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Opened 5 years ago
Closed 5 years ago
#3617 closed defect (duplicate)
Cartoon() 'atoms' parameter type changed
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.93 (2020-03-23) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. > open F:\1_80S\80S\Withbothsubunit.cxs format session Log from Fri Aug 7 13:31:55 2020UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. > open F:\1_80S\80S\Withbothsubunit.cxs format session Log from Fri Aug 7 12:16:07 2020UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. > open > C:\Users\rupa.ale\Desktop\TOKYO\scratch2\jrai\80Sproject\19aug30d\colormethylation\color_chimerx.cxs Log from Tue Mar 24 18:08:37 2020UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. > open > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/colormethylation/color_chimerx.cxs Log from Mon Mar 23 21:07:15 2020UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Publications/60S/29feb_60S_coot- > coot-1_edited_real_space_refined_edited.pdb Chain information for 29feb_60S_coot- coot-1_edited_real_space_refined_edited.pdb #1 --- Chain | Description 1 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available > open > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Publications/40S/40SwithRNA_metyl_actyl_protein_real_space_refined.pdb Chain information for 40SwithRNA_metyl_actyl_protein_real_space_refined.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available > style stick Changed 195537 atom styles > show cartoons > hide atoms > set bgColor white > select ::name="1MA" 46 atoms, 50 bonds, 1 model selected > show sel target ab > style sel sphere Changed 46 atom styles > color sel yellow > select clear > select ::name="3MH" 11 atoms, 11 bonds, 1 model selected > show sel target ab > style sel sphere Changed 11 atom styles > color sel cyan > select ::name="5MC" 42 atoms, 44 bonds, 1 model selected > show sel target ab > style sel sphere Changed 42 atom styles > color sel pink > select ::name="A2M" 437 atoms, 476 bonds, 2 models selected > show sel target ab > style sel sphere Changed 437 atom styles > color sel red > select ::name="AC4" 46 atoms, 48 bonds, 1 model selected > save session > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/colormethylation/color_chimerx.cxs > show sel target ab > style sel sphere Changed 46 atom styles > color sel blue > select ::name="OMC" 168 atoms, 176 bonds, 2 models selected > show sel target ab > style sel sphere Changed 168 atom styles > color sel purple > select ::name="OMG" 336 atoms, 364 bonds, 2 models selected > show sel target ab > style sel sphere Changed 336 atom styles > color sel turquoise > select ::name="OMU" 168 atoms, 176 bonds, 2 models selected > show sel target ab > style sel sphere Changed 168 atom styles Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel violet > select ::name="UR3" 21 atoms, 22 bonds, 1 model selected > show sel target ab > style sel sphere Changed 21 atom styles > color sel green > save session > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/colormethylation/color_chimerx.cxs opened ChimeraX session > hide #1 models > open > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Densities/40S_resample.mrc Opened 40S_resample.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.00549, step 2, values float32 > color zone #3 near #2 distance 10 > surface dust #3 > volume #3 step 1 > volume #3 level 0.01311 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > select > ::name="1MA"::name="3MH"::name="5MC"::name="A2M"::name="AC4"::name="OHX"::name="OMC"::name="OMG"::name="OMU"::name="UR3" 1293 atoms, 1370 bonds, 2 models selected > select ~ sel 194244 atoms, 208432 bonds, 4 pseudobonds, 5 models selected > hide sel target a > hide sel cartoons > show #!3 models > transparency #3 05 > volume sel style image > transparency #3 20 > transparency sel 50 > transparency sel 50 > volume sel style image > transparency #3 100 > volume sel style image > volume #3 style surface > volume sel show > volume sel style image > volume #3 style surface > transparency sel 0 > transparency sel 50 > transparency sel 0 > transparency sel 50 > transparency #3 20 > transparency #3 10 > transparency #3 5 > transparency #3 0 > transparency #3 1 > transparency sel 0 > transparency sel 50 > lighting flat > lighting flat > lighting flat > lighting full > lighting flat > lighting full > lighting soft > lighting soft > lighting flat > lighting soft > lighting flat > lighting full > lighting shadows false > graphics silhouettes false > transparency #3 1 > volume #3 style image > volume #3 maximumIntensityProjection true > volume #3 style surface maximumIntensityProjection false > volume #3 style image > volume #3 region 0,0,215,431,431,215 step 1 showOutlineBox true > volume #3 region 0,0,0,431,431,431 