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Opened 6 years ago
Closed 6 years ago
#1934 closed defect (fixed)
smoothlines: 'NoneType' object has no attribute 'shape'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.15.0-48-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.9 (2019-04-24) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-04-24) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Chain information for 1_colour.pdb #1.1 --- Chain | Description E | No description available Chain information for 6mer.pdb #1.2 --- Chain | Description 3 B I M Q Y | No description available Chain information for dif_colour.pdb #1.3 --- Chain | Description U | No description available > set bgColor white > lighting full > color /3 palegreen > color /b aquamarine > color /e salmon > color /i palegoldenrod > color /m skyblue > color /q "peach puff" > color /u seashell > color /y khaki > select /u sequence PYEWENPQLVSEGTEKSHASFIPYLDPFSGEWEYPEEFISLNGNWRFLFAKNPFEVPEDFFSEKFDDSNWDEIEVPSNWEMKGYGKPIYTNVVYPFEPNPPFVPKDDNPTGVYRRWIEIPEDWFKKEIFLHFEGVRSFFYLWVNGKKIGFSKDSCTPAEFRLTDVLRPGKNLITVEVLKWSDGSYLEDQDMWWFAGIYRDVYLYALPKF 1780 atoms, 1854 bonds, 1 model selected > color sel palegreen > select /u sequence HIRDVFVRTDLDENYRNGKIFLDVEMRNLGEEEEKDLEVTLITPDGDEKTLVKETVKPEDRVLSFAFDVKDPKKWSAETPHLYVLKLKLGEDEKKVNFGFR 837 atoms, 852 bonds, 1 model selected > color sel aquamarine > select /u sequence KIEIKDGTLLFNGKPLYIKGVNRHEFDPDRGHAVTVERMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYFGLYVIDEANIESHGIDWDPEVTLANRWEWEKAHFDRIKRMVERDKNHPSIIFWSLGNEAGDGVNFEKAALWIKKRDNTRLIHYEGTTRRGESYYVDVFSLMYPKMDILLEYASKKREKPFIMCEYAHAMGNSVGNLKDYWDVIEKYPYLHGGCIWDWVDQGIRKKDENGREFWAYGGDFGDTPNDGNFCINGVVLPDRTPEPELYEVKKVY 2357 atoms, 2426 bonds, 1 model selected > color sel plum > select /u sequence QNVKIRQVSKDTYEVENRYLFTNLEMFDGAWKIRKDGEVIEEKTFKIFAEPGEKRLLKIPLPEMDDSEYFLEISFSLSEDTPWAEKGHVVAWEQFLLK 824 atoms, 844 bonds, 1 model selected > color sel palegoldenrod > select /u sequence APAFEKKSISDGVSLREDGKHLTVEAKDTVYVFSKLTGLLEQILHRRKKILKSPVVPNFWRVPTDNDIGNRMPQRLAIWKRASKERKLFKMHWKKEENRVSVHSVFQLPGNSWVYTTYTVFGNGDVLVDLSLIPAEDVPEIPRIGFQFTVPEEFGTVEWYGRGPHETYWDRKESGLFARYRKAVGEMMHRYVRPQETGNRSDVRWFALSDGETKLFVSGMPQIDFSVWPFSMEDLERVQHISELPERDFVTVNVDFRQMGLGGDDSWGAMPHLEYRLLPKPYRFSFRMRISEEIPSWRVLAAI 2501 atoms, 2574 bonds, 1 model selected > color sel skyblue > select /u sequence PETLHVEMSSEDVIREGDTLRVKFSLLNDTPLSKEKQVVLFVDGNEYSVRRVVIPPFKKEELVFKVEGLKKGEHLIHTNLNTRKTIYVR 728 atoms, 740 bonds, 1 model selected > color sel "peach puff" > ~select all Nothing selected > show all models > lighting full > select #1.1 9027 atoms, 9295 bonds, 1 model selected > hide selAtoms > show selAtoms surfaces > hide selAtoms ribbons > select #1.2 54163 atoms, 55770 bonds, 1 model selected > hide selAtoms > hide selAtoms surfaces > show selAtoms ribbons > select #1.3 9027 atoms, 9295 bonds, 1 model selected > hide selAtoms > show selAtoms surfaces > hide selAtoms ribbons > color zone #1.3 near #1.3 distance 3 > ~select all 1 model selected > lighting direction 1,-1,-1 > close #1.2 > view matrix camera -0.56942,0.59784,-0.56422,-69,-0.54459,-0.78848,-0.28586,14.145,-0.61578,0.14449,0.77456,534.07 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera -0.56942,0.59784,-0.56422,-69,-0.54459,-0.78848,-0.28586,14.145,-0.61578,0.14449,0.77456,534.07 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > view cofr false > show selAtoms ribbons > hide selAtoms surfaces > save image /home/smiguez/Documents/dimer.tif width 4000 height 4000 supersample 4 transparentBackground true > save image /home/smiguez/Documents/dimer.tif width 4000 height 4000 supersample 4 transparentBackground true > view matrix camera -0.56942,0.59784,-0.56422,-69,-0.54459,-0.78848,-0.28586,14.145,-0.61578,0.14449,0.77456,534.07 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > view cofr false > save image /home/smiguez/Documents/dimer90.tif width 4000 height 4000 supersample 4 transparentBackground true > save image /home/smiguez/Documents/dimer90.tif width 4000 height 4000 supersample 4 transparentBackground true > select up Nothing selected > view matrix camera -0.56942,0.59784,-0.56422,-69,-0.54459,-0.78848,-0.28586,14.145,-0.61578,0.14449,0.77456,534.07 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > save image /home/smiguez/Documents/dimer90.tif width 4000 height 4000 supersample 4 transparentBackground true QXcbConnection: XCB error: 148 (Unknown), sequence: 21567, resource