<html><head></head><body><div class="yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div>Dear Greg,</div><div><br></div><div dir="ltr" data-setdir="false">Based on your advice, currently the chimera window can display. However by fetching a pdb from RCSB, the protein molecule cannot be shown by default, and for the Presets setting, the protein can only be shown in the all-atoms format.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">In addition, after laoding a mrc map which can be shown very well in the windows version of chimera, this newly installed linux chimera cannot display the mrc map at all.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">I amlloking forward to getting your advice.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Smith.<br></div><div id="yahoo_quoted_9496627708" class="yahoo_quoted">
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On Thursday, August 27, 2020, 3:44:29 PM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
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<p>Okay, that looks like a real bug. And I can reproduce it. For
some reason the X11 server thinks that the physical screen size is
0x0 millimeters (run xdpyinfo to confirm). The solution I found
was to stop using Wayland and go back to use X11. You do that by
editting /etc/gdm/custom.conf and changing "#WaylandEnable=false"
to "WaylandEnable=false", and then rebooting.</p>
<p>Some notes about using Virtual Box, or any virtual machine. In
general, they are not a good idea for running chimera. Even when
they are configured to use 3D acceleration, it is still an extra
layer between chimera and the graphics hardware. And make sure
you have 3D acceleration turned on -- for Virtual Box, you need to
check the "Enable 3D Acceleration" box in the Display settings. </p>
<p> -- Greg<br clear="none">
</p>
<div class="yiv6233896054yqt0086236901" id="yiv6233896054yqt70184"><div class="yiv6233896054moz-cite-prefix">On 8/26/2020 6:30 AM, Smith Lee wrote:<br clear="none">
</div>
<blockquote type="cite">
</blockquote></div></div><div class="yiv6233896054yqt0086236901" id="yiv6233896054yqt68811"><div><div class="yiv6233896054ydp2bd6ecb2yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;">
<div dir="ltr">
<div>Dear Greg,<br clear="none">
<br clear="none">
"libXScrnSaver" was succesffuly installed by "sudo yum
install libXScrnSaver".<br clear="none">
<br clear="none">
Currently when I run "./chimera" in
"UCSF-Chimera64-1.14/bin", the chimera graphical showed
temporarily and immediately disappear, with the following
errot:<br clear="none">
File ".../lib/python2.7/lib-tk/Tkinter.py", line 1947, in
pack_configure<br clear="none">
+self.options(cnf,kw)<br clear="none">
_tkinter.TclError: bad pad value "1p": must be positive
screen distance.<br clear="none">
<br clear="none">
In addition, my Centos 8 was installed in Virtual Box.<br clear="none">
<br clear="none">
I am looking forward to getting your advice on how to solve
the issue.<br clear="none">
<br clear="none">
Smith</div>
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<div class="yiv6233896054yahoo_quoted" id="yiv6233896054yahoo_quoted_9169524441">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div> On Tuesday, August 25, 2020, 4:10:09 PM GMT+8, Smith Lee
<a rel="nofollow" shape="rect" class="yiv6233896054moz-txt-link-rfc2396E" ymailto="mailto:smith_lee123@yahoo.com" target="_blank" href="mailto:smith_lee123@yahoo.com"><smith_lee123@yahoo.com></a>
wrote: </div>
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<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">
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<div class="yiv6233896054yqt9689771960" id="yiv6233896054yqt16098">
<div class="yiv6233896054yahoo_quoted" id="yiv6233896054yahoo_quoted_8428790141">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div> On Tuesday, August 25, 2020, 11:48:06 AM
GMT+8, Greg Couch <a rel="nofollow" shape="rect" class="yiv6233896054moz-txt-link-rfc2396E" ymailto="mailto:gregc@cgl.ucsf.edu" target="_blank" href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a>
wrote: </div>
<div><br clear="none">
</div>
<div><br clear="none">
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<div>
<div id="yiv6233896054">
<div>
<p>You still haven't said which version of
Linux you have. That might be critical.<br clear="none">
</p>
<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">
</p>
<div class="yiv6233896054yqt3548506643" id="yiv6233896054yqt05626">
<div class="yiv6233896054moz-cite-prefix">On
8/24/2020 8:32 PM, Smith Lee wrote:<br clear="none">
</div>
<blockquote type="cite"> </blockquote>
</div>
</div>
<div class="yiv6233896054yqt3548506643" id="yiv6233896054yqt79183">
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<div class="yiv6233896054ydp795bc74cyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;">
<div dir="ltr">Dear All,</div>
<div dir="ltr"><br clear="none">
</div>
<div dir="ltr">With the request from
Greg, the result is as following.<br clear="none">
</div>
<div dir="ltr">
<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>
<div><br clear="none">
</div>
<div dir="ltr">The version of
Chimera involved is: <span><a rel="nofollow" shape="rect" class="yiv6233896054" 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>
<div><br clear="none">
</div>
</div>
<div dir="ltr">
<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">
</div>
<div dir="ltr"><br clear="none">
</div>
<div dir="ltr">Smith<br clear="none">
</div>
<br clear="none">
</div>
</div>
<div><br clear="none">
</div>
</div>
</div>
<div class="yiv6233896054yahoo_quoted" id="yiv6233896054yahoo_quoted_8731858175">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div> On Tuesday, August 25, 2020,
8:48:29 AM GMT+8, Greg Couch <a rel="nofollow" shape="rect" class="yiv6233896054moz-txt-link-rfc2396E" ymailto="mailto:gregc@cgl.ucsf.edu" target="_blank" href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a>
wrote: </div>
<div><br clear="none">
</div>
<div><br clear="none">
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<div>
<div id="yiv6233896054">
<div>
<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">
</p>
<p> HTH,</p>
<p> Greg<br clear="none">
</p>
<div class="yiv6233896054yqt5702304131" id="yiv6233896054yqt52485">
<div class="yiv6233896054moz-cite-prefix">On
8/24/2020 5:07 AM, Smith Lee
wrote:<br clear="none">
</div>
<blockquote type="cite"> </blockquote>
</div>
</div>
<div class="yiv6233896054yqt5702304131" id="yiv6233896054yqt04102">
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<div class="yiv6233896054yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;">
<div dir="ltr">
<div><span style="font-size:12.0pt;" lang="EN-US">Dear All,</span>
<p class="yiv6233896054ydp8588767MsoNormal"><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="yiv6233896054moz-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>
</p>
<p class="yiv6233896054ydp8588767MsoNormal"><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="yiv6233896054ydp8588767MsoNormal"><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="yiv6233896054ydp8588767MsoNormal"><span style="font-size:12.0pt;" lang="EN-US"></span><span style="font-size:12.0pt;" lang="EN-US">Smith</span>
</p>
</div>
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<pre class="yiv6233896054moz-quote-pre">_______________________________________________
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