected
> select subtract #2
3625 atoms, 3248 bonds, 1 pseudobond, 754 residues, 13 models selected
> hide #!2 models
> select subtract #5
116 atoms, 15 residues, 5 models selected
> hide #!5.2 models
> hide #!5.3 models
> select add #5
3625 atoms, 3248 bonds, 1 pseudobond, 754 residues, 4 models selected
> interfaces select & #!5 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> hide #!5 models
> show #!5 models
> select subtract #5
116 atoms, 15 residues, 5 models selected
> select add #5.4
232 atoms, 30 residues, 3 models selected
> interfaces select & #!5 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show Contacts
> show sel & #!5 atoms
> select subtract #5.4
116 atoms, 15 residues, 3 models selected
> select add #5.4
232 atoms, 30 residues, 3 models selected
> contacts sel restrict cross ignoreHiddenModels true
153 contacts
> contacts sel ignoreHiddenModels true
159 contacts
> select add #5
3625 atoms, 3248 bonds, 160 pseudobonds, 754 residues, 6 models selected
> hbonds sel & #!5 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
8289 hydrogen bonds found
> ~hbonds
> color sel & #!5 byhetero
> select subtract #5.4
3509 atoms, 3132 bonds, 1 pseudobond, 739 residues, 7 models selected
> select subtract #5.3
1964 atoms, 1546 bonds, 551 residues, 5 models selected
> select add #5.3
3509 atoms, 1546 bonds, 739 residues, 4 models selected
> select subtract #5.2
2013 atoms, 555 residues, 5 models selected
> select add #5.2
3509 atoms, 739 residues, 4 models selected
> hide sel & #!5 atoms
> select add #5.4
3625 atoms, 754 residues, 5 models selected
> hbonds sel & #!5 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
8289 hydrogen bonds found
> ~hbonds
> interfaces select & #!5 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> hide water
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select subtract #5.4
3509 atoms, 739 residues, 6 models selected
> select add #5.4
3625 atoms, 754 residues, 5 models selected
> select subtract #5.3
2080 atoms, 566 residues, 6 models selected
> select subtract #5.2
584 atoms, 382 residues, 5 models selected
> interfaces select #!5 & protein
Missing required "contacting" argument
> interfaces select #!5 & ~solvent
Missing required "contacting" argument
> hide sel & #!5 atoms
> select add #5
3625 atoms, 3248 bonds, 160 pseudobonds, 754 residues, 6 models selected
> hide sel & #!5 atoms
> select add #1
6608 atoms, 6438 bonds, 224 pseudobonds, 1117 residues, 10 models selected
> select subtract #1
3509 atoms, 3248 bonds, 160 pseudobonds, 739 residues, 9 models selected
> select subtract #3
3509 atoms, 3248 bonds, 1 pseudobond, 739 residues, 5 models selected
> select subtract #5
3 models selected
> hide #3 models
> hide #!5 models
> select add #2
3051 atoms, 3140 bonds, 2 pseudobonds, 375 residues, 2 models selected
> show #!2 models
> hide sel atoms
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #2.4 models
> hide #!2.4 models
> hide #!2.3 models
> hide #2.2 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2
3051 atoms, 3140 bonds, 2 pseudobonds, 375 residues, 2 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> contacts #2/C & protein (#2/A | #2/B) & protein select true makePseudobonds true
Expected a keyword
> contacts #2/C & protein #2/A,B & protein select true makePseudobonds true
Expected a keyword
> contacts #2/C & protein #2/A & protein select true makePseudobonds true
Expected a keyword
> contacts #2/C & protein #2/A
Expected a keyword
> contacts #2/C & protein #2/A & protein select true makePseudobonds true
Expected a keyword
> contacts #2/C
6324 contacts
> show #3 models
> select add #3
3051 atoms, 3140 bonds, 6326 pseudobonds, 375 residues, 6 models selected
> select subtract #2
3 models selected
> hbonds #!2 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
4794 hydrogen bonds found
> hide #3 models
> hide #2.1 models
> show #2.4 models
> hide #!2.4 models
> show #2.3 models
> hide #!2.3 models
> show #2.2 models
> hide #2.2 models
> select add #2.2
104 atoms, 14 residues, 1 model selected
> ~hbonds
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
183 hydrogen bonds found
> select add #2
3051 atoms, 3140 bonds, 145 pseudobonds, 375 residues, 5 models selected
> color sel byhetero
> hide sel atoms
> select subtract #2.1
3051 atoms, 3140 bonds, 143 pseudobonds, 375 residues, 6 models selected
> select add #2
3051 atoms, 3140 bonds, 145 pseudobonds, 375 residues, 7 models selected
> select subtract #2
3 models selected
> select add #2.2
104 atoms, 14 residues, 1 model selected
> show sel atoms
> select add #4
104 atoms, 183 pseudobonds, 14 residues, 3 models selected
> select subtract #4
104 atoms, 14 residues, 2 models selected
> hide #4 models
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
183 hydrogen bonds found
> show #4 models
