volume splitbyzone and color zone issues
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)
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 ----- 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@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)
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@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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participants (3)
-
Elaine Meng -
Tom Goddard -
Yazan Abbas