Hi Paul,

I have installed on my mac Coot 0.9.8.2 (macOS Monterey version 12.4). Every 
time when I clicked “All-atom Refine”, the coot crashed. I also encountered 
errors when I do Real Space Refinement.

Here are the errors:

sys:1: GtkWarning: Attempting to store changes into 
`/Users/ZhenGong/.local/share/recently-used.xbel', but failed: Failed to create 
file '/Users/ZhenGong/.local/share/recently-used.xbel.KSILN1': No such file or 
directory
click on 2 atoms (in the same molecule)
(0) " CA "/1/chainid="C"/415/THR,  occ: 1 with B-factor: 40.23 element: " C" at 
(-19.69,15.03,-34.99) : 0.08046
(0) " CB "/1/chainid="C"/416/LEU,  occ: 1 with B-factor: 37.5 element: " C" at 
(-17.64,12.47,-31.59) : 0.1034
ERROR:: atoms_match_dictionary() --- no restraints
ERROR:: atoms_match_dictionary() --- no restraints
Refinement elapsed time: 0.002
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
sys:1: GtkWarning: Native Windows wider or taller than 32767 pixels are not 
supported
The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadAlloc (insufficient resources for operation)'.
  (Details: serial 49306 error_code 11 request_code 53 minor_code 0)
  (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.)
ObjectCache: Leaked 0002 refs to <P 2ac 2ab CANNOT FORMAT HKL_sampling>
ObjectCache: Leaked 0003 refs to <P 2ac 2ab>
. ------ Coot crashed - trying to diagnose -----
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well.  For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
coot-exe: "/Applications/ccp4-8.0/coot_py2/libexec/coot-bin"
/bin/ls
-rwxr-xr-x  1 root  admin  9906836 Jun 13 15:49 
/Applications/ccp4-8.0/coot_py2/libexec/coot-bin
coot-version: 
/Applications/ccp4-8.0/coot_py2/libexec/coot-bin
Builder_info: CCP4, Oxfordshire, UK
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas 
GSL LibCurl 
Binary type: Darwin-MacOSX-10.13.6-x86_64-python-gtk2
git commit: 36b2422d6a9a006aed969506f45ad84bda495743
Builder_info: CCP4, Oxfordshire, UK
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.8.3 (revision-count 10834)
platform: 
/usr/bin/uname
Darwin MacBook-Pro-ZG-2.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 
21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64
core: #f
No core file found.  No debugging

Any suggestions to what I shall do to fix these problems? Many thanks in 
advance!

Best,
Zhen

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