id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15847	Graphics crash, macOS 13.6.9, Intel UHD Graphics 617	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-13.6.9-x86_64-i386-64bit
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: Aborted

Thread 0x0000700012b97000 (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 0x00007ff8607dd7c0 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 556 in swap_buffers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback
  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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, 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, PIL._imagingmath (total: 59)


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    ""size"" : 32768,
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    ""size"" : 524288,
    ""uuid"" : ""58e1300b-c472-3863-8fc4-4eb27185cbbf"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so"",
    ""name"" : ""mmcif.cpython-311-darwin.so""
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    ""path"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so"",
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    ""uuid"" : ""08a0cdf4-85d3-328a-98ac-8a7ec48356eb"",
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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/katiecasazza/Desktop/Chimera Msh2-Msh3 crosslinking
> analysis.cxs"" format session

opened ChimeraX session  

> ui mousemode right select

> select /A:626

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select /A:626

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /B:549

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /A:307

12 atoms, 12 bonds, 1 residue, 1 model selected  
Drag select of 55 residues  

> ui mousemode right ""translate selected models""

> ui mousemode right translate

> ui mousemode right select

> ui mousemode right distance

> distance /A:626@NZ /B:549@NZ

Distance between /A LYS 626 NZ and /B LYS 549 NZ: 35.097Å  

> ui mousemode right translate

> ui mousemode right select

> select /A:1011

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> select /B:870

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> select /B:890

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> select /A:980

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> select /B:549

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> select /A:626

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> select /a :893

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel red

> ui mousemode right translate

> select /b :980

Nothing selected  

> ui mousemode right select

> select /A:893

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> ui mousemode right distance

> ~distance /B:890@NZ /A:980@NZ

> distance /A:980@NZ /A:893@OG

Distance between /A LYS 980 NZ and SER 893 OG: 33.505Å  

> select /a :549

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel navy

> select /b :549

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right translate

> select /b :549

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /a :549

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel cornflower blue

> select /a :672

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel navy

> show sel atoms

> ui mousemode right distance

> ui mousemode right translate

> ui mousemode right distance

> distance /B:549@NZ /A:672@NZ

Distance between /B LYS 549 NZ and /A LYS 672 NZ: 18.097Å  

> set bgColor black

> set bgColor white

> select /b :575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select color navy

Expected an objects specifier or a keyword  

> color sel navy

> show sel atoms

> distance /A:672@NZ /B:575@NZ

Distance between /A LYS 672 NZ and /B LYS 575 NZ: 13.171Å  

> select /b :950

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel navy

> select /a :999

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel navy

> show sel atoms

> select /b :950

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> distance /A:999@NZ /B:950@NZ

Distance between /A LYS 999 NZ and /B LYS 950 NZ: 27.942Å  

> select /b :549

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /a :667

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel purple

> show sel atoms

> distance /A:667@NZ /B:549@NZ

Distance between /A LYS 667 NZ and /B LYS 549 NZ: 7.714Å  

> select /b :890

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /a :995

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel orange

> show sel atoms

> ui mousemode right translate

> ui mousemode right distance

> distance /A:995@NZ /B:890@NZ

Distance between /A LYS 995 NZ and /B LYS 890 NZ: 16.151Å  

> color #1.1 #ff2600ff models

> select add #1.1

9 atoms, 8 bonds, 1 residue, 3 models selected  

> color #1 #ff2600ff models

> rename #1 ""distances- lines""

> rename #1.1 ""labels- numbers""

> select /b

7655 atoms, 7787 bonds, 964 residues, 1 model selected  

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 XL- updated 8-29-2024.cxs""

