[Chimera-users] On installation of Chimera linux version

Thu Aug 27 04:38:12 PDT 2020

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 at 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 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 
    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> 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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