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Opened 20 months ago
Last modified 20 months ago
#14731 assigned defect
cannot load libXau
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Errors
---
error | Bundle 'ChimeraX-Dicom' custom initialization failed
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/__init__.py", line 17, in <module>
from .dicom import (
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/__init__.py", line 3, in <module>
from .dicom_fetcher import fetchers
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/dicom_fetcher.py", line 2, in <module>
from .databases import TCIADatabase
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/__init__.py", line 1, in <module>
from .tcia import TCIADatabase
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/tcia.py", line 24, in <module>
from tcia_utils import nbia
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tcia_utils/__init__.py", line 1, in <module>
from . import nbia
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tcia_utils/nbia.py", line 12, in <module>
import matplotlib.pyplot as plt
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/__init__.py", line 129, in <module>
from . import _api, _version, cbook, _docstring, rcsetup
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/rcsetup.py", line 27, in <module>
from matplotlib.colors import Colormap, is_color_like
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/colors.py", line 51, in <module>
from PIL import Image
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's
module:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jmadrigal/Box/AlphaFold/outputdir_huwe1_fl_p14arf_1_70/huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
> format pdb
Chain information for
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
> open "/Users/jmadrigal/Box/Tom1 Manuscript/3_Final
> Models/2023Jun16_Tom1ADphenix111-coot-1.pdb"
Chain information for 2023Jun16_Tom1ADphenix111-coot-1.pdb #2
---
Chain | Description
A | No description available
> open "/Users/jmadrigal/Box/Tom1 Manuscript/2_Final
> Maps/cryosparc_P41_J2923_006_volume_map(1).mrc"
Opened cryosparc_P41_J2923_006_volume_map(1).mrc as #3, grid size 320,320,320,
pixel 1.13, shown at level 0.0704, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 84, in <lambda>
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 96, in capture_thumbnails_cb
fs.capture_image(models, ses)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 190, in capture_image
self.image = models_image(session, models, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 252, in models_image
image = v.image(width, height, camera = c, drawings = models)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 448, in image
from PIL import Image
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
Error processing trigger "frame drawn":
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
> select
78849 atoms, 79895 bonds, 7 pseudobonds, 7225 residues, 5 models selected
> view sel
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> 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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1671.6
RMSD between 250 pruned atom pairs is 1.124 angstroms; (across all 2235 pairs:
70.465)
> cofr sel
> ui mousemode right zoom
> select #1:200-500
2387 atoms, 2432 bonds, 301 residues, 1 model selected
> select #1:200-450
1984 atoms, 2022 bonds, 251 residues, 1 model selected
> matchmaker #1 to #2 & sel
No 'to' model specified
> matchmaker #1 to #2 & sel
No 'to' model specified
> matchmaker #1 to #2 & sel
No 'to' model specified
> matchmaker #1/A to #2/A & sel pairing ss
No 'to' chains specified
> select #2:200-450
3660 atoms, 3698 bonds, 1 pseudobond, 229 residues, 2 models selected
> matchmaker #1/A to #2/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 207.6
RMSD between 96 pruned atom pairs is 1.281 angstroms; (across all 212 pairs:
10.480)
> hide #!3 models
> 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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1671.6
RMSD between 250 pruned atom pairs is 1.124 angstroms; (across all 2235 pairs:
70.465)
> matchmaker #1/A to #2/A pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1671.6
RMSD between 250 pruned atom pairs is 1.124 angstroms; (across all 2235 pairs:
70.465)
> select #2:200-450
3660 atoms, 3698 bonds, 1 pseudobond, 229 residues, 2 models selected
> matchmaker #1/A to #2/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 207.6
RMSD between 96 pruned atom pairs is 1.281 angstroms; (across all 212 pairs:
10.480)
> matchmaker #1/A to #2/A pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1671.6
RMSD between 250 pruned atom pairs is 1.124 angstroms; (across all 2235 pairs:
70.465)
> matchmaker #1/A to #2/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 207.6
RMSD between 96 pruned atom pairs is 1.281 angstroms; (across all 212 pairs:
10.480)
> select #2:1-2888
38580 atoms, 38958 bonds, 7 pseudobonds, 2401 residues, 2 models selected
> matchmaker #1/A to #2/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1004.5
RMSD between 216 pruned atom pairs is 1.356 angstroms; (across all 2014 pairs:
47.111)
> matchmaker #1/A to #2/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1004.5
RMSD between 216 pruned atom pairs is 1.356 angstroms; (across all 2014 pairs:
47.111)
> select clear
> select #1/A:1972-1994
188 atoms, 189 bonds, 23 residues, 1 model selected
> rainbow sel
> style sel sphere
Changed 188 atom styles
> show sel atoms
> open /Users/jmadrigal/Box/Maps&PDBs/7jq9_human_HUWE1.pdb
Chain information for 7jq9_human_HUWE1.pdb #4
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #4/A to #2/A pairing ss
Parameters
---
Chain pairing | ss
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
7jq9_human_HUWE1.pdb, chain A (#4), sequence alignment score = 2050.8
RMSD between 185 pruned atom pairs is 1.283 angstroms; (across all 2241 pairs:
16.761)
No reference and/or match structure/chain chosen
> matchmaker #!4 to #1
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
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1) with 7jq9_human_HUWE1.pdb, chain A (#4), sequence alignment score
= 9922.6
RMSD between 1928 pruned atom pairs is 0.864 angstroms; (across all 2427
pairs: 3.401)
> hide #!4 models
> hide #!2 models
> select #1/B
550 atoms, 563 bonds, 70 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> select #2:1100-1201,1260-1320
2676 atoms, 2708 bonds, 163 residues, 1 model selected
> hide #!2 models
> select #2:1100-1201,1260-1320, sel#1:1250-1297,1421-1472
