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<div dir="ltr" data-setdir="false"><div>Dear Greg,<br><br>"libXScrnSaver" was succesffuly installed by "sudo yum install libXScrnSaver".<br><br>Currently when I run "./chimera" in "UCSF-Chimera64-1.14/bin", the chimera graphical showed temporarily and immediately disappear, with the following errot:<br>File ".../lib/python2.7/lib-tk/Tkinter.py", line 1947, in pack_configure<br>+self.options(cnf,kw)<br>_tkinter.TclError: bad pad value "1p": must be positive screen distance.<br><br>In addition, my Centos 8 was installed in Virtual Box.<br><br>I am looking forward to getting your advice on how to solve the issue.<br><br>Smith</div><div><br></div></div><div><br></div>
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On Tuesday, August 25, 2020, 4:10:09 PM GMT+8, Smith Lee <smith_lee123@yahoo.com> wrote:
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<div dir="ltr"><div>Dear Greg,<br clear="none"><br clear="none">Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。<br clear="none"><br clear="none">In the drectory "UCSF-Chimera64-1.14", I run:<br clear="none">ldd ./lib/python2.7/lib-dynload/_tkinter.so<br clear="none"><br clear="none">It gave:<br clear="none"> linux-vdso.so.1 (0x00007ffcd61fa000)<br clear="none"> libtk8.6.so => not found<br clear="none"> libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000)<br clear="none"> libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000)<br clear="none"> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000)<br clear="none"> libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000)<br clear="none"> libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000)<br clear="none"> libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000)<br clear="none"> libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000)<br clear="none"> libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000)<br clear="none"> /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000)<br clear="none"> libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)<br clear="none"><br clear="none">But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib".<br clear="none"><br clear="none">When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following:<br clear="none">“~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module><br clear="none">import_tkinter # If this fails you Python may not be configured for Tk<br clear="none">ImportError: libXss.so.1: cannot open sharted object file: No such file or directory.<br clear="none"><br clear="none">I am looking forward to getting your advice on how to have the issue solved.<br clear="none"><br clear="none">Smith<br clear="none"><br clear="none"></div><div><br clear="none"></div></div><div><br clear="none"></div>
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On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
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<p>You still haven't said which version of Linux you have. That
might be critical.<br clear="none">
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<p>I left out a step for the ldd, do:</p>
<p> env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd
/UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so</p>
<p>It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/.</p>
<p> -- Greg<br clear="none">
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<div class="yiv2202370123yqt3548506643" id="yiv2202370123yqt05626"><div class="yiv2202370123moz-cite-prefix">On 8/24/2020 8:32 PM, Smith Lee wrote:<br clear="none">
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<div dir="ltr">Dear All,</div>
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<div dir="ltr">With the request from Greg,
the result is as following.<br clear="none">
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<div>$ ldd _tkinter.so<br clear="none">
linux-vdso.so.1 (0x00007ffcd61fa000)<br clear="none">
libtk8.6.so => not found<br clear="none">
libtcl8.6.so => /lib64/libtcl8.6.so
(0x00007fe164edd000)<br clear="none">
libX11.so.6 => /lib64/libX11.so.6
(0x00007fe164b99000)<br clear="none">
libpthread.so.0 => /lib64/libpthread.so.0
(0x00007fe164979000)<br clear="none">
libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000)<br clear="none">
libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000)<br clear="none">
libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000)<br clear="none">
libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000)<br clear="none">
libxcb.so.1 => /lib64/libxcb.so.1
(0x00007fe163bf1000)<br clear="none">
/lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000)<br clear="none">
<div> libXau.so.6 => /lib64/libXau.so.6
(0x00007fe1639ed000)</div>
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<div dir="ltr">The version of Chimera
involved is: <span><a rel="nofollow" shape="rect" class="yiv2202370123" target="_blank" href="http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x86_64/chimera-1.14-linux_x86_64.bin">chimera-1.14-linux_x86_64.bin</a></span>
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<div dir="ltr">I am looking forward to
getting your advice on how to solve the issue, and if <span>libtk8.6.so
is what was missing, how to install it especially in
the directory <span>
/UCSF-chimera64-1.14/lib/python2.7/lib-dynload/.</span></span><br clear="none">
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<div dir="ltr">Smith<br clear="none">
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<div> On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg
Couch <a rel="nofollow" shape="rect" class="yiv2202370123moz-txt-link-rfc2396E" ymailto="mailto:gregc@cgl.ucsf.edu" target="_blank" href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a> wrote: </div>
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<p>The CHIMERA/bin directory should not be on your path,
nor should you run chimera when in the CHIMERA/bin
directory. As part of the installation process it
asks you where you want to put a symbolic link to the
chimera binary on your PATH, e.g., if /usr/local/bin
is on your PATH, then one of the choices will be
/usr/local/bin/chimera. If you didn't do that, then
you need to use the full path to the chimera binary.
So go back to your home directory or a directory with
the data you are working on, and run chimera from
there. You can make a symbolic link to the chimera
binary anytime to make running it easier.</p>
<p>If that still doesn't work, then I would suspect that
there is shared library that is missing. Run:</p>
<p> ldd
/UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so</p>
<p>And look for missing libraries. Then use your Linux
distribution's package manager to install it. And
please let everyone know which libraries are missing.
And also please share which version of Linux you are
using. With that information, we should be able to
figure out which system packages are missing.<br clear="none">
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<p> HTH,</p>
<p> Greg<br clear="none">
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<div class="yiv2202370123moz-cite-prefix">On 8/24/2020
5:07 AM, Smith Lee wrote:<br clear="none">
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<div><span style="font-size:12.0pt;" lang="EN-US">Dear
All,</span>
<p class="yiv2202370123ydp8588767MsoNormal"><span style="font-size:12.0pt;" lang="EN-US"></span><span style="font-size:12.0pt;" lang="EN-US">From
<a rel="nofollow" shape="rect" class="yiv2202370123moz-txt-link-freetext" target="_blank" href="https://www.cgl.ucsf.edu/chimera/download.html">https://www.cgl.ucsf.edu/chimera/download.html</a>
I have downloaded the
chimera-1.14-linux_x86_64.bin, and have
tried to install it exactly based on the
accompanied exact "Instructions”. After the
installation completed, I got to the bin
folder, and try to launch chimera with
./chimera. However her</span><span style="font-size:12.0pt;">俄<span lang="EN-US"> it says the installed
/UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py
was not configured for my python.</span></span>
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<p class="yiv2202370123ydp8588767MsoNormal"><span style="font-size:12.0pt;" lang="EN-US"></span><span style="font-size:12.0pt;" lang="EN-US">Will
you please let me know how to configure TK
for my python, which was a downloaded
component of the chimera package?</span> </p>
<p class="yiv2202370123ydp8588767MsoNormal"><span style="font-size:12.0pt;" lang="EN-US"></span><span style="font-size:12.0pt;" lang="EN-US">Best
wishes,</span> </p>
<p class="yiv2202370123ydp8588767MsoNormal"><span style="font-size:12.0pt;" lang="EN-US"></span><span style="font-size:12.0pt;" lang="EN-US">Smith</span>
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