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Opened 82 minutes ago
#20855 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.6.1-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Tried to run Matchmaker
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1_b2_g2_WT.cxs" format session
Log from Tue Aug 18 11:13:16 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1_b2P228del_g2.cxs" format session
Log from Mon Aug 17 10:30:40 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1P233A_b2_g2.cxs"
Log from Fri Aug 14 13:25:06 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/ChimeraX files/9FFO_GABA-A a1b3 asym pre-active
> state branch 1.cxs" format session
Log from Fri Aug 14 09:37:08 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/cmb987/Desktop/ChimeraX files/GABA-A closed_9 and 2.cxs" format
> session
Log from Fri Mar 6 10:11:41 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9ffm
Summary of feedback from opening 9ffm fetched from pdb
---
note | Fetching compressed mmCIF 9ffm from http://files.rcsb.org/download/9ffm.cif
9ffm title:
Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with Mb25 in
the resting state [more info...]
Chain information for 9ffm #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B C E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
F | Megabody25,Outer membrane protein | B5Z8H1_HELPG 14-234 235-403
Non-standard residues in 9ffm #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
D10 — decane
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)
34 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 14509 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
Drag select of 54 residues, 1 pseudobonds
> select up
592 atoms, 597 bonds, 1 pseudobond, 77 residues, 2 models selected
> select up
891 atoms, 915 bonds, 1 pseudobond, 113 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> save "/Users/cmb987/Desktop/ChimeraX files/New Folder/GABA-A alpha1beta3
> resting state_9FFM.cxs"
[Errno 20] Not a directory: '/Users/cmb987/Desktop/ChimeraX files/New Folder'
> save "/Users/cmb987/Desktop/ChimeraX files/GABA-A alpha1beta3/GABA-A
> alpha1beta3 resting state_9FFM.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain /D /A
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain /E /B /C
Alignment identifier is 2
> select /D,A:257
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /D,A:257
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 14 atom styles
> select
> /D,A:12-23,73-76,87-94,142-146,174-177,223-247,251-277,284-310,385-417
2346 atoms, 2390 bonds, 290 residues, 1 model selected
> select /D,A:242
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /D,A:242
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 18 atom styles
> ui tool show "Side View"
> select /D,A:408
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /D,A:408
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 16 atom styles
> select /D,A:411
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /D,A:411
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> select /E,B-C:284
36 atoms, 36 bonds, 3 residues, 1 model selected
> select /E,B-C:284
36 atoms, 36 bonds, 3 residues, 1 model selected
> style sel sphere
Changed 36 atom styles
> show sel atoms
> select clear
> lighting shadows false
> save "/Users/cmb987/Desktop/ChimeraX files/GABA-A alpha1beta3/GABA-A
> alpha1beta3 resting state with residues_9FFM.cxs"
> 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)
> 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
> camera ortho
> select /D:201
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
85 atoms, 84 bonds, 12 residues, 1 model selected
> select up
2744 atoms, 2815 bonds, 339 residues, 1 model selected
> hide sel cartoons
> select /C:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> select /C:7-340
2732 atoms, 2805 bonds, 334 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> sequence chain /E
Alignment identifier is 1/E
> select clear
> select /C:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:252
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:252
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 5 atom styles
> select /E:274
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E:274
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> select /E:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /E:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 6 atom styles
> lighting shadows false
> select clear
> save /Users/cmb987/Desktop/image1.png supersample 3
> save "/Users/cmb987/Desktop/ChimeraX files/GABA-A closed_9 and 2.cxs"
——— End of log from Fri Mar 6 10:11:41 2026 ———
> view name session-start
opened ChimeraX session
> select
13973 atoms, 14366 bonds, 1700 residues, 1 model selected
> hide sel atoms
> select clear
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 6x3s ...
... DSSP completed for 6x3s
DSSP completed.
> select /C:228
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:222-228
59 atoms, 60 bonds, 7 residues, 1 model selected
> select clear
> select /C:222
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:222-227
52 atoms, 52 bonds, 6 residues, 1 model selected
> select
13973 atoms, 14366 bonds, 1700 residues, 1 model selected
> show sel cartoons
> select clear
> save /Users/cmb987/Desktop/image3.png supersample 3
> close session
> open 6CNJ format mmcif fromDatabase pdb
6cnj title:
Structure of the 2alpha3beta stiochiometry of the human Alpha4Beta2 nicotinic
receptor [more info...]
