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Opened 2 years ago
Last modified 2 years ago
#9350 assigned defect
Clipper/ISOLDE version conflict
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | Tristan Croll | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.6.dev202303230759 (2023-03-23 07:59:11 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Errors
---
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed
warnings | Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX_daily\bin\lib\importlib\\__init__.py", line
127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "C:\Users\gdraperbarr\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>
__version__ = _version()
File "C:\Users\gdraperbarr\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 815, in resolve
dist = self._resolve_dist(
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 861, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 364, in initialize
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 509, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
UCSF ChimeraX version: 1.6.dev202303230759 (2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed 'ChimeraX-Clipper==0.21.0'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Collecting ChimeraX-Clipper==0.21.0
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.21.0/ChimeraX_Clipper-0.21.0-cp39-cp39-win_amd64.whl
(7.4 MB)
\---------------------------------------- 7.4/7.4 MB 3.3 MB/s eta 0:00:00
Requirement already satisfied: ChimeraX-Core<1.7,>=1.6.dev202303162359 in
c:\program files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Clipper==0.21.0) (1.6.dev202303230759)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-Clipper==0.21.0)
(1.43.10)
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-Clipper==0.21.0)
(10.0.6)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-Clipper==0.21.0)
(1.1)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0.2)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.1.1)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0.3)
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.7)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.12)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.3)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.2.3)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.5.1)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.10.1)
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.28.4)
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0.1)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.1.4)
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (2.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.10.2)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.2)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (2.1.1)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (2.0.1)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0.1)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0)
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.3.3)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program
files\chimerax_daily\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0)
Installing collected packages: ChimeraX-Clipper
Attempting uninstall: ChimeraX-Clipper
Found existing installation: ChimeraX-Clipper 0.20.0
Uninstalling ChimeraX-Clipper-0.20.0:
Successfully uninstalled ChimeraX-Clipper-0.20.0
Successfully installed ChimeraX-Clipper-0.21.0
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
chimerax-isolde 1.6.dev1 requires ChimeraX-Clipper~=0.20.0, but you have
chimerax-clipper 0.21.0 which is incompatible.
[notice] A new release of pip is available: 23.0 -> 23.1.2
[notice] To update, run: C:\Program Files\ChimeraX_daily\bin\ChimeraX.exe -m
pip install --upgrade pip
> open C:\Users\gdraperbarr\Downloads\CtSla2dimer.pdb format pdb
Chain information for CtSla2dimer.pdb #1
---
Chain | Description
B C | No description available
> open
> C:/Users/gdraperbarr/Downloads/cryosparc_P110_J102_013_volume_map_sharp.mrc
