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Tom
On Jun 25, 2019, at 4:53 PM, Yazan Abbas yazan.abbas@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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