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Opened 5 hours ago
Last modified 5 hours ago
#19566 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: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Messages on the ChimeraX mailing list have suggested that mesh display could be a workaround for ChimeraX's inability to display multiple transparent surfaces, implying that setting one surface to mesh and another to transparent would allow them to display correctly together. However, it appears that the mesh surface display is suffering from the same limitations as the transparent surface display, with mesh being blocked by a transparent surface in front of it. See the attached screenshot, where the ligand has a mesh surface, but the protein's transparent surface blocks it.
(Please consider this another vote for a multi-layer transparency feature! The kind of display I'm trying to produce would be SO useful in educational contexts, where we need to help students understand the space occupied by these molecules while still visualizing the internal structures.)
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/brian/Documents/bch_textbook_git/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_fs.cxs
Log from Fri Jan 2 15:09:06 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/brian/Documents/bch_textbook_git/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_ls.cxs
Log from Fri Jan 2 11:30:46 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/brian/Documents/bch_textbook_git/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_ls.cxs
Log from Fri Jan 2 11:28:58 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/brian/Documents/bch_textbook_git/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_ls.cxs
Log from Fri Jan 2 11:14:29 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/brian/Documents/bch_textbook_git/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/tim_overview_ls.cxs
Log from Thu Jan 1 18:11:09 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025c
> Fall/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics -
> Chimera Structural Models/05_tim_ribbon_helix_interface.cxs" format session
Log from Wed Jan 22 11:11:27 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02f_tim_ribbon_ss_sc_mesh.cxs"
Log from Wed Jan 22 11:06:17 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/01c_tim_bb_sc_dots.cxs"
Log from Wed Jan 22 10:28:45 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/brian/Teaching (Current)/Lecture Slides/Lecture 03 - Protein
> Structure, Folding, and Dynamics - Chimera Structural Models/01a_tim_bb.cxs"
> format session
Log from Wed Jan 22 10:11:16 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/01a_tim_bb_chx.py" format python
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 01a_tim_bb_chx.py
> save "/Users/brian/Teaching (Current)/Lecture Slides/Lecture 03 - Protein
> Structure, Folding, and Dynamics - Chimera Structural Models/01a_tim_bb.cxs"
——— End of log from Wed Jan 22 10:11:16 2025 ———
opened ChimeraX session
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/01b_tim_bb_sc_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 01b_tim_bb_sc_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/01b_tim_bb_sc.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/01c_tim_bb_sc_dots_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 01c_tim_bb_sc_dots_chx.py
> vdw
Unknown command: vdw
> surface style mesh
> style sphere
Changed 8338 atom styles
> style ball
Changed 8338 atom styles
> style sphere
Changed 8338 atom styles
> style stick
Changed 8338 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 8338 atom styles
> show surfaces
> hide surfaces
> surface /A
> surface style /A dots
Missing or invalid "style" argument: Should be one of 'dot', 'mesh', or
'solid'
> surface style /A dot
> surface style /A mesh
> surface close /A
> surface style /A mesh
> surface /A
> surface style dot
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/01c_tim_bb_sc_dots.cxs"
——— End of log from Wed Jan 22 10:28:45 2025 ———
opened ChimeraX session
> surface style mesh
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02a_tim_bb_helix_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 02a_tim_bb_helix_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02a_tim_bb_helix.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02b_tim_bb_sheet_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 02b_tim_bb_sheet_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02b_tim_bb_sheet.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02c_tim_bb_all_ss_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 02c_tim_bb_all_ss_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02c_tim-bb_all_ss.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02d_tim_ribbon_ss_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 02d_tim_ribbon_ss_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02d_tim_ribbon_ss.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02e_tim_ribbon_ss_sc_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 02e_tim_ribbon_ss_sc_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02e_tim_ribbon_ss_sc.cxs"