Opened cryosparc_P110_J102_013_volume_map_sharp.mrc as #2, grid size
220,220,220, pixel 1.7, shown at level 0.295, step 1, values float32
> hide #1 models
> show #1 models
> volume #2 style mesh
> volume #2 level 0.3698
> select add #2
2 models selected
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-197.59,0,1,0,-196.53,0,0,1,-195.63
> hide #!2 models
> open C:/Users/gdraperbarr/Downloads/cryosparc_P118_J143_map_sharp.mrc
Opened cryosparc_P118_J143_map_sharp.mrc as #3, grid size 150,150,150, pixel
1.42, shown at level 0.281, step 1, values float32
> volume #3 level 0.7726
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-249.66,0,1,0,-262.74,0,0,1,-263.69
> select add #3
4 models selected
> select subtract #2
2 models selected
> view matrix models #3,1,0,0,-95.208,0,1,0,-123.23,0,0,1,-108.81
> ui mousemode right translate
> volume #3 level 0.5618
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.77873,0.62719,0.014725,25.776,0.15921,0.22028,-0.96236,32.111,-0.60682,-0.74707,-0.27139,153.17
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.3302, steps = 204
shifted from previous position = 24.5
rotated from previous position = 23 degrees
atoms outside contour = 5108, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
-0.48349169 0.33776142 -0.80755991 110.42700395
0.87324051 0.12211658 -0.47173993 107.17722577
-0.06071909 -0.93327636 -0.35398931 90.13162470
Axis -0.44880809 -0.72624430 0.52071154
Axis point -3.06317047 0.00000000 97.64964154
Rotation angle (degrees) 149.05732872
Shift along axis -80.46480544
> view matrix models
> #3,-0.096905,0.90639,-0.41117,-36.763,0.50485,-0.31126,-0.80513,37.255,-0.85775,-0.2856,-0.42743,145.3
> view matrix models
> #3,0.97007,-0.22088,0.10092,-77.935,0.075619,-0.12017,-0.98987,79.721,0.23077,0.96787,-0.099867,-133.98
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.3301, steps = 156
shifted from previous position = 1.53
rotated from previous position = 28.8 degrees
atoms outside contour = 5106, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.48365576 -0.33788238 0.80741105 102.09172585
-0.87314515 -0.12219511 0.47189607 105.31339730
-0.06078369 -0.93322230 -0.35412074 90.13076391
Axis -0.80927513 0.50003503 -0.30828352
Axis point 0.00000000 110.12341965 -22.48021512
Rotation angle (degrees) 119.75749314
Shift along axis -57.74573620
> view matrix models
> #3,0.49176,-0.41828,0.76368,-67.72,0.61708,-0.45136,-0.64458,25.299,0.61431,0.78823,0.036151,-168.28
> view matrix models
> #3,0.45705,-0.70223,0.54586,-13.625,-0.045667,-0.63144,-0.77408,126.88,0.88827,0.32887,-0.32067,-115.43
> view matrix models
> #3,0.15601,-0.98705,0.037317,95.873,-0.074418,-0.049418,-0.996,88.716,0.98495,0.15261,-0.081164,-129.22
> view matrix models
> #3,0.12377,-0.98835,0.088541,94.678,-0.084579,-0.09941,-0.99145,94.683,0.9887,0.11522,-0.095897,-124.28
> view matrix models
> #3,0.028129,-0.9692,0.24465,88.3,-0.13263,-0.2462,-0.9601,112.47,0.99077,-0.0054403,-0.13547,-108
> view matrix models
> #3,0.13791,-0.9901,0.026075,99.165,0.032094,-0.021846,-0.99925,74.771,0.98993,0.13864,0.028763,-138.48
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.2979, steps = 120
shifted from previous position = 3.26
rotated from previous position = 20.2 degrees
atoms outside contour = 5337, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
-0.39164903 -0.36908409 0.84284517 104.56319321
-0.91859069 0.20954147 -0.33508732 108.75375226
-0.05293562 -0.90546635 -0.42110393 88.26786018
Axis -0.47702279 0.74916472 -0.45956663
Axis point 105.54180137 -0.00000000 55.28015852
Rotation angle (degrees) 143.28371379
Shift along axis -8.96951523
Average map value = 0.2979 for 6672 atoms, 5337 outside contour
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.2979, steps = 36
shifted from previous position = 0.00431
rotated from previous position = 0.00777 degrees
atoms outside contour = 5334, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
-0.39167085 -0.36903558 0.84285627 104.56036114
