Message going to dead viewer's status

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.5.1-x86_64-i386-64bit
ChimeraX Version: 1.7rc202311170002 (2023-11-17 00:02:40 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7rc202311170002 (2023-11-17)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/seanwhittier/Downloads/model_shoichi format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/model_shoichi  
---  
note | Alignment identifier is model_shoichi  
  
Opened 1 sequences from model_shoichi  

> open /Users/seanwhittier/Downloads/model_shoichi format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/model_shoichi  
---  
notes | Destroying pre-existing alignment with identifier model_shoichi  
Alignment identifier is model_shoichi  
  
Opened 1 sequences from model_shoichi  

> open /Users/seanwhittier/Downloads/model_shoichi format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/model_shoichi  
---  
notes | Destroying pre-existing alignment with identifier model_shoichi  
Alignment identifier is model_shoichi  
  
Opened 1 sequences from model_shoichi  

> open /Users/seanwhittier/Downloads/mxigc format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/mxigc  
---  
note | Alignment identifier is mxigc  
  
Opened 1 sequences from mxigc  

> open /Users/seanwhittier/Downloads/mxigc format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/mxigc  
---  
notes | Destroying pre-existing alignment with identifier mxigc  
Alignment identifier is mxigc  
  
Opened 1 sequences from mxigc  

> open /Users/seanwhittier/Downloads/mxigc format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/mxigc  
---  
notes | Destroying pre-existing alignment with identifier mxigc  
Alignment identifier is mxigc  
  
Opened 1 sequences from mxigc  

> open /Users/seanwhittier/Downloads/mxigc format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/mxigc  
---  
notes | Destroying pre-existing alignment with identifier mxigc  
Alignment identifier is mxigc  
  
Opened 1 sequences from mxigc  

> open /Users/seanwhittier/Downloads/mxigc format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/mxigc  
---  
notes | Destroying pre-existing alignment with identifier mxigc  
Alignment identifier is mxigc  
  
Opened 1 sequences from mxigc  

> open /Users/seanwhittier/Downloads/LDBF_truncated.pdb format pdb

Summary of feedback from opening
/Users/seanwhittier/Downloads/LDBF_truncated.pdb  
---  
warning | Ignored bad PDB record found on line 4924  
  
Chain information for LDBF_truncated.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/seanwhittier/Downloads/MxiG_Jian_model.pdb format pdb

Summary of feedback from opening
/Users/seanwhittier/Downloads/MxiG_Jian_model.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 38
GLU A 42 1 5  
Start residue of secondary structure not found: HELIX 2 2 HIS A 125 VAL A 127
1 3  
Start residue of secondary structure not found: HELIX 3 3 PHE A 128 ILE A 156
1 29  
Start residue of secondary structure not found: HELIX 4 4 GLN A 178 LYS A 190
1 13  
Start residue of secondary structure not found: HELIX 5 5 SER A 202 ARG A 216
1 15  
52 messages similar to the above omitted  
  
Chain information for MxiG_Jian_model.pdb  
---  
Chain | Description  
2.1/A 2.2/B 2.3/C 2.4/D 2.5/E 2.6/F 2.7/G 2.8/H 2.9/I 2.10/J 2.11/K 2.12/L
2.13/M 2.14/N 2.15/O 2.16/P 2.17/Q 2.18/R 2.19/S 2.20/T 2.21/U 2.22/V 2.23/W
2.24/X | No description available  
2.49/A 2.50/A 2.51/A 2.52/A 2.53/A 2.54/A 2.55/A 2.56/A 2.57/A 2.58/A 2.59/A
2.60/A | No description available  
2.49/B 2.50/B 2.51/B 2.52/B 2.53/B 2.54/B 2.55/B 2.56/B 2.57/B 2.58/B 2.59/B
2.60/B | No description available  
2.25/a 2.26/b 2.27/c 2.28/d 2.29/e 2.30/f 2.31/g 2.32/h 2.33/i 2.34/j 2.35/k
2.36/l 2.37/m 2.38/n 2.39/o 2.40/p 2.41/q 2.42/r 2.43/s 2.44/t 2.45/u 2.46/v
2.47/w 2.48/x | No description available  
  
