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Opened 4 years ago
Closed 4 years ago
#5289 closed defect (limitation)
Dependency conflict trying to install ISOLDE into 1.2.5 — at Version 2
| 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 (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed show
> help help:user
> help help:user
> toolshed show
> toolshed show
> help help:quickstart
> ui tool show "Command Line Interface"
> ui dockable false "Command Line Interface"
> ui dockable true "Command Line Interface"
> toolshed install isolde
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Requirement already satisfied:
ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2)
Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2)
Collecting ChimeraX-Clipper~=0.16.0 Using cached https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.16.0/ChimeraX_Clipper-0.16.0-cp38-cp38-win_amd64.whl (22.9 MB)
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0)
Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3)
Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages(from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1)
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1)
INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while.
INFO:pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This
could take a while.
INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1\. loosen the range of package versions you've specified 2\. remove package versions to allow pip attempt to solve the
dependency conflict
ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command.
> toolshed uninstall chimerax-nucleotides
Unable to uninstall ChimeraX-Nucleotides because it is needed by another
bundles: ChimeraX-Atomic
> toolshed uninstall ChimeraX-Atomic
Unable to uninstall ChimeraX-Atomic because it is needed by other bundles:
ChimeraX-Markers, ChimeraX-Hbonds, ChimeraX-BuildStructure, ChimeraX-Smiles,
ChimeraX-ModelPanel, ChimeraX-uniprot, ChimeraX-PDBMatrices, ChimeraX-PubChem,
ChimeraX-IHM, ChimeraX-Alignments, ChimeraX-Centroids, ChimeraX-PDBLibrary,
ChimeraX-AxesPlanes, ChimeraX-Maestro, ChimeraX-ReadPbonds, ChimeraX-
coulombic, ChimeraX-ChemGroup, ChimeraX-MDcrds, ChimeraX-SeqView, ChimeraX-
StdCommands, ChimeraX-Nucleotides, ChimeraX-MMTF, ChimeraX-SwapRes, ChimeraX-
TapeMeasure, ChimeraX-mmCIF, ChimeraX-AddH, ChimeraX-PDB, ChimeraX-ShowAttr,
ChimeraX-AddCharge, ChimeraX-ShowSequences, ChimeraX-PDBBio, ChimeraX-
DistMonitor, ChimeraX-Mol2, ChimeraX-Clashes, and ChimeraX-ViewDockX
> toolshed install isolde noDeps true
No bundles were installed
Installed ChimeraX-ISOLDE (1.2.2)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 770, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.16.0'
distribution was not found and is required by ChimeraX-ISOLDE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 357, in initialize
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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: The 'ChimeraX-Clipper~=0.16.0' distribution was not found and is
required by ChimeraX-ISOLDE
ChimeraX-ISOLDE (installed) [version: 1.2.2] [api package: chimerax.isolde]
[category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive
Molecular Dynamics Flexible Fitting (iMDFF)]] [command: isolde [categories:
General] [synopsis: Command-line control of ISOLDE simulations]] [command:
rama [categories: General] [synopsis: Live Ramachandran validation of models]]
[command: rota [categories: General] [synopsis: Live rotamer validation of
models]] [command: ~rama [categories: General] [synopsis: Turn off live
Ramachandran validation of models]] [command: ~rota [categories: General]
[synopsis: Turn off live rotamer validation of models]]: custom initialization
failed
> toolshed show
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 770, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.16.0'
distribution was not found and is required by ChimeraX-ISOLDE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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: The 'ChimeraX-Clipper~=0.16.0' distribution was not found and is
required by ChimeraX-ISOLDE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.16.0' distribution was not found and is required by ChimeraX-ISOLDE
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.16.0' distribution was not found and is required by ChimeraX-ISOLDE
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed install ChimeraX-Clipper
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting ChimeraX-Clipper==0.16.0
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.16.0/ChimeraX_Clipper-0.16.0-cp38-cp38-win_amd64.whl
(22.9 MB) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper==0.16.0) (1.0)
Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper==0.16.0) (1.2.5)
Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper==0.16.0) (3.1.3)
Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper==0.16.0) (1.13.2)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
Clipper==0.16.0) (1.1) Requirement already satisfied: ChimeraX-
Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (2.0.1) Requirement already
satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
Clipper==0.16.0) (2.0) Requirement already satisfied: ChimeraX-Graphics~=1.0
in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (1.0) Requirement already satisfied:
ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (2.3) Requirement already
satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (2.4.1)
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-Clipper==0.16.0)
(1.0) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (1.0.1) Requirement already
satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (1.5) Requirement already satisfied:
ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-Clipper==0.16.0)
(1.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (1.4) Requirement already satisfied:
ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from
ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (1.0.1) Requirement already
satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
Clipper==0.16.0) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in
c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-Clipper==0.16.0) (1.2.1)
INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine
which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-pdb to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-opencommand to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-nucleotides to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-io to determine which version
is compatible with other requirements. This could take a while. INFO: pip is
looking at multiple versions of chimerax-dataformats to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-mmcif to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-graphics to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-geometry to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-core to determine which
version is compatible with other requirements. This could take a while. INFO:
pip is looking at multiple versions of chimerax-atomsearchlibrary to determine
which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of chimerax-connectstructure to
determine which version is compatible with other requirements. This could take
a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary
to determine which version is compatible with other requirements. This could
take a while. INFO: pip is looking at multiple versions of chimerax-atomic to
determine which version is compatible with other requirements. This could take
a while. INFO: pip is looking at multiple versions of chimerax-arrays to
determine which version is compatible with other requirements. This could take
a while. INFO: pip is looking at multiple versions of <Python from Requires-
Python> to determine which version is compatible with other requirements. This
could take a while. INFO: pip is looking at multiple versions of chimerax-
clipper to determine which version is compatible with other requirements. This
could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1
depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-
UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you
could try to: 1\. loosen the range of package versions you've specified 2\.
remove package versions to allow pip attempt to solve the dependency conflict
ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5
and chimerax-savecommand==1.4 because these package versions have conflicting
dependencies. ERROR: ResolutionImpossible: for help visit
https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
WARNING: You are using pip version 21.0.1; however, version 21.2.4 is
available. You should consider upgrading via the 'C:\Program
Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command.
> toolshed install ChimeraX-Clipper noDeps true
Successfully installed ChimeraX-Clipper-0.16.0
Installed ChimeraX-Clipper (0.16.0)
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed install ChimeraX-UI 1.2.1
ChimeraX-UI (1.2.1) is already installed
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed install ChimeraX-UI 1.4
ChimeraX-UI (1.4) does not match any bundles
> toolshed install isolde
ChimeraX-ISOLDE (1.2.2) is already installed
> toolshed install isolde
ChimeraX-ISOLDE (1.2.2) is already installed
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed install isolde
ChimeraX-ISOLDE (1.2.2) is already installed
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed install ChimeraX-UI
ChimeraX-UI (1.2.1) is already installed
> toolshed list full
List of installed bundles:
<string>:7: (WARNING/2) Definition list ends without a blank line; unexpected
unindent.
<string>:1: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
<string>:1: (WARNING/2) Inline literal start-string without end-string.
<string>:1: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
<string>:39: (WARNING/2) Definition list ends without a blank line; unexpected
unindent.