3486 atoms, 3532 bonds, 263 residues, 2 models selected
> show #!2 models
> matchmaker #1 & sel to #2 & sel
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 38.5
RMSD between 4 pruned atom pairs is 1.364 angstroms; (across all 71 pairs:
19.636)
> select #2:1000-1201,1260-1400, sel#1:1100-1250,1421-1500
7431 atoms, 7548 bonds, 574 residues, 2 models selected
> matchmaker #1 & sel to #2 & sel
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 101.5
RMSD between 23 pruned atom pairs is 1.261 angstroms; (across all 205 pairs:
14.247)
> hide #!2 models
> select #1:1550-2000
3521 atoms, 3577 bonds, 451 residues, 1 model selected
> rainbow sel
> select clear
> set bgColor white
> show #!2 models
> hide #1 models
> select #2:1260-1400,1432-1532 sel#1:1421-1500,1753-1891
Expected a keyword
> select #2:1260-1400,1432-1532 sel #1:1421-1500,1753-1891
Expected a keyword
> select #2:1260-1400,1432-1532, sel #1:1421-1500,1753-1891
5670 atoms, 5741 bonds, 461 residues, 2 models selected
> matchmaker #1 & sel to #2 & sel
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 2023Jun16_Tom1ADphenix111-coot-1.pdb, chain A (#2) with
huwe1_fl_p14arf_1-70_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 104.9
RMSD between 40 pruned atom pairs is 0.888 angstroms; (across all 91 pairs:
6.499)
> show #1 models
> save /Users/jmadrigal/Box/Thesis/2024Mar08_deepdive_BH3_compare.cxs
> includeMaps true
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 608, in save
from . import serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 52, in <module>
from . import _serialize
File "src/_serialize.pyx", line 32, in init chimerax.core._serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 608, in save
from . import serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 52, in <module>
from . import _serialize
File "src/_serialize.pyx", line 32, in init chimerax.core._serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
> save
> /Users/jmadrigal/Box/Thesis/2024Mar04_thesisch3_ch4_workingfolder/asf.cxs
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 608, in save
from . import serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 52, in <module>
from . import _serialize
File "src/_serialize.pyx", line 32, in init chimerax.core._serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 608, in save
from . import serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 52, in <module>
from . import _serialize
File "src/_serialize.pyx", line 32, in init chimerax.core._serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
> save
> /Users/jmadrigal/Box/Thesis/2024Mar04_thesisch3_ch4_workingfolder/giu.cmap
> models #3
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 114, in provider_save
remember_file(session, path, data_format.nicknames[0],
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 241, in remember_file
h.remember_file(filename, format, models, database = database, file_saved =
file_saved,
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 79, in remember_file
self.capture_thumbnails_cb()
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 96, in capture_thumbnails_cb
fs.capture_image(models, ses)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 190, in capture_image
self.image = models_image(session, models, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 252, in models_image
image = v.image(width, height, camera = c, drawings = models)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 448, in image
from PIL import Image
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
> cd /Users/jmadrigal/Box/Thesis/2024Mar04_thesisch3_ch4_workingfolder
Current working directory is:
/Users/jmadrigal/Box/Thesis/2024Mar04_thesisch3_ch4_workingfolder
> save
> /Users/jmadrigal/Box/Thesis/2024Mar04_thesisch3_ch4_workingfolder/fy.cxs
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 608, in save
from . import serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 52, in <module>
from . import _serialize
File "src/_serialize.pyx", line 32, in init chimerax.core._serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.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
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 608, in save
from . import serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 52, in <module>
from . import _serialize
File "src/_serialize.pyx", line 32, in init chimerax.core._serialize
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in <module>
from . import _imaging as core
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
ImportError:
dlopen(/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/_imaging.cpython-311-darwin.so, 2): Library not loaded:
@loader_path/libXau.6.0.0.dylib
Referenced from:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libxcb.1.1.0.dylib
Reason: no suitable image found. Did find:
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/.dylibs/libXau.6.0.0.dylib: cannot load 'libXau.6.0.0.dylib'
(load command 0x80000034 is unknown)
File
"/private/var/folders/wm/1s__yqn12ks2ngvcrldy_q000000gp/T/AppTranslocation/F1D14CBC-E29C-4F27-A8D7-0B1C0A5B218C/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 84, in
from . import _imaging as core
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.31
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel 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: MacBookPro15,2
Processor Name: Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G9323)
Kernel Version: Darwin 18.7.0
Time since boot: 5:57
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal: Supported, feature set macOS GPUFamily2 v1
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
Rotation: Supported
Automatically Adjust Brightness: No
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
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: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.7.1
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: 1.1.3
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
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: 2.6.1
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: 1.5.14
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: 1.13.1
ChimeraX-PDB: 2.7.3
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
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
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: 25.1.2
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: 1.0.8
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (1)
comment:1 by , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → cannot load libXau |
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