On installation of Chimera linux version
Dear All, Fromhttps://www.cgl.ucsf.edu/chimera/download.html I have downloaded thechimera-1.14-linux_x86_64.bin, and have tried to install it exactly based onthe accompanied exact "Instructions”. After the installation completed, Igot to the bin folder, and try to launch chimera with ./chimera. However her俄 it says the installed/UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for mypython. Will you please let me know howto configure TK for my python, which was a downloaded component of the chimerapackage? Best wishes, Smith
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. If that still doesn't work, then I would suspect that there is shared library that is missing. Run: ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so 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. HTH, Greg On 8/24/2020 5:07 AM, Smith Lee wrote:
Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package?
Best wishes,
Smith
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear All, With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) The version of Chimera involved is: chimera-1.14-linux_x86_64.bin I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/. Smith On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: 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. If that still doesn't work, then I would suspect that there is shared library that is missing. Run: ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so 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. HTH, Greg On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄 it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package? Best wishes, Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
You still haven't said which version of Linux you have. That might be critical. I left out a step for the ldd, do: env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/. -- Greg On 8/24/2020 8:32 PM, Smith Lee wrote:
Dear All,
With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
The version of Chimera involved is: chimera-1.14-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x86_64/chimera-1.14-linux_x86_64.bin>
I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/.
Smith
On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
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.
If that still doesn't work, then I would suspect that there is shared library that is missing. Run:
ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
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.
HTH,
Greg
On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package?
Best wishes,
Smith
_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Greg, Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。 In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib". When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory. I am looking forward to getting your advice on how to have the issue solved. Smith On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: You still haven't said which version of Linux you have. That might be critical. I left out a step for the ldd, do: env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/. -- Greg On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All, With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) The version of Chimera involved is: chimera-1.14-linux_x86_64.bin I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/. Smith On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: 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. If that still doesn't work, then I would suspect that there is shared library that is missing. Run: ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so 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. HTH, Greg On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄 it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package? Best wishes, Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I would still like to know which version of Linux you have. Red Hat Enterprise Linux 7? Ubuntu 18.10? OpenSUSE Leap 15.2? etc. The "ImportError: libXss.so.1: cannot open sharted object file: No such file or directory." means that your system is missing the X screensaver package. On CentOS/RHEL, that is the libXScrnSaver package. On Debian-based systems, that is the libxss1 pacakge. -- Greg On 8/25/2020 1:10 AM, Smith Lee wrote:
Dear Greg,
Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。
In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so
It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib".
When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory.
I am looking forward to getting your advice on how to have the issue solved.
Smith
On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
You still haven't said which version of Linux you have. That might be critical.
I left out a step for the ldd, do:
env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/.
-- Greg
On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All,
With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
The version of Chimera involved is: chimera-1.14-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x86_64/chimera-1.14-linux_x86_64.bin>
I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/.
Smith
On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> wrote:
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.
If that still doesn't work, then I would suspect that there is shared library that is missing. Run:
ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
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.
HTH,
Greg
On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package?
Best wishes,
Smith
_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Greg, My linus is Centos 8. Smith On Wednesday, August 26, 2020, 1:14:41 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: I would still like to know which version of Linux you have. Red Hat Enterprise Linux 7? Ubuntu 18.10? OpenSUSE Leap 15.2? etc. The "ImportError: libXss.so.1: cannot open sharted object file: No such file or directory." means that your system is missing the X screensaver package. On CentOS/RHEL, that is the libXScrnSaver package. On Debian-based systems, that is the libxss1 pacakge. -- Greg On 8/25/2020 1:10 AM, Smith Lee wrote: Dear Greg, Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。 In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib". When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory. I am looking forward to getting your advice on how to have the issue solved. Smith On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: You still haven't said which version of Linux you have. That might be critical. I left out a step for the ldd, do: env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd/UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/. -- Greg On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All, With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) The version of Chimera involved is: chimera-1.14-linux_x86_64.bin I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/. Smith On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: 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. If that still doesn't work, then I would suspect that there is shared library that is missing. Run: ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so 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. HTH, Greg On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄 it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package? Best wishes, Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
So the administrator of your CentOS 8 computer needs to install the libXScrnSaver package, by running the command: sudo dnf install -y libXscrnSaver Please let me know if that fixes your problem. -- Greg On 8/25/2020 6:15 PM, Smith Lee wrote:
Dear Greg,
My linus is Centos 8.
