Opened 5 years ago
Closed 5 years ago
#4126 closed defect (can't reproduce)
Execution of 'Structure' object's 'atoms' property raised AttributeError
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | 0.91 |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 0.91 (2019-08-20) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-08-20) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open G:/1HNU/yaolab/GFP/1top_preds/2+1/2+1-3.pdb Summary of feedback from opening G:/1HNU/yaolab/GFP/1top_preds/2+1/2+1-3.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T08:22:51Z Chain information for 2+1-3.pdb #1 --- Chain | Description A | No description available X | No description available > rainbow > set bgColor white > lighting soft > lighting full > lighting flat > lighting soft > lighting soft > lighting full > lighting flat > lighting simple Unknown image file format "png image" Unknown image file format "png image" Unknown image file format "png image" Unknown image file format "png image" > save image G:/1HNU/yaolab/GFP/1top_preds/2+1/2+1-3.png width 1341 height 834 > close session > open G:/1HNU/yaolab/t7nie/lys.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/lys.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:30:28Z Chain information for lys.pdb #1 --- Chain | Description X | No description available > open G:/1HNU/yaolab/t7nie/linker.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/linker.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:31:32Z Chain information for linker.pdb #2 --- Chain | Description X | No description available > open G:/1HNU/yaolab/t7nie/thbmdt7.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/thbmdt7.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:32:05Z Chain information for thbmdt7.pdb #3 --- Chain | Description X | No description available > select #1/X 2377 atoms, 2404 bonds, 1 model selected > show sel atoms > hide sel atoms > show sel surfaces > select #3/X 13774 atoms, 13929 bonds, 1 model selected > show sel surfaces > lighting soft > select clear > select #2/X:168 7 atoms, 6 bonds, 1 model selected > undo > undo > select #2 421 atoms, 421 bonds, 1 model selected > ~select #2 Nothing selected > select #2 421 atoms, 421 bonds, 1 model selected > ~select #2 Nothing selected > select #2 421 atoms, 421 bonds, 1 model selected > ~select #2 Nothing selected > select clear > preset "initial styles" "space-filling (chain colors)" Preset implemented in Python; no expansion to individual ChimeraX commands available. > redo > ui favorite true "Model Panel" > hide sel surfaces > lighting soft > mlp sel Map values for surface "linker.pdb_X SES surface": minimum -23.21, mean -7.147, maximum 19.78 > close session > open "G:\\\1HNU\\\yaolab\\\t7nie\\\lys.pdb" Summary of feedback from opening G:\1HNU\yaolab\t7nie\lys.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:30:28Z Chain information for lys.pdb #1 --- Chain | Description X | No description available > open G:/1HNU/yaolab/t7nie/thbmdt7.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/thbmdt7.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:32:05Z Chain information for thbmdt7.pdb #2 --- Chain | Description X | No description available > select clear > open G:/1HNU/yaolab/t7nie/linker.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/linker.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:31:32Z Chain information for linker.pdb #3 --- Chain | Description X | No description available > select clear Invalid "residues" argument: Expected true or false (or 1 or 0) Unknown command: residues 169-179 Unknown command: residues 169 Invalid "residues" argument: Expected true or false (or 1 or 0) Unknown command: 1 Unknown command: 0 > toolshed show Toolbar > select #2 13774 atoms, 13929 bonds, 1 model selected > ~select #2 Nothing selected > select clear > select clear > select #3 421 atoms, 421 bonds, 1 model selected > select clear > show sel cartoons > show sel cartoons > show sel atoms > hide sel atoms > ui favorite true Toolbar > name frozen 1 sel registering illegal selector name "1" Unknown command: 1 > close #3 > close Unknown command: 1 Unknown command: 1 > open "G:\\\1HNU\\\yaolab\\\t7nie\\\thbmdt7.pdb" Summary of feedback from opening G:\1HNU\yaolab\t7nie\thbmdt7.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:32:05Z Chain information for thbmdt7.pdb #1 --- Chain | Description X | No description available > open G:/1HNU/yaolab/t7nie/lys.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/lys.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:30:28Z Chain information for lys.pdb #2 --- Chain | Description X | No description available > open G:/1HNU/yaolab/t7nie/linker.pdb Summary of feedback from opening G:/1HNU/yaolab/t7nie/linker.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:31:32Z Chain information for linker.pdb #3 --- Chain | Description X | No description available > select #3/X:163 7 atoms, 6 bonds, 1 model selected > help help:user/tools/Toolbar.html > select clear > toolshed show "Model Panel" > select #3/X:163 7 atoms, 6 bonds, 1 model selected > toolshed show Toolbar > hide target m > hide target m > show target m > view clip false > select #3/X:164 19 atoms, 18 bonds, 1 model selected > toolshed show Toolbar > distance style color #bbd7ff > distance style color #3edfff > distance style color #29ff66 > distance style color #d7ff0a > distance style color #dfff0a > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > select #3/X:173 11 atoms, 10 bonds, 1 model selected > color gold > color gold Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' 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 'atoms', 