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Opened 4 months ago
Closed 4 months ago
#18453 closed defect (duplicate)
ffmpeg: permission denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Clicked the Spin movie icon
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Library/CloudStorage/Box-Box/Project epilepsy_Human
> Beta2 F200L and L235F/AlphaFold
> models/fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.cxs"
Log from Thu Aug 14 11:50:17 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Library/CloudStorage/Box-Box/TAX-4
> crosslinking/7LFT_human CNGA1_Endog cysteines & F382.cxs"
Log from Fri May 9 12:44:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/GABA-A closed_6X3S_backbone & heteroatom for
> H-bonds.cxs" format session
Log from Mon Apr 21 12:18:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/6X3S_GABAa & bicuculline_Closed.cxs" format
> session
Log from Fri Jul 5 17:36:13 2024UCSF ChimeraX version: 1.8.dev202404300104
(2024-04-30)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Library/CloudStorage/Box-Box/ChimeraX/GABAa receptor
> structures/GABAa a1b2g2_GABA_6X3Z.cxs" format session
Log from Mon Nov 6 17:55:34 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Library/CloudStorage/Box-Box/ChimeraX/6X3X_GABAa a1b2g2
> GABA & DZP.cxs" format session
Log from Fri Nov 3 16:08:28 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Fri Nov 3 13:30:36 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: [Errno 60] Operation timed out
2023-11-03 13:07:13,291 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x28a0e9b50>: Failed to establish a new connection: [Errno 60] Operation timed
out')':
/cxservices/api/v1/chimerax/updates?uuid=b4135827-1a23-5bff-b647-5b8779b2a3f8&OS=macosx&OSVersion=13.6.1&ChimeraXVersion=1.6.1
2023-11-03 13:08:28,295 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x179c06a60>: Failed to establish a new connection: [Errno 60] Operation timed
out')':
/cxservices/api/v1/chimerax/updates?uuid=b4135827-1a23-5bff-b647-5b8779b2a3f8&OS=macosx&OSVersion=13.6.1&ChimeraXVersion=1.6.1
2023-11-03 13:09:43,302 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x16fd34eb0>: Failed to establish a new connection: [Errno 60] Operation timed
out')':
/cxservices/api/v1/chimerax/updates?uuid=b4135827-1a23-5bff-b647-5b8779b2a3f8&OS=macosx&OSVersion=13.6.1&ChimeraXVersion=1.6.1
> ui tool show Registration
> open 6X3T
Summary of feedback from opening 6X3T fetched from pdb
---
notes | Fetching compressed mmCIF 6x3t from http://files.rcsb.org/download/6x3t.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
Fetching CCD ABU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/ABU/ABU.cif
Fetching CCD PFL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/PFL/PFL.cif
6x3t title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus
propofol [more info...]
Chain information for 6x3t #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid type A receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3t #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PFL — 2,6-bis(1-methylethyl)phenol (2,6-diisopropylphenol; propofol)
> select
17415 atoms, 17881 bonds, 2148 residues, 1 model selected
> hide sel atoms
Registration server unavailable. Please try again later.
