Opened 7 hours ago

Closed 2 hours ago

#19995 closed defect (can't reproduce)

Crash in event loop

Reported by: anurag@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.10.dev202501142332 (2025-01-14 23:32:44 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 0x00004afc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x80000003

Thread 0x00000690 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004afc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9hdk

9hdk title:  
Structure of s.c.Osh6 in complex with Ist2 732-756 and POPS [more info...]  
  
Chain information for 9hdk #1  
---  
Chain | Description | UniProt  
A | Oxysterol-binding protein homolog 6 | OSH6_YEAST 31-448  
C | Increased sodium tolerance protein 2 | IST2_YEAST 732-756  
  
Non-standard residues in 9hdk #1  
---  
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)  
  

> set bgColor white

> color byhetero

> color bychain

> select /C

164 atoms, 150 bonds, 36 residues, 1 model selected  

> color sel #9f8cffff

> color sel #9e8bffff

> color sel #9189ffff

> color sel #8789ffff

> color sel #858bffff

> color sel #858dffff

> color sel #8394ffff

> color sel #839affff

> color sel #829fffff

> color sel #82a8ffff

> color sel #81adffff

> color sel #80b3ffff

> color sel #7eb8ffff

> color sel #7dcbffff

> color sel #7dd8ffff

> color sel #7ce9ffff

> color sel #7ceeffff

> color sel #7bf4ffff

> color sel #7bfdffff

> color sel #7bffffff

> color sel #7bfffbff

> color sel #7bfff4ff

> color sel #7bfff0ff

> color sel #7bffebff

> color sel #7cffe9ff

> color sel #7cffe5ff

> color sel #7cffe3ff

> color sel #7cffdeff

> color sel #7cffdaff

> color sel #7dffdaff

> color sel #7dffcdff

> color sel #80ffc6ff

> color sel #81ffb3ff

> color sel #82ffa5ff

> color sel #83ff98ff

> color sel #85ff89ff

> color sel #87ff85ff

> color sel #8cff86ff

> color sel #8eff86ff

> color sel #8fff87ff

> color sel #93ff87ff

> color sel #96ff8aff

> color sel #98ff8cff

> color sel #96ff8eff

> color sel #92ff90ff

> color sel #93ff9aff

> color sel #94ffa6ff

> color sel #97ffb4ff

> color sel #99ffc2ff

> color sel #9dffd3ff

> color sel #a0ffdfff

> color sel #a4ffedff

> color sel #a7fff9ff

> color sel #aafeffff

> color sel #acf7ffff

> color sel #b0f1ffff

> color sel #b4e7ffff

> color sel #b8e3ffff

> color sel #b9deffff

> color sel #bcdfffff

> color sel #bddaffff

> color sel #c0d8ffff

> color sel #c1d9ffff

> color sel #c2d5ffff

> color sel #c5d4ffff

> color sel #c6d3ffff

> color sel #c9d5ffff

> color sel #cad4ffff

> color sel #cfd5ffff

> color sel #d2d7ffff

> color sel #d4d7ffff

> color sel #d7d9ffff

> color sel #dbddffff

> color sel #dcddffff

> color sel #e0e0ffff

> color sel #e2e2ffff

> color sel #e4e4ffff

> color sel #e7e6ffff

> color sel #e8e7ffff

> color sel #eae9ffff

> color sel #ebeaffff

> color sel #ecebffff

> color sel #efeeffff

> color sel #eeedffff

> color sel #ebe9ffff

> color sel #e7e4ffff

> color sel #e5e1ffff

> color sel #e1dbffff

> color sel #ded4ffff

> color sel #decfffff

> color sel #dccaffff

> color sel #ddc4ffff

> color sel #e3bcffff

> color sel #eab4ffff

> color sel #ffaaffff

> color sel #ffa4f0ff

> color sel #ffa0e2ff

> color sel #ff9dd8ff

> color sel #ff98c6ff

> color sel #ff95bfff

> color sel #ff92b8ff

> color sel #ff8fa9ff

> color sel #ff8ca1ff

> color sel #ff868cff

> color sel #ff8385ff

> color sel #ff8183ff

> color sel #ff8082ff

> color sel #ff7e80ff

> color sel #ff7c7eff

> color sel #ff797bff

> color sel #ff787aff

> color sel #ff7779ff

> color sel #ff7476ff

> color sel #ff7375ff

> color sel #ff7072ff

> color sel #ff6e70ff

> color sel #ff6b6dff

> color sel #ff6973ff

> color sel #ff667aff

> color sel #ff6385ff

> color sel #ff638dff

