[Chimera-users] On installation of Chimera linux version

Thu Aug 27 00:44:26 PDT 2020

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 at 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 at 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 at cgl.ucsf.edu> <mailto:gregc at 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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