![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17870 closed defect (duplicate)
Crash destroying OpenGL context on exit
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503180004 (2025-03-18 00:04:20 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001ebfd8840 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 440 in quit
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 805 in closeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, psutil._psutil_osx, psutil._psutil_posix, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.mlp._mlp (total: 56)
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"procLaunch" : "2025-05-30 12:50:45.9975 +0100",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202503180004 (2025-03-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/briaclemetais/Documents/ChimeraX files/C3b FBXO27-FBG5 model
> .cxs"
Log from Wed May 28 13:46:27 2025UCSF ChimeraX version: 1.10.dev202503180004
(2025-03-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/briaclemetais/Documents/ChimeraX files/mapped hydrophobicity
> alphafold models FBGs C3B.cxs" format session
Log from Wed May 28 13:43:16 2025
> hide sel surfaces
> select subtract #9.2
1 model selected
> select add #9.2
5016 atoms, 643 residues, 1 model selected
> select subtract #9.2
1 model selected
> select add #9.1
7931 atoms, 991 residues, 1 model selected
> hide sel surfaces
> color sel byhetero
> select add #9.3
10329 atoms, 1284 residues, 2 models selected
> hbonds sel reveal true
3260 hydrogen bonds found
> select subtract #9.3
7931 atoms, 991 residues, 3 models selected
> select subtract #9.1
1 model selected
> hide #!9 models
> hide #9.1 models
> hide #9.2 models
> hide #9.3 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_0.cif
#15
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #15 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_1.cif
#16
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #16 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_2.cif
#17
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #17 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_3.cif
#18
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #18 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_4.cif
#19
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #19 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif
#20
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> color #20 bychain
> hide #20 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_1.cif
#21
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #21 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_2.cif
#22
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #22 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_3.cif
#23
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #23 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_4.cif
#24
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #24 models
> show #20 models
> select #24/C:1-991
7931 atoms, 8086 bonds, 991 residues, 1 model selected
> select #20/C:1-991
7931 atoms, 8086 bonds, 991 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #20/A:1-296
2352 atoms, 2415 bonds, 296 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hbonds sel reveal true
1096 hydrogen bonds found
> hide #20 models
> open
> "/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b
> 2/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif"
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif
#25
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #25 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_0.cif
#26
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #26 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_1.cif
#27
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #27 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_full_data_1.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_full_data_1.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_full_data_1.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_2.cif
#28
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #28 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_3.cif
#29
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #29 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_4.cif
#30
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #30 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_1.cif
#31
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b alphafold FBXO6
> complete glycan chain 3.cxs"
> hide #31 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_2.cif
#32
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #32 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_3.cif
#33
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b alphafold FBXO6
> complete glycan chain 3- 3rd model.cxs"
> hide #33 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b alphafold FBXO6