> color sel #ff6198ff

> color sel #ff5ea4ff

> color sel #ff5da6ff

> color sel #ff5dabff

> color sel #ff5cabff

> color sel #ff5cb0ff

> color sel #ff5aafff

> color sel #ff5ab2ff

> color sel #ff57b6ff

> color sel #ff55bbff

> color sel #ff53baff

> color sel #ff52baff

> color sel #ff50bcff

> color sel #ff4ec1ff

> color sel #ff4bc0ff

> color sel #ff4ac6ff

> color sel #ff47c8ff

> color sel #ff47ceff

> color sel #ff46d4ff

> color sel #ff43d3ff

> color sel #ff43d6ff

> color sel #ff42dcff

> color sel #ff41dcff

> color sel #ff41dfff

> color sel #ff40dfff

> color sel #ff3edfff

> color sel #ff3de5ff

> color sel #ff3ce5ff

> color sel #ff3aebff

> color sel #ff39ebff

> color sel #ff37f5ff

> color sel #ff35f5ff

> color sel #ff35fcff

> color sel #f134ffff

> color sel #e134ffff

> color sel #b534ffff

> color sel #a034ffff

> color sel #8934ffff

> color sel #6734ffff

> color sel #5735ffff

> color sel #3e37ffff

> color sel #3737ffff

> color sel #385cffff

> color sel #3974ffff

> color sel #3a93ffff

> color sel #3cb1ffff

> color sel #3dd5ffff

> color sel #3efff9ff

> color sel #3effd5ff

> color sel #3effafff

> color sel #3eff95ff

> color sel #3eff75ff

> color sel #3eff4eff

> color sel #48ff3eff

> color sel #58ff3eff

> color sel #5aff3dff

> color sel #67ff3dff

> color sel #70ff3cff

> color sel #76ff3cff

> color sel #7aff3cff

> color sel #80ff3cff

> color sel #87ff3cff

> color sel #8aff3cff

> color sel #90ff3cff

> color sel #94ff3cff

> color sel #9aff3cff

> color sel #a1ff3cff

> color sel #a4ff3cff

> color sel #abff3cff

> color sel #b1ff3cff

> color sel #b4ff3cff

> color sel #bbff3cff

> color sel #c5ff3cff

> color sel #cbff3cff

> color sel #d2ff3cff

> color sel #d5ff3cff

> color sel #dbff3cff

> color sel #dfff3cff

> color sel #e5ff3aff

> color sel #ebff3aff

> color sel #efff39ff

> color sel #f5ff38ff

> color sel #f5ff37ff

> color sel #fcff37ff

> color sel #ffff35ff

> color sel #fff835ff

> color sel #fff834ff

> color sel #fff134ff

> color sel #fff133ff

> color sel #ffee33ff

> color sel #ffee31ff

> color sel #ffe731ff

> color sel #ffd52fff

> color sel #ffc32cff

> color sel #ffbf2bff

> color sel #ffb82bff

> color sel #ffb12aff

> color sel #ffad2aff

> color sel #ffad29ff

> color sel #ffa629ff

> color sel #ffa527ff

> color sel #ff9a26ff

> color sel #ff9225ff

> color sel #ff7e22ff

> color sel #ff7a21ff

> color sel #ff6a20ff

> color sel #ff6720ff

> color sel #ff5f20ff

> color sel #ff5820ff

> color sel #ff5420ff

> color sel #ff4d20ff

> color sel #ff4520ff

> color sel #ff4120ff

> color sel #ff3b21ff

> color sel #ff3422ff

> color sel #ff3223ff

> color sel #ff2a23ff

> color sel #ff2525ff

> color sel #ff2626ff

> color sel #ff2929ff

> color sel #ff2b2bff

> color sel #ff3030ff

> color sel #ff3a3aff

> color sel #ff4545ff

> color sel #ff4e4eff

> color sel #ff5353ff

> color sel #ff5959ff

> color sel #ff6363ff

> color sel #ff6e6eff

> color sel #ff7777ff

> color sel #ff8585ff

> color sel #ff9292ff

> color sel #ffaca1ff

> color sel #ffbcabff

> color sel #ffc4b0ff

> color sel #ffceb8ff

> color sel #ffd8c1ff

> color sel #ffe1c9ff

> color sel #ffe9d2ff

> color sel #ffebd5ff

> color sel #fff0dcff

> color sel #fff2ddff

> color sel #fff4e1ff

> color sel #fff5e2ff

> color sel #fff7e6ff

> color sel #fff8e6ff

> color sel #fff8e7ff

> color sel #fff9eaff

> color sel #fffaedff

> color sel #fffbeeff

> color sel #fffbf0ff

> color sel #fffcf2ff

> color sel #fffcf3ff

> color sel #fffdf4ff

> color sel #fffef4ff

> color sel #fffff4ff

> color sel #fefff4ff

> color sel #fcfff2ff

> color sel #fafff2ff

> color sel #f7fff2ff

> color sel #f4fff2ff

> color sel #f2fff5ff

> color sel #f2fff7ff

> color sel #f2fff9ff

> color sel #f2fffbff