-0.91858689 0.20943878 -0.33516194 108.75546429
-0.05284011 -0.90550988 -0.42102231 88.26798793
Axis -0.47701973 0.74913016 -0.45962613
Axis point 105.54133441 -0.00000000 55.28818083
Rotation angle (degrees) 143.28576953
Shift along axis -8.97563076
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.2979, steps = 40
shifted from previous position = 0.0199
rotated from previous position = 0.0142 degrees
atoms outside contour = 5335, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
-0.39163630 -0.36893708 0.84291544 104.55435147
-0.91861046 0.20923077 -0.33522724 108.77218085
-0.05268609 -0.90559810 -0.42085184 88.26642719
Axis -0.47704050 0.74905334 -0.45972977
Axis point 105.54962987 0.00000000 55.30303968
Rotation angle (degrees) 143.28591244
Shift along axis -8.97919867
> show #!2 models
> view matrix models
> #3,0.14826,-0.98734,0.056345,94.96,0.058007,-0.048195,-0.99715,74.622,0.98725,0.1511,0.050127,-141.51
> view matrix models
> #3,0.18769,-0.98153,0.037146,91.936,0.078521,-0.022703,-0.99665,69.688,0.97909,0.18998,0.07281,-146.88
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.18769,-0.98153,0.037146,44.796,0.078521,-0.022703,-0.99665,7.7021,0.97909,0.18998,0.07281,-203.94
> view matrix models
> #3,0.18769,-0.98153,0.037146,-0.98791,0.078521,-0.022703,-0.99665,35.888,0.97909,0.18998,0.07281,-207.82
> view matrix models
> #3,0.18769,-0.98153,0.037146,8.3553,0.078521,-0.022703,-0.99665,72.08,0.97909,0.18998,0.07281,-217.14
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.74309,-0.62292,-0.24451,-62.588,-0.10182,0.25589,-0.96133,58.358,0.6614,0.73925,0.12673,-246.75
> view matrix models
> #3,0.38016,-0.74244,-0.5516,17.203,-0.36277,0.4289,-0.82731,55.251,0.85081,0.51462,-0.10629,-221.36
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.38016,-0.74244,-0.5516,34.579,-0.36277,0.4289,-0.82731,61.612,0.85081,0.51462,-0.10629,-208.38
> view matrix models
> #3,0.38016,-0.74244,-0.5516,33.838,-0.36277,0.4289,-0.82731,-3.6243,0.85081,0.51462,-0.10629,-173.32
> ui tool show "Fit to Segments"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right rotate
> volume #2 color #aa0000
> volume #2 color #aa00ff
> volume #2 color lime
> volume #2 level 0.5249
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.91998,0.19759,-0.33852,52.302,0.037286,0.90384,0.42624,-213.06,0.39019,0.37951,-0.83888,-41.953
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.91998,0.19759,-0.33852,47.486,0.037286,0.90384,0.42624,-210.39,0.39019,0.37951,-0.83888,-18.54
> view matrix models
> #3,-0.91998,0.19759,-0.33852,22.973,0.037286,0.90384,0.42624,-175.03,0.39019,0.37951,-0.83888,-62.683
> view matrix models
> #3,-0.91998,0.19759,-0.33852,50.394,0.037286,0.90384,0.42624,-177.51,0.39019,0.37951,-0.83888,-90.016
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.51042,0.67952,-0.52699,-26.814,0.67744,0.69522,0.2403,-206.08,0.52967,-0.23435,-0.81519,-41.815
> view matrix models
> #3,0.92746,0.36821,-0.065065,-189.43,0.060734,-0.32005,-0.94545,77.485,-0.36895,0.87292,-0.3192,-110.07
> view matrix models
> #3,0.91845,0.33496,-0.21035,-171.44,-0.045666,-0.43847,-0.89758,96.925,-0.39289,0.83399,-0.38742,-97.05
> view matrix models
> #3,0.9553,0.27566,-0.10686,-178.67,0.017634,-0.41393,-0.91014,88.759,-0.29513,0.86756,-0.40029,-109.81
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.9553,0.27566,-0.10686,-176.33,0.017634,-0.41393,-0.91014,89.341,-0.29513,0.86756,-0.40029,-113.18
> view matrix models
> #3,0.9553,0.27566,-0.10686,-176.21,0.017634,-0.41393,-0.91014,84.608,-0.29513,0.86756,-0.40029,-117.86
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.72946,0.5969,-0.33407,-165.24,0.13704,-0.60602,-0.78356,80.569,-0.67015,0.52579,-0.52387,-30.214
> view matrix models
> #3,0.65052,0.57307,-0.49841,-139.05,0.090551,-0.71009,-0.69827,88.642,-0.75407,0.40911,-0.51382,-9.8337
> open C:\Users\gdraperbarr\Downloads\AF-G0S106-F1-model_v4.pdb format pdb
AF-G0S106-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (G0S106) [more
info...]