Chain information for 6cnj #1
---
Chain | Description | UniProt
A D | Neuronal acetylcholine receptor subunit alpha-4 | ACHA4_HUMAN 1-338 345-386
B C E | Neuronal acetylcholine receptor subunit beta-2 | ACHB2_HUMAN 1-328 337-393
F H J | IgG1 Kappa Light Chain |
G I K | IgG1 Heavy Chain |
Non-standard residues in 6cnj #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
NA — sodium ion
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)
NCT — (S)-3-(1-methylpyrrolidin-2-yl)pyridine ((S)-(-)-nicotine;
3-[(2S)-1-methyl-2-pyrrolidinyl] pyridine)
Y01 — cholesterol hemisuccinate
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 24893 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 /G/I/K
4959 atoms, 5100 bonds, 654 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /F/H/J
5085 atoms, 5211 bonds, 654 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ligand
449 atoms, 487 bonds, 23 residues, 1 model selected
> hide sel atoms
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 6cnj ...
... DSSP completed for 6cnj
DSSP completed.
> lighting shadows false
> save /Users/cmb987/Desktop/image4.png supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain /B /C /E
Alignment identifier is 1
> select /B-C,E:217
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /B-C,E:213-217
117 atoms, 114 bonds, 15 residues, 1 model selected
> select /D:222
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
61 atoms, 63 bonds, 7 residues, 1 model selected
> select up
2722 atoms, 2799 bonds, 331 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /D
Alignment identifier is 1
> select /A,D:221
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /A,D:221-225
78 atoms, 76 bonds, 10 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #00fdff dashes 6 interModel false distSlop 1.0 angleSlop
> 60.0 twoColors true slopColor #0096ff intraRes false select true reveal true
> retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 60 degrees
Models used:
1 6cnj
28 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A THR 221 N /A PRO 217 O no hydrogen 3.124 N/A
/A THR 221 N /A LEU 218 O no hydrogen 3.462 N/A
/A ILE 222 N /A LEU 218 O no hydrogen 3.277 N/A
/A ILE 222 N /A PHE 219 O no hydrogen 3.842 N/A
/A ILE 222 N /A TYR 220 O no hydrogen 3.188 N/A
/A ASN 223 N /A TYR 220 O no hydrogen 3.379 N/A
/A ASN 223 ND2 /A PHE 219 O no hydrogen 3.282 N/A
/A LEU 224 N /A TYR 220 O no hydrogen 2.942 N/A
/A ILE 225 N /A TYR 220 O no hydrogen 3.435 N/A
/A CYS 228 N /A LEU 224 O no hydrogen 3.685 N/A
/A CYS 228 N /A ILE 225 O no hydrogen 3.547 N/A
/A CYS 228 SG /A LEU 224 O no hydrogen 3.542 N/A
/A CYS 228 SG /A ILE 225 O no hydrogen 3.084 N/A
/A LEU 229 N /A ILE 225 O no hydrogen 2.903 N/A
/D THR 221 N /D PRO 217 O no hydrogen 3.041 N/A
/D THR 221 N /D LEU 218 O no hydrogen 3.421 N/A
/D ILE 222 N /D LEU 218 O no hydrogen 2.945 N/A
/D ILE 222 N /D PHE 219 O no hydrogen 3.091 N/A
/D ASN 223 N /D PHE 219 O no hydrogen 2.946 N/A
/D ASN 223 N /D TYR 220 O no hydrogen 3.804 N/A
/D ASN 223 ND2 /D PHE 219 O no hydrogen 3.859 N/A
/D LEU 224 N /D TYR 220 O no hydrogen 3.007 N/A
/D ILE 225 N /D TYR 220 O no hydrogen 3.134 N/A
/D CYS 228 N /D LEU 224 O no hydrogen 4.012 N/A
/D CYS 228 N /D ILE 225 O no hydrogen 3.501 N/A
/D CYS 228 SG /D LEU 224 O no hydrogen 3.808 N/A
/D CYS 228 SG /D ILE 225 O no hydrogen 3.099 N/A
/D LEU 229 N /D ILE 225 O no hydrogen 2.912 N/A
28 hydrogen bonds found
7 strict hydrogen bonds found
> close session
> open 9FFS
Summary of feedback from opening 9FFS fetched from pdb
---
note | Fetching compressed mmCIF 9ffs from http://files.rcsb.org/download/9ffs.cif
9ffs title:
Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and
Mb25 in the short-lived asymmetric open state of branch 2 [more info...]
