Error finding files in same folder as session file (previously: Error restoring frozen selection)

[wieland@…]

The following bug report has been submitted:
Platform:        Darwin-16.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-07)
Description
When trying to open an older version (that I saved but did not open, since I kept using the same session and saved it to the latest version) I am asked to replace missing files, which are in fact not missing but still in the very same directory and with the very same name, so it feels like the real error lies elsewhere? Can I make it reopen the session without reopening the volume? 
The latest version I can open without a problem is close to two weeks old, I named some selections in the meantime, could that cause such an error? 
I use ChimeraX on MacOS X 10.12.6

Log:
UCSF ChimeraX version: 0.92 (2020-02-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/wieland/Desktop/old_argyrin_chX_sesh.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 653, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot  
cmd.name_frozen(session, name, Objects(**value))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/cmd.py", line 54, in name_frozen  
raise UserError("nothing is selected by specifier")  
chimerax.core.errors.UserError: nothing is selected by specifier  
  
opened ChimeraX session  




OpenGL version: 4.1 ATI-1.54.3
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Also, files are not being found despite being in the same locations.

[Conrad Huang]

The problem with restoring frozen names that no longer refer to anything is "fixed" in 78b8af251. Instead of terminating session restoration, ChimeraX now just reports a warning and continues.

Reassigning to TomG to take a look at the "missing file" problem in the description.

[Tom Goddard]

I have never seen session restore not find volume files unless those volume files were really gone. You would have to provide an example session to debug that.

[Maximiliane.Wieland@…]

Hi,
I hope it is okay I am responding here.
I am thinking the error was indeed due to frozen names no longer  
referring to anything. I closed a pdb the selections referred to.  
maybe making me reopen volumes was the programme's way trying to take  
care of it?

 From the prevoius email I gather that the bug has been corrected in  
the new daily build?
"The problem with restoring frozen names that no longer refer to anything
  is "fixed" in [changeset:78b8af251].  Instead of terminating session
  restoration, ChimeraX now just reports a warning and continues."
If so, I will try tomorrow and report back, so possibly the bug has  
been solved.
Can I delete frozen name selections?

Thank you very much for your help!
Best,
Maxi

ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> schrieb/wrote::

[Tom Goddard]

Yes, replying to these emails is the right way to discuss this bug.

I don't think finding volumes linked to the session is related to named selections, but I agree you should try with the new ChimeraX build.

The command "~namesel somename" deletes the named selection "somename" as described in the documentation

	https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/namesel.html

[wieland@…]

Hi,

I actually have a different problem now that the application will not start at all, also without opening a session.
The latest daily build I can find on the webpage is 20-02-2020?

[wieland@…]

Unfortunately the system tells me that they new daily 2020-02-25 build does not run on MacOs 10.12, only on 10.13
When trying to figure out why the 2020-02-20 wouldn’t work, I eventually got an error telling me that the encoded QtCore was built for Mac OS X 10.13 (see below), but wanted to wait for the newest daily build in case the error was just temporary

 wieland$ /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX ; exit;
Traceback (most recent call last):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ChimeraX_main.py", line 894, in <module>
    exit_code = init(sys.argv)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ChimeraX_main.py", line 517, in init
    from chimerax.ui import initialize_qt
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/__init__.py", line 21, in <module>
    from .gui import MainToolWindow, initialize_qt, menu_capitalize
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/gui.py", line 88, in <module>
    from PyQt5.QtWidgets import QApplication
ImportError: dlopen(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyQt5/QtWidgets.abi3.so, 2): Symbol not found: _futimens
  Referenced from: /Applications/ChimeraX_Daily.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/lib/QtCore.framework/Versions/5/QtCore (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib
 in /Applications/ChimeraX_Daily.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/lib/QtCore.framework/Versions/5/QtCore
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
…completed.

[Tom Goddard]

ChimeraX requires macOS 10.13 or higher. Current macOS is 10.15 and 10.13 was released in 2017. We started requiring 10.13 I believe about a week ago because we updated the Qt window toolkit ChimeraX is based on from 5.12 to 5.14 which required 10.13. In general our policy is to only support the most recent 3 versions of macOS.

I see the ChimeraX download page has not been updated (currently says macOS 10.12 is required).

[Tom Goddard]

If you eventually are able to reproduce the session restore error finding volume files, please report a new bug.