> complete glycan chain 3- 4th model.cxs"
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_4.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> color #34 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_3.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_3.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_3.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> hide #34 models
> show #33 models
> color #33 bychain
> color #33 byhetero
> hbonds #33 reveal true
11998 hydrogen bonds found
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> show #33 surfaces
> hide #!33 models
> show #32 models
> hide #32 models
> show #34 models
> color #34 byhetero
> show #34 surfaces
> hide #!34 models
> show #!33 models
> hide #!33 surfaces
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_0.cif
#35
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #!33 models
> color #35 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_1.cif
#36
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #35 models
> color #36 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_2.cif
#37
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #36 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_3.cif
#38
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #37 models
> color #38 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #38 models
> color #39 bychain
> style #39 stick
Changed 15346 atom styles
> select #39/A:1-283
2222 atoms, 2279 bonds, 283 residues, 1 model selected
> hbonds sel reveal true
1917 hydrogen bonds found
> color sel byhetero
> select #39/B:1-643
5016 atoms, 5117 bonds, 643 residues, 1 model selected
> color sel byhetero
> select #39/C:1-991
7931 atoms, 8086 bonds, 991 residues, 1 model selected
> color sel byhetero
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_summary_confidences_4.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_summary_confidences_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_summary_confidences_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> hide #39 models
> show #38 models
> hide #38 models
> show #37 models
> hide #37 models
> show #36 models
> hide #36 models
> show #36 models
> hide #36 models
> show #35 models
> hide #35 models
> show #!34 models
> hide #!34 models
> show #!33 models
> show #32 models
> hide #!33 models
> show #!33 models
> hide #32 models
> hide #!33 models
> show #!34 models
> save "/Users/briaclemetais/Documents/ChimeraX files/FBG2-final version
> alphafold model.cxs"
> mlp #!34
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_A
SES surface": minimum -26.17, mean -4.163, maximum 23.4
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_B
SES surface": minimum -28.54, mean -5.415, maximum 23.79
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_C
SES surface": minimum -30.51, mean -5.323, maximum 24.86
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!34 models
> hide #34.1 models
> hide #34.2 models
> hide #34.3 models
> show #36 models
> hide #36 models
> show #39 models
> show sel surfaces
> mlp sel
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!39 models
> show #38 models
> hide #38 models
> show #37 models
> hide #37 models
> show #36 models
> hide #36 models
> show #!39 models
> select #1/A
4907 atoms, 5005 bonds, 2 pseudobonds, 630 residues, 2 models selected
> mlp #!39
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface": minimum -25.92, mean -4.556, maximum 21.58
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface": minimum -27.38, mean -5.37, maximum 23.83
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> hide #39.3 models
> show #39.3 models
> hide #39.2 models
> hide #39.3 models
> show #39.3 models
> hide #!39 models
> show #!39 models
> hide #39.1 models
> mlp #!39
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface": minimum -25.92, mean -4.556, maximum 21.58
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface": minimum -27.38, mean -5.37, maximum 23.83
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> hide #39.3 models
> show #39.3 models
> hide #39.2 models
> show #39.2 models
> hide #39.2 models
> show #39.2 models
> hide #39.2 models
> show #39.2 models
> hide #39.2 models
> ui mousemode right distance
> select #1/A#1/B
12118 atoms, 12369 bonds, 4 pseudobonds, 1532 residues, 2 models selected
> show #!39 atoms
> select up
12157 atoms, 12411 bonds, 4 pseudobonds, 1535 residues, 2 models selected
> select down
12118 atoms, 12369 bonds, 4 pseudobonds, 1532 residues, 2 models selected
> show #39.2 models
> hide #39.2 models
> distance #39/C:313@CG2 #39/C:272@CG1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C THR 313 CG2 and VAL 272 CG1: 11.658Å
> ~distance #39/C:313@CG2 #39/C:272@CG1
> hide #39.3 models
> show #39.3 models
> hide #39.1 models
> distance #39/C:272@CG1 #39/A:201@CE
