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Opened 14 months ago
Last modified 14 months ago
#15921 feedback defect
Could not instantiate StructureSeq.structure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000382313000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001ffaacc00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91 in get_prop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1255 in _changes_cb
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1069 in proxy_handler
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 54 in check_for_changes
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3318 in command_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3203 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 225 in delete
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 308 in _key_closed
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py", line 105 in delete
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 1010 in close
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/close.py", line 43 in close
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 64)
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-
> Helden@univ-amu.fr/My
> Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin/1MBN_myoglobin_rolling.cxc"
> cd /Users/jvanheld/structures/1MBN_myoglobin/
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin
> close session
> open 1MBN
1mbn title:
The stereochemistry of the protein myoglobin [more info...]
Chain information for 1mbn #1
---
Chain | Description | UniProt
A | MYOGLOBIN | MYG_PHYCA 1-153
Non-standard residues in 1mbn #1
---
HEM — protoporphyrin IX containing Fe (HEME)
OH — hydroxide ion
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> view orient
> color byelement
> movie record
> wait 20
> roll axis y angle 3 frames 120
> wait
> roll axis x angle 3 frames 120
> wait
> view orient
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save 1MBN_myoglobin_white-bg.png width 1984 height 1240 supersample 3
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save 1MBN_myoglobin_black-bg.png width 1984 height 1240 supersample 3
> movie encode output 1MBN_myoglobin_rolling.mov
Movie saved to 1MBN_myoglobin_rolling.mov
> view orient
> movie record
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> transparency 50
> wait 50
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A GLY 153 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09,
maximum 9.92
> transparency 50
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 50
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 50
> wait 100
> view orient
> roll axis y angle 1 frames 25
> wait
> wait 30
> roll axis z angle 1 frames 10
> wait
> wait 30
> roll axis x angle 3 frames 36
> wait
> wait 30
> roll axis y angle -1 frames 10
> wait
> wait 30
> transparency 0
> wait 50
> zoom 2.0 frames 100
> wait 100
> rock y 20 400
> wait 400
> zoom 0.5 frames 100
> wait 100
> roll axis x angle 3 frames 120
> wait 200
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save 1MBN_myoglobin_heme-pocket_white-bg.png width 1984 height 1240
> supersample 3
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save 1MBN_myoglobin_heme-pocket_black-bg.png width 1984 height 1240
> supersample 3
> save 1MBN_myoglobin_rolling.cxs
executed 1MBN_myoglobin_rolling.cxc
> view orient
> movie record
Already recording a movie
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> transparency 50
> wait 50
> coulombic
Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09,
maximum 9.92
> transparency 50
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 50
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 30
> wait 100
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> transparency 30
> wait 50
> coulombic
Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09,
maximum 9.92
> transparency 30
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 30
> wait 100## Show hydrostatic profile
Expected an integer >= 1 or a keyword
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 30
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 30
> wait 100
> view orient
> roll axis y angle 1 frames 25
> wait
> wait 30
> roll axis z angle 1 frames 10
> wait
> wait 30
> roll axis x angle 3 frames 36
> wait
> wait 30
> roll axis y angle -1 frames 10
> wait
> wait 30
> transparency 0
> wait 50
> zoom 2.0 frames 100
> wait 100
> zoom 2.0 frames 60
> wait
> wait 30
> zoom 0.25
> zoom 2.0 frames 30
> wait
> wait 30
> rock y 20 300
> rock y 20 180
> wait
> wait 30
> rock y 20 80
> wait
> wait 30
> rock y 20 80
> wait
> wait 30
> rock y 20 80
> wait
> wait 30
> rock y 20 240
> wait
> wait 30
> zoom 0.5 frames 100
> wait 100
> zoom 2.0 frames 30
> wait
> wait 30
> zoom 0.5 frames 30
> wait
> wait 30
> zoom 2.0 frames 60
> wait
> wait 30
> zoom 0.5 frames 30
> wait
> wait 30
> roll axis x angle 3 frames 120
> wait
> wait 30
> open "/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-
> Helden@univ-amu.fr/My
> Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin/1MBN_myoglobin_rolling.cxc"
> cd /Users/jvanheld/structures/1MBN_myoglobin/
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin
> close session
> open 1MBN
1mbn title:
The stereochemistry of the protein myoglobin [more info...]
