Hi Abril,

There are separate mailing list for Chimera and ChimeraX, so you should send ChimeraX questions to chimerax-users@cgl.ucsf.edu .  The problem you ran into has been fixed and the fix is in the 1.7 release candidate, so if you use that then things will work.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Nov 28, 2023, at 10:25 AM, Abril Gijsbers via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear community, 

I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions.

<image.png>

When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :(

ui tool show "Render By Attribute"

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 759, in _set_value_cb
    self._redraw_cb()
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb
    self._bins = left + filled_bins + right
ValueError: operands could not be broadcast together with shapes (0,) (157,)

ValueError: operands could not be broadcast together with shapes (0,) (157,)

File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb
self._bins = left + filled_bins + right

See log for complete Python traceback.

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 760, in _set_value_cb
    self._move_cur_marker(v)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 570, in _move_cur_marker
    self._active_markers._update_plot()
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1222, in _update_plot
    self._update_marker_coordinates()
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1207, in _update_marker_coordinates
    x, y = self._scene_xy(m.xy)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1090, in _scene_xy
    return self.histogram._scene_xy(abs_xy)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy
    num_bins = len(self._bins)
TypeError: object of type 'function' has no len()

TypeError: object of type 'function' has no len()

File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy
num_bins = len(self._bins)

See log for complete Python traceback.

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