> surface /A
> surface style mesh
> surface close
> surface /A color mint cream
> surface style mesh
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/02f_tim_ribbon_ss_sc_mesh.cxs"
——— End of log from Wed Jan 22 11:06:17 2025 ———
opened ChimeraX session
> surface style mesh
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/03a_tim_bb_helix_closeup_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 03a_tim_bb_helix_closeup_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/03a_tim_bb_helix_closeup.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/03b_tim_bb_helix_closeup_sc_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 03b_tim_bb_helix_closeup_sc_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/03b_tim_bb_helix_closeup_sc.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/03c_tim_bb_helix_closeup_ribbon_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 03c_tim_bb_helix_closeup_ribbon_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/03c_tim_bb_helix_closeup_ribbon.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/04a_tim_bb_sheet_closeup_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 04a_tim_bb_sheet_closeup_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/04a_tim_bb_sheet_closeup.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/04b_tim_bb_sheet_closeup_sc_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 04b_tim_bb_sheet_closeup_sc_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/04b_tim_bb_sheet_closeup_sc.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/04c_tim_bb_sheet_closeup_ribbon_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 04c_tim_bb_sheet_closeup_ribbon_chx.py
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/04c_tim_bb_sheet_closeup_ribbon.cxs"
> open "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/06a_tim_ribbon_interface_chx.py"
> close session
1ney.pdb title:
Triosephosphate isomerase In complex with dhap [more info...]
Chain information for 1ney.pdb #1
---
Chain | Description | UniProt
A B | TIM | TPIS_YEAST 2-248
Non-standard residues in 1ney.pdb #1
---
13P — 1,3-dihydroxyacetonephosphate
FTR — fluorotryptophane
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
executed 06a_tim_ribbon_interface_chx.py
> ui tool show "Side View"
> save "/Users/brian/Library/CloudStorage/Dropbox/Lab/Teaching/BCH 301 2025a
> Spring/Lecture Slides/Lecture 03 - Protein Structure, Folding, and Dynamics
> - Chimera Structural Models/05_tim_ribbon_helix_interface.cxs"
——— End of log from Wed Jan 22 11:11:27 2025 ———
> view name session-start
opened ChimeraX session
> close session
> open 9lyz fromDatabase pdb format mmcif
Summary of feedback from opening 9lyz fetched from pdb
---
notes | Fetching compressed mmCIF 9lyz from http://files.rcsb.org/download/9lyz.cif
Fetching CCD AMU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/AMU/AMU.cif
9lyz title:
X-ray crystallography of the binding of the bacterial cell wall trisaccharide
nam-nag-nam to lysozyme [more info...]
Chain information for 9lyz #1
---
Chain | Description | UniProt
A | HEN EGG WHITE LYSOZYME | LYSC_CHICK 1-129
Non-standard residues in 9lyz #1
---
AMU — N-acetyl-beta-muramic acid (N-acetyl-muramic acid; BETA-N-ACETYLMURAMIC
ACID)
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)
> close session
> open 7rb5 fromDatabase pdb format mmcif
Summary of feedback from opening 7rb5 fetched from pdb
---
notes | Fetching compressed mmCIF 7rb5 from http://files.rcsb.org/download/7rb5.cif
Fetching CCD NWA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NWA/NWA.cif
7rb5 title:
Room temperature structure of hAChE in complex with substrate analog 4K-TMA
[more info...]
Chain information for 7rb5 #1
---
Chain | Description | UniProt
A | Acetylcholinesterase | ACES_HUMAN 1-547
Non-standard residues in 7rb5 #1
---
NWA — 4,4-dihydroxy-N,N,N-trimethylpentan-1-aminium
7rb5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close session
> open 4y8w fromDatabase pdb format mmcif
Summary of feedback from opening 4y8w fetched from pdb
---
notes | Fetching compressed mmCIF 4y8w from http://files.rcsb.org/download/4y8w.cif
Fetching CCD HEM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
Fetching CCD STR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/STR/STR.cif
4y8w title:
Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex [more
info...]
