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Opened 3 hours ago
#19771 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.12.dev202512040236 (2025-12-04 02:36:31 UTC)
Description
No idea what happened got very buggy and then crashed, I'm trying to work with multiple files at a time, maybe overloaded the system? I'm not sure
Log:
UCSF ChimeraX version: 1.12.dev202512040236 (2025-12-04)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\jaidy\OneDrive - University of Glasgow\Honours
> Project\Tetrahymena_ComplexII.cxs" format session
Log from Sat Jan 24 15:50:17 2026 Startup Messages
---
warning | Unknown Vendor ID: 0x4d4f4351
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11rc202512032208 (2025-12-03)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif" format mmcif
No such file/path: C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif
> open "C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif" format mmcif
No such file/path: C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif
> open "C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif" format mmcif
No such file/path: C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif
> open "C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif" format mmcif
No such file/path: C:\Users\jaidy\Downloads\Tetrahymena Complex II.cif
> open "C:\Users\jaidy\Downloads\8B6G (1).cif" format mmcif
Summary of feedback from opening C:\Users\jaidy\Downloads\8B6G (1).cif
---
warnings | Atom H76 is not in the residue template for 3PE /CK:101
Atom H76 is not in the residue template for 3PE /CC:301
Atom H76 is not in the residue template for 3PE /CD:302
8B6G (1).cif title:
Cryo-EM structure of succinate dehydrogenase complex (complex-II) in
respiratory supercomplex of Tetrahymena thermophila [more info...]
Chain information for 8B6G (1).cif #1
---
Chain | Description | UniProt
CA | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | Q23DI3_TETTS 1-636
CB | Succinate dehydrogenase (quinone) | I7M403_TETTS 1-312
CC | Cytochrome b-c1 complex subunit 8 | Q23RH8_TETTS 1-60
CD | SDHD |
CE | NmrA domain-containing protein | Q24I09_TETTS 1-322
CF | Transmembrane protein, putative | Q248F8_TETTS 1-296
CG | SDHTT3 | I7MEX7_TETTS 1-198
CH | Diphthamide synthesis protein | I7LX66_TETTS 1-195
CI | DUF4885 domain-containing protein | Q22YL0_TETTS 1-114
CJ | Transmembrane protein, putative | Q23S01_TETTS 1-103
CK | Transmembrane protein, putative | Q24CW6_TETTS 1-93
CL | Transposase | W7XBF5_TETTS 1-89
CM | Transmembrane protein, putative | Q22HD6_TETTS 1-76
CN | Transmembrane protein, putative | W7XF00_TETTS 1-62
CO | SDHTT11 |
Non-standard residues in 8B6G (1).cif #1
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CA — calcium ion
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
F3S — FE3-S4 cluster
FAD — flavin-adenine dinucleotide
FES — FE2/S2 (inorganic) cluster
HEC — heme C
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
SF4 — iron/sulfur cluster
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc
taen-1-yl]cyclohexa-2,5-diene-1,4-dione)
> style stick
Changed 41412 atom styles
> style stick
Changed 41412 atom styles
> style ball
Changed 41412 atom styles
> style ball
Changed 41412 atom styles
> style ball
Changed 41412 atom styles
> style stick
Changed 41412 atom styles
> hide atoms
> show cartoons
> show surfaces
[Repeated 1 time(s)]
> hide surfaces
> show atoms
> hide atoms
> ui tool show "Change Chain IDs"
> ui tool show "Model Panel"
[Repeated 1 time(s)]
> hide #1.14 models
> show #1.14 models
> hide #1.14 models
> show #1.14 models
> hide #1.15 models
> show #1.15 models
> show #1.14 target m
> ui tool show "Model Panel"
> select add #1.13
1522 atoms, 88 residues, 1 model selected
> select subtract #1.13
1 model selected
> select add #1.13
1522 atoms, 88 residues, 1 model selected
> select subtract #1.13
1 model selected
> select add #1.14
1232 atoms, 74 residues, 1 model selected
> select subtract #1.14
1 model selected
> select add #1.15
1029 atoms, 62 residues, 1 model selected
> select subtract #1.15
1 model selected
> select add #1.16
742 atoms, 43 residues, 1 model selected
> select subtract #1.16
1 model selected
> view #1.13-16 clip false
No displayed objects specified.
