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<p class="MsoNormal"><span style="color:#1F497D">Thank you Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I was trying to install chimeraX 1.5 on linux.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from
<a href="https://www.cgl.ucsf.edu/chimerax/download.html">https://www.cgl.ucsf.edu/chimerax/download.html</a></span><span style="color:#002060"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#002060">However, apparently it contains binaries and not source code.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#002060">The binaries did not work in our centos 7.9 (glibc)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#002060">So I tried to use singularity – I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">However, got the pyqt6 error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">The singularity file I have built is attached<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I activated it within command<o:p></o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph" style="color:#1F497D;margin-left:0cm;mso-list:l0 level1 lfo1">
singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build<o:p></o:p></li></ul>
<p class="MsoNormal"><span style="color:#1F497D">While putting the binaries in a directory I transferred to the image<o:p></o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph" style="color:#1F497D;margin-left:0cm;mso-list:l0 level1 lfo1">
singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img<o:p></o:p></li></ul>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">And then within singularity:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> echo $PATH<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> export PATH=/chimerax-1.5/bin:$PATH<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> echo $LD_LIBRARY_PATH<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/chimerax-1.5/lib:/.singularity.d/libs<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> ls /chimerax-1.5/lib/libQt6Core.so.6<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/chimerax-1.5/lib/libQt6Core.so.6<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity><o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> ChimeraX<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">NOTE: Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">_run_module_as_main<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> return _run_code(code, main_globals, None,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> exec(code, run_globals)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">line 1035, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> exit_code = init(sys.argv)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">line 579, in init<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> from chimerax.ui import initialize_qt<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py",<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">line 21, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> from .gui import MainToolWindow, initialize_qt, menu_capitalize<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">29, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> from Qt.QtWidgets import QApplication<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:red"> <span style="background:yellow;mso-highlight:yellow">from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">ImportError: libQt6Core.so.6: cannot open shared object file: No such file or<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">_See log for complete Python traceback._<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity><o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity> </span></b><span style="color:#1F497D">python<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Python 3.9.11 (main, Nov 28 2022, 23:56:15)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">[GCC 8.3.0] on linux<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Type "help", "copyright", "credits" or "license" for more information.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">>>> import PyQt6<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">>>> import PyQt6.QtCore<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "<stdin>", line 1, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">>>><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b>From:</b> Tom Goddard <goddard@sonic.net> <br>
<b>Sent:</b> Saturday, December 10, 2022 12:39 AM<br>
<b>To:</b> Barak Yariv <barakyariv@gmail.com><br>
<b>Cc:</b> 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><br>
<b>Subject:</b> Re: [chimerax-users] using chimerx on unix<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Barak,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> 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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Dec 9, 2022, at 10:45 AM, Barak Yariv via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Dear Chimera team,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I'm from the ConSurf webservere<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="https://consurf.tau.ac.il/consurf_index.php">https://consurf.tau.ac.il/consurf_index.php</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">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<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Can you help us?<o:p></o:p></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Barak<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
ChimeraX-users mailing list<br>
<a href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a><br>
Manage subscription:<br>
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><o:p></o:p></p>
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</blockquote>
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<p class="MsoNormal"><o:p> </o:p></p>
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