Smith
On Wednesday, August 26, 2020, 1:14:41 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
I would still like to know which version of Linux you have. Red Hat Enterprise Linux 7? Ubuntu 18.10? OpenSUSE Leap 15.2? etc.
The "ImportError: libXss.so.1: cannot open sharted object file: No such file or directory." means that your system is missing the X screensaver package. On CentOS/RHEL, that is the libXScrnSaver package. On Debian-based systems, that is the libxss1 pacakge.
-- Greg
On 8/25/2020 1:10 AM, Smith Lee wrote: Dear Greg,
Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。
In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so
It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib".
When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory.
I am looking forward to getting your advice on how to have the issue solved.
Smith
On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> wrote:
You still haven't said which version of Linux you have. That might be critical.
I left out a step for the ldd, do:
env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/.
-- Greg
On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All,
With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
The version of Chimera involved is: chimera-1.14-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x86_64/chimera-1.14-linux_x86_64.bin>
I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/.
Smith
On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> wrote:
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.
If that still doesn't work, then I would suspect that there is shared library that is missing. Run:
ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
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.
HTH,
Greg
On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package?
Best wishes,
Smith
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Dear Greg, "libXScrnSaver" was succesffuly installed by "sudo yum install libXScrnSaver". Currently when I run "./chimera" in "UCSF-Chimera64-1.14/bin", the chimera graphical showed temporarily and immediately disappear, with the following errot: File ".../lib/python2.7/lib-tk/Tkinter.py", line 1947, in pack_configure +self.options(cnf,kw) _tkinter.TclError: bad pad value "1p": must be positive screen distance. In addition, my Centos 8 was installed in Virtual Box. I am looking forward to getting your advice on how to solve the issue. Smith On Tuesday, August 25, 2020, 4:10:09 PM GMT+8, Smith Lee <smith_lee123@yahoo.com> wrote: Dear Greg, Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。 In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib". When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory. I am looking forward to getting your advice on how to have the issue solved. Smith On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: You still haven't said which version of Linux you have. That might be critical. I left out a step for the ldd, do: env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/. -- Greg On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All, With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) The version of Chimera involved is: chimera-1.14-linux_x86_64.bin I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/. Smith On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: 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. If that still doesn't work, then I would suspect that there is shared library that is missing. Run: ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so 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. HTH, Greg On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄 it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package? Best wishes, Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. 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. -- Greg On 8/26/2020 6:30 AM, Smith Lee wrote:
Dear Greg,
"libXScrnSaver" was succesffuly installed by "sudo yum install libXScrnSaver".
Currently when I run "./chimera" in "UCSF-Chimera64-1.14/bin", the chimera graphical showed temporarily and immediately disappear, with the following errot: File ".../lib/python2.7/lib-tk/Tkinter.py", line 1947, in pack_configure +self.options(cnf,kw) _tkinter.TclError: bad pad value "1p": must be positive screen distance.
In addition, my Centos 8 was installed in Virtual Box.
I am looking forward to getting your advice on how to solve the issue.
Smith
On Tuesday, August 25, 2020, 4:10:09 PM GMT+8, Smith Lee <smith_lee123@yahoo.com> wrote:
Dear Greg,
Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。
In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so
It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib".
When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory.
I am looking forward to getting your advice on how to have the issue solved.
Smith
On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
You still haven't said which version of Linux you have. That might be critical.
I left out a step for the ldd, do:
env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/.
-- Greg
On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All,
With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000)
The version of Chimera involved is: chimera-1.14-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x86_64/chimera-1.14-linux_x86_64.bin>
I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/.
