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Opened 19 months ago
Closed 19 months ago
#14919 closed defect (duplicate)
Log volume level: local variable 'levels' referenced before assignment
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 0.94 (2020-04-17) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.94.dev202004170644 (2020-04-17) © 2016-2020 Regents of the University of California. All rights reserved. > open "D:\\\PRDM1\\\manuscipt\\\figure\\\figure2\\\449 surface .cxs" Log from Sat Apr 6 23:16:22 2024UCSF ChimeraX version: 0.94.dev202004170644 (2020-04-17) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > D:\\\PRDM1\\\crystal\\\Yangsy001\\\Sample-3-01\\\Refine_21\\\449_refine_21.pdb Summary of feedback from opening D:\\\PRDM1\\\crystal\\\Yangsy001\\\Sample-3-01\\\Refine_21\\\449_refine_21.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2024-03-30 Time 14:24:47 ???????????? +0800 (1711779887.93 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : D:\PRDM1\crystal\Yangsy001\Sample-3-01\Refine_19\449_refine_19.mtz 54 messages similar to the above omitted Chain information for 449_refine_21.pdb #1 --- Chain | Description B | No description available > hide #1.1 models > show #1.1 models > hide #1.1 models > set bgColor white > show surfaces > show #1.1 models > hide #1.1 models > color mediumturquoise target s halfbond true transparency 0 > lighting soft > 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 ::name="LIG" 140 atoms, 150 bonds, 1 model selected > select clear > color ::name="LIG" @C* light salmon target a > color ::name="LIG" @C* thistle target a > color ::name="LIG" @C* pink target a > color ::name="LIG" @C* violet target a > select /B:163@OH 1 atom, 1 model selected > select clear > select clear > select ::name="LIG" 140 atoms, 150 bonds, 1 model selected > select clear Drag select of 4 atoms, 3 bonds > select clear Drag select of 3 atoms, 3 bonds > select up 4 atoms, 3 bonds, 1 model selected > select up 70 atoms, 75 bonds, 1 model selected > color ::sel @C* gold target a Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Invalid "target" argument: Character 'e' is not an allowed target, must be one of acrsbpfl Expected a keyword > help help:user Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > show target m > select #1 3247 atoms, 3240 bonds, 1 pseudobond, 2 models selected > ~select #1 1 model selected > hide #1.1 models > select up 2 atoms, 1 bond, 1 model selected > select up 70 atoms, 75 bonds, 1 model selected > color :sel @C* gold target a > color ::sel @C* gold target a > style sel ball Changed 70 atom styles > select ::name="LIG" 140 atoms, 150 bonds, 1 model selected > style sel ball Changed 140 atom styles > color sel gold target a > select clear > select /A:2@S39 1 atom, 1 model selected > select up 70 atoms, 75 bonds, 1 model selected > color sel gold target a > select clear > select /A:2@C38 1 atom, 1 model selected > select up 70 atoms, 75 bonds, 1 model selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select clear > select /A:2@N01 1 atom, 1 model selected > select /A:2@N09 1 atom, 1 model selected > select /A:2@N01 1 atom, 1 model selected > select /A:2@N09 1 atom, 1 model selected > color sel blue target a > select /A:2@N01 1 atom, 1 model selected > color sel blue target a > select /A:2@N03 1 atom, 1 model selected > color sel blue target a > select /A:2@N23 1 atom, 1 model selected > color sel blue target a > select /A:2@N11 1 atom, 1 model selected > color sel blue target a > select /A:2@N17 1 atom, 1 model selected > color sel blue target a > select /A:2@C33 1 atom, 1 model selected > select /A:2@N30 1 atom, 1 model selected > color sel blue target a > select clear > select /A:2@O34 1 atom, 1 model selected > color sel red target a > select /A:2@O41 1 atom, 1 model selected > color sel red target a > select clear > select /A:2@F21 1 atom, 1 model selected > color sel palegreen target a > select /A:2@F22 1 atom, 1 model selected > color sel palegreen target a > select /A:2@F20 1 atom, 1 model selected > color sel palegreen target a > select clear > select /A:2@H231 1 atom, 1 model selected > color sel white target a > select /A:2@S39 1 atom, 1 model selected > color sel sandybrown target a > select clear > select /A:1@S39 1 atom, 1 model selected > color sel sandybrown target a > select clear > save2 "D:/PRDM1/manuscipt/figure/figure2/449 surface .cxs" opened ChimeraX session > 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 . > open2 D:/PRDM1/manuscipt/figure/figure2/449mesh.mrc Opened 449mesh.mrc, grid size 45,45,47, pixel 0.466,0.455,0.449, shown at