[chimerax-users] using chimerx on unix

[Dvora Shait]

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

  *   singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build
While putting the binaries in a directory I transferred to the image

  *   singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img

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 at sonic.net>
Sent: Saturday, December 10, 2022 12:39 AM
To: Barak Yariv <barakyariv at gmail.com>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>; Nir Ben-Tal <bental at tauex.tau.ac.il>; Dvora Shait <dvory at tauex.tau.ac.il>; Danny Shaked <danny at 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



On Dec 9, 2022, at 10:45 AM, Barak Yariv via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Dear Chimera team,

I'm from the ConSurf webservere
https://consurf.tau.ac.il/consurf_index.php

We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error:  missing library PyQT6

Can you help us?

Barak
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