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C VAL 272 CG1 and /A MET 201 CE: 3.735Å
> distance #39/A:201@SD #39/C:272@CB
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 201 SD and /C VAL 272 CB: 5.063Å
> show #39.1 models
> ui mousemode right translate
> hide #39.1 models
> show #39.1 models
> hide #39.1 models
> show #39.2 models
> hide #39.2 models
> ui mousemode right distance
> distance #39/C:311@CB #39/A:262@CE2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C GLN 311 CB and /A PHE 262 CE2: 7.046Å
> ~distance #39/C:311@CB #39/A:262@CE2
> distance #39/A:262@CZ #39/C:272@CG1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A PHE 262 CZ and /C VAL 272 CG1: 4.384Å
> ui mousemode right translate
> ui mousemode right distance
> distance #39/C:309@CD2 #39/A:262@CE1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C LEU 309 CD2 and /A PHE 262 CE1: 4.611Å
> distance #39/C:647@CD2 #39/A:262@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C LEU 647 CD2 and /A PHE 262 CD1: 5.689Å
> hide #39.3 models
> ui mousemode right translate
> show #39.1 models
> show #39.2 models
> hide #39.1 models
> hide #39.2 models
> ui mousemode right distance
> distance #39/A:128@SD #39/C:578@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 128 SD and /C PRO 578 CG: 5.639Å
> show #39.1 models
> hide #39.1 models
> ui mousemode right translate
> ui mousemode right distance
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right distance
> distance #39/C:318@CE #39/A:129@CG2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C MET 318 CE and /A VAL 129 CG2: 4.632Å
> distance #39/A:129@CB #39/C:318@CE
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A VAL 129 CB and /C MET 318 CE: 4.731Å
> show #39.2 models
> hide #39.2 models
> hide #!39 models
> show #38 models
> hide #38 models
> show #!39 models
> show #39.2 models
> ui mousemode right translate
> hide #39.2 models
> ui mousemode right distance
> distance #39/A:159@CB #39/A:158@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A SER 159 CB and PHE 158 CZ: 5.519Å
> ~distance #39/A:159@CB #39/A:158@CZ
> distance #39/A:158@CZ #39/C:647@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A PHE 158 CZ and /C LEU 647 CD1: 5.494Å
> show #39.2 models
> show #39.1 models
> ui mousemode right translate
> hide #39.2 models
> hide #39.1 models
> ui mousemode right distance
> distance #39/C:318@CE #39/A:124@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C MET 318 CE and /A LEU 124 CD1: 6.185Å
> show #39.1 models
> show #39.2 models
> hide #39.2 models
> ui mousemode right translate
> show #39.2 models
> hide #39.2 models
> ui mousemode right distance
> distance #39/C:316@CB #39/A:128@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C ALA 316 CB and /A MET 128 CG: 11.813Å
> ~distance #39/C:316@CB #39/A:128@CG
> hide #39.1 models
> distance #39/A:128@CG #39/C:318@SD
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 128 CG and /C MET 318 SD: 5.696Å
> distance #39/A:128@CG #39/C:318@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 128 CG and /C MET 318 CG: 6.380Å
> ui mousemode right translate
> show #39.1 models
> hide #39.1 models
> show #39.1 models
> show #39.2 models
> hide #!39 models
> hide #39.1 models
> hide #39.2 models
> hide #!40 models
> hide #40.1 models
> show #40.1 models
> hide #!40 models
> show #39.3 models
> show #39.2 models
> show #39.1 models
> show #!40 models
> hide #!39 models
> show #!34 models
> show #!34 atoms
> mlp #!34
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_A
SES surface": minimum -26.17, mean -4.163, maximum 23.4
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_B
SES surface": minimum -28.54, mean -5.415, maximum 23.79
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_C
SES surface": minimum -30.51, mean -5.323, maximum 24.86
To also show corresponding color key, enter the above mlp command and add key
true
> hide #34.1 models
> hide #34.2 models
> show #34.2 models
> hide #34.2 models
> hide #34.3 models
> show #34.1 models
> show #34.2 models
> hide #34.2 models
> show #34.3 models
> show #34.2 models
> hide #34.2 models
> hide #34.1 models
> hide #34.3 models
> ui mousemode right distance
> distance #34/C:318@CE #34/A:145@CD2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A LEU 145 CD2: 4.308Å
> distance #34/C:318@CE #34/A:192@CE1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A TYR 192 CE1: 5.101Å
> distance #34/C:318@CE #34/A:231@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A LEU 231 CD1: 5.490Å
> distance #34/C:318@CE #34/A:194@CG2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A VAL 194 CG2: 9.663Å
> ~distance #34/C:318@CE #34/A:194@CG2
> distance #34/C:318@SD #34/A:192@CB
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 SD and /A TYR 192 CB: 5.041Å
> distance #34/A:193@CZ #34/C:579@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/A PHE 193 CZ and /C PRO 579 CG: 3.520Å