Chain information for 9ffs #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B C E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
F | Megabody25,Outer membrane protein | B5Z8H1_HELPG 14-234 235-403
Non-standard residues in 9ffs #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)
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 14509 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 /F
891 atoms, 915 bonds, 1 pseudobond, 113 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select ligand
403 atoms, 424 bonds, 33 residues, 1 model selected
> hide sel atoms
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 9ffs ...
... DSSP completed for 9ffs
DSSP completed.
> save /Users/cmb987/Desktop/image1.png supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain /E /B /C
Alignment identifier is 1
> select /E,B-C:226
36 atoms, 36 bonds, 3 residues, 1 model selected
> select /E,B-C:222-226
132 atoms, 132 bonds, 15 residues, 1 model selected
> save "/Users/cmb987/Desktop/ChimeraX files/9FFS_GABA-A a1b3 asym open state
> branch 2.cxs"
> close session
> open 9FFR
Summary of feedback from opening 9FFR fetched from pdb
---
notes | Fetching compressed mmCIF 9ffr from http://files.rcsb.org/download/9ffr.cif
Fetching CCD CLR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/CLR/CLR.cif
9ffr title:
Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and
Mb25 in the short-lived asymmetric bound-closed state of branch 2 [more
info...]
Chain information for 9ffr #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B C E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
F | Megabody25,Outer membrane protein | B5Z8H1_HELPG 14-234 235-403
Non-standard residues in 9ffr #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CLR — cholesterol
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)
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /F
891 atoms, 915 bonds, 1 pseudobond, 113 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 13618 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 up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select ligand
431 atoms, 455 bonds, 34 residues, 1 model selected
> hide sel atoms
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 9ffr ...
... DSSP completed for 9ffr
DSSP completed.
> ui tool show "Show Sequence Viewer"
> sequence chain /E /B /C
Alignment identifier is 1
> select /E,B-C:222
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /E,B-C:222-226
132 atoms, 132 bonds, 15 residues, 1 model selected
> select clear
> lighting shadows false
> save "/Users/cmb987/Desktop/ChimeraX files/9FFR_GABA-A a1b3 asym pre-active
> state branch 2.cxs"
> save /Users/cmb987/Desktop/image2.png supersample 3
> close session
> open 9FFP
Summary of feedback from opening 9FFP fetched from pdb
---
note | Fetching compressed mmCIF 9ffp from http://files.rcsb.org/download/9ffp.cif
9ffp title:
Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and
Mb25 in the short-lived asymmetric open state of branch 1 [more info...]
Chain information for 9ffp #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B C E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
F | Megabody25,Outer membrane protein | B5Z8H1_HELPG 14-234 235-403
Non-standard residues in 9ffp #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)
27 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /F
891 atoms, 915 bonds, 1 pseudobond, 113 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 13618 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 ligand
403 atoms, 424 bonds, 33 residues, 1 model selected
> hide sel atoms
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 9ffp ...
... DSSP completed for 9ffp
DSSP completed.
> save /Users/cmb987/Desktop/image1.png supersample 3
> sequence chain #1/B#1/C#1/E
Alignment identifier is 1
> select /B-C,E:222
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /B-C,E:222-226
132 atoms, 132 bonds, 15 residues, 1 model selected
> sequence chain #1/A#1/D
Alignment identifier is 1
> select /A,D:227
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /A,D:227-231
86 atoms, 86 bonds, 10 residues, 1 model selected
> save "/Users/cmb987/Desktop/ChimeraX files/9FFP_GABA-A a1b3 asym open state
> branch 1.cxs"
> close session
> open 9FFO
Summary of feedback from opening 9FFO fetched from pdb
---
notes | Fetching compressed mmCIF 9ffo from http://files.rcsb.org/download/9ffo.cif
Fetching CCD D10 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/D10/D10.cif
9ffo title:
Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and
Mb25 in the short-lived asymmetric bound-closed 2 state of branch 1 [more
info...]
Chain information for 9ffo #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B C E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
F | Megabody25,Outer membrane protein | B5Z8H1_HELPG 14-234 235-403
Non-standard residues in 9ffo #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
D10 — decane
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)
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /F
891 atoms, 915 bonds, 1 pseudobond, 113 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 13618 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 ligand
475 atoms, 493 bonds, 36 residues, 1 model selected
> hide sel atoms
> lighting shadows false
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 9ffo ...
