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#1889 closed defect (can't reproduce)
Incorrect ChimeraX version for ISOLDE
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | pett, Conrad Huang | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.7 (2018-08-07) 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: 0.7 (2018-08-07) OpenGL version: 4.1 ATI-1.68.20 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl Downloading bundle ChimeraX_ISOLDE-0.9.24-cp36-cp36m-macosx_10_9_x86_64.whl Traceback (most recent call last): File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/widgets/htmlview.py", line 366, in download_finished session=self.session) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py", line 841, in _pip_install results = self._run_pip(command) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip raise RuntimeError(s) RuntimeError: Processing /Users/martinf/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl Requirement not upgraded as not directly required: ChimeraX-Atomic>=0.7 in /Applications/ChimeraX.app/Contents/lib/python3.6/site-packages (from ChimeraX-ISOLDE==1.0b2) Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2) Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-macosx_10_9_x86_64.whl (36.1MB) Collecting ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) Cache entry deserialization failed, entry ignored Could not find a version that satisfies the requirement ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) (from versions: ) No matching distribution found for ChimeraX-Core==0.8 (from ChimeraX- ISOLDE==1.0b2) You are using pip version 9.0.3, however version 19.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. RuntimeError: Processing /Users/martinf/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl Requirement not upgraded as not directly required: ChimeraX-Atomic>=0.7 in /Applications/ChimeraX.app/Contents/lib/python3.6/site-packages (from ChimeraX-ISOLDE==1.0b2) Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2) Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-macosx_10_9_x86_64.whl (36.1MB) Collecting ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) Cache entry deserialization failed, entry ignored Could not find a version that satisfies the requirement ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) (from versions: ) No matching distribution found for ChimeraX-Core==0.8 (from ChimeraX- ISOLDE==1.0b2) You are using pip version 9.0.3, however version 19.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip raise RuntimeError(s) See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. Successfully installed ChimeraX-Clipper-0.3 ChimeraX-ISOLDE-0.9.24 Installed ChimeraX-ISOLDE (0.9.24) toolshed show ISOLDE Traceback (most recent call last): File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py", line 527, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py", line 1183, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) File "/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/__init__.py", line 29, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/tools.py", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File "/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/tool.py", line 166, in __init__ self.isolde = isolde.Isolde(self) File "/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/isolde.py", line 310, in __init__ self.omega_validator = validation.OmegaValidator(self._annotations) File "/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/validation.py", line 687, in __init__ self._initialize_drawings() File "/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/validation.py", line 708, in _initialize_drawings d.vertices = numpy.zeros([0,3],numpy.float32) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 220, in __setattr__ super(Drawing, self).__setattr__(key, value) AttributeError: can't set attribute During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py", line 846, in <lambda> run(ses, "toolshed show %s" % quote_if_necessary(tool_name))) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2561, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show bi.start_tool(session, tool_name) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py", line 533, 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: can't set attribute chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: can't set attribute File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py", line 533, 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. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. OpenGL version: 4.1 ATI-1.68.20 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (11)
comment:1 by , 6 years ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
| Resolution: | → not a bug |
| Status: | new → closed |
| Summary: | ChimeraX bug report submission → Incorrect ChimeraX version for ISOLDE |
follow-up: 2 comment:2 by , 6 years ago
Hi!
I tried ChimeraX 0.8 and installed ISOLDE 1.0b2. I could launch both of them and open a pdb and mrc file, but they suddenly crashed and ChimeraX does not start any more (and cannot trace any error message). This is why I tried ChimeraX 0.7.
I could not find anything on the internet. Any suggestion?
Thank you in advance,
Best
Fab
On 25/04/2019, 13:26, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#1889: Incorrect ChimeraX version for ISOLDE
-----------------------------------------+--------------------
Reporter: fabrizio.martino@… | Owner: (none)
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Unassigned | Version:
Resolution: not a bug | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+--------------------
Changes (by tic20):
* project: => ChimeraX
* platform: => all
* status: new => closed
* resolution: => not a bug
Comment:
You'll need to be using the ChimeraX 0.8 release version to install
ISOLDE. Once you have that running, make sure you choose ISOLDE 1.0b2 from
the ToolShed (not the 0.9.24 version).