Chain information for AF-G0S106-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | uncharacterized protein | G0S106_CHATD 1-1050
> select add #4
8343 atoms, 8461 bonds, 1050 residues, 3 models selected
> select subtract #3
8343 atoms, 8461 bonds, 1050 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-22.546,0,1,0,-32.964,0,0,1,-82.43
> view matrix models #4,1,0,0,-89.548,0,1,0,-48.046,0,0,1,-104.56
> view matrix models #4,1,0,0,-87.898,0,1,0,-43.358,0,0,1,-108.7
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.06756,0.24528,-0.9671,-106.94,-0.94556,-0.32505,-0.016384,-71.904,-0.31837,0.91334,0.25388,-108.02
> view matrix models
> #4,-0.51008,-0.57217,-0.64222,-121.5,0.16088,-0.79694,0.58224,-54.511,-0.84495,0.19367,0.49855,-123.43
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.51008,-0.57217,-0.64222,-49.033,0.16088,-0.79694,0.58224,-30.164,-0.84495,0.19367,0.49855,-99.611
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.14543,-0.87083,-0.46958,-44.521,0.2331,-0.49142,0.83915,-25.946,-0.96152,0.012573,0.27446,-103.57
> view matrix models
> #4,-0.92905,-0.1914,-0.31658,-53.203,-0.28522,-0.17442,0.94246,-32.785,-0.2356,0.96589,0.10746,-82.43
> view matrix models
> #4,-0.95843,0.080543,-0.27372,-51.434,-0.28262,-0.39972,0.87198,-34.701,-0.039179,0.91309,0.40587,-78.828
> view matrix models
> #4,-0.90126,-0.43078,-0.046426,-54.314,-0.11886,0.14279,0.98259,-27.015,-0.41665,0.89109,-0.17989,-86.791
> view matrix models
> #4,-0.57204,0.12404,-0.81079,-44.629,-0.75615,-0.46277,0.46269,-44.549,-0.31782,0.87776,0.35852,-84.349
> view matrix models
> #4,0.55004,-0.60178,0.57906,-27.994,-0.13967,0.61732,0.77421,-23.741,-0.82337,-0.50673,0.25551,-105.35
> hide #4 models
> select subtract #4
Nothing selected
> show #4 models
> fitmap #4 inMap #3
Fit molecule AF-G0S106-F1-model_v4.pdb (#4) to map
cryosparc_P118_J143_map_sharp.mrc (#3) using 8343 atoms
average map value = 0.1007, steps = 340
shifted from previous position = 5.2
rotated from previous position = 8.44 degrees
atoms outside contour = 7710, contour level = 0.56184
Position of AF-G0S106-F1-model_v4.pdb (#4) relative to
cryosparc_P118_J143_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.94377789 0.10805637 0.31242137 132.72784347
0.17798268 -0.96249364 -0.20476369 100.45712942
0.27857756 0.24885703 -0.92761238 72.79050343
Axis 0.98565035 0.07353757 0.15193947
Axis point 0.00000000 42.31276912 31.45874810
Rotation angle (degrees) 166.69631122
Shift along axis 149.27036994
> ui mousemode right "translate selected models"
> select add #4
8343 atoms, 8461 bonds, 1050 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.5771,-0.60531,0.54823,-77.309,-0.23544,0.51947,0.82141,-36.102,-0.782,-0.60311,0.15727,-102.27
> select #4:650-1050
3049 atoms, 3079 bonds, 401 residues, 1 model selected
> hide sel cartoons
> select #4:650-1050
3049 atoms, 3079 bonds, 401 residues, 1 model selected
> show sel cartoons
> select #4
8343 atoms, 8461 bonds, 1050 residues, 1 model selected
> hide sel cartoons
> select #4:650-1050
3049 atoms, 3079 bonds, 401 residues, 1 model selected
> show sel cartoons
> fitmap sel inMap #3
Fit molecule AF-G0S106-F1-model_v4.pdb (#4) to map
cryosparc_P118_J143_map_sharp.mrc (#3) using 3049 atoms
average map value = 0.3225, steps = 192
shifted from previous position = 22.9
rotated from previous position = 28.8 degrees
atoms outside contour = 2345, contour level = 0.56184
Position of AF-G0S106-F1-model_v4.pdb (#4) relative to
cryosparc_P118_J143_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.85202654 -0.37816716 0.36199499 84.46313644
-0.25532130 -0.90385975 -0.34329081 113.87712735
0.45701401 0.20006786 -0.86666664 102.50665095
Axis 0.96149594 -0.16814014 0.21738090
Axis point 0.00000000 58.01117934 51.30936309
Rotation angle (degrees) 163.58700648
Shift along axis 84.34663398
> view matrix models
> #4,0.18017,-0.86369,0.47071,-66.205,-0.060664,0.46788,0.88171,-38.351,-0.98176,-0.18741,0.031901,-52.701
> undo
> volume #3 style mesh
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.18017,-0.86369,0.47071,-68.857,-0.060664,0.46788,0.88171,-59.454,-0.98176,-0.18741,0.031901,-86.354
> select #4:650-1007