> show #1.13-16 target m
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #1.8 models
> hide #1.10 models
> hide #1.9 models
> hide #1.11 models
> hide #1.16 models
> hide #1.15 models
> hide #1.14 models
> hide #1.13 models
> hide #1.12 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #1.1 models
> show #1.2 models
> show #1.3 models
> show #1.4 models
> show #1.5 models
> show #1.7 models
> show #1.6 models
> show #1.8 models
> show #1.9 models
> show #1.11 models
> show #1.10 models
> show #1.12 models
> show #1.13 models
> show #1.14 models
> show #1.15 models
> show #1.16 models
> hide #!1 models
> hide #!1 target m
> show #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #1.8 models
> hide #1.9 models
> hide #1.10 models
> hide #1.11 models
> hide #1.13 models
> hide #1.12 models
> hide #1.14 models
> hide #1.15 models
> hide #1.16 models
> select add #1
41412 atoms, 41879 bonds, 13 pseudobonds, 2428 residues, 2 models selected
> select subtract #1.1
41412 atoms, 41879 bonds, 2428 residues, 16 models selected
> select add #1.1
41412 atoms, 41879 bonds, 13 pseudobonds, 2428 residues, 17 models selected
> select subtract #1
15 models selected
> select add #1.1
13 pseudobonds, 1 model selected
> select add #1.2
9198 atoms, 13 pseudobonds, 599 residues, 2 models selected
> select subtract #1.1
9198 atoms, 599 residues, 2 models selected
> select subtract #1.2
1 model selected
> select clear
[Repeated 1 time(s)]
> select /CA:138
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /CA:337
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /CA:337
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /CA:338
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select clear
> label #!1 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> ~label #1.17#!1 residues
> ui tool show "Color Actions"
> color bychain
> color red
> color bychain
> ui tool show "Color Actions"
Cannot color background by chain
> color bychain target acspfl
> color medium turquoise target acspfl
> color bychain target acspfl
> select /CA
9283 atoms, 9386 bonds, 3 pseudobonds, 601 residues, 2 models selected
> color (#!1 & sel) red
> select clear
> select /CL
1522 atoms, 1540 bonds, 88 residues, 1 model selected
> ui tool show "Model Panel"
> show #1.13 models
> hide #1.13 models
> hide #1.1 target m
[Repeated 6 time(s)]
> select subtract #1.13
1 model selected
> select add #1.13
1522 atoms, 88 residues, 1 model selected
> hide target m
[Repeated 1 time(s)]
> show target m
> hide #1.13 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #1.8 models
> hide #1.10 models
> hide #1.9 models
> show #1.13 models
> hide #1.11 models
> hide #1.13 models
> hide #1.12 models
> hide #1.14 models
> hide #1.15 models
> hide #1.16 models
> select add #1
41412 atoms, 41879 bonds, 13 pseudobonds, 2428 residues, 3 models selected
> select subtract #1
15 models selected
> select add #1.13
1522 atoms, 88 residues, 1 model selected
> select subtract #1.13
1 model selected
> select add #1.13
1522 atoms, 88 residues, 1 model selected
> select /CA
9283 atoms, 9386 bonds, 3 pseudobonds, 601 residues, 2 models selected
> color sel dark blue target acspfl
[Repeated 1 time(s)]
> select /CB
4581 atoms, 4641 bonds, 4 pseudobonds, 289 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark red target acspfl
> select /CD
1196 atoms, 1205 bonds, 46 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chocolate target acspfl
[Repeated 1 time(s)]
> select /CO
998 atoms, 1008 bonds, 44 residues, 1 model selected
> ui tool show "Color Actions"
> color sel teal target acspfl
> select /CA
9283 atoms, 9386 bonds, 3 pseudobonds, 601 residues, 2 models selected
> select /CA
9283 atoms, 9386 bonds, 3 pseudobonds, 601 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark blue target acspfl
> ui tool show "Color Actions"
> color sel navy target acspfl
[Repeated 1 time(s)]
> select /CB
4581 atoms, 4641 bonds, 4 pseudobonds, 289 residues, 2 models selected
> select /CB
4581 atoms, 4641 bonds, 4 pseudobonds, 289 residues, 2 models selected
> ui tool show "Color Actions"
> color sel maroon target acspfl
> color sel fire brick target acspfl
> select /CC
1378 atoms, 1388 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chocolate target acspfl
> select /CD
1196 atoms, 1205 bonds, 46 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chocolate target acspfl
> select /CC
1378 atoms, 1388 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel teal target acspfl
> color sel sea green target acspfl
> select /CE
5190 atoms, 5248 bonds, 6 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light green target acspfl
> select /CF
3598 atoms, 3643 bonds, 218 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red target acspfl
> select clear
> select /CG
3759 atoms, 3802 bonds, 198 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime target acspfl
> select /CF
3598 atoms, 3643 bonds, 218 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid target acspfl
> select /CG
3759 atoms, 3802 bonds, 198 residues, 1 model selected
> color (#!1 & sel) lime
> select /CH
1700 atoms, 1712 bonds, 110 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon target acspfl
> select /CI
1805 atoms, 1820 bonds, 114 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lavender target acspfl
> help help:user/tools/coloractions.html
> color sel thistle target acspfl
> select /CJ
1919 atoms, 1945 bonds, 104 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light cyan target acspfl
> select /CK
1966 atoms, 1990 bonds, 95 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium spring green target acspfl
> select /CL
1522 atoms, 1540 bonds, 88 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light goldenrod yellow target acspfl
> color sel lemon chiffon target acspfl
> select /CM
1488 atoms, 1506 bonds, 75 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple target acspfl
> select /CN
1029 atoms, 1045 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light cyan target acspfl
> select /CO
998 atoms, 1008 bonds, 44 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sky blue target acspfl
> select clear
> set bgColor white
> set bgColor #ffffff00
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> select /CC
1378 atoms, 1388 bonds, 62 residues, 1 model selected
> select /CG
3759 atoms, 3802 bonds, 198 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light green target acspfl
> color sel dark sea green target acspfl