> show sel cartoons
Drag select of 207 residues
> select up
1709 atoms, 1750 bonds, 221 residues, 1 model selected
> select up
17415 atoms, 17881 bonds, 2148 residues, 1 model selected
Drag select of 168 residues
> select up
1580 atoms, 1615 bonds, 203 residues, 1 model selected
> select up
1709 atoms, 1750 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 89 residues
> select up
909 atoms, 919 bonds, 121 residues, 1 model selected
> select up
1725 atoms, 1766 bonds, 223 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ligand
329 atoms, 343 bonds, 27 residues, 1 model selected
> show sel atoms
> hide sel atoms
Drag select of 521 residues
> log metadata #1
Metadata for 6x3t #1
---
Title | Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus propofol
Citation | Kim, J.J., Gharpure, A., Teng, J., Zhuang, Y., Howard, R.J., Zhu, S., Noviello, C.M., Walsh Jr., R.M., Lindahl, E., Hibbs, R.E. (2020). Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature, 585, 303-308. PMID: 32879488. DOI: 10.1038/s41586-020-2654-5
Non-standard residues | ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PFL — 2,6-bis(1-methylethyl)phenol (2,6-diisopropylphenol; propofol)
Source (natural) | Mus musculus
Gene sources | Homo sapiens
Homo sapiens (human)
CryoEM Map | EMDB 22032 — open map
Experimental method | Electron microscopy
Resolution | 2.55Å
> log chains #1
Chain information for 6x3t #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid type A receptor subunit gamma-2 | GBRG2_HUMAN 3-322
> select :PFL
26 atoms, 26 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 26 atom styles
> select :ABU
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 14 atom styles
> color sel black
> set bgColor white
> select :PFL
26 atoms, 26 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel fire brick
> select clear
> save "/Users/cmb987/Desktop/GABAa a1b2g2_GABA & Propofol.cxs"
——— End of log from Fri Nov 3 13:30:36 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> sequence chain /B /D
Alignment identifier is 2
> select /A,C:271
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /A,C:271-278
130 atoms, 134 bonds, 16 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict both reveal true
2 hydrogen bonds found
> select /B,D:276
12 atoms, 10 bonds, 2 residues, 1 model selected
> select /B,D:276-283
118 atoms, 120 bonds, 16 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict both reveal true
1 hydrogen bonds found
> close session
> open 6X3X
Summary of feedback from opening 6X3X fetched from pdb
---
notes | Fetching compressed mmCIF 6x3x from http://files.rcsb.org/download/6x3x.cif
Fetching CCD DZP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/DZP/DZP.cif
6x3x title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus
diazepam [more info...]
Chain information for 6x3x #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3x #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
DZP — 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select
17470 atoms, 17944 bonds, 2150 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Drag select of 185 residues
> select up
1613 atoms, 1650 bonds, 206 residues, 1 model selected
> select up
1709 atoms, 1750 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 166 residues
> select up
1515 atoms, 1545 bonds, 195 residues, 1 model selected
> select up
1725 atoms, 1766 bonds, 223 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 188 residues
> show sel atoms
> hide sel atoms
> log metadata #1
Metadata for 6x3x #1
---
Title | Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus diazepam
Citation | Kim, J.J., Gharpure, A., Teng, J., Zhuang, Y., Howard, R.J., Zhu, S., Noviello, C.M., Walsh Jr., R.M., Lindahl, E., Hibbs, R.E. (2020). Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature, 585, 303-308. PMID: 32879488. DOI: 10.1038/s41586-020-2654-5
Non-standard residues | ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
DZP — 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Source (natural) | Mus musculus
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 22036 — open map
Experimental method | Electron microscopy
Resolution | 2.92Å
> log chains #1
Chain information for 6x3x #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
> select :DZP
80 atoms, 88 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 80 atom styles
> color sel cyan
> select :ABU
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 14 atom styles
> color sel black
> set bgColor white
> select clear
> select /C:406@C4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 22 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:406@C4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 22 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /E:403@C8
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 22 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "/Users/cmb987/Library/CloudStorage/Box-Box/ChimeraX/GABAa a1b2g2 GABA
> & DZP_6X3X_top view.jpg" width 9360 height 7150 supersample 3
> save "/Users/cmb987/Library/CloudStorage/Box-Box/ChimeraX/GABAa a1b2g2 GABA
> & DZP_6X3X_side view.jpg" width 9360 height 7150 supersample 4
> save "/Users/cmb987/Library/CloudStorage/Box-Box/ChimeraX/6X3X_GABAa a1b2g2
> GABA & DZP.cxs"
——— End of log from Fri Nov 3 16:08:28 2023 ———
opened ChimeraX session
> close session
> open 6X3Z format mmcif fromDatabase pdb
6x3z title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA [more
info...]
