id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2118 Color zone sharp: Cut fraction is out of range yazan.abbas@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-51-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-25) Description volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 color zone #2 near #1 distance 3 sharpEdges true update false After applying colorzone, portions of the map appear clipped. See attached images. Log: UCSF ChimeraX version: 0.91 (2019-06-25) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open maps_and_models/State1_composite.cif name State1 Summary of feedback from opening maps_and_models/State1_composite.cif --- warnings | skipping chem_comp category: Missing column 'type' near line 297 Unknown polymer entity '?' near line 342 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. skipping chem_comp category: Missing column 'type' near line 72840 skipping chem_comp category: Missing column 'type' near line 72867 Chain information for State1 #1 --- Chain | Description A1 A2 A3 | No description available B1 | No description available B2 | No description available B3 | No description available C | No description available D | No description available E1 E2 E3 | No description available F | No description available G1 | No description available G2 | No description available G3 | No description available K1 | No description available K2 | No description available K3 | No description available a | No description available ac | No description available b | No description available c1 c2 c3 c4 c5 c6 c7 c8 c9 | No description available d | No description available e | No description available f | No description available pr | No description available > open maps_and_models/J1509_state1_Vo.mrc Opened J1509_state1_Vo.mrc, grid size 340,340,340, pixel 1.06, shown at level 0.16, step 2, values float32 > set bgColor white > set silhouettes true > camera ortho > surface cap true > lighting soft shadows true intensity 0.1 > close #1.1 > split #1 chains Chain information for State1 A1 #1.1 --- Chain | Description A1 | No description available Chain information for State1 A2 #1.2 --- Chain | Description A2 | No description available Chain information for State1 A3 #1.3 --- Chain | Description A3 | No description available Chain information for State1 B1 #1.4 --- Chain | Description B1 | No description available Chain information for State1 B2 #1.5 --- Chain | Description B2 | No description available Chain information for State1 B3 #1.6 --- Chain | Description B3 | No description available Chain information for State1 C #1.7 --- Chain | Description C | No description available Chain information for State1 D #1.8 --- Chain | Description D | No description available Chain information for State1 E1 #1.9 --- Chain | Description E1 | No description available Chain information for State1 E2 #1.10 --- Chain | Description E2 | No description available Chain information for State1 E3 #1.11 --- Chain | Description E3 | No description available Chain information for State1 F #1.12 --- Chain | Description F | No description available Chain information for State1 G1 #1.13 --- Chain | Description G1 | No description available Chain information for State1 G2 #1.14 --- Chain | Description G2 | No description available Chain information for State1 G3 #1.15 --- Chain | Description G3 | No description available Chain information for State1 K1 #1.16 --- Chain | Description K1 | No description available Chain information for State1 K2 #1.17 --- Chain | Description K2 | No description available Chain information for State1 K3 #1.18 --- Chain | Description K3 | No description available Chain information for State1 a #1.19 --- Chain | Description a | No description available Chain information for State1 ac #1.20 --- Chain | Description ac | No description available Chain information for State1 b #1.21 --- Chain | Description b | No description available Chain information for State1 c1 #1.22 --- Chain | Description c1 | No description available Chain information for State1 c2 #1.23 --- Chain | Description c2 | No description available Chain information for State1 c3 #1.24 --- Chain | Description c3 | No description available Chain information for State1 c4 #1.25 --- Chain | Description c4 | No description available Chain information for State1 c5 #1.26 --- Chain | Description c5 | No description available Chain information for State1 c6 #1.27 --- Chain | Description c6 | No description available Chain information for State1 c7 #1.28 --- Chain | Description c7 | No description available Chain information for State1 c8 #1.29 --- Chain | Description c8 | No description available