> color sel lime green target acspfl
> select clear
> select /CE
5190 atoms, 5248 bonds, 6 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light green target acspfl
> color sel pale green target acspfl
> color sel light green target acspfl
> color sel dark sea green target acspfl
> color sel light green target acspfl
> color sel medium spring green target acspfl
> color sel light green target acspfl
> color sel aquamarine target acspfl
> color sel pale turquoise target acspfl
> color sel pale green target acspfl
> select clear
> select /CC
1378 atoms, 1388 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium sea green target acspfl
> color sel olive drab target acspfl
> color sel dark olive green target acspfl
> color sel olive drab target acspfl
> color sel medium sea green target acspfl
> color sel olive drab target acspfl
> select clear
> select /CC
1378 atoms, 1388 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green target acspfl
> select clear
> select /CI:86
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /CF
3598 atoms, 3643 bonds, 218 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pink target acspfl
> color sel plum target acspfl
> color sel violet target acspfl
> color sel orchid target acspfl
> color sel pale violet red target acspfl
> color sel medium orchid target acspfl
> color sel orchid target acspfl
> color sel pale violet red target acspfl
> color sel orchid target acspfl
> color sel light pink target acspfl
> select /CI
1805 atoms, 1820 bonds, 114 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light green target acspfl
> color sel pale green target acspfl
> color sel light green target acspfl
[Repeated 1 time(s)]
> select /CE
5190 atoms, 5248 bonds, 6 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle target acspfl
> select clear
> lighting full
> lighting soft
> lighting simple
> set bgColor black
> set bgColor transparent
> select /CJ
1919 atoms, 1945 bonds, 104 residues, 1 model selected
> ui tool show "Color Actions"
> color sel powder blue target acspfl
> select clear
> select /CJ
1919 atoms, 1945 bonds, 104 residues, 1 model selected
> select /CN
1029 atoms, 1045 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light cyan target acspfl
[Repeated 1 time(s)]
> select clear
> select /CN
1029 atoms, 1045 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel teal target acspfl
> color sel dark cyan target acspfl
> color sel cadet blue target acspfl
> select clear
> select /CJ
1919 atoms, 1945 bonds, 104 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium turquoise target acspfl
> color sel cornflower blue target acspfl
> undo
[Repeated 1 time(s)]
> select clear
> select /CK
1966 atoms, 1990 bonds, 95 residues, 1 model selected
> select clear
> select /CO
998 atoms, 1008 bonds, 44 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum target acspfl
> color sel medium aquamarine target acspfl
> color sel pale violet red target acspfl
> color sel violet target acspfl
[Repeated 1 time(s)]
> color sel pink target acspfl
> color sel light pink target acspfl
> color sel sky blue target acspfl
> color sel teal target acspfl
> color sel dark cyan target acspfl
> color sel deep sky blue target acspfl
> color sel medium sea green target acspfl
> color sel sea green target acspfl
> color sel medium aquamarine target acspfl
> color sel cadet blue target acspfl
> color sel light slate gray target acspfl
> color sel turquoise target acspfl
> color sel medium spring green target acspfl
> color sel yellow green target acspfl
> select clear
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> lighting soft
> lighting full
> ui tool show "Selection Inspector"
> lighting shadows false
> lighting shadows true
> set bgColor gray
> set bgColor #80808000
> ui tool show "Side View"
> lighting shadows false
> show surfaces
> hide surfaces
> ui tool show "Model Panel"
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select add #1.2
9198 atoms, 599 residues, 1 model selected
> select add #1.3
13759 atoms, 884 residues, 2 models selected
> select add #1.4
14735 atoms, 943 residues, 3 models selected
> select add #1.5
15542 atoms, 987 residues, 4 models selected
> select add #1.6
20657 atoms, 1308 residues, 5 models selected
> select add #1.7
24255 atoms, 1526 residues, 6 models selected
> select add #1.8
27502 atoms, 1722 residues, 7 models selected
> select add #1.9
29202 atoms, 1832 residues, 8 models selected
> select add #1.10
31007 atoms, 1946 residues, 9 models selected
> select add #1.11
32670 atoms, 2049 residues, 10 models selected
> select add #1.12
34247 atoms, 2142 residues, 11 models selected
> select add #1.13
35769 atoms, 2230 residues, 12 models selected
> select add #1.14
37001 atoms, 2304 residues, 13 models selected
> select add #1.15
38030 atoms, 2366 residues, 14 models selected
> show sel surfaces
> select add #1.16
38772 atoms, 2409 residues, 15 models selected
> show sel surfaces
> transparency (#!1 & sel) 60
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 70
> surface style mesh
> surface style dot
> select clear
> surface style mesh
> surface style solid
> transparency 70
> transparency 80
[Repeated 1 time(s)]
> select add #1.1
13 pseudobonds, 1 model selected
> select add #1.3
4561 atoms, 13 pseudobonds, 285 residues, 2 models selected
> select add #1.2
13759 atoms, 13 pseudobonds, 884 residues, 3 models selected
> select subtract #1.1
13759 atoms, 884 residues, 3 models selected
> select add #1.4
14735 atoms, 943 residues, 3 models selected
> select add #1.5
15542 atoms, 987 residues, 4 models selected
> select add #1.6
20657 atoms, 1308 residues, 5 models selected
> select add #1.7
24255 atoms, 1526 residues, 6 models selected
> select add #1.8
27502 atoms, 1722 residues, 7 models selected
> select add #1.9
29202 atoms, 1832 residues, 8 models selected
> select add #1.10
31007 atoms, 1946 residues, 9 models selected
> select add #1.11
32670 atoms, 2049 residues, 10 models selected
> select add #1.12
34247 atoms, 2142 residues, 11 models selected
> select add #1.13
35769 atoms, 2230 residues, 12 models selected
> select add #1.14
37001 atoms, 2304 residues, 13 models selected
> select add #1.15
38030 atoms, 2366 residues, 14 models selected
> select add #1.16
38772 atoms, 2409 residues, 15 models selected
> ui tool show "Selection Inspector"
> ui tool show "Color Actions"
> color sel light gray target s
> transparency (#!1 & sel) 80
> set bgColor white
> set bgColor #ffffff00