> show #34.3 models
> hide #34.3 models
> show #34.1 models
> hide #34.1 models
> show #34.1 models
> show #34.3 models
> ui mousemode right translate
> hide #34.3 models
> show #34.3 models
> hide #34.3 models
> hide #34.1 models
> ui mousemode right distance
> distance #34/C:315@CG2 #34/A:105@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C VAL 315 CG2 and /A PHE 105 CZ: 5.543Å
> show #34.1 models
> show #34.3 models
> hide #34.3 models
> hide #34.1 models
> show #34.3 models
> hide #34.3 models
> distance #34/C:673@CG2 #34/A:241@CE1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C VAL 673 CG2 and /A TYR 241 CE1: 3.410Å
> distance #34/C:671@CB #34/A:241@CE2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C SER 671 CB and /A TYR 241 CE2: 4.746Å
> distance #34/C:309@CD1 #34/A:241@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C LEU 309 CD1 and /A TYR 241 CZ: 4.632Å
> ~distance #34/C:671@CB #34/A:241@CE2
> distance #34/C:671@CB #34/A:241@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C SER 671 CB and /A TYR 241 CZ: 4.491Å
> distance #34/C:272@CG2 #34/A:241@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C VAL 272 CG2 and /A TYR 241 CZ: 6.000Å
> ~distance #34/C:272@CG2 #34/A:241@CZ
> show #34.3 models
> show #34.1 models
> ui mousemode right translate
> hide #34.3 models
> hide #34.1 models
> ui mousemode right distance
[Repeated 1 time(s)]
> distance #34/A:241@CE2 #34/C:272@CG2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/A TYR 241 CE2 and /C VAL 272 CG2: 5.249Å
> hbonds #!34 reveal true
13903 hydrogen bonds found
> ui mousemode right translate
> coulombic #!34
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_A
SES surface #34.1: minimum, -18.55, mean -1.60, maximum 9.28
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_B
SES surface #34.2: minimum, -21.54, mean -1.03, maximum 13.89
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_C
SES surface #34.3: minimum, -19.18, mean -2.64, maximum 13.44
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> hide #34.1 models
> hide #34.2 models
> show #34.2 models
> hide #34.3 models
> show #34.3 models
> show #34.1 models
> hide #34.1 models
> hide #34.3 models
> ui mousemode right distance
> distance #34/A:155@OE1 #34/C:588@NH2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/A GLU 155 OE1 and /C ARG 588 NH2: 5.248Å
> show #34.3 models
> show #34.1 models
> hide #34.1 models
> show #34.1 models
> hide #34.3 models
> ui mousemode right translate
> show #34.3 models
> hide #34.3 models
> hide #!34 models
> hide #39.1 models
> show #39.1 models
> coulombic #!39
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface #39.2: minimum, -25.09, mean 0.72, maximum 14.62
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface #39.3: minimum, -22.04, mean -0.98, maximum 13.10
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface #39.1: minimum, -18.54, mean -2.60, maximum 13.40
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #39.1 models
> show #39.1 models
> hide #39.1 models
> show #39.1 models
> hide #39.2 models
> hide #39.1 models
> show #39.2 models
> ui mousemode right translate
> show #39.1 models
> hide #39.2 models
> show #39.2 models
> hide #39.1 models
> show #39.1 models
> hide #39.1 models
> show #39.1 models
> hide #39.2 models
> hide #39.1 models
> hide #39.3 models
> hbonds #!39 reveal true
13675 hydrogen bonds found
> show #39.3 models
> show #39.2 models
> show #39.1 models
> save "/Users/briaclemetais/Documents/ChimeraX files/mapped hydrophobicity
> alphafold models FBGs C3B.cxs"
——— End of log from Wed May 28 13:43:16 2025 ———
> view name session-start
opened ChimeraX session
> color #!39 bychain
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b FBXO27-FBG5 model
> .cxs"
——— End of log from Wed May 28 13:46:27 2025 ———
> view name session-start
opened ChimeraX session
> hide #!39 surfaces
> show #!39 atoms
> color #!39 byhetero
> mlp #!39
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface": minimum -25.92, mean -4.556, maximum 21.58
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface": minimum -27.38, mean -5.37, maximum 23.83
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor #!39
15346 atoms, 1932 residues, 3 surfaces, atom bfactor range 2.36 to 98.4
> select #1/A
4907 atoms, 5005 bonds, 2 pseudobonds, 630 residues, 2 models selected
> hide #!39 surfaces
> mlp #!39
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface": minimum -25.92, mean -4.556, maximum 21.58
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface": minimum -27.38, mean -5.37, maximum 23.83
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor #!39
15346 atoms, 1932 residues, 3 surfaces, atom bfactor range 2.36 to 98.4
> rainbow #!39
> color #!39 bychain
> color #!39 bypolymer
> color #!39 byhetero
