id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18453 ffmpeg: permission denied cborghese@… Zach Pearson "{{{ 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(': 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(': 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(': 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 }}} " defect closed normal Build System duplicate all ChimeraX