Chain information for 4y8w #1
---
Chain | Description | UniProt
A B C | Cytochrome P450 21-hydroxylase | Q16874_HUMAN 30-495
Non-standard residues in 4y8w #1
---
HEM — protoporphyrin IX containing Fe (HEME)
SO4 — sulfate ion
STR — progesterone
4y8w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> close session
> open 6zeg fromDatabase pdb format mmcif
Summary of feedback from opening 6zeg fetched from pdb
---
notes | Fetching compressed mmCIF 6zeg from http://files.rcsb.org/download/6zeg.cif
Fetching CCD 16P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/16P/16P.cif
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif
6zeg title:
Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 +
IRSp53(449-465)] bound to Phactr1 (516-580) [more info...]
Chain information for 6zeg #1
---
Chain | Description | UniProt
A B | Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2 | PP1A_HUMAN 7-304, BAIP2_HUMAN 323-339
C D | Phosphatase and actin regulator | Q4VY12_HUMAN 516-580
Non-standard residues in 6zeg #1
---
16P — 3,6,9,12,15,18-hexaoxaicosane
EDO — 1,2-ethanediol (ethylene glycol)
MN — manganese (II) ion
PO4 — phosphate ion
6zeg mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
801 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6889 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close session
> open 6zeh fromDatabase pdb format mmcif
Summary of feedback from opening 6zeh fetched from pdb
---
note | Fetching compressed mmCIF 6zeh from http://files.rcsb.org/download/6zeh.cif
6zeh title:
Structure of PP1-spectrin α II chimera [PP1(7-304) + linker (G/S)x9 + spectrin
α II (1025-1039)] bound to Phactr1 (516-580) [more info...]
Chain information for 6zeh #1
---
Chain | Description | UniProt
A B | Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1 | PP1A_HUMAN 7-304, SPTN1_HUMAN 323-337
C D | Phosphatase and actin regulator | Q4VY12_HUMAN 516-580
Non-standard residues in 6zeh #1
---
MN — manganese (II) ion
PO4 — phosphate ion
SO4 — sulfate ion
6zeh mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
359 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6627 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close session
> open 6lyz fromDatabase pdb format mmcif
Summary of feedback from opening 6lyz fetched from pdb
---
note | Fetching compressed mmCIF 6lyz from http://files.rcsb.org/download/6lyz.cif
6lyz title:
Real-space refinement of the structure of hen egg-white lysozyme [more
info...]
Chain information for 6lyz #1
---
Chain | Description | UniProt
A | HEN EGG WHITE LYSOZYME | LYSC_CHICK 1-129
> close session
> open 9lyz fromDatabase pdb format mmcif
9lyz title:
X-ray crystallography of the binding of the bacterial cell wall trisaccharide
nam-nag-nam to lysozyme [more info...]
Chain information for 9lyz #1
---
Chain | Description | UniProt
A | HEN EGG WHITE LYSOZYME | LYSC_CHICK 1-129
Non-standard residues in 9lyz #1
---
AMU — N-acetyl-beta-muramic acid (N-acetyl-muramic acid; BETA-N-ACETYLMURAMIC
ACID)
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)
> graphics silhouettes true
> color /a #ccebc5 cartoons
> hide :hoh
> color /b & @c* gray(10%)
> color /a & @c* #ccebc5 atoms
> surface ligand
> surface style ligand dot
> surface ligand transparency 50
> surface ligand transparency 30
> surface ligand transparency 80
> surface ligand transparency 90
> surface style dot
> surface style solid
> surface ligand @<5
> surface close /b
> surface close /a
> surface /a
> surface /a transparency 90
> surface /a transparency 50
> surface close /a
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/lysozyme_overview.cxs
> close session
> open 1ney fromDatabase pdb format mmcif
Summary of feedback from opening 1ney fetched from pdb
---
notes | Fetching compressed mmCIF 1ney from http://files.rcsb.org/download/1ney.cif
Fetching CCD 13P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/13P/13P.cif
Fetching CCD FTR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/FTR/FTR.cif
1ney title:
Triosephosphate Isomerase in Complex with DHAP [more info...]