> ui mousemode right translate

> select /b

7655 atoms, 7787 bonds, 964 residues, 1 model selected  

> color sel light blue

> color sel green

> color sea green

> select /b

7655 atoms, 7787 bonds, 964 residues, 1 model selected  

> color sea green

> select /a

8196 atoms, 8344 bonds, 1 pseudobond, 1018 residues, 2 models selected  

> color sel dodger blue

> color sel steel blue

> select /b :549,870,890,893

36 atoms, 32 bonds, 4 residues, 1 model selected  

> ui mousemode right label

> label #4/A:1010

> label #4/A:1012

> label #4/A:1009

> select add #1

36 atoms, 32 bonds, 8 pseudobonds, 4 residues, 4 models selected  

> delete sel

> ui mousemode right translate

> delete sel

> ui mousemode right select

> select /B:546

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> delete sel

> select add #4.3

5 pseudobonds, 2 models selected  

> show #4.3 target m

> close #4.3

> select add #1

3 pseudobonds, 2 models selected  

> open
> /Users/katiecasazza/Downloads/output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> undo

> close session

> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select /A

8196 atoms, 8344 bonds, 1018 residues, 1 model selected  

> select /a :672

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /a

8196 atoms, 8344 bonds, 1018 residues, 1 model selected  

> color sel teal

> color sel steel blue

> select /b

7655 atoms, 7787 bonds, 964 residues, 1 model selected  

> color sel medium sea green

> show sel atoms

> hide sel atoms

> select /b :498,502

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel red

> show sel atoms

> label sel

> distance /b:498@NZ /b:502@NZ

Distance between /B LYS 498 NZ and LYS 502 NZ: 8.080Å  

> select /b :890,893

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel red

> label sel

> show sel atoms

> distance /b:890@NZ /b:893@NZ

Distance between /B LYS 890 NZ and LYS 893 NZ: 14.201Å  

> select /b:950

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> label sel

> show sel atoms

> distance /b:950@NZ /b:893@NZ

Distance between /B LYS 950 NZ and LYS 893 NZ: 30.413Å  

> select /957

Nothing selected  

> select /b:957

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> show sel atoms

> label sel

> distance /b:957@NZ /b:893@NZ

Distance between /B LYS 957 NZ and LYS 893 NZ: 15.865Å  

> select /a:77,70

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel red

> label sel

> show sel atoms

> distance /a:77@NZ /a:70@NZ

Distance between /A LYS 77 NZ and LYS 70 NZ: 30.219Å  

> select /a:92

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /a:92,140,126,160,626,634,959,965,999,995

90 atoms, 80 bonds, 10 residues, 1 model selected  

> color sel red

> show sel atoms

> label sel

> distance /a:92@NZ /a:70@NZ

Distance between /A LYS 92 NZ and LYS 70 NZ: 36.097Å  

> distance /a:140@NZ /a:126@NZ

Distance between /A LYS 140 NZ and LYS 126 NZ: 23.560Å  

> distance /a:160@NZ /a:126@NZ

Distance between /A LYS 160 NZ and LYS 126 NZ: 32.057Å  

> distance /a:626@NZ /a:634@NZ

Distance between /A LYS 626 NZ and LYS 634 NZ: 18.029Å  

> distance /a:959@NZ /a:965@NZ

Distance between /A LYS 959 NZ and LYS 965 NZ: 6.074Å  

> distance /a:999@NZ /a:995@NZ

Distance between /A LYS 999 NZ and LYS 995 NZ: 4.190Å  

> select /b :549,870 /a:1011,980

36 atoms, 32 bonds, 4 residues, 1 model selected  

> color sel red

> show sel atoms

> label sel

> ui mousemode right ""color key""

> key delete

> ui mousemode right select

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs""

> ui tool show Distances

> distance style color #005493

> distance style color #ff2600

Exactly two atoms must be selected!  

