Hi all,
I haven't seen any recent posts in the mailing list about any coot
updates related to crashing. It keeps happening to me in two different
mac computers without any apparent pattern:
OS system: 10.15.7 or 12.2.1
Xquartz 2.8.1 (xorg-server 1.20.11)
Coot: 0.9.8.1
It seems that the last time Coot crashed there was a problem with ATP/Mg
(see below), however it the same happens without ATP in the structure.
Any suggestions?
thanks
Nikos
get_rotamer_probability: caught: Failed to find atom name quads for
residue type MG
get_rotamer_probability: caught: Failed to find atom name quads for
residue type ATP
debug:: in clear_all_atom_pull_restraints() 0
Stack trace (most recent call last):
#31 Object "coot-bin", at 0x10f1d3b79, in inner_main(void*, int,
char**) + 1257
#30 Object "libgtk-x11-2.0.0.dylib", at 0x1125d58bf, in gtk_main + 191
#29 Object "libglib-2.0.0.dylib", at 0x112a9d62f, in g_main_loop_run + 191
#28 Object "libglib-2.0.0.dylib", at 0x112a9d313, in
g_main_context_iterate + 515
#27 Object "libglib-2.0.0.dylib", at 0x112a9cf86, in
g_main_context_dispatch + 310
#26 Object "libgdk-x11-2.0.0.dylib", at 0x1120fad61, in
gdk_event_dispatch + 81
#25 Object "libgtk-x11-2.0.0.dylib", at 0x1125d6008, in
gtk_main_do_event + 1144
#24 Object "libgtk-x11-2.0.0.dylib", at 0x1125d6422, in
gtk_propagate_event + 322
#23 Object "libgtk-x11-2.0.0.dylib", at 0x11270acd3, in
gtk_widget_event_internal + 659
#22 Object "libgobject-2.0.0.dylib", at 0x112270812, in g_signal_emit
+ 130
#21 Object "libgobject-2.0.0.dylib", at 0x1122702e7, in
g_signal_emit_valist + 2695
#20 Object "libgobject-2.0.0.dylib", at 0x11226f4c4, in
signal_emit_unlocked_R + 2068
#19 Object "libgobject-2.0.0.dylib", at 0x11225a5dc, in
g_closure_invoke + 204
#18 Object "libgtk-x11-2.0.0.dylib", at 0x1125d83b4, in
_gtk_marshal_BOOLEAN__BOXED + 100
#17 Object "libgtk-x11-2.0.0.dylib", at 0x11251fcc7, in
gtk_button_button_release + 71
#16 Object "libgobject-2.0.0.dylib", at 0x112270812, in g_signal_emit
+ 130
#15 Object "libgobject-2.0.0.dylib", at 0x11226fdad, in
g_signal_emit_valist + 1357
#14 Object "libgobject-2.0.0.dylib", at 0x11225a7d5, in
_g_closure_invoke_va + 213
#13 Object "libgtk-x11-2.0.0.dylib", at 0x1126adb36, in
gtk_toggle_button_released + 54
#12 Object "libgobject-2.0.0.dylib", at 0x112270812, in g_signal_emit
+ 130
#11 Object "libgobject-2.0.0.dylib", at 0x11226fdad, in
g_signal_emit_valist + 1357
#10 Object "libgobject-2.0.0.dylib", at 0x11225a7d5, in
_g_closure_invoke_va + 213
#9 Object "libgtk-x11-2.0.0.dylib", at 0x1126adb98, in
gtk_toggle_button_clicked + 72
#8 Object "libgobject-2.0.0.dylib", at 0x112270812, in g_signal_emit
+ 130
#7 Object "libgobject-2.0.0.dylib", at 0x11226fdad, in
g_signal_emit_valist + 1357
#6 Object "libgobject-2.0.0.dylib", at 0x11225a7d5, in
_g_closure_invoke_va + 213
#5 Object "coot-bin", at 0x10f6ba0ef, in
coot::rama_plot::show_selection_widget(int) + 143
#4 Object "coot-bin", at 0x10f6b1e23, in
coot::rama_plot::generate_phi_psis(mmdb::Manager*, bool) + 707
#3 Object "libmmdb2.0.dylib", at 0x110eb7995, in
mmdb::Model::GetNumberOfChains() + 5
#2 Object "libsystem_platform.dylib", at 0x7ff81bf37e2c, in _sigtramp
+ 28
#1 Object "libcoot-utils.0.dylib", at 0x110221b4d, in
backward::SignalHandling::sig_handler(int, __siginfo*, void*) + 13
#0 Object "libcoot-utils.0.dylib", at 0x110221bb8, in
backward::SignalHandling::handleSignal(int, __siginfo*, void*) + 72
/opt/ccp4-8.0/coot_py2/bin/coot: line 272: 62093 Segmentation fault: 11
$coot_bin "$@"
. ------ 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: "/opt/ccp4-8.0/coot_py2/libexec/coot-bin"
/bin/ls
-rwxr-xr-x 1 ubcg54bm staff 9902700 Mar 25 21:39
/opt/ccp4-8.0/coot_py2/libexec/coot-bin
coot-version:
/opt/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: 58ccfeebc5f76e5e4373269c1fa510dec22e3a8d
Builder_info: CCP4, Oxfordshire, UK
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.8.1 (revision-count 10823)
platform:
/usr/bin/uname
Darwin ubcg54bm-02.dongle.cryst.bbk.ac.uk 21.3.0 Darwin Kernel Version
21.3.0: Wed Jan 5 21:37:58 PST 2022;
root:xnu-8019.80.24~20/RELEASE_X86_64 x86_64
core: #f
No core file found. No debugging
--
Dr. Nikos Pinotsis
Protein Crystallography and Biophysics Centre
Institute of Structural and Molecular Biology
Department of Biological Sciences, Room B16b
Birkbeck College
Malet Street
London WC1E 7HX
Direct: +44 (0)20 3926 3507
Office: +44 (0)207 631 6458
Mobile: +44 (0)792 384 3593
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