Chain information for 1mbn #1
---
Chain | Description | UniProt
A | MYOGLOBIN | MYG_PHYCA 1-153
Non-standard residues in 1mbn #1
---
HEM — protoporphyrin IX containing Fe (HEME)
OH — hydroxide ion
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> view orient
> color byelement
> movie record
Already recording a movie
> movie stop
> close session
> open "/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-
> Helden@univ-amu.fr/My
> Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin/1MBN_myoglobin_rolling.cxc"
> cd /Users/jvanheld/structures/1MBN_myoglobin/
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin
> close session
> open 1MBN
1mbn title:
The stereochemistry of the protein myoglobin [more info...]
Chain information for 1mbn #1
---
Chain | Description | UniProt
A | MYOGLOBIN | MYG_PHYCA 1-153
Non-standard residues in 1mbn #1
---
HEM — protoporphyrin IX containing Fe (HEME)
OH — hydroxide ion
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> view orient
> color byelement
> movie record
> wait 20
> roll axis y angle 3 frames 120
> wait
> wait 30
> roll axis x angle 3 frames 120
> wait
> wait 30
> view orient
> wait 180
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save 1MBN_myoglobin_white-bg.png width 1984 height 1240 supersample 3
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save 1MBN_myoglobin_black-bg.png width 1984 height 1240 supersample 3
> movie encode output 1MBN_myoglobin_rolling.mov
Movie saved to 1MBN_myoglobin_rolling.mov
> view orient
> movie record
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> transparency 30
> wait 50
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A GLY 153 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09,
maximum 9.92
> transparency 30
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 30
> wait 100
> view orient
> roll axis y angle 1 frames 25
> wait
> wait 30
> roll axis z angle 1 frames 10
> wait
> wait 30
> roll axis x angle 3 frames 36
> wait
> wait 30
> roll axis y angle -1 frames 10
> wait
> wait 30
> transparency 0
> wait 50
> zoom 2.0 frames 60
> wait
> wait 30
> rock y 20 260
> wait
> wait 30
> zoom 0.5 frames 30
> wait
> wait 30
> roll axis x angle 3 frames 120
> wait
> wait 30
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save 1MBN_myoglobin_heme-pocket_white-bg.png width 1984 height 1240
> supersample 3
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save 1MBN_myoglobin_heme-pocket_black-bg.png width 1984 height 1240
> supersample 3
> movie encode output 1MBN_myoglobin_heme-pocket.mov
Movie saved to 1MBN_myoglobin_heme-pocket.mov
> save 1MBN_myoglobin_rolling.cxs
executed 1MBN_myoglobin_rolling.cxc
> close session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close session
> cd /Users/jvanheld/structures/1MBN_myoglobin/
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin
> close session
> open 1MBN
1mbn title:
The stereochemistry of the protein myoglobin [more info...]
Chain information for 1mbn #1
---
Chain | Description | UniProt
A | MYOGLOBIN | MYG_PHYCA 1-153
Non-standard residues in 1mbn #1
---
HEM — protoporphyrin IX containing Fe (HEME)
OH — hydroxide ion
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> view orient
> color byelement
> movie record
> wait 20
> roll axis y angle 3 frames 120
> wait
> wait 30
> roll axis x angle 3 frames 120
> wait
> wait 30
> view orient
> wait 180
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save 1MBN_myoglobin_white-bg.png width 1984 height 1240 supersample 3
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save 1MBN_myoglobin_black-bg.png width 1984 height 1240 supersample 3
> movie encode output 1MBN_myoglobin_rolling.mov
Movie saved to 1MBN_myoglobin_rolling.mov
> movie stop
No movie being recorded.