> color sel #f2fffcff

> color sel #f2fffeff

> color sel #f2feffff

> color sel #f2fdffff

> color sel #f2fcffff

> color sel #f2faffff

> color sel #f2f9ffff

> color sel #f2f6ffff

> color sel #f2f4ffff

> color sel #f2f2ffff

> color sel #f3f2ffff

> color sel #f4f2ffff

> color sel #f5f2ffff

> color sel #f6f2ffff

> color sel #f7f2ffff

> color sel #f8f2ffff

> color sel #f9f2ffff

> color sel #faf0ffff

> color sel #fbf0ffff

> color sel #fdefffff

> color sel #ffeeffff

> color sel #ffeefdff

> color sel #ffeefcff

> color sel #ffeefbff

> color sel #ffedfaff

> color sel #ffebf9ff

> color sel #ffebf7ff

> color sel #ffeaf7ff

> color sel #ffe6f5ff

> color sel #ffdbecff

> color sel #ffcbdfff

> color sel #ffc6d8ff

> color sel #ffb3c3ff

> color sel #ffa6b9ff

> color sel #ff9eb3ff

> color sel #ff93aaff

> color sel #ff8ba6ff

> color sel #ff81a3ff

> color sel #ff7ba5ff

> color sel #ff74a5ff

> color sel #ff6ea8ff

> color sel #ff66a8ff

> color sel #ff62a9ff

> color sel #ff61a8ff

> color sel #ff60adff

> color sel #ff5eacff

> color sel #ff5eb1ff

> color sel #ff60bfff

> color sel #ff62c8ff

> color sel #ff66e3ff

> color sel #ff6af0ff

> color sel #ff6bfdff

> color sel #ff6bffff

> color sel #fa6cffff

> color sel #f36effff

> color sel #ee6effff

> color sel #e96effff

> color sel #db6effff

> color sel #c96bffff

> color sel #bc6affff

> color sel #ac69ffff

> color sel #a467ffff

> color sel #9f67ffff

> color sel #9a67ffff

> color sel #9966ffff

> color sel #9166ffff

> color sel #8c66ffff

> color sel #8c65ffff

> color sel #7d63ffff

> color sel #7462ffff

> color sel #6661ffff

> color sel #6068ffff

> color sel #5e69ffff

> color sel #5e6effff

> color sel #5d73ffff

> color sel #5c74ffff

> color sel #5c7affff

> color sel #5a78ffff

> color sel #5473ffff

> color sel #4b66ffff

> color sel #435cffff

> color sel #3e51ffff

> color sel #3a47ffff

> color sel #3946ffff

> color sel #3845ffff

> color sel #3744ffff

> color sel #3542ffff

> color sel #3442ffff

> color sel #3341ffff

> color sel #333dffff

> color sel #313bffff

> color sel #303affff

> color sel #2f39ffff

> color sel #2e38ffff

> color sel #2c37ffff

> color sel #2b36ffff

> color sel #2934ffff

> color sel #2732ffff

> color sel #2631ffff

> color sel #2530ffff

> color sel #232effff

> color sel #222dffff

> color sel #212cffff

> color sel #202bffff

> color sel #1e29ffff

> color sel #1d28ffff

> color sel #1d2cffff

> color sel #1c2bffff

> color sel #1a29ffff

> color sel #1928ffff

> color sel #1930ffff

> color sel #182fffff

> color sel #1837ffff

> color sel #1736ffff

> color sel #1534ffff

> color sel #1538ffff

> color sel #1437ffff

> color sel #1336ffff

> color sel #133effff

> color sel #113dffff

> color sel #103cffff

> color sel #0f3bffff

> color sel #0e3affff

> color sel #0e32ffff

> color sel #0f33ffff

> color sel #113dffff

> color sel #184effff

> color sel #1d61ffff

> color sel #2277ffff

> color sel #2785ffff

> color sel #2b91ffff

> color sel #2f9effff

> color sel #31a6ffff

> color sel #33a7ffff

> color sel #33adffff

> color sel #33b1ffff

> color sel #34b1ffff

> color sel #34bfffff

> color sel #34c9ffff

> color sel #34f5ffff

> color sel #35ffe7ff

> color sel #35ffd7ff

> color sel #35ffd3ff

> color sel #37ffc6ff

> color sel #37ffc3ff

> color sel #38ffc3ff

> color sel #38ffc7ff

> color sel #38ffcdff

> color sel #38ffd4ff

> color sel #38ffd7ff

> color sel #39ffd7ff

> color sel #39ffdeff

> color sel #39ffe1ff

> color sel #39ffe8ff

> color sel #3affe8ff

> color sel #3dffe8ff

> color sel #3effe8ff

> color sel #40ffe9ff

> color sel #45ffe9ff

> color sel #4cffe4ff

> color sel #57ffe6ff

> color sel #5cffe4ff

> color sel #63ffe5ff

> color sel #6affe1ff