> ui mousemode right select

> color sel blye

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel blue

> undo

> hide #2.1 models

> distance /b:549@NZ /a:626@NZ

Distance between /B LYS 549 NZ and /A LYS 626 NZ: 35.097Å  

> ui mousemode right select

> color sel navy

> color sel magenta

> color sel gold

> color sel bue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel blue

> color sel dark magenta

> color sel dark blue

> color sel darkred purple

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel purple

> color sel lime

> color sel midnight blue

> color sel midnightblue golden rod

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel goldenrod

> distance style color #ff2f92

> distance style color #0433ff

> distance style color #531b93

> distance style color #945200

> distance style color #ff2600

> distance style color #ff2f92

> distance style color #ff2600

> color sel black

> select clear

> color sel coral

> select clear

> color sel saddle brown

> set bgColor black

> set bgColor white

> select /b

7655 atoms, 7787 bonds, 4 pseudobonds, 964 residues, 2 models selected  

> color sel pale green

> select /a

8196 atoms, 8344 bonds, 7 pseudobonds, 1018 residues, 2 models selected  

> set bgColor black

> color sel light pink

> set bgColor black

> set bgColor white

> select clear

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> set bgColor black

> color sel midnight blue

> select /a

8196 atoms, 8344 bonds, 7 pseudobonds, 1018 residues, 2 models selected  

> color sel midnight blue

> select /b

7655 atoms, 7787 bonds, 4 pseudobonds, 964 residues, 2 models selected  

> color sel teal

> set bgColor white

> select /A:325

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> hide #2.1 models

> color sel red

> select /b :498,502,890,893,950,957,549,870,890

72 atoms, 64 bonds, 4 pseudobonds, 8 residues, 2 models selected  

> color sel red

> show sel atoms

> label sel

> select /a :77,70,92,140,126,160,626,634,959,965,999,995

108 atoms, 96 bonds, 7 pseudobonds, 12 residues, 2 models selected  

> select /a :77,70,92,140,126,160,626,634,959,965,999,995,626,1011,980

126 atoms, 112 bonds, 7 pseudobonds, 14 residues, 2 models selected  

> color sel red

> show sel atoms

> label sel

> color sel lime

> color sel cyan

> color sel blue

> color sel dodger blue

> select clear

> color sel magneta

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel magenta

> color sel gold

> select clear

> ui mousemode right translate

> color sel lime

> ui mousemode right select

> color sel lime

> distance /b:870@NZ /a:1011@NZ

Distance between /B LYS 870 NZ and /A LYS 1011 NZ: 13.674Å  

> color sel lime

> distance style dashes 6

> distance style dashes 7

> distance style dashes 8

> distance style dashes 9

> distance style dashes 8

> distance style dashes 7

> distance style dashes 6

> distance style dashes 5

> distance style dashes 4

> distance style dashes 5

> distance style dashes 6

> distance style dashes 7

> distance style dashes 8

> distance style dashes 9

> distance style dashes 10

> distance style dashes 11

> distance style dashes 12

> distance style dashes 13

> distance style dashes 14

> distance style dashes 15

> distance style dashes 16

> distance style dashes 25

> distance /b:890@NZ /a:980@NZ

Distance between /B LYS 890 NZ and /A LYS 980 NZ: 10.736Å  

> color sel lime

> distance /b:893@NZ /a:980@NZ

Distance between /B LYS 893 NZ and /A LYS 980 NZ: 18.731Å  

> color sel lime

> label height 8

> label height 4

> label height 3

> label color white

> set bgColor black

> ui mousemode right ""move label""

> move label

Missing or invalid ""axis"" argument: Expected 3 floats or ""x"", or ""y"", or ""z""
or two atoms  

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs""

> view #2.1 clip false

No displayed objects specified.  

> ui mousemode right select

> select /A:1011

9 atoms, 8 bonds, 1 residue, 1 model selected  

> label sel

> label number

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label sel number

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label number

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label residues number

Expected a keyword  

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs""

> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb

Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb

Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/katiecasazza/Downloads/output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
> format pdb

Chain information for
output_msh2msh6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> undo

> close session

> open ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"" format session

opened ChimeraX session  

> close session

> open ""/Users/katiecasazza/Desktop/Msh2-Msh3 XL- updated 8-29-2024.cxs""
> format session

opened ChimeraX session  

> select /A:371

9 atoms, 8 bonds, 1 residue, 1 model selected  

> label (#!4 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label (#!4 & sel) residues attribute number