<string>:39: (WARNING/2) Inline literal start-string without end-string.
<string>:39: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
<string>:45: (ERROR/3) Unexpected indentation.
<string>:41: (WARNING/2) Inline literal start-string without end-string.
<string>:41: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
<string>:46: (WARNING/2) Block quote ends without a blank line; unexpected
unindent.
<string>:46: (WARNING/2) Inline literal start-string without end-string.
<string>:46: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
<string>:52: (WARNING/2) Inline literal start-string without end-string.
<string>:52: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
<string>:57: (ERROR/3) Unexpected indentation.
<string>:55: (WARNING/2) Inline strong start-string without end-string.
<string>:61: (WARNING/2) Block quote ends without a blank line; unexpected
unindent.
<string>:61: (WARNING/2) Inline literal start-string without end-string.
<string>:61: (WARNING/2) Inline interpreted text or phrase reference start-
string without end-string.
* AddCharge (1.0.1): Add partial charges to atoms
Category: Structure Editing
Add partial charges to atoms
* AddH (2.1.6): Add hydrogens
Category: Structure Editing
Add hydrogens, using steric criteria and optionally H-bonds
Command:
---
addh | Add hydrogens
* AlignmentAlgorithms (2.0): Sequence alignment algorithms
Category: Sequence alignment
This bundle provides a collection of sequence alignment algorithms.
* AlignmentHdrs (3.2): Alignment header support
Category: Sequence
Default useful alignment headers, and support for creating custom headers
* AlignmentMatrices (2.0): Sequence alignment similarity matrices
Category: Sequence alignment
Provide common sequence alignment BLOSUM similarity matrices.
* Alignments (2.1): Sequence alignment support
Category: Sequence
Sequence alignment support
Command:
---
sequence | control/open sequence alignments
* AmberInfo (1.0): Provide information about AmberTools installation
Category: Structure Editing
Provide information about AmberTools installation
* Arrays (1.0): C++ library for parsing numpy arrays
Category: Utility
C++ library for parsing numpy arrays passed from Python to C++ modules.
* Atomic (1.13.2): Atomic-structure functionality
Categories: Structure Analysis and Structure Editing
Python support for handling atomic structures
Selectors:
C1 | sp-hybridized carbon bonded to 2 other atoms
C1- | sp-hybridized carbon bonded to 1 other atom
C2 | sp2-hybridized carbon
C3 | sp3-hybridized carbon
Cac | carboxylate carbon
Car | aromatic carbon
D | other deuterium
DC | deuterium bonded to carbon
H | H (element)
HC | hydrogen bonded to carbon
N1 | sp-hybridized nitrogen bonded to 1 other atom
N1+ | sp-hybridized nitrogen bonded to 2 other atoms
N2 | sp2-hybridized nitrogen, double bonded
N2+ | sp2-hybridized nitrogen, double bonded, formal positive charge
N3 | sp3-hybridized nitrogen, neutral
N3+ | sp3-hybridized nitrogen, formal positive charge
Ng+ | guanidinium/amidinium nitrogen, partial positive charge
Npl | sp2-hybridized nitrogen, not double bonded
Ntr | nitro nitrogen
O1 | sp-hybridized oxygen
O1+ | sp-hybridized oxygen, formal positive charge
O2 | sp2-hybridized oxygen
O2- | carboxylate oxygen sharing formal negative charge; nitro group oxygen
O3 | sp3-hybridized oxygen
O3- | phosphate or sulfate oxygen sharing formal negative charge
Oar | aromatic oxygen
Oar+ | aromatic oxygen, formal positive charge
P3+ | sp3-hybridized phosphorus, formal positive charge
Pac | phosphate phosphorus
Pox | P-oxide phosphorus
S2 | sp2-hybridized sulfur
S3 | sp3-hybridized sulfur, neutral
S3+ | sp3-hybridized sulfur, formal positive charge
S3- | thiophosphate sulfur, sharing formal negative charge
Sac | sulfate, sulfonate, or sulfamate sulfur
Sar | aromatic sulfur
Son | sulfone sulfur
Sxd | sulfoxide sulfur
He | He (element)
Li | Li (element)
Be | Be (element)
B | B (element)
C | C (element)
N | N (element)
O | O (element)
F | F (element)
Ne | Ne (element)
Na | Na (element)
Mg | Mg (element)
Al | Al (element)
Si | Si (element)
P | P (element)
S | S (element)
Cl | Cl (element)
Ar | Ar (element)
K | K (element)
Ca | Ca (element)
Sc | Sc (element)
Ti | Ti (element)
V | V (element)
Cr | Cr (element)
Mn | Mn (element)
Fe | Fe (element)
Co | Co (element)
Ni | Ni (element)
Cu | Cu (element)
Zn | Zn (element)
Ga | Ga (element)
Ge | Ge (element)
As | As (element)
Se | Se (element)
Br | Br (element)
Kr | Kr (element)
Rb | Rb (element)
Sr | Sr (element)
Y | Y (element)
Zr | Zr (element)
Nb | Nb (element)
Mo | Mo (element)
Tc | Tc (element)
Ru | Ru (element)
Rh | Rh (element)
Pd | Pd (element)
Ag | Ag (element)
Cd | Cd (element)
In | In (element)
Sn | Sn (element)
Sb | Sb (element)
Te | Te (element)
I | I (element)
Xe | Xe (element)
Cs | Cs (element)
Ba | Ba (element)
La | La (element)
Ce | Ce (element)
Pr | Pr (element)
Nd | Nd (element)
Pm | Pm (element)
Sm | Sm (element)
Eu | Eu (element)
Gd | Gd (element)
Tb | Tb (element)
Dy | Dy (element)
Ho | Ho (element)
Er | Er (element)
Tm | Tm (element)
Yb | Yb (element)
Lu | Lu (element)
Hf | Hf (element)
Ta | Ta (element)
W | W (element)
Re | Re (element)
Os | Os (element)
Ir | Ir (element)
Pt | Pt (element)
Au | Au (element)
Hg | Hg (element)
Tl | Tl (element)
Pb | Pb (element)
Bi | Bi (element)
Po | Po (element)
At | At (element)
Rn | Rn (element)
Fr | Fr (element)
Ra | Ra (element)
Ac | Ac (element)
Th | Th (element)
Pa | Pa (element)
U | U (element)
Np | Np (element)
Pu | Pu (element)
Am | Am (element)
Cm | Cm (element)
Bk | Bk (element)
Cf | Cf (element)
Es | Es (element)
Fm | Fm (element)
Md | Md (element)
No | No (element)
Lr | Lr (element)
Rf | Rf (element)
Db | Db (element)
Sg | Sg (element)
Bh | Bh (element)
Hs | Hs (element)
Mt | Mt (element)
Ds | Ds (element)
Rg | Rg (element)
Cn | Cn (element)
Uut | Uut (element)
Fl | Fl (element)
Uup | Uup (element)
Uuh | Uuh (element)
Uus | Uus (element)
Uuo | Uuo (element)
backbone | backbone atoms
mainchain | backbone atoms
ions | ions
ligand | ligands
main | main structure
solvent | solvent
protein | proteins
nucleic | nucleic acids
nucleic-acid | nucleic acids
sel-residues | current selection promoted to full residues
strand | beta sheet strands
helix | protein helices
coil | protein coils
sidechain | side-chain atoms
sideonly | side-chain atoms
ribose | ribose
template-mismatch | residues whose heavy atoms don't match the residue
template
* AtomicLibrary (3.1.3): Atomic-structure C++ library
Categories: Structure Analysis and Structure Editing
C++ support for handling atomic structures
* AtomSearch (2.0): 3D atom search
Category: Structure Analysis
Quickly search 3D space for atom within a certain distance of another atom or
a xyz point.
