*Dear all:**
I have been experiencing some problems with Coot when making zone
restrained refinement. I'm using Cento5, 32 bit. The problem appeared
recently using Coot version 0.6-pre-1 Miramar revision 3364, but also
happens if I turn back to the previous Coot 0.6-pre.
At the terminal you can read:*
SUCCESS
TIME:: (dragged refinement): 77.457
Refinement elapsed time: 0.378
INFO:: backup file
coot-backup/_home_hbotti_Comini_Ortiz_G6PDH_1_5_CCP4_G6PDH_1_set_5_refmac45.pdb_Fri_Feb_11_17:02:33_2011_modification_2.pdb.gz
INFO:: replace_coords: 21 atoms updated.
sys:1: Warning: invalid unclassed pointer in cast to `GtkObject'
sys:1: GtkWarning: gtk_object_destroy: assertion `GTK_IS_OBJECT
(object)' failed
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot: line 247:
15305 Segmentation fault (core dumped) $coot_real $@
coot-exe: "/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot-real"
coot-version:
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot-real
platform:
/bin/uname
core: "core.15305"
/usr/bin/gdb
warning: Can't read pathname for load map: Input/output error.
Cannot access memory at address 0x7d1
* Coot message from core dumps:*
Using host libthread_db library "/lib/libthread_db.so.1".
Core was generated by
`/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot-real'.
Program terminated with signal 11, Segmentation fault.
#0 0x00a92692 in g_type_check_instance_cast () from
/lib/libgobject-2.0.so.0
#0 0x00a92692 in g_type_check_instance_cast () from
/lib/libgobject-2.0.so.0
#1 0x08281478 in coot::geometry_graphs::update_omega_blocks
(this=0xb3bb6e8,
om_dist=@0xbfe0b08c, chain_number=0, chain_id=@0xbfe0b0c0)
at geometry-graphs.cc:764
#2 0x082e451a in graphics_info_t::update_geometry_graphs (this=0xbfe0b143,
moving_atoms_asc_local=@0x98803d8, imol_moving_atoms=2)
at graphics-info-graphs.cc:310
#3 0x082bea6d in graphics_info_t::accept_moving_atoms (this=0xbfe0b143)
at graphics-info.cc:1084
#4 0x08132e22 in accept_regularizement () at c-interface-build.cc:5715
#5 0x08232472 in on_accept_reject_refinement_accept_button_clicked (
button=0xa6c16d0, user_data=0x0) at callbacks.c:2394
#6 0x00a84189 in g_cclosure_marshal_VOID__VOID ()
from /lib/libgobject-2.0.so.0
#7 0x00a76e3b in g_closure_invoke () from /lib/libgobject-2.0.so.0
#8 0x00a87db3 in g_signal_override_class_closure ()
from /lib/libgobject-2.0.so.0
#9 0x00a892af in g_signal_emit_valist () from /lib/libgobject-2.0.so.0
#10 0x00a89469 in g_signal_emit () from /lib/libgobject-2.0.so.0
#11 0x02a2ec23 in gtk_button_clicked () from /usr/lib/libgtk-x11-2.0.so.0
#12 0x02a3086e in gtk_button_set_alignment () from
/usr/lib/libgtk-x11-2.0.so.0
#13 0x00a84189 in g_cclosure_marshal_VOID__VOID ()
from /lib/libgobject-2.0.so.0
#14 0x00a75629 in g_value_set_static_boxed () from /lib/libgobject-2.0.so.0
#15 0x00a76e3b in g_closure_invoke () from /lib/libgobject-2.0.so.0
#16 0x00a8824a in g_signal_override_class_closure ()
from /lib/libgobject-2.0.so.0
#17 0x00a892af in g_signal_emit_valist () from /lib/libgobject-2.0.so.0
#18 0x00a89469 in g_signal_emit () from /lib/libgobject-2.0.so.0
#19 0x02a2ecb3 in gtk_button_released () from /usr/lib/libgtk-x11-2.0.so.0
#20 0x02a2ed11 in gtk_button_released () from /usr/lib/libgtk-x11-2.0.so.0
#21 0x02aff030 in gtk_marshal_BOOLEAN__VOID ()
from /usr/lib/libgtk-x11-2.0.so.0
#22 0x00a75629 in g_value_set_static_boxed () from /lib/libgobject-2.0.so.0
#23 0x00a76e3b in g_closure_invoke () from /lib/libgobject-2.0.so.0
#24 0x00a88403 in g_signal_override_class_closure ()
from /lib/libgobject-2.0.so.0
#25 0x00a89077 in g_signal_emit_valist () from /lib/libgobject-2.0.so.0
#26 0x00a89469 in g_signal_emit () from /lib/libgobject-2.0.so.0