> close session
> open 1MBN
1mbn title:
The stereochemistry of the protein myoglobin [more info...]
Chain information for 1mbn #1
---
Chain | Description | UniProt
A | MYOGLOBIN | MYG_PHYCA 1-153
Non-standard residues in 1mbn #1
---
HEM — protoporphyrin IX containing Fe (HEME)
OH — hydroxide ion
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> view orient
> color byelement
> movie record
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> transparency 30
> wait 50
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A GLY 153 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09,
maximum 9.92
> transparency 30
> wait 100
> mlp
Map values for surface "1mbn_A SES surface": minimum -28.73, mean -3.303,
maximum 24.18
> transparency 30
> wait 100
> view orient
> roll axis y angle 1 frames 25
> wait
> wait 30
> roll axis z angle 1 frames 10
> wait
> wait 30
> roll axis x angle 3 frames 36
> wait
> wait 30
> roll axis y angle -1 frames 10
> wait
> wait 30
> transparency 0
> wait 50
> zoom 2.0 frames 60
> wait
> wait 30
> rock y 20 260
> wait
> wait 30
> zoom 0.5 frames 30
> wait
> wait 30
> roll axis x angle 3 frames 120
> wait
> wait 30
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save 1MBN_myoglobin_heme-pocket_white-bg.png width 1984 height 1240
> supersample 3
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> save 1MBN_myoglobin_heme-pocket_black-bg.png width 1984 height 1240
> supersample 3
> movie encode output 1MBN_myoglobin_heme-pocket.mov
Movie saved to 1MBN_myoglobin_heme-pocket.mov
> movie stop
No movie being recorded.
> save 1MBN_myoglobin_rolling.cxs
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
Summary of feedback from opening 2HBS fetched from pdb
---
note | Fetching compressed mmCIF 2hbs from http://files.rcsb.org/download/2hbs.cif
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> show atoms
> hide atoms
> hide cartoons
> hide surfaces
> show cartoons
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view
> view orient
> select #1
4993 atoms, 4686 bonds, 4 pseudobonds, 1027 residues, 2 models selected
> view matrix models #1,1,0,0,-50,0,1,0,+25,0,0,1,0
> wait 20
> close session
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #1
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #1
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> cd "/Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT""
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS-
vs-1A3N_haemoglibin_mutant-vs-WT
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides ribbons/slabspreset cartoons/nucleotides
> ribbons/slabs
No preset name in category 'Cartoons/Nucleotides' matches 'ribbons/slabspreset
cartoons/nucleotides ribbons/slabs'
> view orient
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> select #2/A
1167 atoms, 1147 bonds, 1 pseudobond, 197 residues, 2 models selected
> select down
1167 atoms, 1147 bonds, 1 pseudobond, 197 residues, 2 models selected
> view matrix models #1,1,0,0,-100,0,1,0,0,0,0,1,0
> wait 20
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-100,0,1,0,+25,0,0,1,0
> wait 20
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E
1174 atoms, 1147 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #2/Eselect #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> hide sel
> select #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> hide sel
> cartoon hide (#!2 & sel)
> cartoon hide (#!2 & sel)view orient ;
Expected an atoms specifier or a keyword
> view matrix models #1,1,0,0,1,0,1,0,+75,0,0,1,0
> wait 20
> view orient
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> cartoon hide (#!2 & sel)
> view orient
> hide (#!2 & sel) target a
> cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS-
vs-1A3N_haemoglibin_mutant-vs-WT
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> color red #1:.A,.B # Colorer les chaînes A et B de l'hémoglobine normale en
> rouge
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> All hide (#!2 & sel)
Unknown command: All hide (#!2 & sel)
> All hide (#!2 & sel)# Charger les structures d'hémoglobine sauvage et mutée
Unknown command: All hide (#!2 & sel)# Charger les structures d'hémoglobine
sauvage et mutée
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #3
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #3
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #4
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #4
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> color green #1/A /B /C /D
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green #1/A /B /C /D# Charger les structures d'hémoglobine sauvage et
> mutée
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #5
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #5
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #6
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #6
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> color green #1/A /B /C /D
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green #1/A /B /C /D
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS-
vs-1A3N_haemoglibin_mutant-vs-WT
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS-
vs-1A3N_haemoglibin_mutant-vs-WT
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> color green #1/A /B /C /Dcolor green #1/A /B /C /D ;
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green #1/A /B /C /Dcolor green #1/A /B /C /D ; color green #1/A /B /C