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202503180004 (2025-03-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/briaclemetais/Documents/ChimeraX files/C3b FBXO27-FBG5 model
> .cxs"
Log from Wed May 28 13:46:27 2025UCSF ChimeraX version: 1.10.dev202503180004
(2025-03-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/briaclemetais/Documents/ChimeraX files/mapped hydrophobicity
> alphafold models FBGs C3B.cxs" format session
Log from Wed May 28 13:43:16 2025
> hide sel surfaces
> select subtract #9.2
1 model selected
> select add #9.2
5016 atoms, 643 residues, 1 model selected
> select subtract #9.2
1 model selected
> select add #9.1
7931 atoms, 991 residues, 1 model selected
> hide sel surfaces
> color sel byhetero
> select add #9.3
10329 atoms, 1284 residues, 2 models selected
> hbonds sel reveal true
3260 hydrogen bonds found
> select subtract #9.3
7931 atoms, 991 residues, 3 models selected
> select subtract #9.1
1 model selected
> hide #!9 models
> hide #9.1 models
> hide #9.2 models
> hide #9.3 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_0.cif
#15
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #15 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_1.cif
#16
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #16 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_2.cif
#17
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #17 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_3.cif
#18
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #18 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo6_c3b_model_4.cif
#19
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #19 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif
#20
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> color #20 bychain
> hide #20 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_1.cif
#21
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #21 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_2.cif
#22
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #22 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_3.cif
#23
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #23 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_4.cif
#24
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #24 models
> show #20 models
> select #24/C:1-991
7931 atoms, 8086 bonds, 991 residues, 1 model selected
> select #20/C:1-991
7931 atoms, 8086 bonds, 991 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #20/A:1-296
2352 atoms, 2415 bonds, 296 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hbonds sel reveal true
1096 hydrogen bonds found
> hide #20 models
> open
> "/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b
> 2/fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif"
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_2_from_c3bbb_fbxo2_c3b_model_0.cif
#25
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #25 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_0.cif
#26
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #26 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_1.cif
#27
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #27 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_full_data_1.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_full_data_1.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_full_data_1.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_2.cif
#28
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #28 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_3.cif
#29
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #29 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo2_c3b_model_4.cif
#30
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #30 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_1.cif
#31
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b alphafold FBXO6
> complete glycan chain 3.cxs"
> hide #31 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_2.cif
#32
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #32 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_3.cif
#33
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b alphafold FBXO6
> complete glycan chain 3- 3rd model.cxs"
> hide #33 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b alphafold FBXO6
> complete glycan chain 3- 4th model.cxs"
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_4.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> color #34 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_3.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_3.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_summary_confidences_3.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> hide #34 models
> show #33 models
> color #33 bychain
> color #33 byhetero
> hbonds #33 reveal true
11998 hydrogen bonds found
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> Saltonly
Unknown command: Saltonly
> show #33 surfaces
> hide #!33 models
> show #32 models
> hide #32 models