step 1 > volume #3 style surface region 0,0,0,431,431,431 step 1 > volume #3 > volume #3 style image > color zone #3 near #2 distance 10 > volume #3 style surface > volume sel showOutlineBox false > volume sel step 1 > volume sel step 2 > volume sel step 2 > volume sel step 2 > volume sel step 1 > transparency sel 50 > transparency sel 0 > transparency #3 10 > transparency #3 -5 Missing or invalid "percent" argument: Expected a number > transparency #3 80 > transparency #3 90 > select #2/i 37833 atoms, 42292 bonds, 1 model selected > show sel target ab > style sel stick Changed 37833 atom styles > show sel cartoons > hide sel atoms > select > ::name="1MA"::name="3MH"::name="5MC"::name="A2M"::name="AC4"::name="OHX"::name="OMC"::name="OMG"::name="OMU"::name="UR3" 1293 atoms, 1370 bonds, 2 models selected > style sel sphere Changed 1293 atom styles > show sel target ab > transparency #3 80 > transparency #3 85 > save image > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Densities/40sdensity_backgrounddim.bmp > width 1341 height 806 supersample 4 > graphics silhouettes true > graphics silhouettes false > lighting shadows true > lighting simple > lighting soft > select clear > lighting full > lighting soft > lighting simple > lighting simple > lighting simple > lighting soft > save image > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Densities/40sdensity_backgrounddim.bmp > width 1341 height 806 supersample 4 > save image > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Densities/40sdensity_backgrounddim_zoom.bmp > width 1341 height 806 supersample 4 > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting simple > lighting soft > lighting full > lighting full > lighting simple > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting flat > lighting full > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > save session > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/colormethylation/color_chimerx.cxs > open > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/Densities/60S_resample.mrc Opened 60S_resample.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.00538, step 2, values float32 > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > show #1 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > transparency #4 80 > volume #4 step 1 > select #1/j:101@N1 1 atom, 1 model selected > delete sel > delete sel Drag select of 8 atoms > delete sel > select #1/j:103@N2 1 atom, 1 model selected > delete sel Expected a keyword > hide #1 models > show #1 models Expected a keyword > color zone #4 near #1 distance 10 > volume #4 level 0.01233 > volume #4 level 0.01738 > show #!2 models > hide #!2 models > transparency #4 90 > select #4/1 Nothing selected > select #1/1 69716 atoms, 78023 bonds, 1 model selected > show sel target ab > show sel cartoons > hide sel atoms > select > ::name="1MA"::name="3MH"::name="5MC"::name="A2M"::name="AC4"::name="OMC"::name="OMG"::name="OMU"::name="UR3" 1275 atoms, 1370 bonds, 2 models selected > style sel sphere Changed 1275 atom styles > show sel target ab > hide #!4 models > save session > C:/Users/rupa.ale/Desktop/TOKYO/scratch2/jrai/80Sproject/19aug30d/colormethylation/color_chimerx.cxs opened ChimeraX session > show #!2 models > close Expected a models specifier or a keyword > open F:/1_80S/80S/Refinemodels/80s_job189_14052020_edited-coot-1.pdb Summary of feedback from opening F:/1_80S/80S/Refinemodels/80s_job189_14052020_edited-coot-1.pdb --- warning | Ignored bad PDB record found on line 199863 END Chain information for 80s_job189_14052020_edited-coot-1.pdb #1 --- Chain | Description 1 | No description available 3 | No description available 4 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M Y | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available > show cartoons > hide atoms > hide cartoons > show cartoons > color bynucleotide > rainbow > color bychain > select /1 67679 atoms, 75142 bonds, 1 model selected > hide sel cartoons > show sel cartoons > select /1/2 67679 atoms, 75142 bonds, 1 model selected > select /1/23/4 71059 atoms, 78888 bonds, 1 model selected > select /1/23/4/i 109808 atoms, 121989 bonds, 1 pseudobond, 2 models selected > select ~ /1/23/4/i 89971 atoms, 91665 bonds, 1 pseudobond, 2 models selected > select ~ /1/2/3/4/i 87392 atoms, 88782 bonds, 1 pseudobond, 2 models selected > hide sel cartoons > select /3 2579 atoms, 2883 bonds, 1 model selected > color sel bychain Expected a keyword Expected a keyword Expected a keyword Expected a keyword Expected a keyword > color /3 sky blue cartoons > color /3 blue cartoons > color /4 sky blue cartoons > open F:/1_80S/80S/Composite80S.mrc Opened Composite80S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.0386, step 2, values float32 > transparency #2 50 > select clear > select clear > transparency #2 