* AtomSearchLibrary (1.0): 3D atom search support library
Category: Structure Analysis
C++ library for quickly search 3D space for atom within a certain distance of
another atom or a xyz point.
* AxesPlanes (2.0): Depict axes or planes
Category: Structure Analysis
Define and depict axes or planes, and make measurements involving them
Command:
---
define plane | Create a plane in the scene
* BasicActions (1.1): Basic actions for user-defined specifier names
Category: General
Manager for user-defined specifier names.
Names are listed and may be used to display, hide or color associated atoms,
cartoons and surfaces.
Tool:
---
Basic Actions | show/hide atoms, ribbons and surfaces
Commands:
name | Define specifier name as a string
name frozen | Define specifier name as atoms in current session matching a
string
name delete | Remove user-defined specifier name
name list | List user-defined specifier names
* BILD (1.0): BILD file reader
Category: Generic 3D objects
BILD is a simple text format that describes lines, polygons, and geometric
primitives such as spheres, boxes, cylinders, and cones with commands that was
used in UCSF Chimera. Character strings can also be included. The objects can
be specified in absolute coordinates and/or transformed and scaled
coordinates.
* BlastProtein (1.1): Search PDB/NR using BLAST
Category: Sequence
Use RBVI web service to search the PDB or NR database using BLAST. Results are
shown in a tool when a graphical interface is available; otherwise, the
results are logged.
Tool:
---
Blast Protein | Search PDB/NR using BLAST
Commands:
blastprotein | Search PDB/NR using BLAST
blastprotein mav | Display BLAST results in MultAlign Viewer
blastpdb | Search PDB/NR using BLAST
* BondRot (2.0): Bond rotation support
Category: Structure Editing
Bond rotation support
Command:
---
torsion | Report torsion angle of 4 atoms, or set it (middle two atoms must be
bonded for setting)
* BugReporter (1.0): Report bugs when an error occurs
Category: General
Tool to allow sending a ChimeraX bug report when an error occurs.
* BuildStructure (2.5.2): Create/modify structures
Category: Structure Analysis
Create/modify atomic structures
Tool:
---
Build Structure | Create/modify structures
Commands:
build | Create/modify structures
bond | Create bond(s)
~bond | Remove bond(s)
* Bumps (1.0): Find protrusions in density maps
Category: Volume Data
Find protrusions of cells in light microscopy 3d images.
Commands:
---
bumps | find protrusions in density maps
cbumps | find convex surface patches
* ButtonPanel (1.0): Create custom user interface panels
Category: General
Create custom user interface panels with buttons that run specified commands.
Command:
---
buttonpanel | Create custom user interface panels
* CageBuilder (1.0): Build polygonal meshes for oligomeric molecular assemblies
Category: Higher-Order Structure
Cage Builder creates polyhedral cages composed of hexagons, pentagons, squares
and other polygons. The cages can be decorated with atomic models to create
oligomeric molecular assemblies.
Tool:
---
Cage Builder | Build polygonal meshes
Command:
cage | Place copies of model on polygons of cage
* CellPack (1.0): Fetch cellPACK models from web
Category: Molecular structure
The ChimeraX-CellPack bundle provides support fo reading cellPack data files
via the Internet. See http://www.cellpack.org for more information.
* Centroids (1.1): Depict centroid of atoms
Category: Structure Analysis
Depict centroid of atoms
Command:
---
define centroid | Depict centroid
* ChemGroup (2.0): Detect chemically functional groups
Category: Structure Analysis
This bundle provides the ability for detection of functional groups in a
structure.
Selectors:
acyl-halide | R(C=O)X
adenine | 6-aminopurine
aldehyde | R(C=O)H
amide | R(C=O)NR2
amine | RxNHy
aliphatic-amine | RxNHy
aliphatic-primary-amine | RNH2
aliphatic-secondary-amine | R2NH
aliphatic-tertiary-amine | R3N
aliphatic-quaternary-amine | R4N+
aromatic-amine | RxNHy
aromatic-primary-amine | RNH2
aromatic-secondary-amine | R2NH
aromatic-tertiary-amine | R3N
aromatic-ring | aromatic
carbonyl | R2C=O
carboxylate | RCOO-
cytosine | 2-oxy-4-aminopyrimidine
disulfide | RSSR
ester | R(C=O)OR
ether-O | ROR
guanine | 2-amino-6-oxypurine
halide | RX
hydroxyl | COH or NOH
imine | R2C=NR
ketone | R2C=O
methyl | RCH3
nitrile | RC*N
nitro | RNO2
phosphate | PO4
phosphinyl | R2PO2-
phosphonate | RPO3-
purines | purine-like rings
pyrimidines | pyrimidine-like rings
sulfate | SO4
sulfonamide | RSO2NR2
sulfonate | RSO3-
sulfone | R2SO2
sulfonyl | R2SO2
thiocarbonyl | C=S
thioether | RSR
thiol | RSH
thymine | 5-methyl-2,4-dioxypyrimidine
uracil | 2,4-dioxypyrimidine
sulphate | SO4
sulphonamide | RSO2NR2
sulphonate | RSO3-
sulphone | R2SO2
sulphonyl | R2SO2
aromatic | aromatic
* Clashes (2.1): Find clashes/contacts in structures
Category: Structure Analysis
Find atomic clashes/contacts in structures
Tools:
---
Clashes | Find atom-atom clashes
Contacts | Find atom-atom contacts
Commands:
clashes | Find atoms with steric clashes
contacts | Finds atoms in contact with one another
~clashes | Clear clash pseudobond
~contacts | Clear contact pseudobond
* Clipper (0.16.0): Clipper: Efficient handling of volumetric data and symmetry
Category: General
Missing bundle description
Commands:
---
clipper | Command-line control of Clipper plugin for symmetry and map
visualisation
cview | Re-center view on a selection, and set view mode to centerOfView with
pivot indicator
* ColorActions (1.0): Simple interface for coloring objects
Category: Depiction
Simple interface for coloring atoms, bonds, surfaces, etc.
Tool:
---
Color Actions | color items
* ColorGlobe (1.0): Show directional resolution colored sphere
Category: General
Show directional resolution colored sphere.
* ColorKey (1.2.1): Add color key to graphics
Category: Depiction
Overlay color key on graphics scene.
Tool:
---
Color Key | add color key to graphics
Commands:
key | add color key to graphics
~key | remove color key
* CommandLine (1.1.4): Command line support
Category: General
Provide command line tool with command history.
Tool:
---
Command Line Interface | Command Line Interface
* ConnectStructure (2.0): Add bonds to structures that lack them
Category: Structure Analysis
Add bonds to structures based on inter-atomic distances
* Contacts (1.0): Display chain contact maps
Category: Molecular structure
Display chain contact maps.