#27 0x02c13118 in gtk_widget_get_default_style ()
from /usr/lib/libgtk-x11-2.0.so.0
#28 0x02af84d3 in gtk_propagate_event () from /usr/lib/libgtk-x11-2.0.so.0
#29 0x02af96d7 in gtk_main_do_event () from /usr/lib/libgtk-x11-2.0.so.0
#30 0x00b91ffa in gdk_add_client_message_filter ()
from /usr/lib/libgdk-x11-2.0.so.0
#31 0x05b49272 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#32 0x05b4c24f in g_main_context_check () from /lib/libglib-2.0.so.0
#33 0x05b4c5f9 in g_main_loop_run () from /lib/libglib-2.0.so.0
#34 0x02af9b54 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#35 0x081328fa in c_inner_main (closure=0xbfe0c4b8, argc=1, argv=0xbfe0c7b4)
at c-inner-main.c:311
#36 0x0016b70a in invoke_main_func ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#37 0x0013ce6a in c_body ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#38 0x001b047a in scm_c_catch ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#39 0x0013d2f9 in scm_i_with_continuation_barrier ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#40 0x0013d3c4 in scm_c_with_continuation_barrier ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#41 0x001af14d in scm_i_with_guile_and_parent ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#42 0x001af231 in scm_with_guile ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#43 0x0016b6a8 in scm_boot_guile ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#44 0x08132257 in c_wrapper_scm_boot_guile (argc=1, argv=0xbfe0c7b4,
pcld=0xbfe0c4b8) at c-inner-main.c:366
#45 0x08127753 in main (argc=) at main.cc:605
* It is a reproducible error:
terminal:*
click on 2 atoms (in the same molecule)
pick_mode: 0
(0) " CA "/1/chainid="B"/29/GLU, occ: 1 with B-factor: 23.78 element: "
C" at (-10.823,-72.563,30.605) : 0.185707
pick_mode: 0
(0) " N "/1/chainid="B"/27/ALA, occ: 1 with B-factor: 61.64 element: "
N" at (-10.585,-76.745,36.075) : 0.16172
created 19 bond restraints
created 21 angle restraints
created 1 plane restraints
created 3 chiral vol restraints
created 44 restraints
INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link
restraints) between (and including) residues 27 and 29 of chain B
Link restraints:
2 bond links
6 angle links
4 plane links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues
(flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues
(flanking restraints)
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
INFO:: made 324 non-bonded restraints
initial distortion_score: -2115.77
Initial Chi Squareds
bonds: 0.731319
angles: 0.975354
torsions: N/A
planes: 2.47154
non-bonded: 0
chiral vol: 1.07711
rama plot: N/A
Minimum found (iteration number 76) at -2422.67
Final Estimated RMS Z Scores:
bonds: 1.2342
angles: 1.60291
torsions: N/A
planes: 2.84646
non-bonded: 0.000855816
chiral vol: 1.59474
rama plot: N/A
SUCCESS
TIME:: (dragged refinement): 251.185
Refinement elapsed time: 0.407
INFO:: backup file
coot-backup/_home_hbotti_Comini_Ortiz_G6PDH_1_5_CCP4_G6PDH_1_set_5_refmac45.pdb_Fri_Feb_11_17:30:54_2011_modification_6.pdb.gz
INFO:: replace_coords: 21 atoms updated.
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot: line 247:
3736 Segmentation fault $coot_real $@
coot-exe: "/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot-real"
coot-version:
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot-real
platform:
/bin/uname
core: "core.15305"
/usr/bin/gdb
warning: Can't read pathname for load map: Input/output error.
Cannot access memory at address 0x7d1
*
Coot message:*
Using host libthread_db library "/lib/libthread_db.so.1".
Core was generated by
`/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/bin/coot-real'.
Program terminated with signal 11, Segmentation fault.