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "move planes"
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Color Actions"
> color cadet blue target s
[Repeated 1 time(s)]
> color dark gray target s
> transparency 80
> graphics silhouettes false
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select /CC
1378 atoms, 1388 bonds, 62 residues, 1 model selected
> select /CE
5190 atoms, 5248 bonds, 6 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle target s
> ui tool show "Color Actions"
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui tool show "Selection Inspector"
> color sel #d6bdd6 atoms
> color sel #d5bcd5 atoms
> color sel #d1b8d1 atoms
> color sel #bfa9bf atoms
> color sel #baa4ba atoms
> color sel #b5a0b5 atoms
> color sel #b6a1b6 atoms
> color sel #b8a2b8 atoms
> color sel #bfa9bf atoms
> color sel #c1aac1 atoms
> color sel #c2abc2 atoms
> color sel #c7b0c7 atoms
> color sel #c8b0c8 atoms
> color sel #cab2ca atoms
> transparency (#!1 & sel) 80
> ui tool show "Color Actions"
> color sel gray target s
> transparency (#!1 & sel) 80
> color (#!1 & sel) dark gray
> transparency (#!1 & sel) 80
> ui tool show "Color Actions"
> color sel thistle target c
> color sel plum target c
> color sel thistle target c
> ui tool show "Color Actions"
> color (#!1 & sel) #aaaaffff target c
> color (#!1 & sel) #a9a9feff target c
> color (#!1 & sel) #a5a5f8ff target c
> color (#!1 & sel) #9b9be8ff target c
> color (#!1 & sel) #9797e3ff target c
> color (#!1 & sel) #9595dfff target c
> color (#!1 & sel) #9494deff target c
> color (#!1 & sel) #9595dfff target c
> color (#!1 & sel) #9797e2ff target c
> color (#!1 & sel) #9999e5ff target c
> color (#!1 & sel) #9999e6ff target c
> color (#!1 & sel) #9a9ae7ff target c
> color (#!1 & sel) #9b9be8ff target c
> color (#!1 & sel) #9d9debff target c
> color (#!1 & sel) #9d9decff target c
> color (#!1 & sel) #000038ff target c
> color (#!1 & sel) #f5f5f5ff target c
> color (#!1 & sel) #fdfdfdff target c
> color (#!1 & sel) #ad97c8ff target c
> color (#!1 & sel) #f5f5f5ff target c
> color (#!1 & sel) #863500ff target c
> color (#!1 & sel) #f6f6f6ff target c
> color (#!1 & sel) #efefefff target c
> color (#!1 & sel) #f7f7f7ff target c
> color (#!1 & sel) #f9f9f9ff target c
> color (#!1 & sel) #fdfdfdff target c
> color (#!1 & sel) #61adf2ff target c
> color (#!1 & sel) #f7d48aff target c
> color (#!1 & sel) #f7f7f7ff target c
> color (#!1 & sel) #f5f5f5ff target c
> color (#!1 & sel) #ad6100ff target c
> color (#!1 & sel) #360036ff target c
> color (#!1 & sel) #f4d188ff target c
> color (#!1 & sel) #f0f0f0ff target c
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> color (#!1 & sel) #dec2ffff target c
> select clear
> ui tool show "Selection Inspector"
> ui tool show "Task Manager"
> hide #2 models
> ui mousemode right translate
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> cd "C:/Users/jaidy/OneDrive - University of Glasgow/Honours Project"
Current working directory is: C:\Users\jaidy\OneDrive - University of
Glasgow\Honours Project
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting soft
> lighting full
> save "C:/Users/jaidy/OneDrive - University of Glasgow/Honours
> Project/Tetrahymena_ComplexII.cxs" includeMaps true
> select /CL
1522 atoms, 1540 bonds, 88 residues, 1 model selected
> select clear
> select /CL
1522 atoms, 1540 bonds, 88 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lemon chiffon target c
> color sel light goldenrod yellow target c
> color sel light coral target c
> color sel light goldenrod yellow target c
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> color (#!1 & sel) #f7ff8eff target c
> color (#!1 & sel) #f9ff8eff target c
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> color (#!1 & sel) #fbff8eff target c
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> color (#!1 & sel) #fffab8ff target c
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
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> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 2 time(s)]
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> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
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> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
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> lighting full
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> lighting shadows false
> lighting full
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> lighting simple
[Repeated 1 time(s)]
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> lighting full
> lighting soft
[Repeated 1 time(s)]
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> graphics silhouettes false
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> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> transparency #1 60
> lighting soft
> transparency #1 60
> transparency #1 70
> transparency #1 80
> transparency #1 70
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
[Repeated 2 time(s)]
> transparency #1 80
> ui tool show "Color Actions"
> color royal blue target s
> color gray target s
> transparency #1 80
> ui tool show "Color Actions"
> color dark gray target s
> transparency #1 70
> transparency #1 80
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting soft
> transparency #1 80
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> transparency #1 70
> transparency #1 80
> lighting soft
> save "C:/Users/jaidy/OneDrive - University of Glasgow/Honours
> Project/Tetrahymena Structure .png" width 637 height 513 supersample 3
> save "C:/Users/jaidy/OneDrive - University of Glasgow/Honours
> Project/Tetrahymena_ComplexII.cxs"
——— End of log from Sat Jan 24 15:50:17 2026 ———
> view name session-start
opened ChimeraX session
> open "C:/Users/jaidy/OneDrive - University of Glasgow/Documents/Honours
> Project/Complex I 8b6f.cif"
Summary of feedback from opening C:/Users/jaidy/OneDrive - University of
Glasgow/Documents/Honours Project/Complex I 8b6f.cif
---
warnings | Atom HN76 is not in the residue template for 3PE /A2:401
Atom HN76 is not in the residue template for 3PE /A9:602
Atom HN76 is not in the residue template for 3PE /A9:603
Atom HN76 is not in the residue template for 3PE /AJ:502
Atom HN76 is not in the residue template for 3PE /BA:301
1 messages similar to the above omitted
Complex I 8b6f.cif title:
Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) from
respiratory supercomplex of Tetrahymena thermophila [more info...]