> /D ;
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green #1
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green #1 cartoons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> cartoons color green #1
Unknown command: cartoons color green #1
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1
4993 atoms, 4686 bonds, 4 pseudobonds, 1027 residues, 2 models selected
> color sel forest green
> color sel bychain
> color sel forest green
> select #1/A
1235 atoms, 1147 bonds, 1 pseudobond, 265 residues, 2 models selected
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color green sel ; # WT alpha chains
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel cyan
> color sel cornflower blue
> select down
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green
> select #1/B #1/D
2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected
> color sel cornflowerblue
> select none
Expected an objects specifier or a keyword
> select noneselect clear
Expected an objects specifier or a keyword
> select noneselect clear
Expected an objects specifier or a keyword
> select clear
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green
> select clear
> select #1/B #1/D
2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected
> color sel cornflowerblue
> select clear
> select #2/A #2/C
2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected
> color sel red
> select clear
> select #2/B #2/D
2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected
> color sel yellow
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #2:.B at 6 # Sélectionner la position 6 de la chaîne B (mutation E6V)
Expected an objects specifier or a keyword
> select #2/B:6 # Sélectionner la position 6 de la chaîne B (mutation E6V)
Expected a keyword
> select #2/B
1240 atoms, 1201 bonds, 1 pseudobond, 223 residues, 2 models selected
> select #2/B:6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:6-6 # Sélectionner la position 6 de la chaîne B (mutation E6V)
Expected a keyword
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color green #2:.A,.B ; # Colorer les chaînes A et B de l'hémoglobine mutée
> en vert
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color magenta sel ; # Colorer ce résidu en magenta
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> color sel magenta
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green
> select clear
> select #1/B #1/D
2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected
> color sel cornflowerblue
> select clear
> select #2/A #2/C
2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected
> color sel purple
> select clear
> select #2/B #2/D
2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected
> color sel yellow
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> matchmaker #1 to #2 computeSS true # Calculer les RMSD pour chaque résidu
Expected a keyword
> matchmaker #1 to #2 computeSS true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon
> la RMSD par rapport à la structure normale
Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la
structure mutée selon la RMSD par rapport à la structure normale
> rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon
> la RMSD par rapport à la structure normaleview
Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la
structure mutée selon la RMSD par rapport à la structure normaleview
> rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon
> la RMSD par rapport à la structure normaleviewview orient
Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la
structure mutée selon la RMSD par rapport à la structure normaleviewview
orient
> view orient
> transparency 0.5
> transparency 0.5 All
> select
14670 atoms, 14078 bonds, 12 pseudobonds, 2756 residues, 4 models selected
> ui tool show "Color Actions"
> transparency 70,s #0
Missing or invalid "percent" argument: Expected a number
> transparency 70 #0
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 70
> transparency 70 cartoons
> select clear
> transparency 100,s #0
Missing or invalid "percent" argument: Expected a number
> transparency 100 #0
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100
> transparency 100 cartoons
> transparency 70 cartoons
> transparency 70 All
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 15 residues, 1 model selected
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 15 residues, 1 model selected
> transparency 0 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 0s
Missing or invalid "percent" argument: Expected a number
> transparency 0
> transparency 0
> transparency 0 target sel
Invalid "target" argument: Character 'e' is not an allowed target, must be one
of acrsbmpfl
> transparency 0 target s
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #3
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #3
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #4
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #4
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E #2/F #2/G #2/H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green transparency 50
> select clear
> cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT
Current working directory is:
/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ-
amu.fr/My
Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS-
vs-1A3N_haemoglibin_mutant-vs-WT
> close session
> open 1A3N
1a3n title:
Deoxy human hemoglobin [more info...]
