<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 25, 2019, at 4:53 PM, Yazan Abbas <<a href="mailto:yazan.abbas@gmail.com" class="">yazan.abbas@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi, <div class=""><br class=""></div><div class="">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:</div><div class=""><br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">Traceback (most recent call last):<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py", line 130, in invoke<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> return self._func(self._name, data)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 3557, in _update_drawings<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> v.update_drawings()<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 701, in update_drawings<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> self._update_surfaces()<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 724, in _update_surfaces<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> s.update_surface(ro)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 1953, in update_surface<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, level, rendering_options)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 2048, in _calculate_contour_surface<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> rendering_options, level)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 2071, in _adjust_surface_geometry<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> varray, tarray, narray = subdivide_triangles(varray, tarray, narray)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">ValueError: not enough values to unpack (expected 3, got 2)</span><br style="font-family: "DejaVu Serif"; font-size: inherit;" class=""><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">Error processing trigger "graphics update": not enough values to unpack (expected 3, got 2):<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">ValueError: not enough values to unpack (expected 3, got 2)</span><br style="font-family: "DejaVu Serif"; font-size: inherit;" class=""><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", line 2071, in _adjust_surface_geometry<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">varray, tarray, narray = subdivide_triangles(varray, tarray, narray)</span></blockquote><div class=""><br class=""></div>I also get the following when using the color zone command, even though color zone works (most of the times, sometimes it fails)<div class=""><br class=""><div class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">Traceback (most recent call last):<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 254, in execute<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> cmd.run(cmd_text)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2641, in run<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> result = ci.function(session, **kw_args)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/std_commands/color.py", line 1248, in color_zone<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges, auto_update = update)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 14, in color_zone<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> zc.set_vertex_colors()<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 84, in set_vertex_colors<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> replace = True)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 123, in color_zone_sharp_edges<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 147, in _edge_cuts<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, distance)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class=""> raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">ValueError: Cut fraction 1.8061 is out of range (0,1)</span><br style="font-family: "DejaVu Serif"; font-size: inherit;" class=""><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">ValueError: Cut fraction 1.8061 is out of range (0,1)</span><br style="font-family: "DejaVu Serif"; font-size: inherit;" class=""><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position<br class=""></span><span style="font-family: "DejaVu Serif"; font-size: inherit;" class="">raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)</span></blockquote><br class=""></div></div></div>
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