... DSSP completed for 9ffo
DSSP completed.
> save /Users/cmb987/Desktop/image2.png supersample 3
> save "/Users/cmb987/Desktop/ChimeraX files/9FFO_GABA-A a1b3 asym pre-active
> state branch 1.cxs"
——— End of log from Fri Aug 14 09:37:08 2026 ———
> view name session-start
opened ChimeraX session
> save /Users/cmb987/Desktop/image3.png supersample 3
> save "/Users/cmb987/Desktop/ChimeraX files/9FFO_GABA-A a1b3 asym pre-active
> state branch 1.cxs"
> close session
> open 9FFX
Summary of feedback from opening 9FFX fetched from pdb
---
note | Fetching compressed mmCIF 9ffx from http://files.rcsb.org/download/9ffx.cif
9ffx title:
Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with
GABA and Nb38 in the short-lived asymmetric bound-closed state [more info...]
Chain information for 9ffx #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
C | Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 1-322 400-428
F | Nanobody38 |
Non-standard residues in 9ffx #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 14603 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 /F
950 atoms, 972 bonds, 123 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ligand
412 atoms, 437 bonds, 34 residues, 1 model selected
> hide sel atoms
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 9ffx ...
... DSSP completed for 9ffx
DSSP completed.
> ui tool show "Show Sequence Viewer"
> sequence chain /B /E
Alignment identifier is 1
> select /B,E:226
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /B,E:222-226
88 atoms, 88 bonds, 10 residues, 1 model selected
> select clear
> save /Users/cmb987/Desktop/image1.png supersample 3
> save "/Users/cmb987/Desktop/ChimeraX files/9FFX_GABA-A a1b3g2 asym pre-
> active state.cxs"
> close session
> open 9FFW
Summary of feedback from opening 9FFW fetched from pdb
---
note | Fetching compressed mmCIF 9ffw from http://files.rcsb.org/download/9ffw.cif
9ffw title:
Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with
GABA and Nb38 in the short-lived symmetric bound-closed state [more info...]
Chain information for 9ffw #1
---
Chain | Description | UniProt
A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 5-312 391-429
B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN 1-307 422-448
C | Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 1-322 400-428
F | Nanobody38 |
Non-standard residues in 9ffw #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
D10 — decane
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 /F
950 atoms, 972 bonds, 123 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 13653 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 ligand
469 atoms, 488 bonds, 40 residues, 1 model selected
> hide sel atoms
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 9ffw ...
... DSSP completed for 9ffw
DSSP completed.
> lighting shadows false
> save /Users/cmb987/Desktop/image2.png supersample 3
> save "/Users/cmb987/Desktop/ChimeraX files/9FFW_GABA-A a1b3g2 sym pre-active
> state.cxs"
> close session
> open 6PM5
Summary of feedback from opening 6PM5 fetched from pdb
---
note | Fetching compressed mmCIF 6pm5 from http://files.rcsb.org/download/6pm5.cif
6pm5 title:
CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in
SMA, desensitized state [more info...]
Chain information for 6pm5 #1
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-436
Non-standard residues in 6pm5 #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
GLY — glycine
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 13755 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 ligand
220 atoms, 225 bonds, 20 residues, 1 model selected
> hide sel atoms
> lighting shadows false
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 6pm5 ...
... DSSP completed for 6pm5
DSSP completed.
> save /Users/cmb987/Desktop/image3.png supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D /E
Alignment identifier is 1
> select /A-E:244
60 atoms, 60 bonds, 5 residues, 1 model selected
> select /A-E:240-244
225 atoms, 225 bonds, 25 residues, 1 model selected
> select clear
> save "/Users/cmb987/Desktop/ChimeraX files/6PM5_GlyR a1 desensitized
> state.cxs"
> close session
> open 6PM6
Summary of feedback from opening 6PM6 fetched from pdb
---
note | Fetching compressed mmCIF 6pm6 from http://files.rcsb.org/download/6pm6.cif
6pm6 title:
CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in
SMA, open state [more info...]
Chain information for 6pm6 #1
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-436
Non-standard residues in 6pm6 #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
GLY — glycine
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 13880 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 ligand
220 atoms, 225 bonds, 20 residues, 1 model selected
> hide sel atoms
> lighting shadows false
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 6pm6 ...
... DSSP completed for 6pm6
DSSP completed.