Chain information for Complex I 8b6f.cif #3
---
Chain | Description | UniProt
A0 | Lipid-A-disaccharide synthase | Q22E24_TETTS 1-516
A1 | NAD-dependent epimerase/dehydratase family protein | I7MLH2_TETTS 1-362
A2 | DnaJ domain protein | Q22DR7_TETTS 1-317
A3 | Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II | Q24HK5_TETTS 1-333
A4 | RNase III domain-containing protein | I7LUQ4_TETTS 1-311
A5 | 37S ribosomal protein S25, mitochondrial | I7MIJ7_TETTS 1-282
A6 | Transmembrane protein, putative | Q24C39_TETTS 1-251
A7 | CX9C domain-containing protein | I7MMF4_TETTS 1-238
A8 | NDUTT15 |
A9 | Transmembrane protein, putative | Q24F24_TETTS 1-231
AA | NADH dehydrogenase subunit 5 | Q950Z0_TETTH 1-750
AB | NADH-ubiquinone oxidoreductase 75 kDa subunit | Q23KA9_TETTS 1-718
AC | NADH-ubiquinone oxidoreductase chain 4 | Q950X9_TETTH 1-505
AD | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial | Q23KE4_TETTS 1-474
AE | NADH dehydrogenase subunit 7 | Q951B1_TETTH 1-442
AF | Ymf65 | Q951A3_TETTH 1-360
AG | Transcription factor apfi protein, putative | I7M8Q7_TETTS 1-346
AH | NADH-ubiquinone oxidoreductase chain 1 | Q950Y3_TETTH 1-284
AI | NADH-ubiquinone oxidoreductase 24 kDa subunit | I7MEP0_TETTS 1-274
AJ | Ymf62 | Q950Y2_TETTH 1-255
AK | Gamma-carbonic anhydrase | Q22XU5_TETTS 1-257
AL | NADH-ubiquinone oxidoreductase 1, chain, putative | I7MDW5_TETTS 1-236
AM | Gamma-carbonic anhydrase | I7M6S0_TETTS 1-233
AN | ETC complex I subunit motif protein | Q23ND5_TETTS 1-206
AO | NADH dehydrogenase subunit 9 | Q950Z3_TETTH 1-198
AP | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | A4VDQ6_TETTS 1-194
AQ | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | Q233X7_TETTS 1-189
AR | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | I7MK61_TETTS 1-185
AS | NADH dehydrogenase, putative | I7M2Y3_TETTS 1-172
AT | NADH dehydrogenase subunit 10 | Q951B4_TETTH 1-162
AU | NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit | I7LT42_TETTS 1-150
AV | Acyl carrier protein | Q22XT6_TETTS 1-138
AW | Acyl carrier protein | I7MD12_TETTS 1-133
AX | NADH-ubiquinone oxidoreductase chain 3 | Q950Z7_TETTH 1-121
AY | Ymf58 | Q950Z5_TETTH 1-116
AZ | Ribosomal protein L51/S25/CI-B8 domain protein | I7MA77_TETTS 1-103
B0 | Transmembrane protein, putative | I7MI60_TETTS 1-94
B1 | ATP synthase subunit e, mitochondrial | Q22E95_TETTS 1-93
B2 | GRAM domain protein | W7X4R4_TETTS 1-94
B3 | Transmembrane protein, putative | A4VD20_TETTS 1-83
B4 | Transmembrane protein, putative | Q22DC2_TETTS 1-73
B5 | Transmembrane protein, putative | I7MIK1_TETTS 1-71
B6 | ND1b |
BA | Transmembrane protein | I7MIE0_TETTS 1-212
BB | Transmembrane protein, putative | Q22Z32_TETTS 1-214
BC | NDUB8 | I7M855_TETTS 1-207
BD | Transmembrane protein, putative | I7LT77_TETTS 1-205
BE | NDUPH2 | Q23KE0_TETTS 1-189
BF | NDUB10 | Q23KG0_TETTS 1-188
BG | NDUA13 | I7M2U4_TETTS 1-175
BH | NADH dehydrogenase subunit 2 | Q951B2_TETTH 1-178
BI | 2 iron, 2 sulfur cluster-binding protein | Q22W11_TETTS 1-172
BJ | Thioredoxin | Q22AI5_TETTS 1-166
BK | COX assembly mitochondrial protein | I7M1N8_TETTS 1-144
BL | Transmembrane protein, putative | Q22HE4_TETTS 1-143
BM | Transmembrane protein, putative | I7M9B3_TETTS 1-135
BN | PH domain-containing protein | Q22SC4_TETTS 1-135
BO | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | Q23B10_TETTS 1-136
BP | NDUB6 | Q231G0_TETTS 1-129
BQ | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | I7MAF0_TETTS 1-127