> color sel #6effe2ff

> color sel #74ffe1ff

> color sel #7dffe3ff

> color sel #82ffe0ff

> color sel #87ffe1ff

> color sel #8affe2ff

> color sel #8bffe2ff

> color sel #8cffe2ff

> color sel #8effe3ff

> color sel #8fffe3ff

> select clear

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> cartoon style xsection rectangle modeHelix default

> graphics silhouettes true

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> select ligand

53 atoms, 52 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> cartoon style modeHelix tube sides 20

> cartoon style xsection oval modeHelix default

> select /A

3617 atoms, 3413 bonds, 690 residues, 1 model selected  

> color sel dark gray

> select clear

> select /C

164 atoms, 150 bonds, 36 residues, 1 model selected  

> color sel purple

> ui tool show "Color Actions"

> color sel medium purple

> select clear

> lighting soft

> graphics silhouettes false

> lighting shadows true intensity 0.5

> graphics silhouettes true

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> select ligand

53 atoms, 52 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> select /C

164 atoms, 150 bonds, 36 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> color sel #af7961ff

> color sel #4b4b4bff

> color sel #505050ff

> color sel #171717ff

> color sel #1e1e1eff

> color sel #c885b6ff

> color sel #a477c8ff

> color sel #8e73c8ff

> color sel #7f6cc8ff

> color sel #6a67c8ff

> color sel #6567c8ff

> color sel #6469c8ff

> color sel #6368c8ff

> color sel #6267c7ff

> color sel #6065c3ff

> color sel #5e63bfff

> color sel #585db3ff

> color sel #5559acff

> color sel #5458aaff

> color sel #4e529eff

> color sel #4c509aff

> color sel #4d519cff

> color sel #4c509aff

> color sel #4b4f98ff

> color sel #424686ff

> color sel #3a3d75ff

> color sel #313464ff

> color sel #2a2d56ff

> color sel #282a50ff

> color sel #242548ff

> color sel #1f203eff

> color sel #1d1f3bff

> color sel #1d1e3aff

> color sel #222344ff

> color sel #232547ff

> color sel #2c2f5aff

> color sel #2e305dff

> color sel #303261ff

> color sel #333567ff

> color sel #34376aff

> color sel #35386bff

> color sel #36396dff

> color sel #373a6fff

> color sel #373a70ff

> color sel #383b71ff

> color sel #393c73ff

> color sel #393c74ff

> color sel #3a3d75ff

> color sel #3b3e78ff

> color sel #3c3f79ff

> color sel #3c3f7aff

> color sel #3d407cff

> color sel #3e417dff

> color sel #3f427fff

> color sel #404381ff

> color sel #414584ff

> color sel #434687ff

> color sel #434788ff

> color sel #44488aff

> color sel #45488bff

> select clear

> select sequence k145

Nothing selected  

> view

> select /C

164 atoms, 150 bonds, 36 residues, 1 model selected  

> view sel

> view

> select clear

> save C:\Users\Admin/Desktop\image26.png supersample 3

> show surfaces

> select /C

164 atoms, 150 bonds, 36 residues, 1 model selected  

> color (#!1 & sel) dark gray

> select clear

> color #1 #aa557fff

> color #1 #aa55ffff

> color #1 #ff55ffff

> color #1 #ff557fff

> color #1 #aa557fff

> graphics silhouettes false

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> color #1 #6a3faaff

> color #1 #aa1f9eff

> color #1 #aa1977ff

> color #1 #aa007fff

> color #1 #aa00ffff

> color #1 #aa557fff

> view orient

> color purple

> color #1 #ca00caff

> color #1 #f900f9ff

> color #1 #aa007fff

> color #1 #ff00bfff

> color #1 magenta

> color #1 #ff55ffff

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting soft

> color #1 #ed89ffff

> color #1 #e978ffff

> color #1 #cb8bffff

> view orient

> save C:\Users\Admin/Desktop\image27.png supersample 3

> hide surfaces

> show atoms

> hide atoms

> select ligand

53 atoms, 52 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> lighting soft