Command:
---
interfaces | Display chain contact maps
* Core (1.2.5): ChimeraX Core Package
Category: Core
Missing bundle description
* CoreFormats (1.0): ChimeraX session support
Category: Atomic Data
ChimeraX session support
* coulombic (1.1.1): Compute/show electrostatic potential
Category: Surface/Binding Analysis
Compute and electrostatic potential according to Coulomb's law and either
create a corresponding volume (three-dimensional grid) or color a surface.
Command:
---
coulombic | Color surface based on electrostatics
* Crosslinks (1.0): Analyze crosslinks
Category: General
Plot or minimize crosslink lengths.
Command:
---
crosslinks | Plot or minimize crosslink lengths
* Crystal (1.0): Crystal symmetries
Category: Generic 3D objects
Provide matrices for crystallographic space groups.
* CrystalContacts (1.0): Show contacting asymmetric units in a crystal
Category: Higher-Order Structure
Makes copies of a crystal asymmetric unit for all contacting asymmetric units.
Tool:
---
Crystal Contacts | Show contacting subunits in a crystal
Command:
crystalcontacts | Make contacting copies of a crystal asymmetric unit
* DataFormats (1.1): Data format management
Category: Utilities
Manager for data format information
* DevelExtras (0.4.0): Implements commands and a tool to use non installed Bundles.
Category: Utilities
DevelExtras is a ChimeraX Bundle that implements commands and a tool to use
non installed Bundles. Intended for use only in development of Bundles.
Tool :: DevelExtras Tool :: Utilities :: A tool to open non installed Bundle
Tools Command :: devel module :: Utilities :: Imports Python module from file
path Command :: devel module reload :: Utilities :: Reloads the specified
Python module and its submodules Command :: devel module register :: Utilities
:: Registers a module's bundle Command :: devel bundle :: Utilities :: Loads a
Bundle from a folder path Command :: devel bundle info :: Utilities :: Loads a
BundleInfo object from a folder path Command :: devel bundle register ::
Utilities :: Registers a loaded bundle Command :: devel bundle onstart ::
Utilities :: Controls whether a bundle is loaded at the ChimeraX start
The next functionalities are supported and have been tested on ChimeraX
version 1.1:
* (Re)loading of Python modules
* Starting of Tools using the DevelExtras Tool
* Initialization of managers
* Adding of providers
* Registration of commands
* Registration of selectors
You can use the command devel bundle or the DevelExtras Tool to load your
bundle from the folder that contains the bundle_info.xml, resulting in the
creation of a BundleInfo object accesible from the session.devel.bundles
object, the loading (or reloading) of the corresponding Python module, the
initialization of managers, the adding of providers, the registration of
commands and the registration of selectors specified in the XML, also all the
tools specified in the XML can be started through the DevelExtras Tool.
In most cases is NOT necessary to restart ChimeraX to reload a bundle or a
module but some specific cases may not work. Follow the next link to see some
caveats of module reloading:
https://docs.python.org/3/library/importlib.html#importlib.reload
Currently, every time that the information in the bundle_info.xml changes, is
necessary to build the bundle in order to collect the generated metadata.
If you want your Bundle loaded at the ChimeraX start, you should execute the
next command:
devel bundle onload true BUNDLE_PATH
BUNDLE_PATH must be a directory and it must follow the standard source code
organization. It must contain a bundle_info.xml and a src folder with an
__init__.py that implements a bundle_api.
Tool:
---
DevelExtras Tool | A tool to open non installed Bundle Tools
Commands:
devel module | Imports Python module from file path
devel module reload | Reloads the specified Python module and its submodules
devel module register | Registers a module's bundle
devel bundle | Loads a Bundle from a folder path
devel bundle info | Loads a BundleInfo object from a folder path
devel bundle register | Registers a loaded bundle
devel bundle onstart | Controls whether a bundle is loaded at the ChimeraX
start
* Dicom (1.0): Read medical imaging and segmentations in DICOM format
Category: Volume Data
Read medical imaging and segmentations in DICOM format.
* DistMonitor (1.1.3): Interactive distance display
Category: Structure Analysis
Support for showing interactive distances on pseudobonds
Commands:
---
distance | determine distance
~distance | remove distance monitors
* DistUI (1.0): Distance measurement user interface
Category: Structure Analysis
Distance measurement tool, mouse mode, and context-menu entry
Tool:
---
Distances | inter-atomic distances
* Dssp (2.0): Compute/assign secondary structure
Category: Structure Analysis
Use Kabsch and Sander 'Define Secondary Structure of Proteins' algorithm to
compute and assign secondary structure. See
https://en.wikipedia.org/wiki/DSSP_(hydrogen_bond_estimation_algorithm)
* EMDB-SFF (1.0): EMDB SFF file reader
Category: Volume Data
Read segmentation files in EMDB SFF format.
* ExperimentalCommands (1.0): Experimental commands
Category: General
A collection of commands that might become a standard part of ChimeraX.
Commands:
---
ribbon | show cartoon for selected residues
ribbon hide | hide cartoon for selected residues
~ribbon | hide cartoon for selected residues
getcrd | report atomic coordinates
debug dumpspec | report what a specifier matches
* FileHistory (1.0): File History Panel
Category: General
Display thumbmails of the list of recently opened files in a panel.
Tool:
---
File History | Show recently opened files
* FunctionKey (1.0): Assign function keys to run commands
Category: General
Assign function keys to run commands
Commands:
---
ui functionkey | Assign function keys to run commands
functionkey | Assign function keys to run commands
* Geometry (1.1): Vector and coordinate system routines
Category: Utility
Routines for vectors, rotations, coordinate transformations, bounding boxes
and miscellaneous 3D scene geometry calculations.
* gltf (1.0): Read/write glTF 3d scene files
Category: Generic 3D objects
Read and write glTF 3d scene files.
* Graphics (1.0): OpenGL graphics rendering
Category: Graphics
Render scenes using a camera, view and hierarchy of drawings.
* Hbonds (2.1): Identify hydrogen bonds in and among structures
Category: Structure Analysis
Identify hydrogen bonds in and among structures
Tool:
---
H-Bonds | Find hydrogen bonds
Commands:
hbonds | Find hydrogen bonds
~hbonds | Clear hydrogen bonds
* Help (1.1): Show ChimeraX Help
Category: Documentation
Support help command and GUI.
Command:
---
help | Display ChimeraX help
* HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
Category: Higher-Order Structure
Create icosahedral mesh of hexagons and pentagons using h and k lattice
parameters.
Command:
---
hkcage | Create icosahedral cage
* IHM (1.0): Integrative Hybrid Models file reader
Category: Higher-Order Structure
Support Integrative Hybrid Models.
* ImageFormats (1.1): Support for saving images
Category: I/O
Support for saving images
* IMOD (1.0): IMOD model file reader
Category: Volume Data
Read meshes and contours from IMOD model files.
* IO (1.0.1): Python convenience input/output functions
Category: Input/Output
Python functions to more easily open files while allowing for comression, home
directory or environment variable expansion, etc.