> save /Users/cmb987/Desktop/image4.png supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain /A /D /B /C /E
Alignment identifier is 1
> select /A,D,B-C,E:244
60 atoms, 60 bonds, 5 residues, 1 model selected
> select /A,D,B-C,E:240-244
225 atoms, 225 bonds, 25 residues, 1 model selected
> select /A,D,B-C,E:245
40 atoms, 35 bonds, 5 residues, 1 model selected
> select /A,D,B-C,E:245-247
105 atoms, 105 bonds, 15 residues, 1 model selected
> select clear
> save "/Users/cmb987/Desktop/ChimeraX files/6PM6_GlyR a1 open state.cxs"
> close session
> open 6PM4
Summary of feedback from opening 6PM4 fetched from pdb
---
note | Fetching compressed mmCIF 6pm4 from http://files.rcsb.org/download/6pm4.cif
6pm4 title:
CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in
SMA, super-open state [more info...]
Chain information for 6pm4 #1
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-436
Non-standard residues in 6pm4 #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
GLY — glycine
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 13835 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 ligand
220 atoms, 225 bonds, 20 residues, 1 model selected
> hide sel atoms
> lighting shadows false
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for 6pm4 ...
... DSSP completed for 6pm4
DSSP completed.
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D /E
Alignment identifier is 1
> select /A-E:240
40 atoms, 35 bonds, 5 residues, 1 model selected
> select /A-E:240-244
225 atoms, 225 bonds, 25 residues, 1 model selected
> select clear
> save /Users/cmb987/Desktop/image5.png supersample 3
> save "/Users/cmb987/Desktop/ChimeraX files/6PM4_GlyR a1 extended open
> state.cxs"
> close session
> open /Users/cmb987/Library/CloudStorage/Box-
> Box/Downloads_Box/fold_2026_08_14_human_gaba_a_a1p233a_b2_g2/fold_2026_08_14_human_gaba_a_a1p233a_b2_g2_model_0.cif
Chain information for fold_2026_08_14_human_gaba_a_a1p233a_b2_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18389 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
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1p233a_b2_g2_model_0.cif
...
... DSSP completed for fold_2026_08_14_human_gaba_a_a1p233a_b2_g2_model_0.cif
DSSP completed.
> save /Users/cmb987/Library/CloudStorage/Box-
> Box/Downloads_Box/Fold_gaba_a_a1P233A_b2_g2.cxs
——— End of log from Fri Aug 14 13:25:06 2026 ———
> view name session-start
opened ChimeraX session
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18393 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
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif
...
... DSSP completed for
fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif
DSSP completed.
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1_b2P228del_g2.cxs"
——— End of log from Mon Aug 17 10:30:40 2026 ———
> view name session-start
opened ChimeraX session
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1v227del_b2_g2_true/fold_2026_08_14_human_gaba_a_a1v227del_b2_g2_true_model_0.cif"
Chain information for
fold_2026_08_14_human_gaba_a_a1v227del_b2_g2_true_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18379 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
> ui tool show "Modern DSSP Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for
fold_2026_08_14_human_gaba_a_a1v227del_b2_g2_true_model_0.cif ...
Traceback (most recent call last):
File "/Users/cmb987/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/dssp/tool.py", line 324, in color_ribbons
for key, selection in data['selections'].items():
^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'items'
AttributeError: 'NoneType' object has no attribute 'items'
File "/Users/cmb987/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/dssp/tool.py", line 324, in color_ribbons
for key, selection in data['selections'].items():
^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
... DSSP completed for
fold_2026_08_14_human_gaba_a_a1v227del_b2_g2_true_model_0.cif
DSSP completed.
> lighting shadows false
> toolshed uninstall ChimeraX-ModernDSSP
unloading module chimerax.dssp
Successfully uninstalled ChimeraX-ModernDSSP-0.1
Removed ChimeraX-ModernDSSP (0.1)
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1V227del_b2_g2.cxs"
> close session
> cd /Users/cmb987/Desktop/ChimeraX-SecondaryStructure-main
Current working directory is: /Users/cmb987/Desktop/ChimeraX-
SecondaryStructure-main
> devel build .