> show #34 models
> color #34 byhetero
> show #34 surfaces
> hide #!34 models
> show #!33 models
> hide #!33 surfaces
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_0.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_0.cif
#35
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #!33 models
> color #35 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_1.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_1.cif
#36
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #35 models
> color #36 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_2.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_2.cif
#37
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #36 models
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_3.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_3.cif
#38
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #37 models
> color #38 bychain
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
Chain information for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #38 models
> color #39 bychain
> style #39 stick
Changed 15346 atom styles
> select #39/A:1-283
2222 atoms, 2279 bonds, 283 residues, 1 model selected
> hbonds sel reveal true
1917 hydrogen bonds found
> color sel byhetero
> select #39/B:1-643
5016 atoms, 5117 bonds, 643 residues, 1 model selected
> color sel byhetero
> select #39/C:1-991
7931 atoms, 8086 bonds, 991 residues, 1 model selected
> color sel byhetero
> open
> /Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_summary_confidences_4.json
Failed opening file
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_summary_confidences_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/briaclemetais/Downloads/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b/fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_summary_confidences_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> hide #39 models
> show #38 models
> hide #38 models
> show #37 models
> hide #37 models
> show #36 models
> hide #36 models
> show #36 models
> hide #36 models
> show #35 models
> hide #35 models
> show #!34 models
> hide #!34 models
> show #!33 models
> show #32 models
> hide #!33 models
> show #!33 models
> hide #32 models
> hide #!33 models
> show #!34 models
> save "/Users/briaclemetais/Documents/ChimeraX files/FBG2-final version
> alphafold model.cxs"
> mlp #!34
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_A
SES surface": minimum -26.17, mean -4.163, maximum 23.4
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_B
SES surface": minimum -28.54, mean -5.415, maximum 23.79
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_C
SES surface": minimum -30.51, mean -5.323, maximum 24.86
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!34 models
> hide #34.1 models
> hide #34.2 models
> hide #34.3 models
> show #36 models
> hide #36 models
> show #39 models
> show sel surfaces
> mlp sel
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!39 models
> show #38 models
> hide #38 models
> show #37 models
> hide #37 models
> show #36 models
> hide #36 models
> show #!39 models
> select #1/A
4907 atoms, 5005 bonds, 2 pseudobonds, 630 residues, 2 models selected
> mlp #!39
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface": minimum -25.92, mean -4.556, maximum 21.58
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface": minimum -27.38, mean -5.37, maximum 23.83
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> hide #39.3 models
> show #39.3 models
> hide #39.2 models
> hide #39.3 models
> show #39.3 models
> hide #!39 models
> show #!39 models
> hide #39.1 models
> mlp #!39
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface": minimum -25.92, mean -4.556, maximum 21.58
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface": minimum -27.38, mean -5.37, maximum 23.83
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface": minimum -29.91, mean -5.247, maximum 24.18
To also show corresponding color key, enter the above mlp command and add key
true
> hide #39.3 models
> show #39.3 models
> hide #39.2 models
> show #39.2 models
> hide #39.2 models
> show #39.2 models
> hide #39.2 models
> show #39.2 models
> hide #39.2 models
> ui mousemode right distance
> select #1/A#1/B
12118 atoms, 12369 bonds, 4 pseudobonds, 1532 residues, 2 models selected
> show #!39 atoms
> select up
12157 atoms, 12411 bonds, 4 pseudobonds, 1535 residues, 2 models selected
> select down
12118 atoms, 12369 bonds, 4 pseudobonds, 1532 residues, 2 models selected
> show #39.2 models
> hide #39.2 models
> distance #39/C:313@CG2 #39/C:272@CG1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C THR 313 CG2 and VAL 272 CG1: 11.658Å
> ~distance #39/C:313@CG2 #39/C:272@CG1
> hide #39.3 models
> show #39.3 models
> hide #39.1 models
> distance #39/C:272@CG1 #39/A:201@CE
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C VAL 272 CG1 and /A MET 201 CE: 3.735Å