* ISOLDE (1.2.2): ISOLDE: Interactive Structure Optimisation by Local Direct Exploration
Category: General
ISOLDE is a next-generation environment for interactive building and real-
space refinement of atomic models into electron density maps. It applies
interactive molecular dynamics to allow real-time, intuitive performance of
structural rearrangements from the small to the quite drastic, while
constantly maintaining physically reasonable interactions with the
surroundings.
Tool:
---
ISOLDE | Interactive Molecular Dynamics Flexible Fitting (iMDFF)
Commands:
isolde | Command-line control of ISOLDE simulations
rama | Live Ramachandran validation of models
rota | Live rotamer validation of models
~rama | Turn off live Ramachandran validation of models
~rota | Turn off live rotamer validation of models
* Label (1.0): Add text labels to graphics
Category: General
Overlay 2D text on graphics scene.
Commands:
---
2dlabels | add text labels to graphics
label | add 3d labels to graphics
~label | remove 3d labels from graphics
* ListInfo (1.1.1): Report attributes for selected atomic data
Category: General
Report attributes for selected atomic data
Command:
---
info | Report attributes for models and atomic data
* Log (1.1.2): Log support
Category: General
The ChimeraX-Log bundle provides a tool for viewing a log of what the user has
done.
Tool:
---
Log | Log of information and output
Commands:
echo | Log a line of text
log | manipulate the Log tool
* LookingGlass (1.1): LookingGlass holographic display
Category: General
Show graphics on LookingGlass holographic display.
Commands:
---
lookingglass | Render to LookingGlass holographic display
device lookingglass | Render to LookingGlass holographic display
* Maestro (1.8.1): Maestro reader
Category: I/O
Schrodinger Maestro input.
* Map (1.0.2): Density maps
Category: Volume Data
Display and analyze 3d image data
Tools:
---
Volume Viewer | Show density maps info
Map Coordinates | Adjust density map coordinates
Map Statistics | Report map minimum, maximum, mean, standard deviation, and
root mean square
Commands:
volume | control volume data display
vop | filter volume data
molmap | create density map for molecule
measure mapstats | report map statistics
* MapData (2.0): Volume data file formats
Category: Volume Data
Open and save volume data.
* MapEraser (1.0): Map eraser
Category: Volume data
Erase image data within a sphere.
Tool:
---
Map Eraser | Erase part of a density map within a sphere
Command:
volume erase | Erase part of a density map within a sphere
* MapFilter (2.0): Operations on maps
Category: Volume Data
Volume subcommands that create a new map from an existing map
* MapFit (2.0): Fit molecules into maps
Category: Volume Data
Rigid body motion of molecules and maps into other maps.
Tool:
---
Fit in Map | Fit molecules in maps
Command:
fitmap | fit molecules in maps
* MapSeries (2.0): Volume series
Category: Volume Data
Display and analyze 3d image time series.
Commands:
---
vseries | volume series
measure motion | volume series cactus prickles
* Markers (1.0): Place markers on density maps
Category: Volume Data
Mouse mode to place markers on density maps.
Tool:
---
Marker Placement | Place markers on density maps
Command:
marker | Place markers
* Mask (1.0): Mask a volume to a surface
Category: Volume Data
Copy a volume setting values outside a surface to zero
Commands:
---
volume mask | Mask a map to a surface
volume onesmask | Create a onesmask inside a surface
* MatchMaker (1.2.1): Superimpose structures
Category: Sequence
MatchMaker superimposes protein or nucleic acid structures by first creating
pairwise sequence alignments, then fitting the aligned residue pairs. Residue
types and/or secondary structure information can be used to create the initial
sequence alignments. Fitting uses one point per residue. Optionally, a
structure-based multiple sequence alignment can be computed after the
structures have been superimposed.
Tool:
---
Matchmaker | superimpose structures/chains
Commands:
matchmaker | Superimpose structures
mmaker | alias of matchmaker
* MDcrds (2.2): Molecular dynamics support
Category: Molecular Dynamics
This bundle provides parsers for various molecular dynamics file formats.
* MedicalToolbar (1.0.1): Toolbar for medical image analysis
Category: Toolbar
Provide a toolbar tab including buttons useful for medical image
visualization.
* Meeting (1.0): Shared interactive VR sessions.
Category: General
Show virtual reality hand controllers or mouse from ChimeraX running on a
remote machine.
Tool:
---
Meeting | Multi-person sessions
Commands:
meeting start | Create a ChimeraX meeting
meeting join | Join a ChimeraX meeting
meeting | Same as meeting join
meeting close | Close a ChimeraX meeting
meeting info | Report ChimeraX meeting info
meeting settings | Report or set meeting default settings
meeting server | Report or define meeting server names
meeting unname | Deregister a meeting name
meeting send | Copy my scene to all other meeting participants
* MLP (1.1): Molecular lipophilicity calculation
Category: Molecular structure
Molecular lipophilicity calculation
Based on:
> pyMLP Molecular Lipophilic Potential evaluator Copyright (c) 2006-2007
> Julien Lefeuvre <lefeuvrejulien@yahoo.fr>
>
> Software License Agreement (BSD-new License)
>
> Copyright (c) 2006-2015, Julien Lefeuvre <julien@lefeuv.re> Contributors: -
> Julien Lefeuvre <julien@lefeuv.re>
>
> All rights reserved.
Command:
---
mlp | Molecular lipophilicity calculation
* mmCIF (2.3): mmCIF format read/write
Category: Molecular structure
This bundle provides the abiility to fetch and read Macromolecular CIF files.
* MMTF (2.1): MMTF format read/write
Category: Molecular structure
This bundle provides the abiility to fetch and read MMTF files.
* Modeller (1.0.1): Interface to Modeller
Category: Sequence
Perform comparitive or loop modeling.
Tool:
---
Modeller Comparative | Generate comparative models
Commands:
modeller comparative | Generate comparative model
modeller scores | Fetch Modeller scores for a model
* ModelPanel (1.0.1): ChimeraX Model Panel
Category: General
ChimeraX Model Panel.
Tool:
---
Model Panel | model panel
* ModelSeries (1.0): Display sequences of models one by one
Category: General
Display sequences of models one by one.
Command:
---
mseries | Display sequence of models one by one
* Mol2 (2.0): Mol2 reader/writer
Category: I/O
Sybyl Mol2 input/output.
* MolecularDynamicsViewer (1.2): A UI tool for loading and viewing a multiframe pdb file
Categories: MolecularDynamics, MD, and Visualization
Loads a multiframe pdb file for people to view. Generally used for loading
molecular dynamics simulations to be viewed within ChimeraX.
Tool:
---
Molecular Dynamics Viewer | Shows a UI to display Molecular Dynamics
* Morph (1.0): Morph atomic structures
Category: Morph Structures
This bundle provides the morph command to smoothly interpolate between
different conformations of an atomic structure.
Command:
---
morph | morph atomic structures
* MouseModes (1.1): Provide right button mouse mode tool
Category: Toolbar
Provide a series of icons for changing the assigment of the right mouse
button.
Commands:
---
ui mousemode | set/list mouse modes
mousemode | set/list mouse modes
* Movie (1.0): Commands to record movies
Category: General
Provide commands for capturing images and assembling them into movies.
Command:
---
movie | record movies
* Neuron (1.0): Read SWC neuron trace files
Category: Generic 3D objects
Read SWC neuron trace files.