> select /A:166

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:469

9 atoms, 8 bonds, 1 residue, 1 model selected  

> label (#!4 & sel) text ""{0.name} {0.number}{0.insertion_code}""

> label (#!4 & sel) text ""/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label (#!4 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label (#!4 & sel) residues attribute number

> close session

> open ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"" format session

opened ChimeraX session  

> select /b:498,502,890,893,950,957,549,870,890,893
> /a:77,70,92,140,126,160,626,634,959,965,999,995,626,1011,980,980

198 atoms, 176 bonds, 15 pseudobonds, 22 residues, 2 models selected  

> label (#!1 & sel) residues attribute number

> select clear

Drag select of 22 residues  

> ui mousemode right translate

> ui mousemode right select

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katiecasazza/Desktop/movie1.mp4

Movie saved to /Users/katiecasazza/Desktop/movie1.mp4  
  

> close session

> open
> /Users/katiecasazza/Downloads/output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
output_msh23_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> sel/b

Unknown command: sel/b  

> select /b

7655 atoms, 7787 bonds, 964 residues, 1 model selected  

> color sel teal

> select /a

8196 atoms, 8344 bonds, 1018 residues, 1 model selected  

> color sel midnight blue

> select clear

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 HOMODUPLEX XLs.cxs""

> open ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs"" format session

opened ChimeraX session  

> select /a :176,158

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel red

> show sel atoms

> label sel

> label height 4

> label sel residues attribute number

> select add #2.1

18 atoms, 16 bonds, 2 residues, 2 models selected  

> label height 4

> label (#!1 & sel) residues attribute number

> select clear

> select add #2.1

1 model selected  
No visible residues selected  

> select subtract #2.1

Nothing selected  

> select add #1.1

1 model selected  
No visible residues selected  

> select subtract #1.1

Nothing selected  

> select /b:498,502,890,893,950,893,957,549,870,890,893
> /a:176,158,77,70,92,140,126,160,626,634,959,965,999,995,626,1011,980

216 atoms, 192 bonds, 15 pseudobonds, 24 residues, 2 models selected  

> label (#!1 & sel) residues attribute number

> label height 6

> label height 4

> label height 4.5

> ui mousemode right translate

> ui mousemode right distance

> distance /A:176@NZ /A:158@NZ

Distance between /A LYS 176 NZ and LYS 158 NZ: 11.661Å  

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs""

> ui mousemode right select

> select clear

> show #!2 target m

> ui tool show Distances

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katiecasazza/Desktop/movie1.mp4

Movie saved to /Users/katiecasazza/Desktop/movie1.mp4  
  

> save ""/Users/katiecasazza/Desktop/Msh2-Msh3 NO DNA XLs.cxs""

> open ""/Users/katiecasazza/Desktop/Msh2-Msh3 HOMODUPLEX XLs.cxs"" format
> session

opened ChimeraX session  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /b:549,890,575,870,498,502,893,890,957,893
> /a:672,980,995,672,1011,999,995,131,140,241,248,626,634,959,965,705,248

198 atoms, 176 bonds, 22 residues, 1 model selected  

> select /b:549,890,575,870,498,502,893,890,957,893
> /a:672,980,995,672,1011,999,995,131,140,241,248,626,634,959,965,705,248

198 atoms, 176 bonds, 22 residues, 1 model selected  


===== 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 INTEL-20.7.2
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.

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 Air
      Model Identifier: MacBookAir8,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 577.140.2~22

Software:

    System Software Overview:

      System Version: macOS 13.6.9 (22G830)
      Kernel Version: Darwin 22.6.0
      Time since boot: 9 hours, 42 minutes

Graphics/Displays:

    Intel UHD Graphics 617:

      Chipset Model: Intel UHD Graphics 617
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x87c0
      Revision ID: 0x0002
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL S2721NX:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 9BGB9H3     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI


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
}}}
"	defect	closed	normal		Graphics		nonchimerax						all	ChimeraX