Opened 2 months ago

Closed 2 months ago

#18453 closed defect (duplicate)

ffmpeg: permission denied

Reported by: cborghese@… 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 Tom Goddard, 2 months ago

Component: UnassignedBuild System
Owner: set to Zach Pearson
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionffmpeg: permission denied

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

$ chmod a+x /Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg

But probably better just to get the ChimeraX 1.10.1 release.

comment:2 by Tom Goddard, 2 months ago

Resolution: duplicate
Status: assignedclosed
Note: See TracTickets for help on using tickets.