* Nucleotides (2.0.1): Create nucleotide-specific displays
Category: General
Create special nucleotide-specific displays of the base and sugar moieties.
Such displays are generally combined with various atomic representations
and/or cartoons.
See also
Nucleic acid visualization with UCSF Chimera.
System Message: WARNING/2 (`<string>`, line 7)
Definition list ends without a blank line; unexpected unindent.
Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res. 2006 Feb 14;34(4):e29.
Commands:
---
nucleotides | Manipulate nucleotide representations
~nucleotides | Undo nucleotide representations
* OpenCommand (1.5): Manages 'open' command extensibility
Category: Commands
Handles 'open' command and manages bundles extending its capabilities
Commands:
---
open | Open/fetch data files
usage open | Show syntax of 'open' command
* PDB (2.4.1): PDB format read/write
Category: Molecular structure
This bundle provides the abiility to fetch and read PDB files.
* PDBBio (1.0): PDB biological assembly fetch
Category: Molecular structure
Fetch biological assembly models from the PDB database.
* PDBLibrary (1.0.1): C++ PDB support
Category: Molecular structure
This provides a PDB-related C++ library.
* PDBMatrices (1.0): Crystal and biological unit matrices
Category: Molecular structure
Extract crystal and biological unit matrices from mmCIF and PDB files.
* PickBlobs (1.0): Measure and color blobs
Category: Volume data
Measure and color connected parts of a surface.
Tool:
---
Measure and Color Blobs | Measure and color connected parts of surfaces
Command:
measure blob | Measure and color connected parts of surfaces
* Positions (1.0): Read and write model position matrices
Category: Generic 3D objects
Read and write model position matrices.
* PresetMgr (1.0.1): Preset management
Category: Depiction
Manager for preset information
Command:
---
preset | apply "preset" depiction to models
* PubChem (2.0.1): PubChem fetch
Category: Molecular structure
This bundle provides the abiility to fetch PubChem files.
* ReadPbonds (1.0): Read in pseudobonds from a file
Category: Generic 3D objects
Read in pseudobonds from a text file.
* Registration (1.1): Register ChimeraX
Category: Utilities
Register ChimeraX with RBVI and help us document the impact this software is
having in the scientific community. The information you supply will only be
used for reporting summary statistics to NIH.
Tool:
---
Registration | Register ChimeraX with RBVI
Commands:
registration status | Report registration status
registration file | Report registration file location or apply registration
file
* RemoteControl (1.0): Control ChimeraX from other apps
Category: General
Provide the ability to send commands to ChimeraX from other applications.
Command:
---
remotecontrol xmlrpc | synopsis
* ResidueFit (1.0): Display fit of residues to density map
Category: General
Display fit of residues to density map.
Command:
---
resfit | Display slider to show fit of each residue in density map
* RestServer (1.1): Starts REST server to execute commands from network requests
Category: General
Starts REST server to execute commands from network requests
Server is listening on a local port for HTTP requests. The request content is
executed as a ChimeraX command and the generated output is returned as the
response.
Command:
---
remotecontrol rest | Control REST server
* RNALayout (1.0): Make RNA models
Category: Structure Editing
Create RNA models from secondary structure information.
Commands:
---
rna path | make RNA marker model
rna model | make RNA atomic model
* RotamerLibMgr (2.0): Manage rotamer libraries
Category: Structure Editing
Manager for rotamer libraries (provided by other bundles)
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
Category: Structure Editing
Dunbrack 2010 backbone-dependent rotamer library -- 5% stepdown
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
Category: Structure Editing
Dynameomics backbone-independent rotamer library -- March '12
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
Category: Structure Editing
Richardson lab backbone-independent rotamer libraries
* SaveCommand (1.4): Manages 'save' command extensibility
Category: Commands
Handles 'save' command and manages bundles extending its capabilities
Commands:
---
save | Save data files
usage save | Show 'save' command syntax
* SchemeMgr (1.0): HTTP scheme management
Category: Utilities
Manager for tracking HTTP schemes used in ChimeraX bundles
* SDF (2.0): SDF file reader
Category: Atomic Data
The ChimeraX-SDF bundle provides support for reading structures from MDL
SDF/MOL files
* Segger (1.0): Segment map
Category: Volume data
Segment density maps using Segger watershed methods.
Tools:
---
Segment Map | Segment density maps using Segger algorithms
Fit to Segments | Fit atomic models in segmented maps
Command:
segger | Operate on Segger segmentations
* Segment (1.0): Watershed segment calculation
Category: Volume data
Calculate watershed segmentation regions for density maps.
Command:
---
segmentation | color and surface segmentations
* SeqView (2.3): Sequence viewer
Category: Sequence
Sequence/alignment viewer.
* Shape (1.0.1): Make models for geometric shapes
Category: Generic 3D objects
Create geometric shapes like spheres, cylinders, cones, tubes, icosahedrons.
Commands:
---
shape boxPath | create a box beam model
shape cone | create a cone model
shape cylinder | create a cylinder model
shape ellipsoid | create an ellipsoid model
shape icosahedron | create a icosahedron model
shape rectangle | create a rectangle model
shape ribbon | create a ribbon model
shape sphere | create a sphere model
shape triangle | create a triangle model
shape tube | create a tube model
* Shell (1.0): Interactive Python shell
Category: General
Provide IPython interactive shell, https://ipython.org/ipython-
doc/3/interactive/qtconsole.html. The current ChimeraX session is available in
the global variable 'session'.
Tool:
---
Shell | Python shell
* Shortcuts (1.0): Button and keyboard shortcuts
Category: Toolbar
Provide button and keyboard shortcuts for common commands.
Command:
---
ks | keyboard shortcuts
Selectors:
selAtoms | Selected atoms, or if none selected then all atoms.
selMaps | Selected maps, or if none selected then displayed maps.
selModels | Selected models, or if none selected then all models.
* ShowAttr (1.0): Render/select by attribute
Category: Depiction
Change coloring or depiction or selection based on attribute value
* ShowSequences (1.0): Choose/show structure sequences
Category: Sequence
Simgle interface to bring up a sequence viewer for structure chains
Tool:
---
Show Sequence Viewer | show chain sequences
* SideView (1.0): Side view of scene
Category: General
Show camera settings (eye position and clipping planes) overlayed on the scene
and allow for them to be interactively changed.
Tool:
---
Side View | Show side view interface
* Smiles (2.0.1): SMILES fetch
Category: Molecular structure
This bundle provides the abiility to get 3D structures for SMILES strings.
* SmoothLines (1.0): Smooth network of lines
Category: General
Smooth network of lines.
Command:
---
smoothlines | Smooth networks of lines
* SpaceNavigator (1.0): Space Navigator device support
Category: General
This bundle allows using 3dconnexion space navigator devices to move models.