2691 atoms, 2717 bonds, 358 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule AF-G0S106-F1-model_v4.pdb (#4) to map
cryosparc_P118_J143_map_sharp.mrc (#3) using 2691 atoms
average map value = 0.3353, steps = 196
shifted from previous position = 2.38
rotated from previous position = 14.7 degrees
atoms outside contour = 2041, contour level = 0.56184
Position of AF-G0S106-F1-model_v4.pdb (#4) relative to
cryosparc_P118_J143_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.78144476 -0.57940936 0.23157909 91.83607639
-0.43526852 -0.77210615 -0.46302637 120.17792778
0.44708545 0.26103044 -0.85555697 106.51683015
Axis 0.94146332 -0.28021466 0.18742081
Axis point 0.00000000 63.89229968 59.04434638
Rotation angle (degrees) 157.38493952
Shift along axis 72.74815117
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.0085369,-0.98517,0.17138,-62.698,0.8012,0.10929,0.58834,-73.442,-0.59834,0.13228,0.79025,-92.972
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.0085369,-0.98517,0.17138,-66.292,0.8012,0.10929,0.58834,-66.446,-0.59834,0.13228,0.79025,-96.633
> fitmap sel inMap #3
Fit molecule AF-G0S106-F1-model_v4.pdb (#4) to map
cryosparc_P118_J143_map_sharp.mrc (#3) using 2691 atoms
average map value = 0.3707, steps = 88
shifted from previous position = 4.82
rotated from previous position = 11.4 degrees
atoms outside contour = 1955, contour level = 0.56184
Position of AF-G0S106-F1-model_v4.pdb (#4) relative to
cryosparc_P118_J143_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.38588931 -0.81702399 -0.42844048 97.28881689
-0.90809394 -0.41827591 -0.02026488 116.44722652
-0.16264944 0.39688421 -0.90334274 115.21958077
Axis 0.82941572 -0.52847117 -0.18107399
Axis point 0.00000000 80.36575568 77.13059254
Rotation angle (degrees) 165.43538556
Shift along axis -1.70939676
> select #4:1007-1050
364 atoms, 367 bonds, 44 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule AF-G0S106-F1-model_v4.pdb (#4) to map
cryosparc_P118_J143_map_sharp.mrc (#3) using 364 atoms
average map value = 0.4746, steps = 184
shifted from previous position = 12.1
rotated from previous position = 32.9 degrees
atoms outside contour = 228, contour level = 0.56184
Position of AF-G0S106-F1-model_v4.pdb (#4) relative to
cryosparc_P118_J143_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.30087048 -0.95149670 0.06427271 95.67244729
-0.92319952 -0.30749553 -0.23054101 123.36187470
0.23912258 0.01002645 -0.97093763 91.08340584
Axis 0.80527223 -0.58529006 0.09472161
Axis point 0.00000000 92.26127457 46.03534876
Rotation angle (degrees) 171.40956541
Shift along axis 13.46745301
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.084672,0.42813,0.89974,-58.53,0.87411,0.46536,-0.13917,-56.73,-0.47829,0.77469,-0.41364,-80.057
> view matrix models
> #4,-0.059869,0.54994,0.83306,-58.71,0.85168,0.46342,-0.24471,-56.076,-0.52063,0.69485,-0.49612,-79.168
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.059869,0.54994,0.83306,-45.605,0.85168,0.46342,-0.24471,-65.843,-0.52063,0.69485,-0.49612,-78.328
> view matrix models
> #4,-0.059869,0.54994,0.83306,-57.895,0.85168,0.46342,-0.24471,-77.678,-0.52063,0.69485,-0.49612,-89.92
> fitmap sel inMap #3
Fit molecule AF-G0S106-F1-model_v4.pdb (#4) to map
cryosparc_P118_J143_map_sharp.mrc (#3) using 364 atoms
average map value = 0.5532, steps = 400
shifted from previous position = 3.46
rotated from previous position = 36 degrees
atoms outside contour = 197, contour level = 0.56184
Position of AF-G0S106-F1-model_v4.pdb (#4) relative to
cryosparc_P118_J143_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.32402534 -0.30182343 0.89661040 98.56787568
-0.51060546 0.74205490 0.43432316 130.71596068
-0.79642304 -0.59854587 0.08633190 136.30995618
Axis -0.51794063 0.84898549 -0.10469546
Axis point 178.84292221 0.00000000 -1.47213816
Rotation angle (degrees) 85.62947695
Shift along axis 45.65261241
> view matrix models
> #4,0.31512,0.52722,0.78913,-49.617,0.94803,-0.13631,-0.2875,-59.91,-0.04401,0.83872,-0.54278,-74.898
> hide #4 models
> hide #1 models
> show #1 models
> view matrix models
> #4,0.31512,0.52722,0.78913,-50.8,0.94803,-0.13631,-0.2875,-62.951,-0.04401,0.83872,-0.54278,-76.944