running build
running build_py
creating build/lib/chimerax/secondarystructure
copying src/__init__.py -> build/lib/chimerax/secondarystructure
copying src/tool.py -> build/lib/chimerax/secondarystructure
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
running install_egg_info
running egg_info
creating ChimeraX_SecondaryStructure.egg-info
writing ChimeraX_SecondaryStructure.egg-info/PKG-INFO
writing dependency_links to ChimeraX_SecondaryStructure.egg-
info/dependency_links.txt
writing requirements to ChimeraX_SecondaryStructure.egg-info/requires.txt
writing top-level names to ChimeraX_SecondaryStructure.egg-info/top_level.txt
writing manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
reading manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
Copying ChimeraX_SecondaryStructure.egg-info to
build/bdist.macosx-10.9-universal2/wheel/./ChimeraX_SecondaryStructure-0.9.1-py3.11.egg-
info
running install_scripts
creating
build/bdist.macosx-10.9-universal2/wheel/chimerax_secondarystructure-0.9.1.dist-
info/WHEEL
creating 'dist/chimerax_secondarystructure-0.9.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/secondarystructure/__init__.py'
adding 'chimerax/secondarystructure/tool.py'
adding 'chimerax_secondarystructure-0.9.1.dist-info/licenses/LICENSE'
adding 'chimerax_secondarystructure-0.9.1.dist-info/METADATA'
adding 'chimerax_secondarystructure-0.9.1.dist-info/WHEEL'
adding 'chimerax_secondarystructure-0.9.1.dist-info/top_level.txt'
adding 'chimerax_secondarystructure-0.9.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in ./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl
> devel install .
running build
running build_py
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
running install_egg_info
running egg_info
writing ChimeraX_SecondaryStructure.egg-info/PKG-INFO
writing dependency_links to ChimeraX_SecondaryStructure.egg-
info/dependency_links.txt
writing requirements to ChimeraX_SecondaryStructure.egg-info/requires.txt
writing top-level names to ChimeraX_SecondaryStructure.egg-info/top_level.txt
reading manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
Copying ChimeraX_SecondaryStructure.egg-info to
build/bdist.macosx-10.9-universal2/wheel/./ChimeraX_SecondaryStructure-0.9.1-py3.11.egg-
info
running install_scripts
creating
build/bdist.macosx-10.9-universal2/wheel/chimerax_secondarystructure-0.9.1.dist-
info/WHEEL
creating 'dist/chimerax_secondarystructure-0.9.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/secondarystructure/__init__.py'
adding 'chimerax/secondarystructure/tool.py'
adding 'chimerax_secondarystructure-0.9.1.dist-info/licenses/LICENSE'
adding 'chimerax_secondarystructure-0.9.1.dist-info/METADATA'
adding 'chimerax_secondarystructure-0.9.1.dist-info/WHEEL'
adding 'chimerax_secondarystructure-0.9.1.dist-info/top_level.txt'
adding 'chimerax_secondarystructure-0.9.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in ./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl
[toolshed install ./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-
any.whl](cxcmd:toolshed install
./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl)
Installed ChimeraX-SecondaryStructure (0.9.1)
> ui tool show "Secondary Structure"
> toolshed uninstall ChimeraX-SecondaryStructure
unloading module chimerax.secondarystructure
Successfully uninstalled ChimeraX-SecondaryStructure-0.9.1
Removed ChimeraX-SecondaryStructure (0.9.1)
> cd /Users/cmb987/Desktop/ChimeraX-SecondaryStructure-main
Current working directory is: /Users/cmb987/Desktop/ChimeraX-
SecondaryStructure-main
> devel build .
running build
running build_py
creating build/lib/chimerax/secondarystructure
copying src/__init__.py -> build/lib/chimerax/secondarystructure
copying src/tool.py -> build/lib/chimerax/secondarystructure
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
running install_egg_info
running egg_info
creating ChimeraX_SecondaryStructure.egg-info
writing ChimeraX_SecondaryStructure.egg-info/PKG-INFO
writing dependency_links to ChimeraX_SecondaryStructure.egg-
info/dependency_links.txt
writing requirements to ChimeraX_SecondaryStructure.egg-info/requires.txt
writing top-level names to ChimeraX_SecondaryStructure.egg-info/top_level.txt
writing manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
reading manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
Copying ChimeraX_SecondaryStructure.egg-info to
build/bdist.macosx-10.9-universal2/wheel/./ChimeraX_SecondaryStructure-0.9.1-py3.11.egg-
info
running install_scripts
creating
build/bdist.macosx-10.9-universal2/wheel/chimerax_secondarystructure-0.9.1.dist-
info/WHEEL
creating 'dist/chimerax_secondarystructure-0.9.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/secondarystructure/__init__.py'
adding 'chimerax/secondarystructure/tool.py'
adding 'chimerax_secondarystructure-0.9.1.dist-info/licenses/LICENSE'
adding 'chimerax_secondarystructure-0.9.1.dist-info/METADATA'
adding 'chimerax_secondarystructure-0.9.1.dist-info/WHEEL'
adding 'chimerax_secondarystructure-0.9.1.dist-info/top_level.txt'
adding 'chimerax_secondarystructure-0.9.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in ./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl
> devel install .