Command:
---
device snav | Control SpaceNavigator device
* StdCommands (1.3.1): Standard commands
Category: Structure Analysis
General purpose commands always available in ChimeraX
Commands:
---
alias | create shorthand version of command
alias list | list command aliases
alias delete | remove command alias
~alias | remove command alias
align | superimpose specific parts of structures
angle | Report or set angle between atoms/objects
camera | change "camera" parametrs of main viewing window
cartoon | show stylized representation of structure
~cartoon | stop show stylized representation of structure
cd | change ChimeraX's current working directory
clip | control clipping of models
~clip | stop clipping of models
close | close models
cofr | set center of rotation
~cofr | revert to default center of rotation
color | change model colors
colour | change model colors
color delete | delete custom color names
color list | list custom color names
color name | define custom color names
color show | show definition of custom color names
colordef | define custom color names
~colordef | remove custom color names
colourdef | define custom color names
~colourdef | remove custom color names
coordset | show specific coordinate set (a.k.a. frame or conformer)
crossfade | fade from one view to another
defattr | set many Python attribute values for structure elements from a file
delete | delete parts of a structure
dssp | compute/assign secondary structure
exit | quit ChimeraX
quit | quit ChimeraX
fly | interpolate motions for animations
graphics | control 3D graphics parameters
hide | stop displaying (parts of) a model
~show | stop displaying (parts of) a model
~display | stop displaying (parts of) a model
lighting | change lighting
lighting model | change per-model lighting
material | change visual surface properties of 3D objects
measure buriedarea | measure surface area buried by contacting structures
measure center | measure center of mass of maps or atoms
measure convexity | color surface based on local convexity
measure inertia | measure moments of inertia
measure length | measure path length of connected markers
measure rotation | measure rotation of one model relative to another
measure symmetry | compute map symmetry
move | move (parts of) a model relative to others
palette | list available color palettes
perframe | execute commands every frame
~perframe | stop execution of commands every frame
pwd | report current working directory
rainbow | "rainbow" color (parts of) structures
rename | change name or ID of model
rmsd | measure RMSD between two sets of atoms
rock | rock models back and forth
roll | continuously turn model(s) about an axis
runscript | run a Python script with arguments
select | select models or parts thereof
~select | unselect models or parts thereof
set | set various global parameters
~set | revert various global parameters to their default value
setattr | set Python attribute values for structure elements
show | display (parts of) a model
display | display (parts of) a model
size | change display size of structural elements
split | split a model into multiple models
stop | stop an ongoing motion
style | change style of depiction for strcutural elements
sym | generate symmetry mates
tile | tile models onto grid
time | time execution and redisplay of commands
transparency | change transparency of (parts of) models
turn | rotate a model about an axis
undo | undo a command
redo | redo an undone command
usage | show the required syntax for a command
version | report ChimeraX version number
view | change/save/restore 3D view
wait | wait a given amount of frames before executing the next command
windowsize | set the size of the 3D window
wobble | move models in figure 8 motion
select zone | select (parts of) models within a 3D zone
zoom | zoom in/out
Selectors:
sel | selected atoms
all | everything
pbonds | pseudobonds
hbonds | hydrogen bonds
hbondatoms | hydrogen bond atoms
* STL (1.0): STL file read/write
Category: Generic 3D objects
This bundle provides the ability to read and write StereoLithography (STL)
files.
* Storm (1.0): STORM file reader
Category: Generic 3D object
Read STORM microscopy text files with x,y,z points and widths.
* StrudelScore (0.1.9): Strudel score visualisation tool
Category: General
* Tool:
---
Strudel Score | Strudel score visualisation
Command:
strudel | Print center of mass of atoms
* Struts (1.0): struts for 3D printing
Category: Molecular structure
Add bonds between atoms of a molecule to strengthen it for 3-d printing.
Command:
---
struts | provide struts for 3D printing
* Surface (1.0): Surface calculations
Category: Generic 3D objects
Routines to calculate and manipulate triangulated surfaces.
Tools:
---
Hide Dust | hide small surface blobs
Surface Zone | show surface near atoms
Color Zone | color surface to match nearby atoms
Measure Volume and Area | measure surface area and enclosed volume
Surface Color | Color surface by geometry or map value
Commands:
color electrostatic | color surface by electrostatic potential map
color sample | color surface by map value
color gradient | color surface by map gradient norm
color radial | color surface by distance from a point
color cylindrical | color surface by distance from an axis
color height | color surface by distance from a plane
color image | color surface using an image file
surface | create/modify surfaces
~surface | delete surface
surface showPatches | show atom surface patches for existing surfaces
surface hidePatches | hide patches of existing surfaces for specified atoms
surface close | close surfaces for specified atoms
surface style | set surface mesh, solid, or dot display style
surface squaremesh | mask mesh lines that are not parallel x, y or z
surface showall | turn of maskig of triangles and edges
surface cap | control surface caps when clipping
surface dust | hide small pieces of surfaces
surface undust | show small pieces of surfaces
surface zone | show surface near atoms
surface unzone | show all of surface
surface check | check surface topology
sop | alias for surface commands
volume splitbyzone | split volume by color zone
measure sasa | measure solvent-accessible surface area
measure volume | measure enclosed surface volume
measure area | measure surface area
* SwapAA (2.0): Swap amino acid
Category: Structure Editing
Swap amino acid
Command:
---
swapaa mousemode | Replaces amino acid with a specified standard amino acid
* SwapRes (2.1): Swap residue side chains
Category: Structure Editing
Swap amino/nucleic acid side chains, using rotamer libraries where applicable
Tool:
---
Rotamers | swap residue side chain
Command:
swapaa | swap residue side chain
* TapeMeasure (1.0): Tape measure mouse mode
Category: General
Measure distance between two points in scene
* Test (1.0): simple regression test
Category: General
Execute a series of commands to test for regressions.
Commands:
---
debug test | Run through test sequence of commands to check for errors
debug exectest | Test running executable from bundle
debug expectfail | Expect command to fail
* TestManager (0.3): manager for test cases
Category: Utilities
Manager for test cases (à la unittest) for ChimeraX bundles. Creating test
cases can allow bundle developers to quickly test the functionality of their
bundle and whether their bundle remains functioning after code is edited or
ChimeraX updates. Test cases can be created by subclassing the TestWithSession
class of this bundle. For convenience, this subclass of unittest.TestCase has
a session attribute, which can be used to execute commands or start tools in
the same way a user would. Tests can be implemented either as methods of a
TestWithSession subclass with names that begin with "test_" or by implementing
the runTest method, as is standard with unittest.TestCase. A structure
validation function is also included, which can be used to compare two
`chimerax.atomic.AtomicStructure`s based on their elements, bonding, and RMSD
between the two structures. As an example: ```python from
chimerax.core.commands import run
System Message: WARNING/2 (`<string>`, line 1); backlink
Inline interpreted text or phrase reference start-string without end-string.
System Message: WARNING/2 (`<string>`, line 1); backlink
Inline literal start-string without end-string.
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from TestManager import TestWithSession from TestManager.validation import
validate_atomic_structures as validate
class AngleCmdTest(TestWithSession):
"""tests associated with the angle command"""
def test_change_angle(self):
"""test setting the angle of a simple structure" # open a water molecule
run(self.session, "open
/home/CoolUser/my_bundle/tests/structures/water_molecule.mol2") # set the
H-O-H angle to 104.5 degrees run(self.session, "angle @H1 @O1 @H2 104.5")
# grab the water model # before and after every test, all open models are
closed # therefore, our water molecule should be the first and only open model
mdl = self.session.models.list()[0]
# open a reference structure, which has an H-O-H angle of 104.5 and the same
bonding pattern as the previous water molecule run(self.session, "open
/home/CoolUser/my_bundle/tests/structures/water_angle_ref.mol2") # grab this
reference structure ref_mdl = self.session.models.list()[1]
# the test will fail if the two water molecules are dissimilar # the "thresh"
keyword specifies the tolerance on the RMSD # see the documentation associated
with this method for more details self.assertTrue(validate(mdl, ref_mdl,
thresh="tight"))
System Message: WARNING/2 (`<string>`, line 39)
Definition list ends without a blank line; unexpected unindent.
