Opened 5 years ago

Last modified 5 years ago

#4015 assigned defect

ISOLDE installed but not Clipper dependency

Reported by: l.loeff@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version: 1.1
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-20.1.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed ChimeraX-HKCage-1.3 ChimeraX-ISOLDE-1.1.0 ChimeraX-
Phenix-0.1  
Installed ChimeraX-HKCage (1.3)  
Installed ChimeraX-ISOLDE (1.1.0)  
Installed ChimeraX-Phenix (0.1)  

Traceback (most recent call last):  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import  
File "<frozen importlib._bootstrap>", line 983, in _find_and_load  
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 728, in exec_module  
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed  
File "/Users/luukloeff/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 41, in <module>  
__version__ = _version()  
File "/Users/luukloeff/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 39, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 899, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 785, in resolve  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.15.0'
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
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, 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~=0.15.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  

ChimeraX-ISOLDE (installed) [version: 1.1.0] [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  

> ui tool show ISOLDE

Traceback (most recent call last):  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import  
File "<frozen importlib._bootstrap>", line 983, in _find_and_load  
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 728, in exec_module  
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed  
File "/Users/luukloeff/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 41, in <module>  
__version__ = _version()  
File "/Users/luukloeff/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 39, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 899, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 785, in resolve  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.15.0'
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
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 530, in start_tool  
api = self._get_api(session.logger)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, 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~=0.15.0' 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
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.15.0' 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~=0.15.0' distribution was not found and is required by ChimeraX-ISOLDE  
  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  

> ui tool show ISOLDE

Traceback (most recent call last):  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import  
File "<frozen importlib._bootstrap>", line 983, in _find_and_load  
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 728, in exec_module  
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed  
File "/Users/luukloeff/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 41, in <module>  
__version__ = _version()  
File "/Users/luukloeff/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 39, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 899, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 785, in resolve  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.15.0'
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
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 530, in start_tool  
api = self._get_api(session.logger)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, 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~=0.15.0' 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
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.15.0' 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~=0.15.0' distribution was not found and is required by ChimeraX-ISOLDE  
  
File
"/private/var/folders/0j/gkf3rvnj1ws6jdndk5mt83s80000gn/T/AppTranslocation/99A585F3-786A-41B7-AC0C-CC1F613BB379/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.0.47
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 1554.60.15.0.0 (iBridge: 18.16.13026.5.2,0)

Software:

    System Software Overview:

      System Version: macOS 11.0.1 (20B50)
      Kernel Version: Darwin 20.1.0
      Time since boot: 32 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        VG27A:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: L1LMQS059457
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-Phenix: 0.1
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (1)

comment:1 by pett, 5 years ago

Cc: Tristan Croll added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE installed but not Clipper dependency
Version: → 1.1

Reported by Luuk Loeff

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