Smith
On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> wrote:
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.
If that still doesn't work, then I would suspect that there is shared library that is missing. Run:
ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so
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.
HTH,
Greg
On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄it says the installed /UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package?
Best wishes,
Smith
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Dear Greg, 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. 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. I amlloking forward to getting your advice. Smith. On Thursday, August 27, 2020, 3:44:29 PM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: 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. 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. -- Greg On 8/26/2020 6:30 AM, Smith Lee wrote: Dear Greg, "libXScrnSaver" was succesffuly installed by "sudo yum install libXScrnSaver". Currently when I run "./chimera" in "UCSF-Chimera64-1.14/bin", the chimera graphical showed temporarily and immediately disappear, with the following errot: File ".../lib/python2.7/lib-tk/Tkinter.py", line 1947, in pack_configure +self.options(cnf,kw) _tkinter.TclError: bad pad value "1p": must be positive screen distance. In addition, my Centos 8 was installed in Virtual Box. I am looking forward to getting your advice on how to solve the issue. Smith On Tuesday, August 25, 2020, 4:10:09 PM GMT+8, Smith Lee <smith_lee123@yahoo.com> wrote: Dear Greg, Version: chimera-1.14-linux_x86_64.bin （Is it waht you mean for Version?）。 In the drectory "UCSF-Chimera64-1.14", I run: ldd ./lib/python2.7/lib-dynload/_tkinter.so It gave: linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) But "libtk8.6.so" was really in "UCSF-Chimera64-1.14/lib". When I run "./chimera" in "UCSF-Chimera64-1.14/bin", the last 3 sentences of the error message was as following: “~/.local/UCSF-Chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py",line 39, in <module> import_tkinter # If this fails you Python may not be configured for Tk ImportError: libXss.so.1: cannot open sharted object file: No such file or directory. I am looking forward to getting your advice on how to have the issue solved. Smith On Tuesday, August 25, 2020, 11:48:06 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: You still haven't said which version of Linux you have. That might be critical. I left out a step for the ldd, do: env LD_LIBRARY_PATH=/UCSF-chimera64-1.14/lib ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so It should find the libtk8.6.so in /UCSF-chimera64-1.14/lib/. -- Greg On 8/24/2020 8:32 PM, Smith Lee wrote: Dear All, With the request from Greg, the result is as following. $ ldd _tkinter.so linux-vdso.so.1 (0x00007ffcd61fa000) libtk8.6.so => not found libtcl8.6.so => /lib64/libtcl8.6.so (0x00007fe164edd000) libX11.so.6 => /lib64/libX11.so.6 (0x00007fe164b99000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe164979000) libc.so.6 => /lib64/libc.so.6 (0x00007fe1645b7000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fe1643b3000) libz.so.1 => /lib64/libz.so.1 (0x00007fe16419c000) libm.so.6 => /lib64/libm.so.6 (0x00007fe163e1a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007fe163bf1000) /lib64/ld-linux-x86-64.so.2 (0x00007fe1654af000) libXau.so.6 => /lib64/libXau.so.6 (0x00007fe1639ed000) The version of Chimera involved is: chimera-1.14-linux_x86_64.bin I am looking forward to getting your advice on how to solve the issue, and if libtk8.6.so is what was missing, how to install it especially in the directory /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/. Smith On Tuesday, August 25, 2020, 8:48:29 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: 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. If that still doesn't work, then I would suspect that there is shared library that is missing. Run: ldd /UCSF-chimera64-1.14/lib/python2.7/lib-dynload/_tkinter.so 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. HTH, Greg On 8/24/2020 5:07 AM, Smith Lee wrote: Dear All,
From https://www.cgl.ucsf.edu/chimera/download.html 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俄 it says the installed/UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for my python.