> ui mousemode right "translate selected models"
> select add #1
7036 atoms, 7099 bonds, 920 residues, 2 models selected
> select add #4
15015 atoms, 15193 bonds, 1926 residues, 2 models selected
> select subtract #4
6672 atoms, 6732 bonds, 876 residues, 1 model selected
> view matrix models
> #1,0.85414,-0.28165,0.43718,-67.351,0.060145,0.8885,0.45491,-75.658,-0.51656,-0.36226,0.77584,-57.71
> view matrix models
> #1,0.85414,-0.28165,0.43718,-64.319,0.060145,0.8885,0.45491,-30.986,-0.51656,-0.36226,0.77584,-83.037
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.2628, steps = 228
shifted from previous position = 15.3
rotated from previous position = 31.9 degrees
atoms outside contour = 5454, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.74657379 0.09418489 -0.65860216 102.48015304
0.47247874 -0.77199671 0.42518812 99.14784029
-0.46839240 -0.62860982 -0.62085286 92.86059809
Axis -0.92789789 -0.16748489 0.33309807
Axis point 0.00000000 60.42536775 50.45451810
Rotation angle (degrees) 145.40015307
Shift along axis -80.76519674
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.95853,0.26701,0.099649,-62.609,-0.20347,0.88596,-0.41675,-40.441,-0.19956,0.3792,0.90354,-95.632
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.95853,0.26701,0.099649,-55.758,-0.20347,0.88596,-0.41675,-36.474,-0.19956,0.3792,0.90354,-85.904
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.2684, steps = 148
shifted from previous position = 3.35
rotated from previous position = 5.58 degrees
atoms outside contour = 5421, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.73604361 0.03586715 -0.67598325 99.82956138
0.65995509 -0.26027370 0.70478145 106.00908964
-0.15066216 -0.96486847 -0.21524349 87.89277035
Axis -0.89849545 -0.28269316 0.33584297
Axis point 0.00000000 81.90611759 32.20682579
Rotation angle (degrees) 111.69938520
Shift along axis -90.14628297
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.6312,0.06029,0.77327,-51.12,0.22727,0.93884,-0.25871,-38.551,-0.74157,0.33904,0.57889,-88.713
> view matrix models
> #1,0.18282,-0.13786,0.97343,-48.795,0.23649,0.96722,0.092565,-36.023,-0.95428,0.21328,0.20942,-90.976
> view matrix models
> #1,0.15233,-0.14778,0.97722,-48.715,0.25669,0.96074,0.10528,-35.939,-0.95441,0.2348,0.18429,-91.201
> select #4:650-900
1893 atoms, 1915 bonds, 251 residues, 1 model selected
> select #1:650-900
3786 atoms, 3830 bonds, 502 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 3786 atoms
average map value = 0.348, steps = 116
shifted from previous position = 7.91
rotated from previous position = 21.2 degrees
atoms outside contour = 2803, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.66954444 -0.26709157 0.69308899 103.25140175
-0.73028247 -0.40710798 0.54858966 105.82672869
0.13563838 -0.87345590 -0.46762918 87.86849434
Axis -0.89095448 0.34925964 -0.29020308
Axis point 0.00000000 91.17555513 -10.31573665
Rotation angle (degrees) 127.05607499
Shift along axis -80.53100132
> ui tool show "Dock Prep"
Density map not found or not selected
> ui dockable false "Fit to Segments"
> view matrix models
> #1,-0.0095912,-0.12196,0.99249,-54.841,0.32724,0.9375,0.11836,-37.58,-0.94489,0.32592,0.030917,-88.525
> fitmap sel inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 3786 atoms
average map value = 0.3479, steps = 120
shifted from previous position = 2.31
rotated from previous position = 13.2 degrees
atoms outside contour = 2799, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.66979135 -0.26711904 0.69283979 103.25031760
-0.73013783 -0.40680134 0.54900949 105.79696727
0.13519726 -0.87359035 -0.46750574 87.86510532
Axis -0.89101651 0.34926807 -0.29000241
Axis point 0.00000000 91.17173364 -10.31325477
Rotation angle (degrees) 127.03177662
Shift along axis -80.52732786
> select #1:750-900
2318 atoms, 2344 bonds, 302 residues, 1 model selected
> select #1:800-900
1534 atoms, 1550 bonds, 202 residues, 1 model selected
> select #1:800-1007
3130 atoms, 3154 bonds, 416 residues, 1 model selected
> select #1:B 800-1007
Expected a keyword
> select #1/B: 800-1007
1565 atoms, 1577 bonds, 208 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> ui mousemode right pivot
