Opened 2 months ago
Closed 2 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 , 2 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 , 2 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.