'cartoons', 'ribbons', or 'surfaces' or a keyword Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces' or a keyword > name frozen 1 sel registering illegal selector name "1" Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' 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 'atoms', 'cartoons', 'ribbons', or 'surfaces' or a keyword > color byattribute gold No known/registered attribute gold Expected a collection of one of 'atoms', 'cartoons', 'ribbons', 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 'atoms', 'cartoons', 'ribbons', or 'surfaces' or a keyword Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color gold 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 > color random Unknown command: selection > select 16572 atoms, 16754 bonds, 3 models selected Expected an objects specifier or a keyword Invalid "residues" argument: Expected true or false (or 1 or 0) Invalid "residues" argument: Expected true or false (or 1 or 0) Invalid "residues" argument: Expected true or false (or 1 or 0) > select residues true 16572 atoms, 16754 bonds, 3 models selected > select residues true 16572 atoms, 16754 bonds, 3 models selected Expected an objects specifier or a keyword Expected an objects specifier or a keyword Expected an objects specifier or a keyword Expected an objects specifier or a keyword Expected an objects specifier or a keyword > select #1 13774 atoms, 13929 bonds, 1 model selected > select #167 Nothing selected > help help:user > select #179 Nothing selected > style sel stick Changed 132 atom styles > style sel sphere Changed 132 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 132 atom styles > show sel cartoons > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel sphere Changed 96 atom styles > style sel ball Changed 96 atom styles > show sel cartoons > hide sel atoms > rainbow sel > ui mousemode rightMode "crop volume" > show sel atoms > color sel yellow > close session > open "G:\\\1HNU\\\yaolab\\\t7nie\\\thbmdt7.pdb" Summary of feedback from opening G:\1HNU\yaolab\t7nie\thbmdt7.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:32:05Z Chain information for thbmdt7.pdb #1 --- Chain | Description X | No description available > open "G:\\\1HNU\\\yaolab\\\t7nie\\\linker.pdb" Summary of feedback from opening G:\1HNU\yaolab\t7nie\linker.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:31:32Z Chain information for linker.pdb #2 --- Chain | Description X | No description available > open "G:\\\1HNU\\\yaolab\\\t7nie\\\lys.pdb" Summary of feedback from opening G:\1HNU\yaolab\t7nie\lys.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-01-10T12:30:28Z Chain information for lys.pdb #3 --- Chain | Description X | No description available > select #1/X 13774 atoms, 13929 bonds, 1 model selected > show sel surfaces > select #1/X 13774 atoms, 13929 bonds, 1 model selected > show sel surfaces > show sel surfaces > select #3/X 2377 atoms, 2404 bonds, 1 model selected > show sel surfaces Traceback (most recent call last): File "F:\install\ChimeraX\bin\lib\site-packages\chimerax\model_panel\tool.py", line 212, in set_single_color cm.single_color = rgba File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "F:\install\ChimeraX\bin\lib\site-packages\chimerax\atomic\structure.py", line 268, in _set_single_color self.atoms.colors = color File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 65, in get_attr raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'atoms' property raised AttributeError AttributeError: Execution of 'Structure' object's 'atoms' property raised AttributeError File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 65, in get_attr raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. Traceback (most recent call last): File "F:\install\ChimeraX\bin\lib\site-packages\chimerax\model_panel\tool.py", line 212, in set_single_color cm.single_color = rgba File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "F:\install\ChimeraX\bin\lib\site-packages\chimerax\atomic\structure.py", line 268, in _set_single_color self.atoms.colors = color File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 65, in get_attr raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'atoms' property raised AttributeError [lots of these deleted] AttributeError: Execution of 'Structure' object's 'atoms' property raised AttributeError File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 65, in get_attr raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. Traceback (most recent call last): File "F:\install\ChimeraX\bin\lib\site-packages\chimerax\model_panel\tool.py", line 212, in set_single_color cm.single_color = rgba File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "F:\install\ChimeraX\bin\lib\site-packages\chimerax\atomic\structure.py", line 268, in _set_single_color self.atoms.colors = color File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 65, in get_attr raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'atoms' property raised AttributeError AttributeError: Execution of 'Structure' object's 'atoms' property raised AttributeError File "F:\install\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py", line 65, in get_attr raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 456.71 OpenGL renderer: GeForce GTX 960/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 5 years ago
Component: | Unassigned → Structure Analysis |
---|---|
Description: | modified (diff) |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Execution of 'Structure' object's 'atoms' property raised AttributeError |
Version: | → 0.91 |
comment:2 by , 5 years ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.