running build
running build_py
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
copying build/lib/chimerax/secondarystructure/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/./chimerax/secondarystructure
running install_egg_info
running egg_info
writing ChimeraX_SecondaryStructure.egg-info/PKG-INFO
writing dependency_links to ChimeraX_SecondaryStructure.egg-
info/dependency_links.txt
writing requirements to ChimeraX_SecondaryStructure.egg-info/requires.txt
writing top-level names to ChimeraX_SecondaryStructure.egg-info/top_level.txt
reading manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'ChimeraX_SecondaryStructure.egg-info/SOURCES.txt'
Copying ChimeraX_SecondaryStructure.egg-info to
build/bdist.macosx-10.9-universal2/wheel/./ChimeraX_SecondaryStructure-0.9.1-py3.11.egg-
info
running install_scripts
creating
build/bdist.macosx-10.9-universal2/wheel/chimerax_secondarystructure-0.9.1.dist-
info/WHEEL
creating 'dist/chimerax_secondarystructure-0.9.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/secondarystructure/__init__.py'
adding 'chimerax/secondarystructure/tool.py'
adding 'chimerax_secondarystructure-0.9.1.dist-info/licenses/LICENSE'
adding 'chimerax_secondarystructure-0.9.1.dist-info/METADATA'
adding 'chimerax_secondarystructure-0.9.1.dist-info/WHEEL'
adding 'chimerax_secondarystructure-0.9.1.dist-info/top_level.txt'
adding 'chimerax_secondarystructure-0.9.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in ./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl
[toolshed install ./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-
any.whl](cxcmd:toolshed install
./dist/ChimeraX_SecondaryStructure-0.9.1-py3-none-any.whl)
Installed ChimeraX-SecondaryStructure (0.9.1)
> ui tool show "Secondary Structure"
DSSP color scheme saved to /Users/cmb987/Desktop/ChimeraX_colorscheme.json
> cd /Users/cmb987/Desktop
Current working directory is: /Users/cmb987/Desktop
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1p233l_b2_g2/fold_2026_08_14_human_gaba_a_a1p233l_b2_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1p233l_b2_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18409 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
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1p233l_b2_g2_model_0.cif
...
... DSSP completed for fold_2026_08_14_human_gaba_a_a1p233l_b2_g2_model_0.cif
Finished running DSSP.
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:226
22 atoms, 22 bonds, 2 residues, 1 model selected
> select /A-B:226-234
152 atoms, 154 bonds, 18 residues, 1 model selected
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1P233L_b2_g2.cxs"
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1p233s_b2_g2/fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18405 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
> ui tool show "Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif
...
... DSSP completed for fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif
Finished running DSSP.
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1p233s_b2_g2/fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif"
> format mmcif
Chain information for fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> select /A:1-429
3440 atoms, 3529 bonds, 429 residues, 1 model selected
> select clear
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18405 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
> ui tool show "Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif
...
... DSSP completed for fold_2026_08_14_human_gaba_a_a1p233s_b2_g2_model_0.cif
Finished running DSSP.
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1P233S_b2_g2.cxs"
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1_b2p228l_g2/fold_2026_08_14_human_gaba_a_a1_b2p228l_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1_b2p228l_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18409 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
> ui tool show "Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1_b2p228l_g2_model_0.cif
...
... DSSP completed for fold_2026_08_14_human_gaba_a_a1_b2p228l_g2_model_0.cif
Finished running DSSP.
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1_b2P228L_g2.cxs"
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1p233a_b2_g2/fold_2026_08_14_human_gaba_a_a1p233a_b2_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1p233a_b2_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18389 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
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1p233del_b2_g2/fold_2026_08_14_human_gaba_a_a1p233del_b2_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1p233del_b2_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18379 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
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1_b2_g2_wt/fold_2026_08_14_human_gaba_a_a1_b2_g2_wt_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1_b2_g2_wt_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 18407 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
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> ui tool show "Secondary Structure"
Running DSSP at /opt/homebrew/bin/mkdssp ...