Chain information for 6x3z #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3z #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select
17365 atoms, 17829 bonds, 2144 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Drag select of 208 residues
> select up
1645 atoms, 1683 bonds, 212 residues, 1 model selected
> select up
1725 atoms, 1766 bonds, 223 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 216 residues
> select up
1759 atoms, 1800 bonds, 227 residues, 1 model selected
> select up
4439 atoms, 4550 bonds, 559 residues, 1 model selected
Drag select of 240 residues
Drag select of 176 residues
> select up
1536 atoms, 1569 bonds, 198 residues, 1 model selected
> select up
1709 atoms, 1750 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "/Users/cmb987/Desktop/GABAa a1b2g2_GABA_6X3Z.cxs"
——— End of log from Mon Nov 6 17:55:34 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain /B /D
Alignment identifier is 2
> sequence chain /E
Alignment identifier is 1/E
> select /A,C:269
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /A,C:269
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /B,D:274
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /B,D:274
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /E:284
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /E:284
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A,C:271
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /A,C:271-278
130 atoms, 134 bonds, 16 residues, 1 model selected
> ui tool show "Side View"
> select /A,C:269
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /A,C:269
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 22 atom styles
> select #1 A/269@CA | sel CA<10A
Expected a keyword
> select #1 A/269@CA
Expected a keyword
> select /C:269@CA
1 atom, 1 residue, 1 model selected
> select /A:269@CA
1 atom, 1 residue, 1 model selected
> select /A:269@CA
1 atom, 1 residue, 1 model selected
> select /A:279
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select /A,C:282
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:282
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 16 atom styles
> select /A,C:274
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A,C:274
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 18 atom styles
> hide sel atoms
> select /B,D:274
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /B,D:274
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 22 atom styles
> select /B,D:287
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /B,D:287
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 16 atom styles
> select /B,D:331
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /B,D:242-331
1420 atoms, 1456 bonds, 180 residues, 1 model selected
> select /E:284
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /E:284
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select /E:297
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E:297
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select clear
> select /B
2730 atoms, 2800 bonds, 338 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> lighting shadows false
> set bgColor white
> set bgColor #ffffff00
> save /Users/cmb987/Desktop/image2.png supersample 3
> close session
> open 6X3S format mmcif fromDatabase pdb
6x3s title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline
methbromide [more info...]
Chain information for 6x3s #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid type A receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3s #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
J94 —
(5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select
17407 atoms, 17882 bonds, 2144 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select /J/K
1821 atoms, 1865 bonds, 233 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /I/L
1613 atoms, 1651 bonds, 211 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "/Users/cmb987/Desktop/6X3S_GABAa & bicuculline_Closed.cxs"
——— End of log from Fri Jul 5 17:36:13 2024 ———
opened ChimeraX session
> select
13973 atoms, 14366 bonds, 1700 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel ball
Changed 13973 atom styles
> color sel byhetero
> select ligand
320 atoms, 343 bonds, 23 residues, 1 model selected
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> sequence chain /B /D
Alignment identifier is 2
> sequence chain /E
Alignment identifier is 1/E
> select /B,D:281
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /B,D:281
10 atoms, 8 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 interModel false distSlop 2.0 angleSlop 120.0 twoColors