Chain information for 1ney #1
---
Chain | Description | UniProt
A B | triosephosphate isomerase | TPIS_YEAST 2-248
Non-standard residues in 1ney #1
---
13P — 1,3-dihydroxyacetonephosphate
95 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4548 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide /b
> hide /b cartoons
> hide :hoh
> color :13p & @c* gray(10%)
> color /a & ~ligand #b3cde3 cartoons
> color /a & ~ligand & @c* #b3cde3 atoms
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/tim_overview.cxs
> surface :13p transparency 90
> surface close
> surface /a:13p transparency 90
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/tim_overview_ls.cxs
——— End of log from Thu Jan 1 18:11:09 2026 ———
> view name session-start
opened ChimeraX session
> surface /a:13p transparency 65
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/tim_overview_ls.cxs
> close session
> open 7RB5 fromDatabase pdb format mmcif
7rb5 title:
Room temperature structure of hAChE in complex with substrate analog 4K-TMA
[more info...]
Chain information for 7rb5 #1
---
Chain | Description | UniProt
A | Acetylcholinesterase | ACES_HUMAN 1-547
Non-standard residues in 7rb5 #1
---
NWA — 4,4-dihydroxy-N,N,N-trimethylpentan-1-aminium
7rb5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> color :nwa & @c* gray(10%)
> surface :nwa transparency 65
> hide :hoh
> color main #decbe4 cartoons
> color main & @c* #decbe4 atoms
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/hache_overview_ls.cxs
> close session
> open 1XEL fromDatabase pdb format mmcif
1xel title:
UDP-galactose 4-epimerase from escherichia coli [more info...]
Chain information for 1xel #1
---
Chain | Description | UniProt
A | UDP-GALACTOSE 4-EPIMERASE | GALE_ECOLI 1-338
Non-standard residues in 1xel #1
---
EDO — 1,2-ethanediol (ethylene glycol)
NA — sodium ion
NAD — nicotinamide-adenine-dinucleotide
PEG — di(hydroxyethyl)ether
UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl-
monophosphate ester)
1xel mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide :hoh
> color :upg & @c* gray(10%)
> surface :upg transparency 65
> color :nad & @c* sea green atoms
> surface :nad transparency 65
> color :nad sea green surfaces
> surface :nad transparency 65
> hide :na
> color main #decbe4 cartoons
> color main & @c* #decbe4 atoms
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_ls.cxs
——— End of log from Fri Jan 2 11:14:29 2026 ———
> view name session-start
opened ChimeraX session
> hide :edo
> hide :peg
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_ls.cxs
——— End of log from Fri Jan 2 11:28:58 2026 ———
> view name session-start
opened ChimeraX session
> color main & @c* #fed9a6 atoms
> color main #fed9a6 cartoons
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_ls.cxs
——— End of log from Fri Jan 2 11:30:46 2026 ———
> view name session-start
opened ChimeraX session
> surface /a transparency 90
> surface :upg
> hide :334
> hide :216
> save
> /Users/brian/Enzymes/1.2_enzymatic_solutions/figures/float_pdb/as_overview_simple/gale_overview_fs.cxs
——— End of log from Fri Jan 2 15:09:06 2026 ———
> view name session-start
opened ChimeraX session
> surface style #1.2 dot
> surface style #1.2 mesh
> surface style #1.2 dot
> surface style #1.2 mesh
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: Z1FC000HTLL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 1 day, 22 hours, 37 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
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:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
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: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
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: 2.5.3
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
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: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
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: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
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: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
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: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
File attachment: Screenshot 2026-01-02 at 16.06.43.png
Attachments (1)
Change History (2)
by , 5 hours ago
| Attachment: | Screenshot 2026-01-02 at 16.06.43.png added |
|---|
comment:1 by , 5 hours ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
Tom owns the graphics code, but I would be interested in learning more about graphics by implementing OIT.
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