#0 0x00a92692 in g_type_check_instance_cast () from
/lib/libgobject-2.0.so.0
#0 0x00a92692 in g_type_check_instance_cast () from
/lib/libgobject-2.0.so.0
#1 0x08281478 in coot::geometry_graphs::update_omega_blocks
(this=0xb3bb6e8,
om_dist=@0xbfe0b08c, chain_number=0, chain_id=@0xbfe0b0c0)
at geometry-graphs.cc:764
#2 0x082e451a in graphics_info_t::update_geometry_graphs (this=0xbfe0b143,
moving_atoms_asc_local=@0x98803d8, imol_moving_atoms=2)
at graphics-info-graphs.cc:310
#3 0x082bea6d in graphics_info_t::accept_moving_atoms (this=0xbfe0b143)
at graphics-info.cc:1084
#4 0x08132e22 in accept_regularizement () at c-interface-build.cc:5715
#5 0x08232472 in on_accept_reject_refinement_accept_button_clicked (
button=0xa6c16d0, user_data=0x0) at callbacks.c:2394
#6 0x00a84189 in g_cclosure_marshal_VOID__VOID ()
from /lib/libgobject-2.0.so.0
#7 0x00a76e3b in g_closure_invoke () from /lib/libgobject-2.0.so.0
#8 0x00a87db3 in g_signal_override_class_closure ()
from /lib/libgobject-2.0.so.0
#9 0x00a892af in g_signal_emit_valist () from /lib/libgobject-2.0.so.0
#10 0x00a89469 in g_signal_emit () from /lib/libgobject-2.0.so.0
#11 0x02a2ec23 in gtk_button_clicked () from /usr/lib/libgtk-x11-2.0.so.0
#12 0x02a3086e in gtk_button_set_alignment () from
/usr/lib/libgtk-x11-2.0.so.0
#13 0x00a84189 in g_cclosure_marshal_VOID__VOID ()
from /lib/libgobject-2.0.so.0
#14 0x00a75629 in g_value_set_static_boxed () from /lib/libgobject-2.0.so.0
#15 0x00a76e3b in g_closure_invoke () from /lib/libgobject-2.0.so.0
#16 0x00a8824a in g_signal_override_class_closure ()
from /lib/libgobject-2.0.so.0
#17 0x00a892af in g_signal_emit_valist () from /lib/libgobject-2.0.so.0
#18 0x00a89469 in g_signal_emit () from /lib/libgobject-2.0.so.0
#19 0x02a2ecb3 in gtk_button_released () from /usr/lib/libgtk-x11-2.0.so.0
#20 0x02a2ed11 in gtk_button_released () from /usr/lib/libgtk-x11-2.0.so.0
#21 0x02aff030 in gtk_marshal_BOOLEAN__VOID ()
from /usr/lib/libgtk-x11-2.0.so.0
#22 0x00a75629 in g_value_set_static_boxed () from /lib/libgobject-2.0.so.0
#23 0x00a76e3b in g_closure_invoke () from /lib/libgobject-2.0.so.0
#24 0x00a88403 in g_signal_override_class_closure ()
from /lib/libgobject-2.0.so.0
#25 0x00a89077 in g_signal_emit_valist () from /lib/libgobject-2.0.so.0
#26 0x00a89469 in g_signal_emit () from /lib/libgobject-2.0.so.0
#27 0x02c13118 in gtk_widget_get_default_style ()
from /usr/lib/libgtk-x11-2.0.so.0
#28 0x02af84d3 in gtk_propagate_event () from /usr/lib/libgtk-x11-2.0.so.0
#29 0x02af96d7 in gtk_main_do_event () from /usr/lib/libgtk-x11-2.0.so.0
#30 0x00b91ffa in gdk_add_client_message_filter ()
from /usr/lib/libgdk-x11-2.0.so.0
#31 0x05b49272 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#32 0x05b4c24f in g_main_context_check () from /lib/libglib-2.0.so.0
#33 0x05b4c5f9 in g_main_loop_run () from /lib/libglib-2.0.so.0
#34 0x02af9b54 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#35 0x081328fa in c_inner_main (closure=0xbfe0c4b8, argc=1, argv=0xbfe0c7b4)
at c-inner-main.c:311
#36 0x0016b70a in invoke_main_func ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#37 0x0013ce6a in c_body ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#38 0x001b047a in scm_c_catch ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#39 0x0013d2f9 in scm_i_with_continuation_barrier ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#40 0x0013d3c4 in scm_c_with_continuation_barrier ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#41 0x001af14d in scm_i_with_guile_and_parent ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#42 0x001af231 in scm_with_guile ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#43 0x0016b6a8 in scm_boot_guile ()
from
/home/Xtal/Coot/coot-Linux-i386-rhel-5-gtk2-python/lib/libguile.so.17
#44 0x08132257 in c_wrapper_scm_boot_guile (argc=1, argv=0xbfe0c7b4,
pcld=0xbfe0c4b8) at c-inner-main.c:366
#45 0x08127753 in main (argc=) at main.cc:605
* Another example using **Coot 0.6-pre**:*
SUCCESS
TIME:: (dragged refinement): 239.802
Refinement elapsed time: 0.507
INFO:: backup file
coot-backup/_home_hbotti_Comini_Ortiz_G6PDH_1_5_CCP4_G6PDH_1_set_5_refmac45.pdb_Mon_Feb_14_16:19:01_2011_modification_9.pdb.gz
INFO:: replace_coords: 21 atoms updated.
DEBUG:: update omega dist graph chain B 4 blocks
(coot-real:3712): GLib-GObject-WARNING **: invalid uninstantiatable type
`<invalid>' in cast to `GtkObject'
sys:1: GtkWarning: gtk_object_destroy: assertion `GTK_IS_OBJECT
(object)' failed
/home/Xtal/Coot/coot-Linux-i386-centos-4-gtk2-python/bin/coot: line
154: 3712 Segmentation fault $coot_real $*
coot-exe:
"/home/Xtal/Coot/coot-Linux-i386-centos-4-gtk2-python/bin/coot-real"
coot-version:
/home/Xtal/Coot/coot-Linux-i386-centos-4-gtk2-python/bin/coot-real
platform:
/bin/uname
core: #f
No core file found. No debugging
This is not helpful.
Please turn on core dumps before sending a crash report
[hbotti@pxf4 ~]$