> true slopColor #7a81ff reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 2 angstroms and 120 degrees
Models used:
1 6x3s
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ALA 281 N /B ALA 281 O no hydrogen 3.617 N/A
/B ALA 281 N /C PRO 184 O no hydrogen 3.670 N/A
/C TYR 220 N /B ALA 281 O no hydrogen 4.199 N/A
/D ALA 281 N /D ALA 281 O no hydrogen 3.614 N/A
/D ALA 281 N /E TYR 199 O no hydrogen 3.871 N/A
/E GLY 234 N /D ALA 281 O no hydrogen 3.662 N/A
/E TYR 235 N /D ALA 281 O no hydrogen 3.361 N/A
7 hydrogen bonds found
0 strict hydrogen bonds found
> select /B,D:278
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /B,D:278-283
90 atoms, 92 bonds, 2 pseudobonds, 12 residues, 2 models selected
> select /E:199@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /E:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /E:196-202
71 atoms, 74 bonds, 7 residues, 1 model selected
> select /D:281@O
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /E:235@N
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select
> /A,C:36-51,56-68,81-83,96-98,101-106,114-118,123-135,147-156,164-168,175-176,188-200,203-215
1678 atoms, 1690 bonds, 204 residues, 1 model selected
> select /E:235@N
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /C:184@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:220@N
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> save "/Users/cmb987/Desktop/GABA-A closed_6X3S_backbone & heteroatom for
> H-bonds.cxs"
——— End of log from Mon Apr 21 12:18:56 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> select /A,C:8-21,84-90,218-241,246-272,279-306,309-339
2160 atoms, 2210 bonds, 262 residues, 1 model selected
> select /A,C:267
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A,C:267
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A,C:271
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /A,C:271
14 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel saveFile "/Users/cmb987/Desktop/6x3s_Hbonds b2T271" dashes 6
> interModel false distSlop 2.0 angleSlop 120.0 twoColors true slopColor
> #7a81ff reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 2 angstroms and 120 degrees
Models used:
1 6x3s
24 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A TYR 220 OH /A THR 271 OG1 no hydrogen 4.646 N/A
/A THR 271 N /A HIS 267 O no hydrogen 2.901 N/A
/A THR 271 N /A LEU 268 O no hydrogen 2.969 N/A
/A THR 271 N /A ARG 269 O no hydrogen 3.685 N/A
/A THR 271 N /A THR 271 O no hydrogen 3.602 N/A
/A THR 271 N /A THR 271 OG1 no hydrogen 3.693 N/A
/A THR 271 OG1 /A TYR 220 OH no hydrogen 4.646 N/A
/A THR 271 OG1 /A HIS 267 NE2 no hydrogen 4.995 N/A
/A THR 271 OG1 /A HIS 267 O no hydrogen 4.879 N/A
/A THR 271 OG1 /A GLU 270 O no hydrogen 4.959 N/A
/A THR 271 OG1 /A THR 271 O no hydrogen 2.946 N/A
/C GLN 224 NE2 /C THR 271 OG1 no hydrogen 4.124 N/A
/C THR 271 N /C HIS 267 O no hydrogen 2.901 N/A
/C THR 271 N /C LEU 268 O no hydrogen 3.471 N/A
/C THR 271 N /C ARG 269 O no hydrogen 4.124 N/A
/C THR 271 N /C THR 271 O no hydrogen 3.488 N/A
/C THR 271 N /C THR 271 OG1 no hydrogen 2.921 N/A
/C THR 271 OG1 /B ASN 275 OD1 no hydrogen 4.016 N/A
/C THR 271 OG1 /C HIS 267 O no hydrogen 3.179 N/A
/C THR 271 OG1 /C LEU 268 O no hydrogen 5.086 N/A
/C THR 271 OG1 /C GLU 270 O no hydrogen 4.714 N/A
/C THR 271 OG1 /C THR 271 O no hydrogen 4.506 N/A
/E LYS 285 NZ /A THR 271 OG1 no hydrogen 3.810 N/A
/E LYS 289 NZ /A THR 271 O no hydrogen 4.254 N/A
24 hydrogen bonds found
2 strict hydrogen bonds found
> show sel atoms
> select /A,C:8-21,84-90,218-241,246-272,279-306,309-339
2160 atoms, 2210 bonds, 21 pseudobonds, 262 residues, 2 models selected
> select /A,C:272
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:272
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:8-21,84-90,218-241,246-272,279-306,309-339
2160 atoms, 2210 bonds, 21 pseudobonds, 262 residues, 2 models selected
> select /A,C:281
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:281
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:8-21,84-90,218-241,246-272,279-306,309-339
2160 atoms, 2210 bonds, 21 pseudobonds, 262 residues, 2 models selected
> select /A,C:280
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /A,C:280
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /A,C:8-21,84-90,218-241,246-272,279-306,309-339
2160 atoms, 2210 bonds, 21 pseudobonds, 262 residues, 2 models selected
> select /A,C:259
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:259
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:145
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:145
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:277
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /A,C:277
