![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 hours ago
Last modified 6 seconds ago
#19995 accepted defect
Crash in event loop
| Reported by: | 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 (1)
comment:1 by , 6 seconds ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
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