Re: [COOT] toolbox and color of symmetry related chains not working
On 24/05/2026 02:17, Georg Mlynek wrote: Dear Paul, many thanks. It works now. However in my case the difference between the reference and symmetry related chain is not strong. You mean the colour thereof? Changes in bot these lines have no effect coot.set_symmetry_colour(0.4, 0.4, 0.4) Oh, yes - haha, not updated since olden graphics. Noted. coot.set_default_bond_thickness(2) This sets the bond width (thickness) for the next time you generate bonds - e.g. reading a pdb file. The documentation could do with an overhaul. coot.set_bond_thickness(imol, w) is the one that you want. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] toolbox and color of symmetry related chains not working
Dear Paul, many thanks. It works now. However in my case the difference
between the reference and symmetry related chain is not strong.
Changes in bot these lines have no effect
coot.set_symmetry_colour(0.4, 0.4, 0.4)
coot.set_default_bond_thickness(2)
What can I do?
Many thanks for all your efforts, br Georg.
import gi
gi.require_version("Gtk", "4.0")
from gi.repository import Gtk
import coot
import coot_utils
import coot_gui_api
def toggle_quicksymm(button):
"""
Toggle Quick Symmetry based on the button's active state for ALL
open molecules.
Displays ALL ATOMS instead of just C-alphas.
"""
if button.get_active():
# Global settings
coot.set_show_symmetry_master(1)
coot.set_show_unit_cells_all(0)
coot.set_symmetry_colour(0.4, 0.4, 0.4)
coot.set_symmetry_size(15)
coot.set_default_bond_thickness(2)
# Apply to all open molecules
for imol in coot_utils.model_molecule_number_list():
coot.set_symmetry_colour_by_symop(imol, 0)
coot.set_symmetry_molecule_rotate_colour_map(imol, 0)
coot.set_symmetry_whole_chain(imol, 0)
# 0 = False (Show all atoms instead of just C-alphas)
coot.symmetry_as_calphas(imol, 0)
coot.add_status_bar_text("Quick Symmetry: ON (All Atoms)")
else:
coot.set_show_symmetry_master(0)
coot.set_show_unit_cells_all(0)
coot.add_status_bar_text("Quick Symmetry: OFF")
# Create a GTK4 ToggleButton natively
quicksymm_button = Gtk.ToggleButton(label="QuickSymm")
quicksymm_button.connect("toggled", toggle_quicksymm)
coot_gui_api.main_toolbar().append(quicksymm_button)
Am 24.05.2026 um 02:24 schrieb Paul Emsley:
On 23/05/2026 21:42, Georg Mlynek wrote:
I then asked Gemini 3.1 Pro (which has access to the Wincoot folder):
Can you figure out in the code which problem there is in the
coot_gui.coot_toolbar_button function?
9:29 PM
Yes, I can! I looked into the source code for coot_gui.py and found exactly why
it is failing.
The coot_gui.coot_toolbar_button function in your version of Coot 1 is
unfortunately completely broken due to several severe coding errors left by the
Coot developers during their transition to the new GTK4 interface.
Well, yes... I suppose so. We don't use coot_gui (much?) now. It's
basically abandoned since Gtk3+.
I wrote a blog post
https://pemsley.github.io/coot/blog/2026/04/11/adding-toolbar-buttons.html
That should get you going.
Paul.
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Re: [COOT] toolbox and color of symmetry related chains not working
On 23/05/2026 21:42, Georg Mlynek wrote: I then asked Gemini 3.1 Pro (which has access to the Wincoot folder): Can you figure out in the code which problem there is in the coot_gui.coot_toolbar_button function? 9:29 PM Yes, I can! I looked into the source code for coot_gui.py and found exactly why it is failing. The coot_gui.coot_toolbar_button function in your version of Coot 1 is unfortunately completely broken due to several severe coding errors left by the Coot developers during their transition to the new GTK4 interface. Well, yes... I suppose so. We don't use coot_gui (much?) now. It's basically abandoned since Gtk3+. I wrote a blog post https://pemsley.github.io/coot/blog/2026/04/11/adding-toolbar-buttons.html That should get you going. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] toolbox and color of symmetry related chains not working
Dear Bernhard and Paul,
I am running Coot 1.2 on windows.
I tried to implement a toolbox button for showing symmtry, but the toolbox is
not created.