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /B,D:278-283
90 atoms, 92 bonds, 2 pseudobonds, 12 residues, 2 models selected
> select /B,D:281
10 atoms, 8 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select /B,D:281
10 atoms, 8 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select /B,D:280
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B,D:280
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /B,D:282
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /B,D:282
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /A,C:272
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:272-279
134 atoms, 138 bonds, 16 residues, 1 model selected
> ui tool show Matchmaker
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 2.0 angleSlop 120.0 twoColors true
> slopColor #7a81ff reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 2 angstroms and 120 degrees
Models used:
1 6x3s
67 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LEU 140 N /A TYR 277 OH no hydrogen 2.701 N/A
/A ARG 141 N /A TYR 277 OH no hydrogen 3.309 N/A
/A LEU 272 N /A HIS 267 O no hydrogen 4.759 N/A
/A LEU 272 N /A LEU 268 O no hydrogen 2.572 N/A
/A LEU 272 N /A ARG 269 O no hydrogen 4.141 N/A
/A LEU 272 N /A GLU 270 O no hydrogen 3.835 N/A
/A LEU 272 N /A LEU 272 O no hydrogen 2.722 N/A
/A LYS 274 N /A LEU 272 O no hydrogen 3.268 N/A
/A LYS 274 N /A LYS 274 O no hydrogen 3.146 N/A
/A LYS 274 NZ /A ARG 269 O no hydrogen 3.961 N/A
/A LYS 274 NZ /B TYR 225 OH no hydrogen 2.396 N/A
/A ILE 275 N /A PRO 273 O no hydrogen 2.865 N/A
/A ILE 275 N /A ILE 275 O no hydrogen 2.974 N/A
/A TYR 277 N /A ILE 275 O no hydrogen 2.912 N/A
/A TYR 277 N /A TYR 277 O no hydrogen 2.678 N/A
/A TYR 277 OH /A MET 138 O no hydrogen 4.657 N/A
/A TYR 277 OH /A ASP 139 O no hydrogen 4.890 N/A
/A TYR 277 OH /A ASP 139 OD1 no hydrogen 4.777 N/A
/A TYR 277 OH /A LEU 140 O no hydrogen 3.637 N/A
/A VAL 278 N /A VAL 278 O no hydrogen 2.833 N/A
/A LYS 279 N /A TYR 277 O no hydrogen 3.656 N/A
/A LYS 279 N /A LYS 279 O no hydrogen 2.665 N/A
/A LYS 279 N /A ASP 282 OD1 no hydrogen 4.535 N/A
/A LYS 279 N /A ASP 282 OD2 no hydrogen 4.169 N/A
/A LYS 279 NZ /A ILE 275 O no hydrogen 3.825 N/A
/A LYS 279 NZ /A TYR 277 O no hydrogen 3.508 N/A
/A LYS 279 NZ /A ASP 282 OD1 no hydrogen 2.824 N/A
/A LYS 279 NZ /A ASP 282 OD2 no hydrogen 3.010 N/A
/A ILE 281 N /A LYS 279 O no hydrogen 3.880 N/A
/A ASP 282 N /A LYS 279 O no hydrogen 3.813 N/A
/A MET 283 N /A LYS 279 O no hydrogen 3.578 N/A
/A TYR 339 OH /A LYS 279 O no hydrogen 4.577 N/A
/B GLN 190 NE2 /A PRO 276 O no hydrogen 4.928 N/A
/B TYR 225 OH /A ILE 275 O no hydrogen 4.803 N/A
/C LEU 140 N /C TYR 277 OH no hydrogen 2.664 N/A
/C ARG 141 N /C TYR 277 OH no hydrogen 4.093 N/A
/C LEU 272 N /C LEU 268 O no hydrogen 2.987 N/A
/C LEU 272 N /C ARG 269 O no hydrogen 4.536 N/A
/C LEU 272 N /C GLU 270 O no hydrogen 3.623 N/A
/C LEU 272 N /C LEU 272 O no hydrogen 2.749 N/A
/C LYS 274 N /C LEU 272 O no hydrogen 3.402 N/A
/C LYS 274 N /C LYS 274 O no hydrogen 3.045 N/A
/C LYS 274 NZ /C ARG 269 O no hydrogen 2.458 N/A
/C LYS 274 NZ /C GLU 270 OE1 no hydrogen 4.489 N/A
/C LYS 274 NZ /C LEU 272 O no hydrogen 5.067 N/A
/C LYS 274 NZ /D TYR 225 OH no hydrogen 3.969 N/A
/C ILE 275 N /C PRO 273 O no hydrogen 2.921 N/A
/C ILE 275 N /C ILE 275 O no hydrogen 2.973 N/A
/C TYR 277 N /C ILE 275 O no hydrogen 2.909 N/A
/C TYR 277 N /C TYR 277 O no hydrogen 2.685 N/A
/C TYR 277 OH /C MET 138 O no hydrogen 4.676 N/A
/C TYR 277 OH /C ASP 139 O no hydrogen 4.874 N/A
/C TYR 277 OH /C LEU 140 O no hydrogen 4.161 N/A
/C VAL 278 N /C VAL 278 O no hydrogen 2.805 N/A
/C LYS 279 N /C TYR 277 O no hydrogen 3.652 N/A
/C LYS 279 N /C LYS 279 O no hydrogen 2.678 N/A
/C LYS 279 N /C ASP 282 OD2 no hydrogen 4.206 N/A
/C LYS 279 NZ /C ILE 275 O no hydrogen 3.632 N/A
/C LYS 279 NZ /C TYR 277 O no hydrogen 3.195 N/A
/C LYS 279 NZ /C ASP 282 OD1 no hydrogen 4.687 N/A
/C LYS 279 NZ /C ASP 282 OD2 no hydrogen 2.672 N/A
/C ILE 281 N /C LYS 279 O no hydrogen 3.715 N/A
/C ASP 282 N /C LYS 279 O no hydrogen 3.604 N/A
/C MET 283 N /C LYS 279 O no hydrogen 3.371 N/A
/C TYR 339 OH /C LYS 279 O no hydrogen 4.789 N/A
/D ASN 189 ND2 /C LYS 274 O no hydrogen 4.952 N/A
/D TYR 225 OH /C ILE 275 O no hydrogen 4.649 N/A
67 hydrogen bonds found
4 strict hydrogen bonds found
> select /A,C:279
18 atoms, 16 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select /A,C:279
18 atoms, 16 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select /A:279@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> close session
> open 6wej
6wej title:
Structure of cGMP-unbound WT TAX-4 reconstituted in lipid nanodiscs [more
info...]