Chain information for 1a3n #1
---
Chain | Description | UniProt
A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141
B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146
Non-standard residues in 1a3n #1
---
HEM — protoporphyrin IX containing Fe (HEME)
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 2HBS
2hbs title:
The high resolution crystal structure of deoxyhemoglobin S [more info...]
Chain information for 2hbs #2
---
Chain | Description | UniProt
A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141
B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146
Non-standard residues in 2hbs #2
---
HEM — protoporphyrin IX containing Fe (HEME)
2hbs mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8760 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #2/E-H
4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> view orient
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0
> wait 20
> view orient
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green transparency 50
> select clear
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green transparency 40
> select clear
> select #1/B #1/D
2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected
> color sel cornflowerblue transparency 40
> select clear
> select #2/A #2/C
2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected
> color sel purple transparency 40
> select clear
> select #2/B #2/D
2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected
> color sel yellow transparency 40
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> matchmaker #1 to #2 computeSS true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon
> la RMSD par rapport à la structure normale
Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la
structure mutée selon la RMSD par rapport à la structure normale
> matchmaker mmaker
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green transparency 40
> select clear
> select #1/B #1/D
2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected
> color sel cornflowerblue transparency 40
> select clear
> select #2/A #2/C
2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected
> color sel purple transparency 40
> select clear
> select #2/B #2/D
2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected
> color sel yellow transparency 40
> select clear
> select #2/A #2/C
2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected
> color sel purple transparency 40
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> transparency 70 All
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 15 residues, 1 model selected
> transparency 0 target sel
Invalid "target" argument: Character 'e' is not an allowed target, must be one
of acrsbmpfl
> transparency 0 target selsel up ;
Invalid "target" argument: Character 'e' is not an allowed target, must be one
of acrsbmpfl
> transparency 0 target selsel up ; sel up ;
Invalid "target" argument: Character 'e' is not an allowed target, must be one
of acrsbmpfl
> transparency 0 target s
> select up
1121 atoms, 1151 bonds, 146 residues, 1 model selected
> transparency 0 target s
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> view orient
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 15 residues, 1 model selected
> transparency 0 target s
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow transparency 0
> select clear
> transparency 70 All
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow transparency 0
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow transparency 0
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #1/A #1/C
2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected
> color sel green transparency 40
> select clear
> select #1/B #1/D
2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected
> color sel cornflowerblue transparency 40
> select clear
> select #2/A #2/C
2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected
> color sel purple transparency 40
> select clear
> select #2/B #2/D
2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected
> color sel yellow transparency 40
> select clear
> transparency 70 All
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow transparency 0
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 15 residues, 1 model selected
> color sel yellow transparency 0
> select clear
> select #2/B:6-6
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> matchmaker #1 to #2 computeSS true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon
> la RMSD par rapport à la structure normale
Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la
structure mutée selon la RMSD par rapport à la structure normale
> rmsd #2 to #1
Number of atoms from first atom spec (9677) differs from number in second
(4993)
> matchmaker #1 to #2 computeSS true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment
score = 774
RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs:
0.475)
> color byattribute rmsd palette white:red range 0,2 #2
Expected a keyword
> color byattribute rmsd palette white:red range 0,2 #2color #2 byattribute
> "rmsd" palette white:red range 0,2
Expected a keyword
> color #2 byattribute "rmsd" palette white:red range 0,2
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> close
> open 4bql
Summary of feedback from opening 4bql fetched from pdb
---
note | Fetching compressed mmCIF 4bql from http://files.rcsb.org/download/4bql.cif
4bql title:
Crystal structure of archaeal actin [more info...]