> graphics silhouettes true

> save C:\Users\Admin/Desktop\image28.png supersample 3

> show surfaces

> hide surfaces

> show surfaces

> graphics silhouettes false

> transparency 70

> save C:\Users\Admin/Desktop\image29.png supersample 3

> hide surfaces

> graphics silhouettes true

> save C:\Users\Admin/Desktop\image30.png supersample 3

> select ligand

53 atoms, 52 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> open 9hdh

9hdh title:  
Structure of s.c.Osh6 in complex with Ist2 732-761 and POPS [more info...]  
  
Chain information for 9hdh #2  
---  
Chain | Description | UniProt  
A | Oxysterol-binding protein homolog 6 | OSH6_YEAST 31-448  
C | Increased sodium tolerance protein 2 | IST2_YEAST 732-761  
  
Non-standard residues in 9hdh #2  
---  
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)  
  

> hide #!1 models

> color #2 #c780ebff

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> color (#2 & sel) purple

> select clear

> save C:\Users\Admin/Desktop\image31.png supersample 3

> ui tool show "Side View"

> view

> color #2 #9e66bcff

> color #2 #c27de7ff

> save C:\Users\Admin/Desktop\image32.png supersample 3

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> color (#2 & sel) purple

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> view sel

> view

> select clear

> save C:\Users\Admin/Desktop\image33.png supersample 3

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> view sel

> save C:\Users\Admin/Desktop\image34.png supersample 3

> select clear

> save C:\Users\Admin/Desktop\image35.png supersample 3

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> view sel

> surface (#2 & sel)

> select clear

> transparency #2 60

> select clear

> color sel yellow

> select clear

> color sel yellow

> color sel byhetero

> select #2/A:501@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:69

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

> color sel yellow

> color sel byhetero

> select #2/A:501@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:69

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

> color sel byhetero

> select clear

> select #2/A:67

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

> color sel yellow

> select clear

Drag select of 9hdh_A SES surface, 543 of 13738 triangles, 4 atoms, 4
residues, 3 bonds  

> select clear

> select #2/A:64

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

> color sel yellow

> select clear

> select #2/A:501@C34

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:86

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

> color sel yellow

> select clear

> select #2/A:79

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

> color sel yellow

> select clear

> select #2/A:160

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

> color sel yellow

> select clear

> select #2/A:126@CA

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 9hdh_A SES surface, 152 of 13738 triangles, 2 atoms, 1 residues  

> select clear

> select #2/A:501@O18

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:129

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

> color sel yellow

> color sel byhetero

> select clear

> select #2/A:67@CA

1 atom, 1 residue, 1 model selected  

> color sel byhetero

> select #2/A:64@CA

1 atom, 1 residue, 1 model selected  

> color sel byhetero

> select #2/A:79

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

> color sel byhetero

> select clear

> select #2/A:79

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

> color sel byhetero

Drag select of 1 residues, 1 bonds  

> select clear

> select #2/A:164@CA

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 4 residues  

> select clear

> select #2/A:164

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> select #2/A:126@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:126@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:126@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:127

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

> select clear

> select #2/A:126@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:126@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:126

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

> color sel yellow

> select clear

> select #2/A:501@C21

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:126

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

> color sel byhetero

> select clear

> select #2/A:127@N

1 atom, 1 residue, 1 model selected  

> select #2/A:127@N

1 atom, 1 residue, 1 model selected  

> select #2/A:127@N

1 atom, 1 residue, 1 model selected  

> select #2/A:127@N

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:127@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:127@CD

1 atom, 1 residue, 1 model selected  

> select #2/A:127@CD

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:127@N

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:127

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

> color sel yellow

> color sel byhetero

> select #2/A:501@C33

1 atom, 1 residue, 1 model selected  

> select clear

> graphics silhouettes false

> select #2/A:192

5 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> graphics silhouettes true