Chain information for 6wej #1
---
Chain | Description | UniProt
A B C D | Cyclic nucleotide-gated cation channel | CNG_CAEEL 1-733
Non-standard residues in 6wej #1
---
CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl
phosphatidylcholine)
NA — sodium ion
PX2 — 1,2-dilauroyl-Sn-glycero-3-phosphate
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D
Alignment identifier is 1
> select ::name="CYS"
216 atoms, 184 bonds, 36 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 216 atom styles
> color sel orange red
> select
> /A-D:104-112,119-145,193-224,236-263,276-301,303-335,358-375,385-438,441-457,464-489,498-508,592-619
10548 atoms, 10784 bonds, 1236 residues, 1 model selected
> select sequence VTLDL
152 atoms, 148 bonds, 20 residues, 1 model selected
> select /A-D:396
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A-D:396
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 32 atom styles
> color sel medium blue
> select clear
> save "/Users/cmb987/Desktop/6WEJ_TAX-4 closed_Endog cysteines & L396.cxs"
> select ::name="CYS"
216 atoms, 184 bonds, 36 residues, 1 model selected
> color sel light gray
> color sel dim gray
> select /A-D:325
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A-D:325
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel orange red
> save "/Users/cmb987/Desktop/6WEJ_TAX-4 closed_Endog cysteines & L396.cxs"
> select clear
> save "/Users/cmb987/Desktop/6WEJ_TAX-4 closed_Endog cysteines & L396.cxs"
> close session
> open 6wek
Summary of feedback from opening 6wek fetched from pdb
---
notes | Fetching compressed mmCIF 6wek from http://files.rcsb.org/download/6wek.cif
Fetching CCD PCG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PCG/PCG.cif
6wek title:
Structure of cGMP-bound WT TAX-4 reconstituted in lipid nanodiscs [more
info...]
Chain information for 6wek #1
---
Chain | Description | UniProt
A B C D | Cyclic nucleotide-gated cation channel | CNG_CAEEL 1-733
Non-standard residues in 6wek #1
---
CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl
phosphatidylcholine)
PCG — cyclic guanosine monophosphate
PX2 — 1,2-dilauroyl-Sn-glycero-3-phosphate
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select ::name="CYS"
216 atoms, 184 bonds, 36 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 216 atom styles
> color sel dim gray
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D
Alignment identifier is 1
> select
> /A-D:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620
10904 atoms, 11124 bonds, 1284 residues, 1 model selected
> select /A-D:325
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A-D:325
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel orange red
> select
> /A-D:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620
10904 atoms, 11124 bonds, 1284 residues, 1 model selected
> select /A-D:396
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A-D:396
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel medium blue
> style sel sphere
Changed 32 atom styles
> show sel atoms
> select clear
> save "/Users/cmb987/Desktop/6WEK_TAX-4 open_Endog cysteines & L396.cxs"
> close session
> open 5H3o
Summary of feedback from opening 5H3o fetched from pdb
---
note | Fetching compressed mmCIF 5h3o from http://files.rcsb.org/download/5h3o.cif
5h3o title:
Structure of a eukaryotic cyclic nucleotide-gated channel [more info...]