Writing a script for switching on symmtery via keybinding works.
import coot
# Track whether the symmetry is currently on or off
quicksymm_is_on = False
def toggle_quicksymm():
global quicksymm_is_on
if quicksymm_is_on:
coot.set_show_symmetry_master(0)
coot.set_show_unit_cells_all(0)
coot.add_status_bar_text("Quick Symmetry: OFF")
quicksymm_is_on = False
else:
coot.set_show_symmetry_master(1)
coot.set_show_unit_cells_all(1)
coot.set_symmetry_colour_by_symop(0, 0)
coot.set_symmetry_molecule_rotate_colour_map(0, 0)
coot.set_symmetry_colour(0.4, 0.4, 0.4)
coot.set_symmetry_size(10)
coot.set_symmetry_whole_chain(0, 0)
coot.set_default_bond_thickness(2)
coot.symmetry_as_calphas(0, 1)
coot.add_status_bar_text("Quick Symmetry: ON")
quicksymm_is_on = True
# 115 is the ASCII code for lowercase 's'
# 0 means no modifiers (like Ctrl or Shift) are required
coot.add_key_binding_gtk4_py(115, 0, toggle_quicksymm, "Toggle Quick Symmetry")
Additionally, swtching the colors using coot.set_symmetry_colour(0.4, 0.4,
0.4) or the gui is not working.
Is there a command to change the thickness of the symmetry related chains?
For testing if the toolbox works at all I used that script which does not work:
import coot
import coot_gui
def toggle_quicksymm(button):
if button.get_active():
coot.set_show_symmetry_master(1)
coot.set_show_unit_cells_all(1)
coot.add_status_bar_text("Symmetry: ON")
else:
coot.set_show_symmetry_master(0)
coot.set_show_unit_cells_all(0)
coot.add_status_bar_text("Symmetry: OFF")
coot_gui.coot_toolbar_button("QuickSymm", toggle_quicksymm,
icon_name="gtk-yes",
tooltip="Toggle Quick Symmetry on/off",
toggle_button_flag=True,
use_button_flag=True)
I then asked Gemini 3.1 Pro (which has access to the Wincoot folder):
Can you figure out in the code which problem there is in the
coot_gui.coot_toolbar_button function?
9:29 PM
Yes, I can! I looked into the source code for coot_gui.py and found exactly why
it is failing.
The coot_gui.coot_toolbar_button function in your version of Coot 1 is
unfortunately completely broken due to several severe coding errors left by the
Coot developers during their transition to the new GTK4 interface.
Here are the three major bugs present in the coot_gui.py code that cause it to
fail:
1. The "get_label" Crash
At the very beginning of the function, it calls toolbar_label_list() to loop
through every existing item on the toolbar. To get their names, it runs
.get_label() on every single child widget. However, toolbars contain items like
spacer lines (Separators) and raw images, which don't have text labels. When it
hits one of these, Python throws an AttributeError and the script silently
crashes before it even attempts to draw your button!
2. The "String Indexing" Bug
Even if the above crash didn't happen, the new version of toolbar_label_list()
accidentally returns a list of text strings (like ["Update Maps", "Shiftfield
B"]). However, the coot_toolbar_button function was written expecting a list of
pairs [[label, widget_object], ...].
It checks if button_label in f:, and if it matches, it does found_button =
f[1]. Because f is just a text string, f[1] grabs the second letter of the
word. It literally tries to assign a single letter of the alphabet as a GTK
Toolbar Button widget, which is totally invalid.
3. Deprecated GTK4 Icon Methods
At the very end of the function, it tries to assign your icon using
toolbutton.set_stock_id() and toolbutton.set_icon_widget(). Both of these
methods were completely removed by the creators of GTK when they upgraded from
GTK3 to GTK4. Coot will throw a hidden error here because those commands
literally don't exist in GTK4 anymore.
Conclusion: It's structurally impossible for coot_toolbar_button to work in
this build of Coot 1 because it's full of half-finished GTK4 transition code!
The Keyboard Shortcut and Extensions Menu methods I provided earlier are the
official, working replacements that the developers actually finished testing. I
highly recommend using the "s" keyboard shortcut we set up!
Would be curious how good the answer is.
Many thanks to both of you in advance. It is not a urgent issue.
Br, Georg.
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