[chimerax-users] volume splitbyzone and color zone issues

[Yazan Abbas]

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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