[chimerax-users] volume splitbyzone and color zone issues

[Tom Goddard]

When an error like this occurs ChimeraX shows an error dialog that has a "Report a Bug" button.  Please press that button to submit the bug because it will include additional information like exactly what commands led to each error, exactly what ChimeraX version you have, what operating system you are running.

	Tom


> On Jun 25, 2019, at 4:53 PM, Yazan Abbas <yazan.abbas at gmail.com> wrote:
> 
> Hi, 
> 
> I executed 'color zone #2 near #1 distance 5 sharpEdges true' to colour a map I loaded, followed by "volume splitbyzone #2', but repeatedly would get an error that the volume specified is not coloured by zone. Eventually after trying multiple times, it worked, however the log outputted the following:
> 
> Traceback (most recent call last):
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py", line 130, in invoke
>     return self._func(self._name, data)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 3557, in _update_drawings
>     v.update_drawings()
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 701, in update_drawings
>     self._update_surfaces()
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 724, in _update_surfaces
>     s.update_surface(ro)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 1953, in update_surface
>     va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, level, rendering_options)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 2048, in _calculate_contour_surface
>     rendering_options, level)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 2071, in _adjust_surface_geometry
>     varray, tarray, narray = subdivide_triangles(varray, tarray, narray)
> ValueError: not enough values to unpack (expected 3, got 2)
> Error processing trigger "graphics update": not enough values to unpack (expected 3, got 2):
> ValueError: not enough values to unpack (expected 3, got 2)
> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 2071, in _adjust_surface_geometry
> varray, tarray, narray = subdivide_triangles(varray, tarray, narray)
> 
> I also get the following when using the color zone command, even though color zone works (most of the times, sometimes it fails)
> 
> Traceback (most recent call last):
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 254, in execute
>     cmd.run(cmd_text)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2641, in run
>     result = ci.function(session, **kw_args)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/std_commands/color.py", line 1248, in color_zone
>     color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges, auto_update = update)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 14, in color_zone
>     zc.set_vertex_colors()
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 84, in set_vertex_colors
>     replace = True)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 123, in color_zone_sharp_edges
>     ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 147, in _edge_cuts
>     f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, distance)
>   File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position
>     raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)
> ValueError: Cut fraction 1.8061 is out of range (0,1)
> ValueError: Cut fraction 1.8061 is out of range (0,1)
> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position
> raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)
> 
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