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> hide sel & #!2 surfaces

> color sel & #!2 byhetero

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> show sel & #!2 surfaces

> select clear

> select #2/A:112

14 atoms, 15 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> select #2/A

3619 atoms, 3413 bonds, 692 residues, 1 model selected  

> surface (#!2 & sel)

> select add #2

3847 atoms, 3627 bonds, 737 residues, 4 models selected  

> select subtract #2

2 models selected  

> select add #1

3781 atoms, 3563 bonds, 726 residues, 1 model selected  

> select subtract #1

2 models selected  

> select add #2

3847 atoms, 3627 bonds, 737 residues, 2 models selected  

> graphics silhouettes false

> transparency (#!2 & sel) 80

> select clear

> cartoon hide #2

> hide #!2 surfaces

> lighting soft

> graphics silhouettes true

> label #2 text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select clear

> select #2/A:183@O

1 atom, 1 residue, 1 model selected  

> select #2/A:183@O

1 atom, 1 residue, 1 model selected  

> select #2/A:183@N

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:183@OG

1 atom, 1 residue, 1 model selected  

> color sel yellow

> select clear

> select #2/A:183@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:183@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:183@N

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:183@OG

1 atom, 1 residue, 1 model selected  

> select #2/A:183@OG

1 atom, 1 residue, 1 model selected  

> select #2/A:183@O

1 atom, 1 residue, 1 model selected  

> select #2/A:183@O

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:183@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:183@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:65@OG1

1 atom, 1 residue, 1 model selected  

> select #2/A:65@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/A:65@CB

1 atom, 1 residue, 1 model selected  

> select #2/A:65@OG1

1 atom, 1 residue, 1 model selected  

> select #2/A:65@CG2

1 atom, 1 residue, 1 model selected  

> select #2/A:65@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> surface (#!2 & sel)

> set bgColor black

> set bgColor transparent

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Admin/Desktop\movie11.mp4

Movie saved to C:\Users\Admin/Desktop\movie11.mp4  
  

> select clear

> view orient

> view

> set bgColor white

> set bgColor #ffffff00

> view orient

> save C:\Users\Admin/Desktop\image36.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Admin/Desktop\movie12.mp4

Movie saved to C:\Users\Admin/Desktop\movie12.mp4  
  

> set bgColor black

> set bgColor transparent

> show #!2 cartoons

> ~label #2 residues

> set bgColor white

> set bgColor #ffffff00

> view orient

> save C:\Users\Admin/Desktop\image37.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Admin/Desktop\movie13.mp4

Movie saved to C:\Users\Admin/Desktop\movie13.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Admin/Desktop\movie14.mp4

