I have recently upgrade my machine to Ubuntu MATE 1.26 and re-install all crystallography software I often use, including Phenix version dev-5493.

I am working in a structure of a protein bound to a new ligand. I built the ligand with chemDraw, get the SMILE, get a universal SMILE string in cactus.nci.nih.gov, and used eLbow for ligand restraints generation and optimization (using default parameters).

First problem. When I try to open the ligand in REEL. Phenix crash with the following message in the terminal

libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: nouveau
libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: nouveau
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast
The program 'main.py' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue'.
(Details: serial 39668 error_code 2 request_code 152 minor_code 24)
(Note to programmers: normally, X errors are reported asynchronously;
  that is, you will receive the error a while after causing it.
  To debug your program, run it with the --sync command line
  option to change this behavior. You can then get a meaningful
  backtrace from your debugger if you break on the gdk_x_error() function.)

Second, when I open the structure in Coot (0.9.8.95) from Phenix and try to perform real space refine zone to the ligand, the attached window pops-up.