> distance #39/A:201@SD #39/C:272@CB
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 201 SD and /C VAL 272 CB: 5.063Å
> show #39.1 models
> ui mousemode right translate
> hide #39.1 models
> show #39.1 models
> hide #39.1 models
> show #39.2 models
> hide #39.2 models
> ui mousemode right distance
> distance #39/C:311@CB #39/A:262@CE2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C GLN 311 CB and /A PHE 262 CE2: 7.046Å
> ~distance #39/C:311@CB #39/A:262@CE2
> distance #39/A:262@CZ #39/C:272@CG1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A PHE 262 CZ and /C VAL 272 CG1: 4.384Å
> ui mousemode right translate
> ui mousemode right distance
> distance #39/C:309@CD2 #39/A:262@CE1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C LEU 309 CD2 and /A PHE 262 CE1: 4.611Å
> distance #39/C:647@CD2 #39/A:262@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C LEU 647 CD2 and /A PHE 262 CD1: 5.689Å
> hide #39.3 models
> ui mousemode right translate
> show #39.1 models
> show #39.2 models
> hide #39.1 models
> hide #39.2 models
> ui mousemode right distance
> distance #39/A:128@SD #39/C:578@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 128 SD and /C PRO 578 CG: 5.639Å
> show #39.1 models
> hide #39.1 models
> ui mousemode right translate
> ui mousemode right distance
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right distance
> distance #39/C:318@CE #39/A:129@CG2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C MET 318 CE and /A VAL 129 CG2: 4.632Å
> distance #39/A:129@CB #39/C:318@CE
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A VAL 129 CB and /C MET 318 CE: 4.731Å
> show #39.2 models
> hide #39.2 models
> hide #!39 models
> show #38 models
> hide #38 models
> show #!39 models
> show #39.2 models
> ui mousemode right translate
> hide #39.2 models
> ui mousemode right distance
> distance #39/A:159@CB #39/A:158@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A SER 159 CB and PHE 158 CZ: 5.519Å
> ~distance #39/A:159@CB #39/A:158@CZ
> distance #39/A:158@CZ #39/C:647@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A PHE 158 CZ and /C LEU 647 CD1: 5.494Å
> show #39.2 models
> show #39.1 models
> ui mousemode right translate
> hide #39.2 models
> hide #39.1 models
> ui mousemode right distance
> distance #39/C:318@CE #39/A:124@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C MET 318 CE and /A LEU 124 CD1: 6.185Å
> show #39.1 models
> show #39.2 models
> hide #39.2 models
> ui mousemode right translate
> show #39.2 models
> hide #39.2 models
> ui mousemode right distance
> distance #39/C:316@CB #39/A:128@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/C ALA 316 CB and /A MET 128 CG: 11.813Å
> ~distance #39/C:316@CB #39/A:128@CG
> hide #39.1 models
> distance #39/A:128@CG #39/C:318@SD
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 128 CG and /C MET 318 SD: 5.696Å
> distance #39/A:128@CG #39/C:318@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif
#39/A MET 128 CG and /C MET 318 CG: 6.380Å
> ui mousemode right translate
> show #39.1 models
> hide #39.1 models
> show #39.1 models
> show #39.2 models
> hide #!39 models
> hide #39.1 models
> hide #39.2 models
> hide #!40 models
> hide #40.1 models
> show #40.1 models
> hide #!40 models
> show #39.3 models
> show #39.2 models
> show #39.1 models
> show #!40 models
> hide #!39 models
> show #!34 models
> show #!34 atoms
> mlp #!34
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_A
SES surface": minimum -26.17, mean -4.163, maximum 23.4
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_B
SES surface": minimum -28.54, mean -5.415, maximum 23.79
Map values for surface
"fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_C
SES surface": minimum -30.51, mean -5.323, maximum 24.86
To also show corresponding color key, enter the above mlp command and add key
true
> hide #34.1 models
> hide #34.2 models
> show #34.2 models
> hide #34.2 models
> hide #34.3 models
> show #34.1 models
> show #34.2 models
> hide #34.2 models
> show #34.3 models
> show #34.2 models
> hide #34.2 models
> hide #34.1 models
> hide #34.3 models
> ui mousemode right distance
> distance #34/C:318@CE #34/A:145@CD2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A LEU 145 CD2: 4.308Å
> distance #34/C:318@CE #34/A:192@CE1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A TYR 192 CE1: 5.101Å
> distance #34/C:318@CE #34/A:231@CD1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A LEU 231 CD1: 5.490Å
> distance #34/C:318@CE #34/A:194@CG2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 CE and /A VAL 194 CG2: 9.663Å
> ~distance #34/C:318@CE #34/A:194@CG2
> distance #34/C:318@SD #34/A:192@CB
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C MET 318 SD and /A TYR 192 CB: 5.041Å
> distance #34/A:193@CZ #34/C:579@CG
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/A PHE 193 CZ and /C PRO 579 CG: 3.520Å
