Sorry for no log, but I'll do my best to describe it.
I was trying to run Coot through SSH from a CentOS6 machine on my Macbook with OS Sierra. Xquartz turned out to be the problem with Coot not opening. We have confirmed with SBGrid that any version of XQuartz after 2.7.9 will break when running Coot and other programs in the SBGrid package. 2.7.9 didn't work for me on Sierra, but did work with someone running an older OS. I had to revert to 2.7.8 to get it to work. We know that older Mac OS's will work with 2.7.9 and a few Linux distros work with the latest 2.7.11.
Not a major issue, but we wanted it to be known that versions 2.7.9-2.7.11 do not work with Sierra. We have contacted SBGrid to see if there is a fix on their end as well.
Found the error:
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/data/monomers/
INFO:: Reading coordinate file: /export/bwsl1/sbgrid/x86_64-linux/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb
PDB file /export/bwsl1/sbgrid/x86_64-linux/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (integer parameter out of range for operation)'.
(Details: serial 299 error_code 2 request_code 149 minor_code 3)
(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.)
No core file found. No debugging
Please work with SBGrid to figure out what the problem is and file a reduced test case if they believe this is a bug in the X server.
-- GitLab Migration Automatic Message --
This bug has been migrated to freedesktop.org's GitLab instance and has been closed from further activity.
You can subscribe and participate further through the new bug through this link to our GitLab instance: https://gitlab.freedesktop.org/xorg/xserver/issues/784.