--
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comment:3 by , 6 years ago
| Component: | Unassigned → Third Party |
|---|
comment:4 by , 6 years ago
| Resolution: | not a bug |
|---|---|
| Status: | closed → reopened |
comment:5 by , 6 years ago
| Cc: | added |
|---|---|
| Owner: | set to |
| Status: | reopened → assigned |
Start ChimeraX from the Unix command line and see if you get an error message there. If you don't know how to do that, here are the steps:
1) Open Terminal.app, which is in Applications→Utilities
2) type "cd " into Terminal (note the space)
3) Drag and drop the ChimeraX icon onto the terminal window (this should add text after the "cd ")
4) Append "/Contents/MacOS/ChimeraX" to that text (no space in between)
5) Hit Return -- ChimeraX will try to start...
comment:6 by , 6 years ago
| Status: | assigned → feedback |
|---|
follow-up: 7 comment:7 by , 6 years ago
Hi!
Thank you for your prompt reply!
I started ChimeaX from the Terminal using the command
Cd /Applications/ChimeraX.app/Contents/MacOS
Open -a ChimeraX
And it works! ChimeraX launches, I can open Isolde and load the demo pdb.
Double clicking on the icon still does not work, but I am happy to start the software through the terminal.
Thank you!
Best
fab
On 25/04/2019, 18:36, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#1889: Incorrect ChimeraX version for ISOLDE
-----------------------------------------+----------------------
Reporter: fabrizio.martino@… | Owner: tic20
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+----------------------
Changes (by pett):
* cc: pett, conrad (added)
* owner: (none) => tic20
* status: reopened => assigned
Comment:
Start ChimeraX from the Unix command line and see if you get an error
message there. If you don't know how to do that, here are the steps:
1) Open Terminal.app, which is in Applications→Utilities
2) type "cd " into Terminal (note the space)
3) Drag and drop the ChimeraX icon onto the terminal window (this should
add text after the "cd ")
4) Append "/Contents/MacOS/ChimeraX" to that text (no space in between)
5) Hit Return -- ChimeraX will try to start...
--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F1889%23comment%3A5&data=02%7C01%7C%7Cb87b9ffb8a9746b30dc208d6c9a48fe5%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C636918105967290074&sdata=xfNdyo9Hnck9JO6hz1kal7X%2Bv6WSEYiN8kirhO3HdZ0%3D&reserved=0>
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ChimeraX Issue Tracker
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
comment:8 by , 6 years ago
| Status: | feedback → accepted |
|---|
comment:9 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Hi Fabrizio,
I'm glad something is working. :-) FYI, using "open -a ChimeraX" will open *some* ChimeraX, not necessarily the one from the /Applications/ChimeraX.app/Contents/MacOS (if you have more that one ChimeraX version installed). In that directory, typing "./ChimeraX" will definitely execute the one from that directory. But maybe you don't care! :-)
--Eric
follow-up: 10 comment:10 by , 6 years ago
Hi Eric,
Thank you for the tip, did not know that ./ Works in the Mac terminal. I am new to MacOS and still a bit rusty (more comfortable with Ubuntu, but my institution supports apple :( ).
Thank you for your help.
Looking forward to use ChimeraX and Isolde!
Best
Fab
Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, April 26, 2019 6:59:25 PM
Cc: conrad@cgl.ucsf.edu; Fabrizio Martino; pett@cgl.ucsf.edu; tic20@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1889: Incorrect ChimeraX version for ISOLDE
#1889: Incorrect ChimeraX version for ISOLDE
-----------------------------------------+--------------------
Reporter: fabrizio.martino@… | Owner: tic20
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: can't reproduce | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+--------------------
Changes (by pett):
* status: accepted => closed
* resolution: => can't reproduce
Comment:
Hi Fabrizio,
I'm glad something is working. :-) FYI, using "open -a ChimeraX"
will open *some* ChimeraX, not necessarily the one from the
/Applications/ChimeraX.app/Contents/MacOS (if you have more that one
ChimeraX version installed). In that directory, typing "./ChimeraX" will
definitely execute the one from that directory. But maybe you don't care!
:-)
--Eric
--
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You'll need to be using the ChimeraX 0.8 release version to install ISOLDE. Once you have that running, make sure you choose ISOLDE 1.0b2 from the ToolShed (not the 0.9.24 version).