> show #34.3 models
> hide #34.3 models
> show #34.1 models
> hide #34.1 models
> show #34.1 models
> show #34.3 models
> ui mousemode right translate
> hide #34.3 models
> show #34.3 models
> hide #34.3 models
> hide #34.1 models
> ui mousemode right distance
> distance #34/C:315@CG2 #34/A:105@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C VAL 315 CG2 and /A PHE 105 CZ: 5.543Å
> show #34.1 models
> show #34.3 models
> hide #34.3 models
> hide #34.1 models
> show #34.3 models
> hide #34.3 models
> distance #34/C:673@CG2 #34/A:241@CE1
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C VAL 673 CG2 and /A TYR 241 CE1: 3.410Å
> distance #34/C:671@CB #34/A:241@CE2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C SER 671 CB and /A TYR 241 CE2: 4.746Å
> distance #34/C:309@CD1 #34/A:241@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C LEU 309 CD1 and /A TYR 241 CZ: 4.632Å
> ~distance #34/C:671@CB #34/A:241@CE2
> distance #34/C:671@CB #34/A:241@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C SER 671 CB and /A TYR 241 CZ: 4.491Å
> distance #34/C:272@CG2 #34/A:241@CZ
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/C VAL 272 CG2 and /A TYR 241 CZ: 6.000Å
> ~distance #34/C:272@CG2 #34/A:241@CZ
> show #34.3 models
> show #34.1 models
> ui mousemode right translate
> hide #34.3 models
> hide #34.1 models
> ui mousemode right distance
[Repeated 1 time(s)]
> distance #34/A:241@CE2 #34/C:272@CG2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/A TYR 241 CE2 and /C VAL 272 CG2: 5.249Å
> hbonds #!34 reveal true
13903 hydrogen bonds found
> ui mousemode right translate
> coulombic #!34
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_A
SES surface #34.1: minimum, -18.55, mean -1.60, maximum 9.28
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_B
SES surface #34.2: minimum, -21.54, mean -1.03, maximum 13.89
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif_C
SES surface #34.3: minimum, -19.18, mean -2.64, maximum 13.44
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right translate
> hide #34.1 models
> hide #34.2 models
> show #34.2 models
> hide #34.3 models
> show #34.3 models
> show #34.1 models
> hide #34.1 models
> hide #34.3 models
> ui mousemode right distance
> distance #34/A:155@OE1 #34/C:588@NH2
Distance between
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo6_c3b_model_4.cif
#34/A GLU 155 OE1 and /C ARG 588 NH2: 5.248Å
> show #34.3 models
> show #34.1 models
> hide #34.1 models
> show #34.1 models
> hide #34.3 models
> ui mousemode right translate
> show #34.3 models
> hide #34.3 models
> hide #!34 models
> hide #39.1 models
> show #39.1 models
> coulombic #!39
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_A
SES surface #39.2: minimum, -25.09, mean 0.72, maximum 14.62
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_B
SES surface #39.3: minimum, -22.04, mean -0.98, maximum 13.10
Coulombic values for
fold_2025_03_20_11_22_alpha_glycan_chain_3_from_c3bbb_fbxo27_c3b_model_4.cif_C
SES surface #39.1: minimum, -18.54, mean -2.60, maximum 13.40
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #39.1 models
> show #39.1 models
> hide #39.1 models
> show #39.1 models
> hide #39.2 models
> hide #39.1 models
> show #39.2 models
> ui mousemode right translate
> show #39.1 models
> hide #39.2 models
> show #39.2 models
> hide #39.1 models
> show #39.1 models
> hide #39.1 models
> show #39.1 models
> hide #39.2 models
> hide #39.1 models
> hide #39.3 models
> hbonds #!39 reveal true
13675 hydrogen bonds found
> show #39.3 models
> show #39.2 models
> show #39.1 models
> save "/Users/briaclemetais/Documents/ChimeraX files/mapped hydrophobicity
> alphafold models FBGs C3B.cxs"
——— End of log from Wed May 28 13:43:16 2025 ———
> view name session-start
opened ChimeraX session
> color #!39 bychain
> save "/Users/briaclemetais/Documents/ChimeraX files/C3b FBXO27-FBG5 model
> .cxs"
——— End of log from Wed May 28 13:46:27 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z12Q00186B/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 96 days, 2 hours, 35 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202503180004
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.15
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.44
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.7.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.13
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.17.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 1.31.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.4
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.7.3
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pyzmq: 26.3.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash destroying OpenGL context on exit |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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