[Chimera-users] On installation of Chimera linux version

Tue Aug 25 10:14:36 PDT 2020

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 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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