Chain information for 5h3o #1
---
Chain | Description | UniProt
A B C D | Cyclic nucleotide-gated cation channel | CNG_CAEEL 1-733
Non-standard residues in 5h3o #1
---
NA — sodium ion
PCG — cyclic guanosine monophosphate
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D
Alignment identifier is 1
> select ::name="CYS"
216 atoms, 180 bonds, 36 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 216 atom styles
> color sel dim gray
> select /A-D:325
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A-D:325
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel orange red
> select /A-D:396
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A-D:396
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 32 atom styles
> color sel medium blue
> select clear
> save "/Users/cmb987/Desktop/5H3O_TAX-4 closed_Endog cysteines & L396.cxs"
> close session
> open 7LFT
Summary of feedback from opening 7LFT fetched from pdb
---
note | Fetching compressed mmCIF 7lft from http://files.rcsb.org/download/7lft.cif
7lft title:
Cryo-EM structure of human Apo CNGA1 channel in K+/Ca2+ [more info...]
Chain information for 7lft #1
---
Chain | Description | UniProt
A B C D | cGMP-gated cation channel alpha-1 | CNGA1_HUMAN 144-690
Non-standard residues in 7lft #1
---
CLR — cholesterol
CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl
phosphatidylcholine)
K — potassium ion
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D
Alignment identifier is 1
> select ::name="CYS"
144 atoms, 120 bonds, 24 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 144 atom styles
> color sel dim gray
> select /A-D:316
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A-D:316-317
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A-D:316
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A-D:316
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel orange red
> select /A-D:382
44 atoms, 44 bonds, 4 residues, 1 model selected
> select /A-D:382
44 atoms, 44 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 44 atom styles
> color sel cornflower blue
> select clear
> save "/Users/cmb987/Desktop/7LFT_human CNGA1_Endog cysteines & F377.cxs"
[Repeated 1 time(s)]
——— End of log from Fri May 9 12:44:42 2025 ———
> view name session-start
opened ChimeraX session
> close session
> open 6X3X format mmcif fromDatabase pdb
6x3x title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus
diazepam [more info...]
Chain information for 6x3x #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3x #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
DZP — 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> sequence chain /B /D
Alignment identifier is 2
> sequence chain /E
Alignment identifier is 1/E
> select /B,D:12-23,73-76,90-94,174-177,223-247,251-275,284-311,314-346
2192 atoms, 2234 bonds, 272 residues, 1 model selected
> select clear
[Repeated 2 time(s)]
> close session
> open 6X3S
6x3s title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline
methbromide [more info...]
Chain information for 6x3s #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid type A receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3s #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
J94 —
(5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> sequence chain /B /D
Alignment identifier is 2
> sequence chain /E
Alignment identifier is 1/E
> select
> /A,C:36-51,56-68,81-83,96-98,101-106,114-118,123-135,147-156,164-168,175-176,188-200,203-215
1678 atoms, 1690 bonds, 204 residues, 1 model selected
> select /A,C:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A,C:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select
> /A,C:36-51,56-68,81-83,96-98,101-106,114-118,123-135,147-156,164-168,175-176,188-200,203-215
1678 atoms, 1690 bonds, 204 residues, 1 model selected
> select clear
> close session
> open
> /Users/cmb987/Downloads/fold_20250814_human_gabaa_a1_beta2f200l_g2_6x3s/fold_20250814_human_gabaa_a1_beta2f200l_g2_6x3s_model_0.cif
Chain information for
fold_20250814_human_gabaa_a1_beta2f200l_g2_6x3s_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 15036 atom styles
Computing secondary structure
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /A:1-358
2891 atoms, 2965 bonds, 358 residues, 1 model selected
> select /B:1-358
2891 atoms, 2965 bonds, 358 residues, 1 model selected
> select /C:1-364
2944 atoms, 3018 bonds, 364 residues, 1 model selected
> select /D:1-364
2944 atoms, 3018 bonds, 364 residues, 1 model selected
> select /E:1-417
3366 atoms, 3462 bonds, 417 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /C /D
Alignment identifier is 1
> select /C-D:200
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /C-D:200
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> save /Users/cmb987/Desktop/fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.cxs
——— End of log from Thu Aug 14 11:50:17 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /E
Alignment identifier is 1/E
> select /E:60
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /E:1-60
464 atoms, 481 bonds, 60 residues, 1 model selected
> select /E:57-58
16 atoms, 16 bonds, 2 residues, 1 model selected
> select /E:1-58
450 atoms, 466 bonds, 58 residues, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> hide sel cartoons
> save "/Users/cmb987/Library/CloudStorage/Box-Box/Project epilepsy_Human
> Beta2 F200L and L235F/AlphaFold
> models/fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb" relModel #1
> close session
> open 6X3z
6x3z title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA [more
info...]
