[chimerax-users] volume splitbyzone and color zone issues

[Elaine Meng]

Hi Yazan,
For bug reports, it’s generally recommended to use the ChimeraX menu: Help… Report a Bug (rather than this mailing list)  … it will automatically tell us what version/platform you are using, include Log contents, etc. The bug report form also allows attaching a file like data or a session that may help us reproduce the problem.
Thanks,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> 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)
>