C:\Program Files\ChimeraX 1.10.dev202501142332\bin\ffmpeg.exe -r 25 -i
C:\Users\Admin\AppData\Local\Temp\chimovie_Dng2-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\Admin/Desktop\movie14.mp4  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with gcc 6.3.0 (GCC)  
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'C:\Users\Admin\AppData\Local\Temp\chimovie_Dng2-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1116x491, 25 fps, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 0000000001055760] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2  
[libx264 @ 0000000001055760] profile High, level 3.1  
[libx264 @ 0000000001055760] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to 'C:\Users\Admin/Desktop\movie14.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1116x490, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 58 fps=0.0 q=25.0 size= 159kB time=00:00:00.20 bitrate=6511.4kbits/s
speed=0.368x frame= 101 fps= 96 q=25.0 size= 910kB time=00:00:01.92
bitrate=3882.6kbits/s speed=1.83x frame= 145 fps= 93 q=25.0 size= 1657kB
time=00:00:03.68 bitrate=3687.7kbits/s speed=2.37x frame= 180 fps= 77 q=-1.0
Lsize= 3112kB time=00:00:07.08 bitrate=3600.2kbits/s speed=3.04x  
video:3109kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.095030%  
[libx264 @ 0000000001055760] frame I:1 Avg QP: 8.08 size: 28439  
[libx264 @ 0000000001055760] frame P:45 Avg QP:21.44 size: 23225  
[libx264 @ 0000000001055760] frame B:134 Avg QP:26.40 size: 15738  
[libx264 @ 0000000001055760] consecutive B-frames: 0.6% 0.0% 1.7% 97.8%  
[libx264 @ 0000000001055760] mb I I16..4: 84.9% 0.0% 15.1%  
[libx264 @ 0000000001055760] mb P I16..4: 0.5% 0.7% 6.4% P16..4: 2.2% 3.4%
4.6% 0.0% 0.0% skip:82.1%  
[libx264 @ 0000000001055760] mb B I16..4: 0.1% 0.1% 1.2% B16..8: 3.6% 4.2%
7.8% direct: 0.6% skip:82.4% L0:42.7% L1:38.3% BI:19.0%  
[libx264 @ 0000000001055760] 8x8 transform intra:7.2% inter:2.3%  
[libx264 @ 0000000001055760] coded y,uvDC,uvAC intra: 69.6% 74.6% 73.7% inter:
7.4% 5.3% 4.0%  
[libx264 @ 0000000001055760] i16 v,h,dc,p: 87% 7% 6% 0%  
[libx264 @ 0000000001055760] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 5% 7% 85% 1% 0% 0%
0% 0% 0%  
[libx264 @ 0000000001055760] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 14% 11% 21% 7% 10%
10% 11% 9% 8%  
[libx264 @ 0000000001055760] i8c dc,h,v,p: 66% 12% 13% 9%  
[libx264 @ 0000000001055760] Weighted P-Frames: Y:2.2% UV:0.0%  
[libx264 @ 0000000001055760] ref P L0: 53.3% 10.7% 22.0% 13.7% 0.3%  
[libx264 @ 0000000001055760] ref B L0: 82.9% 13.3% 3.7%  
[libx264 @ 0000000001055760] ref B L1: 93.6% 6.4%  
[libx264 @ 0000000001055760] kb/s:3536.13  
Exiting normally, received signal 15.  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 3221225786  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with gcc 6.3.0 (GCC)  
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'C:\Users\Admin\AppData\Local\Temp\chimovie_Dng2-%05d.ppm':  
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1116x491, 25 fps, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 0000000001055760] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2  
[libx264 @ 0000000001055760] profile High, level 3.1  
[libx264 @ 0000000001055760] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to 'C:\Users\Admin/Desktop\movie14.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1116x490, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 58 fps=0.0 q=25.0 size= 159kB time=00:00:00.20 bitrate=6511.4kbits/s
speed=0.368x frame= 101 fps= 96 q=25.0 size= 910kB time=00:00:01.92
bitrate=3882.6kbits/s speed=1.83x frame= 145 fps= 93 q=25.0 size= 1657kB
time=00:00:03.68 bitrate=3687.7kbits/s speed=2.37x frame= 180 fps= 77 q=-1.0
Lsize= 3112kB time=00:00:07.08 bitrate=3600.2kbits/s speed=3.04x  
video:3109kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.095030%  
[libx264 @ 0000000001055760] frame I:1 Avg QP: 8.08 size: 28439  
[libx264 @ 0000000001055760] frame P:45 Avg QP:21.44 size: 23225  
[libx264 @ 0000000001055760] frame B:134 Avg QP:26.40 size: 15738  
[libx264 @ 0000000001055760] consecutive B-frames: 0.6% 0.0% 1.7% 97.8%  
[libx264 @ 0000000001055760] mb I I16..4: 84.9% 0.0% 15.1%  
[libx264 @ 0000000001055760] mb P I16..4: 0.5% 0.7% 6.4% P16..4: 2.2% 3.4%
4.6% 0.0% 0.0% skip:82.1%  
[libx264 @ 0000000001055760] mb B I16..4: 0.1% 0.1% 1.2% B16..8: 3.6% 4.2%
7.8% direct: 0.6% skip:82.4% L0:42.7% L1:38.3% BI:19.0%  
[libx264 @ 0000000001055760] 8x8 transform intra:7.2% inter:2.3%  
[libx264 @ 0000000001055760] coded y,uvDC,uvAC intra: 69.6% 74.6% 73.7% inter:
7.4% 5.3% 4.0%  
[libx264 @ 0000000001055760] i16 v,h,dc,p: 87% 7% 6% 0%  
[libx264 @ 0000000001055760] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 5% 7% 85% 1% 0% 0%
0% 0% 0%  
[libx264 @ 0000000001055760] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 14% 11% 21% 7% 10%
10% 11% 9% 8%  
[libx264 @ 0000000001055760] i8c dc,h,v,p: 66% 12% 13% 9%  
[libx264 @ 0000000001055760] Weighted P-Frames: Y:2.2% UV:0.0%  
[libx264 @ 0000000001055760] ref P L0: 53.3% 10.7% 22.0% 13.7% 0.3%  
[libx264 @ 0000000001055760] ref B L0: 82.9% 13.3% 3.7%  
[libx264 @ 0000000001055760] ref B L1: 93.6% 6.4%  
[libx264 @ 0000000001055760] kb/s:3536.13  
Exiting normally, received signal 15.  
  