Chain information for 6x3z #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3z #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 17087 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /J/K
1821 atoms, 1865 bonds, 233 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /I/L
1613 atoms, 1651 bonds, 211 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open "/Users/cmb987/Library/CloudStorage/Box-Box/Project epilepsy_Human
> Beta2 F200L and L235F/AlphaFold
> models/fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb"
Chain information for fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb #2
---
Chain | Description
A B | No description available
C D | No description available
E | No description available
Drag select of 15036 atoms
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #2/D#2/A#2/C#2/B#2/E to #1/A#1/B#1/C#1/D#1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6x3z, chain A (#1) with
fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb, chain D (#2), sequence
alignment score = 1790.8
Matchmaker 6x3z, chain B (#1) with
fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb, chain A (#2), sequence
alignment score = 1776.9
Matchmaker 6x3z, chain C (#1) with
fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb, chain C (#2), sequence
alignment score = 1785.4
Matchmaker 6x3z, chain D (#1) with
fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb, chain B (#2), sequence
alignment score = 1779.3
Matchmaker 6x3z, chain E (#1) with
fold_20250814_human_gabaa_a1_b2F200L_g2_6x3s.pdb, chain E (#2), sequence
alignment score = 2022.3
RMSD between 1608 pruned atom pairs is 0.762 angstroms; (across all 1677
pairs: 0.911)
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 7 atom styles
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 7 atom styles
> select #2/D:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select #1/A:200
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select :BMA
33 atoms, 33 bonds, 3 residues, 1 model selected
> hide sel atoms
> select :MAN
77 atoms, 82 bonds, 7 residues, 1 model selected
> hide sel atoms
> select :NAG
154 atoms, 158 bonds, 11 residues, 1 model selected
> hide sel atoms
> save "/Users/cmb987/Library/CloudStorage/Box-Box/Project epilepsy_Human
> Beta2 F200L and L235F/AlphaFold models/F200L & 6X3Z superimposed.cxs"
> close session
> open
> /Users/cmb987/Downloads/fold_20250815_e_anthonyi_ache/fold_20250815_e_anthonyi_ache_model_0.cif
Chain information for fold_20250815_e_anthonyi_ache_model_0.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:494
12 atoms, 10 bonds, 2 residues, 1 model selected
> select /A-B:494
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 12 atom styles
> color sel cyan
> select clear
> save /Users/cmb987/Desktop/image5.png supersample 3
> select /A-B:116
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /A-B:116-118
24 atoms, 22 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> color sel cornflower blue
> select /A-B:494
12 atoms, 10 bonds, 2 residues, 1 model selected
> select /A-B:494
12 atoms, 10 bonds, 2 residues, 1 model selected
> color sel forest green
> select clear
> select /A-B:199
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A-B:199-201
40 atoms, 38 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 40 atom styles
> color sel cornflower blue
> select /A-B:204
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /A-B:204
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 10 atom styles
> color sel cornflower blue
> select /A-B:200
12 atoms, 10 bonds, 2 residues, 1 model selected
> select /A-B:200
12 atoms, 10 bonds, 2 residues, 1 model selected
> color sel hot pink
> select /A-B:327
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A-B:327
18 atoms, 16 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 18 atom styles
> show sel atoms
> color sel hot pink
> select /A-B:326-327
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /A-B:326-327
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /A-B:326
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /A-B:326
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 16 atom styles
> color sel red
> select /A-B:440
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A-B:440
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 20 atom styles
> color sel hot pink
> save /Users/cmb987/Desktop/image6.png supersample 3
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/cmb987/Desktop/movie3.mp4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHE3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 14 days, 23 hours, 52 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG ULTRAGEAR:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 144.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Build System |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: permission denied |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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This has been fixed in ChimeraX 1.10.1.
The ffmpeg executable in ChimeraX 1.10 did not have execute permission set and we fixed that in ChimeraX 1.10.1. In your current ChimeraX you could fix it from a terminal with
But probably better just to get the ChimeraX 1.10.1 release.