id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3616 cartoon() 'atoms' parameter type changed chimerax-bug-report@… Tristan Croll "{{{ 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\40S\40S_mainfigure.cxs format session Log from Tue May 19 11:07:14 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 F:/1_80S/40S/40s_job189_14052020_edited-coot-1.pdb Chain information for 40s_job189_14052020_edited-coot-1.pdb #1 --- Chain | Description A F | No description available B | No description available C | No description available D | No description available E | 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 P | No description available N | No description available O | 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 > set bgColor white > show cartoons > hide atoms > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected Expected a keyword Expected a keyword > cartoon sel > select ~sel 38618 atoms, 39237 bonds, 1 model selected > hide sel target a > cartoon hide sel > open F:/1_80S/40S/Composite40S.mrc Opened Composite40S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.028, step 2, values float32 > open F:/1_80S/40S/Averagemap_coot_0.mrc Opened Averagemap_coot_0.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.0143, step 2, values float32 > open F:/1_80S/40S/Composite40S.mrc Opened Composite40S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.028, step 2, values float32 > select clear > show target ab > hide #!2 models > show cartoons > hide atoms > show #!2 models > color zone #2 near #1 distance 10 > volume zone #2 nearAtoms #3 range 2 no atoms specified for zone > surface dust #2 > volume #2 step 1 > hide #!2 models Drag select of 6707 residues Drag select of 6718 residues Missing required ""range"" argument > select sel @< 5 76591 atoms, 81560 bonds, 1 pseudobond, 2 models selected > volume zone #1 nearAtoms #1 range 2 > show #!2 models > volume zone #2 nearAtoms #1 range 2 > color zone #2 near #1 distance 10 > color zone #3 near #1 distance 10 > transparency #3 50 > transparency #3 80 > select clear > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > select ~sel 38618 atoms, 39237 bonds, 5 models selected > hide sel target a > hide #!3 models > hide sel cartoons > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > show #!3 models > hide #!3 models > select ::name=""4ACB"" 46 atoms, 48 bonds, 1 model selected > style sel sphere Changed 46 atom styles > color sel pink > style sel sphere Changed 46 atom styles > show sel target ab > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > nucleotides sel ladder > nucleotides sel stubs > cartoon style sel modeHelix tube sides 20 > nucleotides sel slab > nucleotides sel stubs > show #!2 models > hide #!2 models > display #1 cartoon style nuclix xset oval width 1.6 thick1.6 Expected ',' or a keyword > display #1 cartoon style nuclieic xset oval width 1.6 thick1.6 Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword Expected a keyword > cartoon style nucleic width 1.6 thickness 1.6 > cartoon style nucleic width 1.6 thickness 0.5 > cartoon style nucleic width 0.5 thickness 0.5 > cartoon style nucleic width 0.5 thickness 0.3 > cartoon style nucleic width 1.5 thickness 0.3 > cartoon style nucleic width 0.3 thickness 0.3 > cartoon style nucleic width 0.3 thickness 0.5 > select clear > show #!3 models > volume #!3 style image > volume #!3 style surface > transparency #3.1 0 > transparency #3.1 50 > transparency #3.1 0 > transparency #3.1 50 > transparency #3.1 10 > transparency #3.1 80 > cartoon style nucleic width 1.5 thickness 0.3 > cartoon style nucleic width 1 thickness 0.3 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > open F:/1_80S/40S/Composite40S.mrc Opened Composite40S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.028, step 2, values float32 > volume zone #4 nearAtoms #1/i range 2 > close #5 > display all > volume zone #4 nearAtoms #1/i range 2 > hide #!1 models > volume #5 level 0.02025 > volume zone #4 nearAtoms #1 range 2 > volume #4 step 1 > show #!1 models > show cartoons > hide atoms > transparency #5.1 50 > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > display select Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select ~sel 38618 atoms, 39237 bonds, 10 models selected > hide sel target a > cartoon hide sel > select clear > volume #5 step 1 > graphics silhouettes true > lighting flat > graphics silhouettes false > lighting soft > lighting simple > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting soft > graphics silhouettes false > show #!4 models > hide #!4 models > show #!3 models > hide #!5 models > show #!5 models > hide #!5 models > transparency #3 10 > transparency #3 95 > transparency #3 90 > transparency #1 0 > select ::name=""OMCB"" 63 atoms, 66 bonds, 1 model selected > hide #!3 models > show sel atoms > color sel dark green > select ::name=""OMGB"" 120 atoms, 130 bonds, 1 model selected > show sel atoms > color sel dark cyan > select ::name=""OMUB"" 42 atoms, 44 bonds, 1 model selected > show sel atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel pink > select ::name=""A2MB"" 184 atoms, 200 bonds, 1 model selected > color sel red > show sel atoms > select ::name=""4ACB"" 46 atoms, 48 bonds, 1 model selected > show sel atoms > color sel gray > select ::name=""PS3B"" 28 atoms, 29 bonds, 1 model selected > show sel atoms > color sel light sea green Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel orange red > select ::name=""G7MB"" 24 atoms, 26 bonds, 1 model selected > show sel atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel black > select ::name=""PSUB"" 260 atoms, 273 bonds, 1 model selected > show sel atoms > color sel yellow > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!3 models > save session F:/1_80S/40S/40S_mainfigure.cxs > save image F:/1_80S/40S/40S_front.bmp width 787 height 773 > save image F:/1_80S/40S/Images/subunitjoining.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/headfront.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/bodyfront.bmp width 787 height 773 > supersample 3 > toolshed show ""Side View"" > select ::name=""G7MB"" 24 atoms, 26 bonds, 1 model selected > select ::name=""MA6B"" 48 atoms, 53 bonds, 1 model selected > show sel atoms > color sel goldenrod > volume #3 change image level -1.167e-05,0 level 0.03982,0.8 level 0.3983,1 > save image F:/1_80S/40S/Images/bodyfront_2.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/bodyfront_2.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/bodyfront_2.bmp width 787 height 773 > supersample 3 > save session F:/1_80S/40S/40S_mainfigure.cxs > save image F:/1_80S/40S/Images/subunitjoining.bmp width 787 height 773 > supersample 3 > save session F:/1_80S/40S/40S_mainfigure.cxs Summary of feedback from opening F:\1_80S\40S\40S_mainfigure.cxs --- notes | Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time 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 "" }}} " defect closed normal Third Party fixed Tom Goddard all ChimeraX