BR | Zinc-finger protein | I7MK02_TETTS 1-132
BS | NDUB4 | I7MG29_TETTS 1-126
BT | NDUB15 |
BU | NDUTT16 |
BV | NDUTT17 |
BW | CHCH domain-containing protein | I7MIM0_TETTS 1-120
BX | Transmembrane protein, putative | Q22T55_TETTS 1-113
BY | Ymf57 | Q951C2_TETTH 1-100
BZ | Complex I-MNLL | Q22W63_TETTS 1-102
Non-standard residues in Complex I 8b6f.cif #3
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
8Q1 — S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-
alanyl}amino)ethyl] dodecanethioate (S-dodecanoyl-4'-phosphopantetheine)
ADP — adenosine-5'-diphosphate
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
LPP — 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate
(1,2-dipalmitoyl-Sn-glycero-3-phosphate; L-B,G-dipalmitoyl-A-phosphatidic acid
disodium salt; 3-Sn-phosphatidic acid; 1,2-dipalmitoyldisodium salt)
MG — magnesium ion
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
SF4 — iron/sulfur cluster
UDP — uridine-5'-diphosphate
ZN — zinc ion
> open "C:/Users/jaidy/OneDrive - University of Glasgow/Documents/Honours
> Project/Complex III 8b6j.cif"
Summary of feedback from opening C:/Users/jaidy/OneDrive - University of
Glasgow/Documents/Honours Project/Complex III 8b6j.cif
---
warnings | Atom H1 is not in the residue template for UNK /J:1
Atom H1 is not in the residue template for UNK /j:1
Atom H79 is not in the residue template for PEE /C:512
Atom H79 is not in the residue template for PEE /L:401
note | Fetching CCD PEE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PEE/PEE.cif
Complex III 8b6j.cif title:
Cryo-EM structure of cytochrome bc1 complex (complex-III) from respiratory
supercomplex of Tetrahymena thermophila [more info...]
Chain information for Complex III 8b6j.cif #4
---
Chain | Description | UniProt
A a | Peptidase M16 inactive domain protein | I7MGU2_TETTS 1-513
B b | M16 family peptidase, putative | I7MJ25_TETTS 2-482
C c | Apocytochrome b | Q950Z1_TETTH 1-426
D d | Cytochrome protein c1 | Q24IM5_TETTS 1-319
E e | Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit | I7MIC7_TETTS 1-269
F f | Ubiquinol-cytochrome C reductase hinge protein | Q23K66_TETTS 1-86
G g | UQCRTT1 | Q23F81_TETTS 1-328
H h | Transmembrane protein, putative | I7M484_TETTS 1-130
I i | Transmembrane protein, putative | I7MM45_TETTS 1-119
J j | UQCRTT3/UP1 |
K k | Transmembrane protein, putative | I7MFL6_TETTS 1-62
L l | UQCRTT2 |
Non-standard residues in Complex III 8b6j.cif #4
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
FES — FE2/S2 (inorganic) cluster
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
PEE — 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc
taen-1-yl]cyclohexa-2,5-diene-1,4-dione)
> open "C:/Users/jaidy/OneDrive - University of Glasgow/Documents/Honours
> Project/Complex 4 8b6h.cif"
Summary of feedback from opening C:/Users/jaidy/OneDrive - University of
Glasgow/Documents/Honours Project/Complex 4 8b6h.cif
---
warnings | Atom H76 is not in the residue template for 3PE /DA:708
Atom H76 is not in the residue template for 3PE /DC:606
Atom H76 is not in the residue template for 3PE /DC:607
Atom H76 is not in the residue template for 3PE /DG:204
Atom H76 is not in the residue template for 3PE /DG:205
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
note | Fetching CCD AME from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif
Complex 4 8b6h.cif title:
Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory
supercomplex of Tetrahymena thermophila [more info...]