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #4 models
> select subtract #2.2
1 model selected
> hide #!2 models
> show #!1 models
> hide #!1 cartoons
> show #!1 cartoons
> hide #!1 atoms
> select add #1.4
116 atoms, 15 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
146 hydrogen bonds found
> show #4 models
> select subtract #1.4
1 model selected
> select add #1.4
116 atoms, 15 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select subtract #1.4
1 model selected
> ui tool show "Side View"
> color #4 #003a4dff models
> color #4 #aaffffff models
> color #4 #355050ff models
> color #4 white models
> color #4 #434343ff models
> color #4 #aaffffff models
> color #4 #243636ff models
> color #4 #314a4aff models
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB4_H_bound.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> select add #2.4
1468 atoms, 179 residues, 1 model selected
> select subtract #2.4
1 model selected
> select add #2.2
104 atoms, 14 residues, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
183 hydrogen bonds found
> color #4 #314a4aff models
> save "D:/桌面/BLB4 and BLB21/BLB21_H_bound_1.png" width 1979 height 1169
> supersample 3
> save "D:/桌面/BLB4 and BLB21/BLB21_H_bound_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #4 models
> hide #!2 models
> show #!5 models
> hide #!5 atoms
> select add #5.1
104 atoms, 1 pseudobond, 14 residues, 3 models selected
> select subtract #5.1
104 atoms, 14 residues, 2 models selected
> select add #5.4
220 atoms, 29 residues, 3 models selected
> show sel & #!5 atoms
> hbonds sel & #!5 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
191 hydrogen bonds found
> show #4 models
> hide atoms #5 & solvent
Expected ',' or a keyword
> delete solvent
> color #4 #314a4aff models
> select subtract #5.4
104 atoms, 14 residues, 3 models selected
> select add #5.4
220 atoms, 29 residues, 3 models selected
> hbonds sel & #!5 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
151 hydrogen bonds found
> hide #4 models
> show #4 models
> color #4 #314a4aff models
> save "D:/桌面/BLB4 and BLB21/BLB21_H_bound_2.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!5 models
> show #!2 models
> select subtract #2.2
116 atoms, 15 residues, 3 models selected
> select add #2.2
220 atoms, 29 residues, 3 models selected
> hbonds sel & #!2 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
146 hydrogen bonds found
> select subtract #2.2
116 atoms, 15 residues, 3 models selected
> hide #!2 models
> show #!1 models
> select add #1.4
232 atoms, 30 residues, 3 models selected
> hbonds sel & #!1 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: BLB21_10.pdb #10/A ARG 3 NE
122 hydrogen bonds found
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202508300055 (2025-08-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
zhangnianzhi@cau.edu.cn has been invited to the ChimeraX announcements list
OpenGL version: 3.3.0 NVIDIA 581.63
OpenGL renderer: NVIDIA GeForce RTX 3080/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: 6.9.1
Qt platform: windows
Manufacturer: HP
Model: OMEN by HP 45L Gaming Desktop GT22-0xxx
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 34,105,032,704
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.16
ChimeraX-AtomicLibrary: 14.1.23
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.dev202508300055
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: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
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-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
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: 1.0.1
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: 1.15.1
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: 1.3.1
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: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.1
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: 2.17.2
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: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3.2
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
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.19.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
narwhals: 2.3.0
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: 2.11.0
numpy: 2.2.6
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: 4.4.0
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.1
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 311
pyzmq: 27.0.2
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.13.2
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
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
Change History (2)
comment:1 by , 7 days ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 7 days ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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