Will you please let me know how to configure TK for my python, which was a downloaded component of the chimera package? Best wishes, Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
It works for me. Just much slower than running natively on Windows. Make sure you have 3D acceleration turned on in VirtualBox in the Display settings for your virtual machine. You also need a decent graphics card on the native system for VirtualBox to use. I have a NVIDIA GeForce GTX 970. I've attached a screenshot of a CentOS 8 VirtualBox VM running Chimera 1.14 after fetching the "EMDB & fit PDBs" 1048 example. That said, if Chimera works in Windows, just use Windows :-) -- Greg On 8/27/2020 4:38 AM, Smith Lee wrote:
Dear Greg,
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.
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.
I amlloking forward to getting your advice.
Smith. Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Greg, I have the 3D acceleration turned on inVirtualBox in the Display settings for my virtual machine, it seems with thenative GPU of the VirtualBox， the chimera did not work. The host of my VirtualBox is Windows 10,and it really has an advanced GPU, which is NVIDIA RTX 5000. However I neverhave the experience to have the RTX 5000 work in Centos for my VirtualBox. Infact, I d not know in order to have the RTX 5000 workable in the Centos in theVirtualBox, which steps I need to process, including which NVIDIA relatedsoftwares I need to install, the commands to connect the RTX 5000 with theVirtual Box Centos, and how to verify the RTX 5000 has been successfullyinstalled in the VirtualBox Centos host. I am looking forward to getting your adviceon the above questions, for making my Linux version of chimera workable. Smith On Friday, August 28, 2020, 2:13:03 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote: It works for me. Just much slower than running natively on Windows. Make sure you have 3D acceleration turned on in VirtualBox in the Display settings for your virtual machine. You also need a decent graphics card on the native system for VirtualBox to use. I have a NVIDIA GeForce GTX 970. I've attached a screenshot of a CentOS 8 VirtualBox VM running Chimera 1.14 after fetching the "EMDB & fit PDBs" 1048 example. That said, if Chimera works in Windows, just use Windows :-) -- Greg On 8/27/2020 4:38 AM, Smith Lee wrote: Dear Greg, 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. 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. I amlloking forward to getting your advice. Smith. Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
For 3D graphics, there is one more VirtualBox Display setting -- I have the Graphics Controller set to VMSVGA. If that doesn't fix things, then you might need to update your NVIDIA Windows graphics driver. If that doesn't work, you'll get to ask for help on a VirtualBox forum. This is not a Chimera bug anymore. For help running NVIDIA software in your virtual machine, you will need to ask elsewhere. That is beyond my expertise. And it could change how you need to configure VirtualBox for 3D graphics. I just don't know. Good luck, Greg On 8/27/2020 5:59 PM, Smith Lee wrote:
Dear Greg,
I have the 3D acceleration turned on in VirtualBox in the Display settings for my virtual machine, it seems with the native GPU of the VirtualBox，the chimera did not work.
The host of my VirtualBox is Windows 10, and it really has an advanced GPU, which is NVIDIA RTX 5000. However I never have the experience to have the RTX 5000 work in Centos for my VirtualBox. In fact, I d not know in order to have the RTX 5000 workable in the Centos in the VirtualBox, which steps I need to process, including which NVIDIA related softwares I need to install, the commands to connect the RTX 5000 with the Virtual Box Centos, and how to verify the RTX 5000 has been successfully installed in the VirtualBox Centos host.
I am looking forward to getting your advice on the above questions, for making my Linux version of chimera workable.
Smith
On Friday, August 28, 2020, 2:13:03 AM GMT+8, Greg Couch <gregc@cgl.ucsf.edu> wrote:
It works for me. Just much slower than running natively on Windows. Make sure you have 3D acceleration turned on in VirtualBox in the Display settings for your virtual machine. You also need a decent graphics card on the native system for VirtualBox to use. I have a NVIDIA GeForce GTX 970. I've attached a screenshot of a CentOS 8 VirtualBox VM running Chimera 1.14 after fetching the "EMDB & fit PDBs" 1048 example.
That said, if Chimera works in Windows, just use Windows :-)
-- Greg
On 8/27/2020 4:38 AM, Smith Lee wrote: Dear Greg,
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.
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.
I amlloking forward to getting your advice.
Smith. Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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