Associated MxiG_Jian_model.pdb (2.1) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.2) chain B to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.3) chain C to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.4) chain D to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.5) chain E to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.6) chain F to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.7) chain G to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.8) chain H to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.9) chain I to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.10) chain J to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.11) chain K to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.12) chain L to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.13) chain M to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.14) chain N to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.15) chain O to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.16) chain P to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.17) chain Q to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.18) chain R to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.19) chain S to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.20) chain T to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.21) chain U to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.22) chain V to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.23) chain W to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.24) chain X to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.49) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.49) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.50) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.50) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.51) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.51) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.52) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.52) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.53) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.53) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.54) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.54) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.55) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.55) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.56) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.56) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.57) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.57) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.58) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.58) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.59) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.59) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.60) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.60) chain B to chain A with 9 mismatches  
Associated MxiG_Jian_model.pdb (2.49) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.49) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.50) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.50) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.51) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.51) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.52) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.52) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.53) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.53) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.54) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.54) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.55) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.55) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.56) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.56) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.57) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.57) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.58) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.58) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.59) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.59) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.60) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.60) chain B to chain B with 0 mismatches  

> select add #2

137376 atoms, 139656 bonds, 24 pseudobonds, 16992 residues, 73 models selected  

> select subtract #2

Nothing selected  

> select add #2

137376 atoms, 139656 bonds, 24 pseudobonds, 16992 residues, 73 models selected  

> open /Users/seanwhittier/Downloads/mxigc format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/mxigc  
---  
notes | Destroying pre-existing alignment with identifier mxigc  
Alignment identifier is mxigc  
Associated MxiG_Jian_model.pdb (2.49) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.49) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.50) chain A to chain B with 5 mismatches  
Associated MxiG_Jian_model.pdb (2.50) chain B to chain B with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.51) chain A to chain B with 5 mismatches  
19 messages similar to the above omitted  
  
Opened 1 sequences from mxigc  

> select subtract #2

Nothing selected  

> select add #2

137376 atoms, 139656 bonds, 24 pseudobonds, 16992 residues, 73 models selected  

> select subtract #2

Nothing selected  

> show atoms

[Repeated 1 time(s)]

> hide atoms

[Repeated 2 time(s)]

> movie record

> turn y 2 180

> wait 180

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

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

> ui tool show "Selection Inspector"

> open /Users/seanwhittier/Downloads/model_shoichi format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/model_shoichi  
---  
notes | Destroying pre-existing alignment with identifier model_shoichi  
Alignment identifier is model_shoichi  
Associated MxiG_Jian_model.pdb (2.1) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.2) chain B to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.3) chain C to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.4) chain D to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.5) chain E to chain A with 0 mismatches  
43 messages similar to the above omitted  
  
Opened 1 sequences from model_shoichi  

> open /Users/seanwhittier/Downloads/model_shoichi format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/model_shoichi  
---  
notes | Destroying pre-existing alignment with identifier model_shoichi  
Alignment identifier is model_shoichi  
Associated MxiG_Jian_model.pdb (2.1) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.2) chain B to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.3) chain C to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.4) chain D to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.5) chain E to chain A with 0 mismatches  
20 messages similar to the above omitted  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/__init__.py", line 74, in open  
return open_file(session, data, file_name,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/parse.py", line 75, in open_file  
alignments = [session.alignments.new_alignment(seqs,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/manager.py", line 253, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 134, in __init__  
self.associate([s for s in session.models if isinstance(s, AtomicStructure)],
force=False)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 352, in associate  
do_assoc()  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 269, in do_assoc  
status("Associated %s %s to %s with %d mismatch%s%s" % (struct_name,  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 470, in status  
StatusLogger.status(self, msg, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 210, in status  
if l.status(msg, color, secondary) and getattr(l, "excludes_other_logs",
True):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 929, in status  
sbar.status(msg, color, secondary)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status  
restore_current_opengl_context(cc)  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 421, in
restore_current_opengl_context  
opengl_context.makeCurrent(opengl_surface)  
RuntimeError: wrapped C/C++ object of type StatusOpenGLWindow has been deleted  
  
RuntimeError: wrapped C/C++ object of type StatusOpenGLWindow has been deleted  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 421, in
restore_current_opengl_context  
opengl_context.makeCurrent(opengl_surface)  
  
See log for complete Python traceback.  
  

> open /Users/seanwhittier/Downloads/model_shoichi format fasta

Summary of feedback from opening /Users/seanwhittier/Downloads/model_shoichi  
---  
notes | Alignment identifier is model_shoichi  
Associated MxiG_Jian_model.pdb (2.1) chain A to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.2) chain B to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.3) chain C to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.4) chain D to chain A with 0 mismatches  
Associated MxiG_Jian_model.pdb (2.5) chain E to chain A with 0 mismatches  
43 messages similar to the above omitted  
  
Opened 1 sequences from model_shoichi  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0)
      OS Loader Version: 540.120.3~19

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 23:33

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL S3422DWG:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 144.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 3XZVS63     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.12
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7rc202311170002
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.44.3
    funcparserlib: 1.0.1
    glfw: 2.6.3
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.0.0
    prompt-toolkit: 3.0.41
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.10
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9