> ui mousemode right "translate selected atoms"
> undo
> select #1/B: 805-1007
1526 atoms, 1537 bonds, 203 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 1526 atoms
average map value = 0.3702, steps = 104
shifted from previous position = 7.29
rotated from previous position = 16.1 degrees
atoms outside contour = 1114, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.82452673 -0.17385916 0.53845024 106.19945384
-0.52650096 -0.58430429 0.61756396 96.17958958
0.20724963 -0.79269257 -0.57331152 88.41433498
Axis -0.94589023 0.22214357 -0.23652465
Axis point 0.00000000 75.87332132 2.93506177
Rotation angle (degrees) 131.80092724
Shift along axis -99.99951780
> undo
[Repeated 1 time(s)]
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.27738,0.13434,0.95132,-59.095,0.47079,0.88215,0.012698,-31.81,-0.83751,0.45139,-0.30794,-99.702
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.27738,0.13434,0.95132,-59.265,0.47079,0.88215,0.012698,-41.739,-0.83751,0.45139,-0.30794,-89.293
> view matrix models
> #1,-0.27738,0.13434,0.95132,-57.046,0.47079,0.88215,0.012698,-40.865,-0.83751,0.45139,-0.30794,-88.757
> fitmap #1 inMap #3
Fit molecule CtSla2dimer.pdb (#1) to map cryosparc_P118_J143_map_sharp.mrc
(#3) using 6672 atoms
average map value = 0.3302, steps = 120
shifted from previous position = 4.35
rotated from previous position = 17.5 degrees
atoms outside contour = 5105, contour level = 0.56184
Position of CtSla2dimer.pdb (#1) relative to cryosparc_P118_J143_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.48322813 -0.33764273 0.80776727 102.06954388
-0.87338336 -0.12187742 0.47153729 105.32391624
-0.06076255 -0.93335058 -0.35378614 90.13184229
Axis -0.80908252 0.50019102 -0.30853593
Axis point 0.00000000 110.14837696 -22.51512779
Rotation angle (degrees) 119.75007962
Shift along axis -57.70951820
> select #1/B: 805-1007
1526 atoms, 1537 bonds, 203 residues, 1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX_daily\bin\lib\importlib\\__init__.py", line
127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "C:\Users\gdraperbarr\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>
__version__ = _version()
File "C:\Users\gdraperbarr\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 815, in resolve
dist = self._resolve_dist(
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 861, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 385, in run_provider
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 509, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX_daily\bin\lib\importlib\\__init__.py", line
127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "C:\Users\gdraperbarr\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>
__version__ = _version()
File "C:\Users\gdraperbarr\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 815, in resolve
dist = self._resolve_dist(
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\pkg_resources\\__init__.py", line 861, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 385, in run_provider
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 509, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0
(c:\users\gdraperbarr\appdata\local\ucsf\chimerax\1.6\site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_GB.cp65001
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 3640 Tower
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 68,420,292,608
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202303230759
ChimeraX-CoreFormats: 1.1
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: 1.3.3
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.dev1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.2
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.1.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.5
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.6
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.1.1
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2022.7.1
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.6
WMI: 1.5.1
zipp: 3.15.0
Change History (1)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Clipper/ISOLDE version conflict |
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