Chain information for Complex 4 8b6h.cif #5
---
Chain | Description | UniProt
DA Da | Cytochrome c oxidase subunit 1 | Q950Y4_TETTH 1-688
DB Db | Cytochrome c oxidase subunit 2 | Q950Y9_TETTH 1-604
DC Dc | Ymf68 | Q950Y6_TETTH 1-594
DD Dd | Cytochrome C oxidase subunit Vb protein | Q23FF5_TETTS 1-637
DE De | Transmembrane protein, putative | W7XCY5_TETTS 1-130
DF Df | Structural protein | Q24I72_TETTS 1-230
DG Dg | Transmembrane protein, putative | Q23DS4_TETTS 1-103
DH Dh | Transmembrane protein, putative | I7MGF9_TETTS 1-133
DI Di | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | W7X287_TETTS 1-236
DJ Dj | Transmembrane protein, putative | W7WZP1_TETTS 1-220
DK Dk | CTF/NF-I domain-containing protein | Q22CI1_TETTS -858-131
DL Dl | COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein | Q22RF2_TETTS 83-411
DM Dm | Transmembrane protein, putative | Q22PJ5_TETTS 1-490
DN Dn | Ymf67 | Q950Y7_TETTH 3-455
DO Do | Protein phosphatase 2C, putative | Q22FX8_TETTS 1-473
DP Dp | SURF1-like protein | I7M1Q4_TETTS 1-402
DQ Dq | TraB family protein | Q23DP7_TETTS 1-385
DR Dr | Transmembrane protein, putative | Q23DG8_TETTS 1-348
DS Ds | Oxoglutarate/malate translocator protein, putative | A4VDV3_TETTS 1-346
DT Dt | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial | Q23DZ5_TETTS 1-318
DU Du | Carrier protein | Q22ZA6_TETTS 1-330
DV Dv | 2-oxoglutarate/malate carrier protein | Q23M99_TETTS 1-318
DW Dw | SURF1-like protein | I7LTZ4_TETTS 1-318
DX Dx | COXTT9 | I7LY65_TETTS 1-252
DY Dy | COXTT10 | I7MD70_TETTS 1-234
DZ Dz | 39S ribosomal protein L9, mitochondrial | W7X4J9_TETTS 1-231
EA Ea | COXTT12,Transmembrane protein,Transmembrane protein | I7M3P9_TETTS 22-222
EB Eb | Transmembrane protein, putative | I7LZX8_TETTS 1-210
EC Ec | COXTT27 |
ED Ed | Ymf75 | Q951A7_TETTH 1-190
EE Ee | Mobilization protein | Q23F08_TETTS 1-193
EF Ef | Iron-binding zinc finger CDGSH type protein | I7M8P0_TETTS 1-188
EG Eg | COXTT28 |
EH Eh | Transmembrane protein, putative | Q23D87_TETTS 1-173
EI Ei | Transmembrane protein | I7MKT6_TETTS 1-173
EJ Ej | YflT domain-containing protein | I7M8Y9_TETTS 1-175
EK Ek | Complex III subunit VII | Q230X6_TETTS 1-170
EL El | Transmembrane protein, putative | Q23VY4_TETTS 1-158
EM Em | Transmembrane protein, putative | Q22DP8_TETTS 1-154
EN En | COXTT22 | I7MFV5_TETTS 1-149
EO Eo | Transmembrane protein, putative | Q23TE5_TETTS 1-124
EP Ep | Phage protein | Q24C97_TETTS 1-127
EQ Eq | Transmembrane protein, putative | Q22W32_TETTS 1-122
ER Er | Lysozyme | I7M9E7_TETTS 1-105
ES Es | Ymf70 | Q950Y0_TETTH 1-89
ET Et | Zf-Tim10_DDP domain-containing protein | Q231A8_TETTS 1-93
EU Eu | ABC transporter | I7LTF1_TETTS 1-90
EV Ev | Decapping nuclease | I7LVX0_TETTS 1-88
EW Ew | Cullin domain-containing protein | Q22N23_TETTS 1-81
EX Ex | Zf-Tim10_DDP domain-containing protein | W7XDM6_TETTS 1-72
EY Ey | Annexin | Q233U0_TETTS 1-72
EZ Ez | Transposase | Q22A35_TETTS 7-74
FA Fa | Tim10/DDP family zinc finger protein | W7X3D6_TETTS 1-72
Non-standard residues in Complex 4 8b6h.cif #5
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
ATP — adenosine-5'-triphosphate
CA — calcium ion
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
FES — FE2/S2 (inorganic) cluster
HEA — heme-A
HEM — protoporphyrin IX containing Fe (HEME)
K — potassium ion
LPP — 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate
(1,2-dipalmitoyl-Sn-glycero-3-phosphate; L-B,G-dipalmitoyl-A-phosphatidic acid
disodium salt; 3-Sn-phosphatidic acid; 1,2-dipalmitoyldisodium salt)
MG — magnesium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc
taen-1-yl]cyclohexa-2,5-diene-1,4-dione)
ZN — zinc ion
> open "C:/Users/jaidy/OneDrive - University of Glasgow/Documents/Honours
> Project/ATP Synthase 6YNW.cif"
ATP Synthase 6YNW.cif title:
Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase -
central stalk/cring [more info...]
Chain information for ATP Synthase 6YNW.cif #6
---
Chain | Description | UniProt
H I J K L M N O P Q | subunit c | Q951A5_TETTH 1-76
d | subunit delta | Q22ZH1_TETTS 1-158
e | subunit epsilon | I7MMW3_TETTS 1-71
g | subunit gamma | Q22Z05_TETTS 1-299
> open "C:/Users/jaidy/Downloads/Complex I 8B6G.cif"
Summary of feedback from opening C:/Users/jaidy/Downloads/Complex I 8B6G.cif
---
warnings | Atom H76 is not in the residue template for 3PE /CK:101
Atom H76 is not in the residue template for 3PE /CC:301
Atom H76 is not in the residue template for 3PE /CD:302
Complex I 8B6G.cif title:
Cryo-EM structure of succinate dehydrogenase complex (complex-II) in
respiratory supercomplex of Tetrahymena thermophila [more info...]