Chain information for State1 c9 #1.30 --- Chain | Description c9 | No description available Chain information for State1 d #1.31 --- Chain | Description d | No description available Chain information for State1 e #1.32 --- Chain | Description e | No description available Chain information for State1 f #1.33 --- Chain | Description f | No description available Chain information for State1 pr #1.34 --- Chain | Description pr | No description available Split State1 (#1) into 34 models > dssp > select #1.1-3 13993 atoms, 14279 bonds, 3 models selected > name frozen subunitA sel > select #1.4-6 10847 atoms, 11060 bonds, 3 models selected > name frozen subunitB sel > select #1.7 2927 atoms, 2981 bonds, 1 model selected > name frozen subunitC sel > select #1.8 1726 atoms, 1744 bonds, 1 model selected > name frozen subunitD sel > select #1.9-11 5040 atoms, 5079 bonds, 3 models selected > name frozen subunitE sel > select #1.12 876 atoms, 890 bonds, 1 model selected > name frozen subunitF sel > select #1.13-15 2392 atoms, 2401 bonds, 3 models selected > name frozen subunitG sel > select #1.16-18 5441 atoms, 5542 bonds, 3 models selected > name frozen SidK sel > select #1.19 5615 atoms, 5754 bonds, 1 model selected > name frozen V0a sel > select #1.21 1503 atoms, 1537 bonds, 1 model selected > name frozen V0b sel > select #1.22-30 9612 atoms, 9747 bonds, 9 models selected > name frozen V0cring sel > select #1.31 2833 atoms, 2899 bonds, 1 model selected > name frozen V0d sel > select #1.32 628 atoms, 653 bonds, 1 model selected > name frozen V0e sel > select #1.33 675 atoms, 691 bonds, 1 model selected > name frozen V0RNAseK sel > select #1.20 337 atoms, 347 bonds, 1 model selected > name frozen V0Ac45 sel > select #1.34 443 atoms, 456 bonds, 1 model selected > name frozen V0PRR sel > hide SidK target c > hide subunitG target c > hide subunitF target c > hide subunitE target c > hide subunitC target c > hide subunitA target c > hide subunitB target c > hide subunitD target c > hide subunitF target c > color subunitA #F2EA42 target cabp > color subunitB #D01F26 target cabp > color subunitC #996633 target cabp > color subunitD #3A53A3 target cabp > color subunitE #804F9F target cabp > color subunitF #B9529E target cabp > color subunitG #fce94f target cabp > color SidK #D2D2D2 target cabp > color V0a #8ae234 target cabp > color V0b #9d42bf target cabp > color V0cring #e182d9 target cabp > color V0d #8ab7ff target cabp > color V0e #3465a4 target cabp > color V0RNAseK #cc0000 target cabp > color V0Ac45 #EEEEEC target cabp > color V0PRR #edd400 target cabp > select clear > hide atoms > show cartoons > surface dust #2 size 6 > volume #2 step 1 level 0.5 color #EEEEEC surfaceSmoothing true subdivideSurface true smoothingIterations 4 > cartoon style V0cring modeHelix tube > hide SidK target c > hide subunitG target c > hide subunitF target c > hide subunitE target c > hide subunitC target c > hide subunitA target c > hide subunitB target c > hide subunitD target c > hide subunitF target c > color V0Ac45 #eeeeec target c > ui mousemode rightMode pivot > toolshed show ""Volume Viewer"" > toolshed show ""Model Panel"" > cartoon style V0b modeHelix tube > show #!2 models > color zone #2 near #1 distance 3 sharpEdges true > ui mousemode rightMode rotate > ui mousemode rightMode pivot > volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 > volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 Expected a keyword Expected a keyword > color zone #2 near #1 distance 3 sharpEdges true update false 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 -0.27227 is out of range (0,1) ValueError: Cut fraction -0.27227 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) See log for complete Python traceback. > volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 > color zone #2 near #1 distance 3 sharpEdges true update false > color zone #2 near #1 distance 2.5 sharpEdges true update false 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 1.7919 is out of range (0,1) ValueError: Cut fraction 1.7919 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) See log for complete Python traceback. > volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 > volume #2 step 1 level 0.501 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 > color zone #2 near #1 distance 3 sharpEdges true update false > save after_colorzone.png > volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 > save before_colorzone.png OpenGL version: 3.3.0 NVIDIA 418.56 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: colorzone.tar.gz }}} [attachment:""colorzone.tar.gz""] " defect closed normal Surface fixed all ChimeraX