A few more observations and suggestions for Coot 1.x
I’m using Coot 1.x-pre b9ade0e82fa509f24ea458adf5d2939629bb73ec on MacOS 26.6.2
1.
After deleting a water, the water is still shown until I move away, at which
point it disappears. I think it should disappear immediately just as with
residues etc.
2.
I’ve mapped the “w” key to add a water at the current center, which worked in a
previous version, but now Coot crashes with the info below in the console.
Please let me know if you want additional information.
3.
In the delete menu, I have occasionally mis-clicked on “All Waters” when I
meant to click on just “Water”. Thankfully, the undo mechanism came to the
rescue, but I wonder if it makes any sense to rearrange the list to put
frequently-used (and potentially less destructive) items at the top? For
instance, I typically use Water, Residue, Hydrogen Atoms in Residue, Residue
Atoms with Alt-conf, Residue Range.
4.
I’ll reiterate the suggestion to improve the utility of the “o” keybinding to
cycle among NCS-related chains: when centered on a non-protein (e.g. water),
the “o” key does nothing. Rather, I need to center on a nearby protein atom for
the NCS cycling to work. I would suggest that when the “o” key is hit, that the
closest protein atom is found and then the matching NCS operator is applied to
the view. I hope this makes some sense.
5.
When looking at the list of outliers on the left side (via Validate > Overlaps,
Peptide, etc. or Validate > Validation Outliers - is there a difference between
these two menu items?), would it be possible to add a small region to toggle
on/off certain types of outliers?
6.
When looking at lists of items (validation outliers, difference map peaks,
etc.) the contrast between selected and unselected items is still pretty weak -
could this be made a bit less subtle? Also, it’d be useful if the arrow keys
(or comma and period as in 0.9.x) could be used to move up and down in the list.
Coot is such an amazing tool, so thank you so very much for continuing your
work on it!
Chip
—
The “w” keybinding is defined as follows:
coot.add_key_binding_gtk4_py(119, 0, lambda:
place_typed_atom_at_pointer("Water"), "Add Water") #w key
After hitting the “w” key:
INFO:: key-binding for key: 119 0 Add Water
Fatal Python error: _PyEval_EvalFrameDefault: Executing a cache.
Python runtime state: initialized
Current thread 0x00000001f20b2180 (most recent call first):
<invalid frame>
Extension modules: _coot, gi._gi, cairo._cairo, gi._gi_cairo, coot_gui_api
(total: 5)
Stack trace (most recent call last):
#31 Object "libgtk-4.1.dylib", at 0x107d408fb, in
gdk_macos_event_source_dispatch + 43
#30 Object "libgtk-4.1.dylib", at 0x107d8913b, in gdk_surface_handle_event +
375
#29 Object "libgobject-2.0.0.dylib", at 0x106842b87, in g_signal_emit + 27
#28 Object "libgobject-2.0.0.dylib", at 0x106842063, in g_signal_emit_valist
+ 63
#27 Object "libgobject-2.0.0.dylib", at 0x1068423eb, in
signal_emit_valist_unlocked + 859
#26 Object "libgobject-2.0.0.dylib", at 0x10682e667, in _g_closure_invoke_va
+ 211
#25 Object "libgtk-4.1.dylib", at 0x107d89f23, in
gdk_surface_event_marshallerv + 103
#24 Object "libgtk-4.1.dylib", at 0x107d33477, in
_gdk_marshal_BOOLEAN__POINTERv + 75
#23 Object "libgtk-4.1.dylib", at 0x107af71fb, in gtk_main_do_event + 3003
#22 Object "libgtk-4.1.dylib", at 0x107af77db, in
gtk_propagate_event_internal + 335
#21 Object "libgtk-4.1.dylib", at 0x107bdb5af, in gtk_widget_run_controllers
+ 239
#20 Object "libgtk-4.1.dylib", at 0x107a9095f, in
gtk_event_controller_handle_event + 239
#19 Object "libgtk-4.1.dylib", at 0x107a9206b, in
gtk_event_controller_key_handle_event + 243
#18 Object "libgobject-2.0.0.dylib", at 0x106842b87, in g_signal_emit + 27
#17 Object "libgobject-2.0.0.dylib", at 0x106842063, in g_signal_emit_valist
+ 63
#16 Object "libgobject-2.0.0.dylib", at 0x1068423eb, in
signal_emit_valist_unlocked + 859
#15 Object "libgobject-2.0.0.dylib", at 0x10682e667, in _g_closure_invoke_va
+ 211
#14 Object "libgtk-4.1.dylib", at 0x107a255ef, in
_gtk_marshal_BOOLEAN__UINT_UINT_FLAGSv + 103
#13 Object "MacCoot", at 0x102a51da7, in
on_glarea_key_controller_key_pressed(_GtkEventControllerKey*, unsigned int,
unsigned int, unsigned int, _GtkButton*) + 51
#12 Object "libcootsumo.0.dylib", at 0x10388e00b, in
graphics_info_t::on_glarea_key_controller_key_pressed(_GtkEventControllerKey*,
unsigned int, unsigned int, unsigned int) + 523
#11 Object "libcootsumo.0.dylib", at 0x1039c2917, in key_bindings_t::run()
const + 123
#10 Object "Python", at 0x108a7ec97, in _PyEval_Vector + 267
#9 Object "Python", at 0x108a8b32b, in _PyEval_EvalFrameDefault + 49975
#8 Object "Python", at 0x108aef21b, in _Py_FatalErrorFunc + 55
#7 Object "Python", at 0x108af021f, in fatal_error + 47
#6 Object "Python", at 0x108af0443, in fatal_error_exit + 15
#5 Object "libsystem_c.dylib", at 0x185579977, in abort + 147
#4 Object "libsystem_pthread.dylib", at 0x1856738d7, in pthread_kill + 295
#3 Object "libsystem_platform.dylib", at 0x18567d743, in _sigtramp + 55
#2 Object "libcoot-utils.0.dylib", at 0x10641523f, in
backward::SignalHandling::sig_handler(int, __siginfo*, void*) + 19
#1 Object "libcoot-utils.0.dylib", at 0x1064152a3, in
backward::SignalHandling::handleSignal(int, __siginfo*, void*) + 71
#0 Object "libcoot-utils.0.dylib", at 0x1064153e3, in
backward::StackTraceImpl<backward::system_tag::darwin_tag>::load_from(void*,
unsigned long, void*, void*) + 43
/opt/homebrew/bin/coot: line 9: 10830 Abort trap: 6
${exec_prefix}/libexec/MacCoot "$@"
[cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png]
Charles Lesburg
Senior Vice President, Structural Biology
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