Chain information for Complex I 8B6G.cif #7
---
Chain | Description | UniProt
CA | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | Q23DI3_TETTS 1-636
CB | Succinate dehydrogenase (quinone) | I7M403_TETTS 1-312
CC | Cytochrome b-c1 complex subunit 8 | Q23RH8_TETTS 1-60
CD | SDHD |
CE | NmrA domain-containing protein | Q24I09_TETTS 1-322
CF | Transmembrane protein, putative | Q248F8_TETTS 1-296
CG | SDHTT3 | I7MEX7_TETTS 1-198
CH | Diphthamide synthesis protein | I7LX66_TETTS 1-195
CI | DUF4885 domain-containing protein | Q22YL0_TETTS 1-114
CJ | Transmembrane protein, putative | Q23S01_TETTS 1-103
CK | Transmembrane protein, putative | Q24CW6_TETTS 1-93
CL | Transposase | W7XBF5_TETTS 1-89
CM | Transmembrane protein, putative | Q22HD6_TETTS 1-76
CN | Transmembrane protein, putative | W7XF00_TETTS 1-62
CO | SDHTT11 |
Non-standard residues in Complex I 8B6G.cif #7
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CA — calcium ion
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
F3S — FE3-S4 cluster
FAD — flavin-adenine dinucleotide
FES — FE2/S2 (inorganic) cluster
HEC — heme C
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
SF4 — iron/sulfur cluster
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc
taen-1-yl]cyclohexa-2,5-diene-1,4-dione)
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #6 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!3 models
> view
> view orient
[Repeated 1 time(s)]
> hide #!3 atoms
> show #!3 cartoons
> ui tool show "Color Actions"
> color bychain
[Repeated 2 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> ui tool show "Color Actions"
> color light sea green
> color cyan
> color cornflower blue
> color deep sky blue
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> show #!3 surfaces
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> view orient
[Repeated 1 time(s)]
> hide #!3 models
> show #!7 models
> view orient
> select add #7
41412 atoms, 41879 bonds, 13 pseudobonds, 2428 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting simple
> lighting full
> ui tool show "Color Actions"
> color sel lime green
> color sel forest green
> color sel medium sea green
> select subtract #7
15 models selected
> hide #!7 models
> show #!7 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!4 models
> select add #4
94062 atoms, 95238 bonds, 47 pseudobonds, 5488 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> ui tool show "Color Actions"
> color sel yellow
> color (#!4 & sel) #ffff00ff
> color (#!4 & sel) #fcfc00ff
> color (#!4 & sel) #adad00ff
> color (#!4 & sel) #7e7e00ff
> color (#!4 & sel) #acac00ff
> color (#!4 & sel) #a8a800ff
> color (#!4 & sel) #ffff00ff
> color (#!4 & sel) #d6d600ff
> color (#!4 & sel) #f7f700ff
> color (#!4 & sel) #eeee00ff
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> select subtract #4
24 models selected
> select add #5
436035 atoms, 441334 bonds, 86 pseudobonds, 24033 residues, 3 models selected
> show #!5 models
> show sel cartoons
> show sel surfaces
> hide sel atoms
[Repeated 1 time(s)]
> hide #!4 models
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> lighting full
> view orient
[Repeated 1 time(s)]
> view
> select clear
> select add #5
436035 atoms, 441334 bonds, 86 pseudobonds, 24033 residues, 3 models selected
> ui tool show "Color Actions"
> color sel medium orchid
> color sel medium purple
> color (#!5 & sel) #aa55ffff
> color (#!5 & sel) #9e3cffff
> color (#!5 & sel) #a81cffff
> color (#!5 & sel) #a007ffff
> color (#!5 & sel) #ac07ffff
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1731, in use_color
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']), hex_code) +
cmd_arg)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\std_commands\color.py", line 196, in color
session.logger.status('Colored %s' % commas(items, 'and'))
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 165, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 175, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3177, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3220, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3097, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 165, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 175, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3177, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3220, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3097, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> color (#!5 & sel) #9f06ebff
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1731, in use_color
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']), hex_code) +
cmd_arg)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\std_commands\color.py", line 196, in color
session.logger.status('Colored %s' % commas(items, 'and'))
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\core\logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 165, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 175, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3177, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3220, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX 1.12.dev202512040236\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3097, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
972,
34,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 26.0.0-devel (git-b36be3abdc)
OpenGL renderer: D3D12 (Qualcomm(R) Adreno(TM) X1-45 GPU)
OpenGL vendor: Microsoft Corporation
Python: 3.11.9
Locale: en_GB.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: HP
Model: HP OmniBook 5 Laptop 14-he0xxx
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 16,759,046,144
MaxProcessMemory: 137,438,953,344
CPU: 8 Snapdragon(R) X - X126100 - Qualcomm(R) Oryon(TM) CPU
OSLanguage: en-GB
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.1
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202512040236
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.12.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
pytz: 2025.2
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.3
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
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