\-----------------------------  
  

> ui tool show "Selection Inspector"

> volume planes z style image imageMode "full region"

No volumes specified  

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> view sel

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Admin/Desktop\movie14.mp4

Movie saved to C:\Users\Admin/Desktop\movie14.mp4  
  

> save "C:/Users/Admin/Downloads/cndntng gn.png" width 1116 height 491
> supersample 3

> color #2 #c37ee8ff

> view orient

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> hide sel & #!2 surfaces

> color (#!2 & sel) purple

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> show sel & #!2 surfaces

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> view sel

> select clear

> select ligand

106 atoms, 104 bonds, 2 residues, 2 models selected  

> hide sel & #!2 surfaces

> select clear

> close #1

> color #2 #00aa7fff

> color #2 #50a9aaff

> color #2 #2ba8aaff

> color #2 #3ae2e5ff

> color #2 #32c1c3ff

> select clear

> color #2 #be1fc3ff

> color #2 #aa007fff

> color #2 #ff00bfff

> color byhetero

> color bychain

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> style sel stick

Changed 228 atom styles  

> show sel atoms

> color sel byhetero

> select ::name="HOH"

309 atoms, 309 residues, 1 model selected  

> hide sel atoms

> color #2 #edeee7ff

> color #2 #c6c7c1ff

> color #2 #b8b9b3ff

> color #2 #a7a8a3ff

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> select clear

> color #2 #b7b8b2ff

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> color #2 #aa007fff

> select clear

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> select clear

> select /A

3619 atoms, 3413 bonds, 692 residues, 1 model selected  

> color (#!2 & sel) dark gray

> select clear

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light blue

> color sel dark violet

> select clear

> view orient

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> view sel

> color sel byhetero

> select clear

> view orient

> select /C

228 atoms, 214 bonds, 45 residues, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select clear

> set bgColor white

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> save C:\Users\Admin/Desktop\image38.png supersample 3

> ~label #2 residues

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 2/C  

> select /C:732

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /C:732

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select
> /A:39-56,70-72,79-86,89-98,101-116,169-171,319-323,327-341,343-369,399-411,420-437

1124 atoms, 1139 bonds, 136 residues, 1 model selected  

> select /A:391

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:391

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select /A:420

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:420

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select /A:405

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:405

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select
> /A:39-56,70-72,79-86,89-98,101-116,169-171,319-323,327-341,343-369,399-411,420-437

1124 atoms, 1139 bonds, 136 residues, 1 model selected  

> select /A:408

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

> select /A:408

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

> show sel atoms

> color sel byhetero

> select /A:404

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

> select /A:404

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

> show sel atoms

> color sel byhetero

> select clear

> select
> /A:39-56,70-72,79-86,89-98,101-116,169-171,319-323,327-341,343-369,399-411,420-437

1124 atoms, 1139 bonds, 136 residues, 1 model selected  

> select /A:170

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

> select /A:170

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

> show sel atoms

> color sel byhetero

> select clear

> select /A:145

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

> select /A:145

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

> show sel atoms

> color sel byhetero

> select clear

> hide atoms

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> undo

> hide cartoons

> undo

> save C:\Users\Admin/Desktop\image39.png supersample 3

> hide cartoons

Drag select of 177 atoms, 168 bonds  
Drag select of 169 atoms, 161 bonds  

> hide target m

> undo

> hide sel atoms


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 31.0.101.5522
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: windows

Manufacturer: LENOVO
Model: 82KA
OS: Microsoft Windows 11 Pro (Build 26200)
Memory: 4,084,523,008
MaxProcessMemory: 137,438,953,344
CPU: 4 11th Gen Intel(R) Core(TM) i3-1115G4 @ 3.00GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.12.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202501142332
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NIHPresets: 1.2.8
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    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: 2.5.1
    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: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.11
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.0
    PyQt6-Qt6: 6.8.1
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.1
    PyQt6_sip: 13.9.1
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 hours ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by Eric Pettersen, 2 hours ago

Resolution: → can't reproduce
Status: accepted → closed

Hi Anurag,

Thanks for reporting this problem. I would suggest updating to the latest ChimeraX release, which has many bug fixes relative to the release you're using, and uses a later version of the Qt windowing toolkit, and therefore may already have fixed the problem that caused your crash. Even if it doesn't, getting crash information from a current build will be much more helpful to us in fixing the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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