Chain information for 4bql #1
---
Chain | Description | UniProt
A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432
Non-standard residues in 4bql #1
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
4bql mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> open 4bql
4bql title:
Crystal structure of archaeal actin [more info...]
Chain information for 4bql #2
---
Chain | Description | UniProt
A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432
Non-standard residues in 4bql #2
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
4bql mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> delete /B,C,D
> open 1j6z
Summary of feedback from opening 1j6z fetched from pdb
---
note | Fetching compressed mmCIF 1j6z from http://files.rcsb.org/download/1j6z.cif
1j6z title:
Uncomplexed actin [more info...]
Chain information for 1j6z #3
---
Chain | Description | UniProt
A | ACTIN ALPHA 1 | ACTS_RABIT 2-375
Non-standard residues in 1j6z #3
---
ADP — adenosine-5'-diphosphate
CA — calcium ion
HIC — 4-methyl-histidine
RHO — tetramethylrhodamine-5-maleimide (TMR)
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bql, chain A (#1) with 4bql, chain A (#2), sequence alignment
score = 2308.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 4bql #1/A, 4bql #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 436 pruned atom pairs is 0.000 angstroms; (across all 436 pairs:
0.000)
> select add #1
3465 atoms, 3539 bonds, 437 residues, 1 model selected
> close
> open 4bql
4bql title:
Crystal structure of archaeal actin [more info...]
Chain information for 4bql #1
---
Chain | Description | UniProt
A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432
Non-standard residues in 4bql #1
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
4bql mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
Associated 4bql chain A to 4bql, chain A with 0 mismatches
Associated 4bql chain B to 4bql, chain A with 0 mismatches
Associated 4bql chain C to 4bql, chain A with 0 mismatches
Associated 4bql chain D to 4bql, chain A with 0 mismatches
> delete /B,C,D
> open 1j6z
1j6z title:
Uncomplexed actin [more info...]
Chain information for 1j6z #2
---
Chain | Description | UniProt
A | ACTIN ALPHA 1 | ACTS_RABIT 2-375
Non-standard residues in 1j6z #2
---
ADP — adenosine-5'-diphosphate
CA — calcium ion
HIC — 4-methyl-histidine
RHO — tetramethylrhodamine-5-maleimide (TMR)
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4bql, chain A (#1) with 1j6z, chain A (#2), sequence alignment
score = 412.6
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 4bql #1/A, 1j6z #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 177 pruned atom pairs is 1.198 angstroms; (across all 349 pairs:
4.965)
> ui tool show "Render/Select by Attribute"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Render/Select by Attribute"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color byattribute r:seq_rmsd #!1-2 target csab palette
> 1,#0433ff:3,white:5,red noValueColor #80b180
6810 atoms, 1218 residues, atom seq_rmsd range 0.179 to 25.6
> key #0433ff:1 white:3 red:5 showTool true
> ui mousemode right "color key"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> key #0433ff:1 white:3 red:5 showTool true
> ui mousemode right translate
> key #0433ff:1 white:3 red:5 showTool true
> ui mousemode right "color key"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> key #0433ff:1 white:3 red:5 showTool true
> key pos 0.433902,0.375647 size 0.00997586,0.00432396
> undo
Undo failed, probably because structures have been modified.
> show target m
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #3 target m
> hide #3 target m
> show #3 target m
> open 4bqlcd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT
'4bqlcd' has no suffix
> close
> ui mousemode right translate
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1069, in proxy_handler
s._changes_cb(*args)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1255, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
N10atomstruct9StructureE
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++
N10atomstruct9StructureE
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: Z1AF00123FN/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 11 days, 43 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PHL 272B7QU:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Attachments (1)
Change History (4)
comment:1 by , 14 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Could not instantiate StructureSeq.structure |
comment:2 by , 14 months ago
comment:3 by , 14 months ago
| Status: | accepted → feedback |
|---|
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15991.cxc