... DSSP started for fold_2026_08_14_human_gaba_a_a1_b2_g2_wt_model_0.cif ...
... DSSP completed for fold_2026_08_14_human_gaba_a_a1_b2_g2_wt_model_0.cif
Finished running DSSP.
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/Fold_GABA-A_a1_b2_g2_WT.cxs"
——— End of log from Tue Aug 18 11:13:16 2026 ———
> view name session-start
opened ChimeraX session
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif"
Chain information for fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> open 6X3S
Summary of feedback from opening 6X3S fetched from pdb
---
notes | Fetching compressed mmCIF 6x3s from http://files.rcsb.org/download/6x3s.cif
Fetching CCD J94 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/J94/J94.cif
6x3s title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline
methbromide [more info...]
Chain information for 6x3s #2
---
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 #2
---
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)
Drag select of 739 atoms
> select up
868 atoms, 874 bonds, 112 residues, 1 model selected
> select up
1206 atoms, 1226 bonds, 155 residues, 1 model selected
> select up
1725 atoms, 1766 bonds, 223 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 1967 atoms, 7 bonds
Drag select of 321 atoms
Drag select of 1038 atoms
> select up
1162 atoms, 1179 bonds, 151 residues, 1 model selected
> select up
1480 atoms, 1508 bonds, 191 residues, 1 model selected
> select up
1709 atoms, 1750 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 32046 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
> ui tool show Matchmaker
> matchmaker #1/C#1/B#1/D#1/A#1/E to #2/A#2/B#2/C#2/D#2/E pairing ss
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 318, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 788, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 329, in match
score, s1, s2 = align(session, ref, match, matrix_name, alg,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 75, in align
dssp.compute_ss(s)
^^^^^^^^^^^^^^^
AttributeError: module 'chimerax.dssp' has no attribute 'compute_ss'
AttributeError: module 'chimerax.dssp' has no attribute 'compute_ss'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 75, in align
dssp.compute_ss(s)
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close session
> open "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif"
> format mmcif
Chain information for fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_0.cif
#1
---
Chain | Description
A B | .
C D | .
E | .
> save "/Users/cmb987/Desktop/ChimeraX files/Fold structures_M1 pi-
> helix/fold_2026_08_14_human_gaba_a_a1_b2p228del_g2_model_4.pdb" relModel #1
Computing secondary structure
> open 6X3S
6x3s title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline
methbromide [more info...]
Chain information for 6x3s #2
---
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 #2
---
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)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 35480 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 #2/J#2/K
1821 atoms, 1865 bonds, 233 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/I#2/L
1613 atoms, 1651 bonds, 211 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ligand
320 atoms, 343 bonds, 23 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #1/C#1/B#1/D#1/A#1/E to #2/A#2/B#2/C#2/D#2/E pairing ss
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 318, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 788, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 329, in match
score, s1, s2 = align(session, ref, match, matrix_name, alg,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 75, in align
dssp.compute_ss(s)
^^^^^^^^^^^^^^^
AttributeError: module 'chimerax.dssp' has no attribute 'compute_ss'
AttributeError: module 'chimerax.dssp' has no attribute 'compute_ss'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 75, in align
dssp.compute_ss(s)
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Matchmaker
> matchmaker #1 to #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 318, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 788, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 409, in match
score, s1, s2 = align(session, rseq, mseq,
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 75, in align
dssp.compute_ss(s)
^^^^^^^^^^^^^^^
AttributeError: module 'chimerax.dssp' has no attribute 'compute_ss'
AttributeError: module 'chimerax.dssp' has no attribute 'compute_ss'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 75, in align
dssp.compute_ss(s)
^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
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: 18000.161.9
OS Loader Version: 18000.161.9
Software:
System Software Overview:
System Version: macOS 26.6.1 (25G76)
Kernel Version: Darwin 25.6.0
Time since boot: 9 days, 35 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 4
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
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
autocommand: 2.2.2
babel: 2.18.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
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: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-SecondaryStructure: 0.9.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
more-itertools: 10.3.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
platformdirs: 4.2.2
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomli: 2.0.1
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typeguard: 4.3.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
typing_extensions: 4.12.2
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
zipp: 3.19.2
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