level 1.6, step 1, values float32 > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > ui mousemode rightMode "translate selected models" > hide surfaces > volume #2 style mesh level 0.8 color cornflowerblue level 1.2 color 0,50,80 > ui mousemode rightMode "move planes" > volume #2 region 0,0,0,44,44,46 > volume #2 region 0,0,0,44,44,46 > volume #2 region 0,0,0,44,44,46 > volume #2 region 0,0,0,44,44,46 > volume #2 region 0,0,0,44,44,46 > ui mousemode rightMode "contour level" > volume #2 level 0.7296 level 1.2 > volume #2 level 0.5083 level 0.9787 > volume #2 level 0.3976 level 0.868 > ui mousemode rightMode "move planes" > volume #2 region 0,0,0,44,44,46 > ui mousemode rightMode "play map series" > ui mousemode rightMode rotate > ui mousemode rightMode "contour level" > volume #2 level 0.3289 level 0.7993 > volume #2 level 0.3439 level 0.8144 > open2 D:/PRDM1/manuscipt/figure/figure2/449mesh2.mrc Opened 449mesh2.mrc, grid size 87,89,91, pixel 0.466,0.455,0.449, shown at level 1.41, step 1, values float32 > volume #3 level 1.179 > volume #2 style mesh level 0.8 color cornflowerblue level 1.2 color 0,50,80 > hide #!3 models > show #!3 models > hide #2.2 models > hide #2.1 models Traceback (most recent call last): File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py", line 477, in <lambda> gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_up") File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py", line 402, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 70, in mouse_up self.log_volume_command() File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 100, in log_volume_command log_volume_level_command(v) File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 137, in log_volume_level_command command = 'volume #%s %s' % (v.id_string, levels) UnboundLocalError: local variable 'levels' referenced before assignment UnboundLocalError: local variable 'levels' referenced before assignment File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 137, in log_volume_level_command command = 'volume #%s %s' % (v.id_string, levels) See log for complete Python traceback. Traceback (most recent call last): File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py", line 475, in <lambda> gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_down") File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py", line 396, in _dispatch_mouse_event lm.mouse_up(MouseEvent(event, modifiers=modifiers)) File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 70, in mouse_up self.log_volume_command() File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 100, in log_volume_command log_volume_level_command(v) File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 137, in log_volume_level_command command = 'volume #%s %s' % (v.id_string, levels) UnboundLocalError: local variable 'levels' referenced before assignment UnboundLocalError: local variable 'levels' referenced before assignment File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 137, in log_volume_level_command command = 'volume #%s %s' % (v.id_string, levels) See log for complete Python traceback. Traceback (most recent call last): File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py", line 477, in <lambda> gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_up") File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py", line 402, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 70, in mouse_up self.log_volume_command() File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 100, in log_volume_command log_volume_level_command(v) File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 137, in log_volume_level_command command = 'volume #%s %s' % (v.id_string, levels) UnboundLocalError: local variable 'levels' referenced before assignment UnboundLocalError: local variable 'levels' referenced before assignment File "E:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\map\mouselevel.py", line 137, in log_volume_level_command command = 'volume #%s %s' % (v.id_string, levels) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 31.0.101.4146 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Manufacturer: HUAWEI Model: KLVG-XX OS: Microsoft Windows 11 家庭中文版 (Build 22631) Memory: 34,067,963,904 MaxProcessMemory: 137,438,953,344 CPU: 16 13th Gen Intel(R) Core(TM) i7-1360P"
Change History (2)
comment:1 by , 19 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Log volume level: local variable 'levels' referenced before assignment |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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ChimeraX 0.94!