Thank you Tom,
I was trying to install chimeraX 1.5 on linux.
We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from
https://www.cgl.ucsf.edu/chimerax/download.html
However, apparently it contains binaries and not source code.
The binaries did not work in our centos 7.9 (glibc)
So I tried to use singularity – I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb
However, got the pyqt6 error
I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error
The singularity file I have built is attached
I activated it within command
While putting the binaries in a directory I transferred to the image
And then within singularity:
Singularity> echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Singularity> export PATH=/chimerax-1.5/bin:$PATH
Singularity> echo $LD_LIBRARY_PATH
/chimerax-1.5/lib:/.singularity.d/libs
Singularity> ls /chimerax-1.5/lib/libQt6Core.so.6
/chimerax-1.5/lib/libQt6Core.so.6
Singularity>
Singularity> ChimeraX
NOTE: Traceback (most recent call last):
File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in
_run_module_as_main
return _run_code(code, main_globals, None,
File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 1035, in <module>
exit_code = init(sys.argv)
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 579, in init
from chimerax.ui import initialize_qt
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py",
line 21, in <module>
from .gui import MainToolWindow, initialize_qt, menu_capitalize
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line
29, in <module>
from Qt.QtWidgets import QApplication
File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in
<module>
from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION
ImportError: libQt6Core.so.6: cannot open shared object file: No such file or
directory
BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or
directory
File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in
from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION
_See log for complete Python traceback._
Singularity>
Singularity> python
Python 3.9.11 (main, Nov 28 2022, 23:56:15)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import PyQt6
>>> import PyQt6.QtCore
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
>>>
From: Tom Goddard <goddard@sonic.net>
Sent: Saturday, December 10, 2022 12:39 AM
To: Barak Yariv <barakyariv@gmail.com>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Nir Ben-Tal <bental@tauex.tau.ac.il>; Dvora Shait <dvory@tauex.tau.ac.il>; Danny Shaked <danny@shaked.tau.ac.il>
Subject: Re: [chimerax-users] using chimerx on unix
Hi Barak,
The ChimeraX Linux daily build was broken yesterday, missing Qt, but is fixed today. You might want to use ChimeraX 1.5 instead. We released it just a few weeks ago and that is the version most ChimeraX users will have.
Tom