20 > transparency #2 90 > transparency #2 80 > color #2 gray > surface dust #2 > select ::name="G7MB" 24 atoms, 26 bonds, 1 model selected > show sel atoms > color sel sky blue > color sel black > select ::name="PSUA" 580 atoms, 609 bonds, 1 model selected > color sel yellow > show sel atoms > select ::name="PSUA" 580 atoms, 609 bonds, 1 model selected > select ::name="PSUB" 260 atoms, 273 bonds, 1 model selected > show sel atoms > color sel yellow > select ::name="1MAA" 46 atoms, 50 bonds, 1 model selected > show sel atoms > hide #!2 models > color sel white > select ::name="4ACB" 46 atoms, 48 bonds, 1 model selected > show sel atoms > color sel gray > select ::name="5MCA" 42 atoms, 44 bonds, 1 model selected > save session F:/1_80S/80S/Withbothsubunit.cxs opened ChimeraX session > show sel atoms Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel sienna > select ::name="A2MA" 253 atoms, 276 bonds, 1 model selected Expected an objects specifier or a keyword Unknown command: select::name=A2MA/A2MB Unknown command: select::name=A2MA Expected an objects specifier or a keyword Unknown command: select#1: A2MA Unknown command: select#1:: A2MA > select #1:: A2MA 199779 atoms, 213654 bonds, 2 pseudobonds, 2 models selected > select clear > select clear > select :: A2MA 199779 atoms, 213654 bonds, 2 pseudobonds, 2 models selected > select ::name="A2MA" 253 atoms, 276 bonds, 1 model selected > select #1 :A2MA 253 atoms, 276 bonds, 1 model selected > select #1 :A2MA/A2MB 253 atoms, 276 bonds, 1 model selected > show sel atoms Expected an objects specifier or a keyword > color sel red Expected a keyword > select #1 :A2MA:A2MB 437 atoms, 476 bonds, 1 model selected > show sel atoms > color sel red > select ::name="OMGA" 240 atoms, 260 bonds, 1 model selected > select #1 :OMGC:OMGB 120 atoms, 130 bonds, 1 model selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select #1 :OMGA:OMGB 360 atoms, 390 bonds, 1 model selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel cyan > show sel atoms > select #1 :OMCA:OMCB 210 atoms, 220 bonds, 1 model selected > show sel atoms > color sel darkgreen > select ::name="OMSA" 21 atoms, 22 bonds, 1 model selected > show sel atoms > color sel sky blue > select ::name="UR3A" 21 atoms, 22 bonds, 1 model selected > show sel atoms > save session F:/1_80S/80S/Withbothsubunit.cxs > select ::name="OMUA" 147 atoms, 154 bonds, 1 model selected > select #1 :OMUB:OMUA 189 atoms, 198 bonds, 1 model selected > color sel pink > show sel atoms > select ::name="PS3B" 28 atoms, 29 bonds, 1 model selected > show sel atoms > select #1 :PS3A:PS3B 28 atoms, 29 bonds, 1 model selected > show sel atoms > color sel orange > select #1 :PS3A:PS3B 28 atoms, 29 bonds, 1 model selected > select #1 :5MCA 42 atoms, 44 bonds, 1 model selected > select #1 :5MCB Nothing selected > select #1 :A2MA:A2MB 437 atoms, 476 bonds, 1 model selected > select #1 :G7MB 24 atoms, 26 bonds, 1 model selected > select ::name="1MAA" 46 atoms, 50 bonds, 1 model selected > select #1 :MA6B:MA6A 48 atoms, 53 bonds, 1 model selected > show sel atoms Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel goldenrod > select ::name="UR3A" 21 atoms, 22 bonds, 1 model selected > show sel atoms > color sel khaki > color sel peachpuff > save session F:/1_80S/80S/Withbothsubunit.cxs Summary of feedback from opening F:\1_80S\80S\Withbothsubunit.cxs --- notes | Deleting atomic symmetry model... opened ChimeraX session Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Users\rupa.ale\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py", line 1222, in _set_default_cartoon_cb set_to_default_cartoon(self.session, model = self.structure) File "C:\Users\rupa.ale\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\util.py", line 55, in set_to_default_cartoon cartoon.cartoon(session, atoms = atoms, suppress_backbone_display=False) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\cartoon.py", line 71, in cartoon results = atoms.evaluate(session) AttributeError: 'Atoms' object has no attribute 'evaluate' Error processing trigger "frame drawn": AttributeError: 'Atoms' object has no attribute 'evaluate' File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\cartoon.py", line 71, in cartoon results = atoms.evaluate(session) See log for complete Python traceback. OpenGL version: 3.3.13492 Core Profile Forward-Compatible Context 22.19.677.257 OpenGL renderer: AMD Radeon(TM) R5 Graphics OpenGL vendor: ATI Technologies Inc. Manufacturer: LENOVO Model: 20377 OS: Microsoft Windows 10 Education (Build 17134) Memory: 7,443,828,736 MaxProcessMemory: 137,438,953,344 CPU: 4 AMD A8-6410 APU with AMD Radeon R5 Graphics "
Change History (2)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cartoon() 'atoms' parameter type changed |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #3616