```
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System Message: WARNING/2 (`<string>`, line 39); backlink
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To add this test, include a provider for the test_manager in your
bundle_info.xml file. Whether developers choose to add their test cases to
their main bundle, or create a separate bundle specifically for tests is up to
them. ```xml <Providers manager="test_manager">
System Message: WARNING/2 (`<string>`, line 41); backlink
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System Message: ERROR/3 (`<string>`, line 45)
Unexpected indentation.
> <Provider name="angle_command"/>
System Message: WARNING/2 (`<string>`, line 46)
Block quote ends without a blank line; unexpected unindent.
</Providers> ```
System Message: WARNING/2 (`<string>`, line 46); backlink
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System Message: WARNING/2 (`<string>`, line 46); backlink
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The run_provider method of the bundle containing this test should return their
TestWithSession subclass. Multiple providers can be added to the manager.
```python class _TestBundle(BundleAPI):
System Message: WARNING/2 (`<string>`, line 52); backlink
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System Message: WARNING/2 (`<string>`, line 52); backlink
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> @staticmethod def run_provider(session, name, mgr, **kw):
>
> System Message: WARNING/2 (`<string>`, line 55); backlink
>
> Inline strong start-string without end-string.
>
> System Message: ERROR/3 (`<string>`, line 57)
>
> Unexpected indentation.
>
>> if mgr is session.test_manager:
>>
>>
>> if name == "angle_command":
>> from .tests.angle_command import AngleCmdTest return AngleCmdTest
System Message: WARNING/2 (`<string>`, line 61)
Block quote ends without a blank line; unexpected unindent.
```
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System Message: WARNING/2 (`<string>`, line 61); backlink
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There are two simple ways to run tests. One is using the test command, for
which a list of provider names can be specified to only run certain tests.
When run without arguments, the test command will run all tests. Running help
test will list the available tests in the log. The "Run Tests" tool, found in
the "Utilities" section, can also be used to run your tests. The tool lists
all providers, and the providers can be selected to only run test methods of
those providers. After tests are run, results can be viewed in the tool. For
both the test command the the tool, results are printed to the log.
Tools:
---
Run Tests | run tests
Linter | check for errors in code
Commands:
test | run a test
linter | run a code linter
* Toolbar (1.0.1): Toolbar
Category: General
Tabbed Toolbar
Provides a Windows ribbon-style toolbar interface
Tool:
---
Toolbar | a Windows ribbon-style toolbar
* ToolshedUtils (1.2): Toolshed bundle utilities
Category: Utilities
Utilties for installing, uninstalling, and updating bundles from the ChimeraX
Toolshed
Tool:
---
Updates | synopsis
* Tug (1.0): Tug on atoms with molecular dynamics
Category: Molecular structure
Tug on atoms with molecular dynamics.
* UI (1.2.1): ChimeraX user interface
Category: User Interface
ChimeraX user interface
Commands:
---
ui | control user interface behavior
tool | Manipulate tools
* uniprot (2.1): UniProt database support
Category: Sequence
Fetch Uniprot sequence info
* UnitCell (1.0): Show crystal unit cell
Category: Higher-Order Structure
Copy an atomic model solved by X-ray crystallography to fill out the unit
cell.
Tool:
---
Unit Cell | Show crystal unit cell
Command:
unitcell | Place copies of atomic structure in crystal unit cell
* ViewDockX (1.0): Analyze ligand-receptor docking results
Category: General
Display docking results as structures and table.
UCSF DOCK output in PDB and mol2 formats are supported.
Tool:
---
ViewDockX | display docking results
Commands:
viewdockx | specify models as docking results
viewdockx down | Simulate down-arrow key in ViewDockX
viewdockx up | Simulate up-arrow key in ViewDockX
* Vive (1.1): Virtual reality headset support
Category: General
Use virtual reality headsets with SteamVR.
Commands:
---
vr | Render to virtual reality headsets
device vr | Render to virtual reality headsets
* VolumeMenu (1.0): Volume menu
Category: Volume data
Add a top level volume menu.
Tool:
---
Show Volume Menu | Add a top level volume menu
* VTK (1.0): Legacy VTK file reader and writer
Category: Generic 3D objects
The ChimeraX-VTK bundle provides support for reading polygonal data from
legacy VTK files and writing those files for molecular structures and
surfaces.
* WavefrontOBJ (1.0): Wavefront OBJ file read/write
Category: Generic 3D objects
This bundle provides the ability to read and write Wavefront OBJ files.
* WebCam (1.0): Combine camera video with graphics
Category: General
Produce augmented reality videos combining web cam video with rendered
graphics.
Commands:
---
webcam | Show webcam video
device webcam | Show webcam video
* WebServices (1.0): Web service and HTTP request support
Category: General
Infrastructure support for web services and HTTP requests
* Zone (1.0): Mouse mode to show atom and map zones
Category: Volume Data
Display atoms and density near an atom chosen with the mouse
Command:
---
zone | Show atoms and map in a small region
> ui tool show ISOLDE
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 470, in get_module
m = importlib.import_module(self.package_name)
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 41, in <module>
__version__ = _version()
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\\__init__.py", line 39, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 884, in require
needed = self.resolve(parse_requirements(requirements))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 539, in start_tool
api = self._get_api(session.logger)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 489, in _get_api
m = self.get_module()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 472, 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-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1552, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 203, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1
(c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages),
Requirement.parse('ChimeraX-UI~=1.4'), {'ChimeraX-SaveCommand'})
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 545, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 3.3.14831 Core Profile Forward-Compatible Context 21.5.2 27.20.21003.8013
OpenGL renderer: AMD Radeon R5 430
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Dell Inc.
Model: OptiPlex 5080
OS: Microsoft Windows 10 家庭版 (Build 19043)
Memory: 59,827,888,128
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10500 CPU @ 3.10GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-DevelExtras: 0.4.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StrudelScore: 0.1.9
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-TestManager: 0.3
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.1
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
MolecularDynamicsViewer: 1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Dependency conflict trying to install ISOLDE into 1.2.5 |
comment:2 by , 4 years ago
| Description: | modified (diff) |
|---|---|
| Resolution: | → limitation |
| Status: | assigned → closed |
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Incompatible version of UI bundle was installed. Unfortunately to remove it is complicated because it is in the user customization of ChimeraX.
To fix this, two directories need to be removed. To find out where in the filesystem they are, use the
info path}} command to to find the {{{user versioned data directory.Then use a file browser to go to that directory. On Windows, you might need to check the
Hidden Filesentry in theViewmenu. Then go into thesite-packagesdirectory and remove theChimeraX_UI-1.2.1.dist-infodirectory. And then go into thechimeraxdirectory (inside ofsite-packages) and remove theuidirectory.