id: 0, major code: 140 (Unknown), minor code: 20 > save image /home/smiguez/Documents/dimer90.tif width 4000 height 4000 supersample 4 transparentBackground true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 213, in _update_current_size int(100.0 * window_width / screen_width), ZeroDivisionError: float division by zero Error processing trigger "resized": float division by zero: ZeroDivisionError: float division by zero File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 213, in _update_current_size int(100.0 * window_width / screen_width), See log for complete Python traceback. > movie record > turn y 2 180 > wait 180 > movie encode /home/smiguez/Desktop/movie1.mp4 Movie saved to /home/smiguez/Desktop/movie1.mp4 > open /home/smiguez/emdata/TMBGAL/tmbgal3/final_things/postprocess_masked.mrc Opened postprocess_masked.mrc, grid size 512,512,512, pixel 0.67, shown at level 0.0211, step 2, values float32 > ui mousemode rightMode zoom > close > save image /home/smiguez/Documents/dimer90.tif width 4000 height 4000 supersample 4 transparentBackground true > save image /home/smiguez/Documents/dimer90.tif width 4000 height 4000 supersample 4 transparentBackground true > open /home/smiguez/ccpem_project/Molrep_18/molrep.pdb Chain information for molrep.pdb #1 --- Chain | Description 3 B E I M Q U Y | No description available > preset cartoons/nucleotides ribbons/slabs Changed 72216 atom styles Preset expands to these ChimeraX commands: surf hide; style (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x rect; nucleotides tube/slab shape box > hide selAtoms > open /home/smiguez/emdata/TMBGAL/tmbgal3/final_things/postprocess_masked.mrc Opened postprocess_masked.mrc, grid size 512,512,512, pixel 0.67, shown at level 0.0211, step 2, values float32 > volume #2 level 0.021 step 1 > fitmap #1 inMap #2 Fit molecule molrep.pdb (#1) to map postprocess_masked.mrc (#2) using 72232 atoms average map value = 0.07463, steps = 40 shifted from previous position = 0.00497 rotated from previous position = 0.00291 degrees atoms outside contour = 3339, contour level = 0.021 Position of molrep.pdb (#1) relative to postprocess_masked.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00002254 0.00004361 -0.00429957 0.00002254 1.00000000 -0.00001307 -0.00591895 -0.00004361 0.00001307 1.00000000 0.00283017 Axis 0.25734315 0.85844465 0.44367476 Axis point 115.07913900 0.00000000 69.49579474 Rotation angle (degrees) 0.00291050 Shift along axis -0.00493188 > lighting full > color list all 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 . > show #2 models > surface dust #2.1 size 5 > color /3 palegreen > color /b aquamarine > color /e salmon > color /i palegoldenrod > color /m skyblue > color /q "peach puff" > color /u seashell > color /y khaki > color zone #2 near #1 distance 5 > lighting direction 1,-1,-1 > view matrix camera 0.99819,-0.055785,0.022588,182.51,0.025082,0.044425,-0.9987,-315.59,0.054709,0.99745,0.045743,193.83 models #1,1,-6.6527e-05,4.3276e-05,0.0033002,6.6527e-05,1,-1.3171e-05,-0.013487,-4.3275e-05,1.3173e-05,1,0.0024598,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > surface dust #2.1 size 5 > movie record > turn y 2 180 > wait 180 > movie encode /home/smiguez/Desktop/movie2.mp4 Movie saved to /home/smiguez/Desktop/movie2.mp4 > save /home/smiguez/Desktop/image1.png supersample 3 > close Chain information for 1_colour.pdb #1.1 --- Chain | Description E | No description available Chain information for 6mer.pdb #1.2 --- Chain | Description 3 B I M Q Y | No description available Chain information for dif_colour.pdb #1.3 --- Chain | Description U | No description available > set bgColor white > lighting full > color /3 palegreen > color /b aquamarine > color /e salmon > color /i palegoldenrod > color /m skyblue > color /q "peach puff" > color /u seashell > color /y khaki > select /u sequence PYEWENPQLVSEGTEKSHASFIPYLDPFSGEWEYPEEFISLNGNWRFLFAKNPFEVPEDFFSEKFDDSNWDEIEVPSNWEMKGYGKPIYTNVVYPFEPNPPFVPKDDNPTGVYRRWIEIPEDWFKKEIFLHFEGVRSFFYLWVNGKKIGFSKDSCTPAEFRLTDVLRPGKNLITVEVLKWSDGSYLEDQDMWWFAGIYRDVYLYALPKF 1780 atoms, 1854 bonds, 1 model selected > color sel palegreen > select /u sequence HIRDVFVRTDLDENYRNGKIFLDVEMRNLGEEEEKDLEVTLITPDGDEKTLVKETVKPEDRVLSFAFDVKDPKKWSAETPHLYVLKLKLGEDEKKVNFGFR 837 atoms, 852 bonds, 1 model selected > color sel aquamarine > select /u sequence KIEIKDGTLLFNGKPLYIKGVNRHEFDPDRGHAVTVERMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYFGLYVIDEANIESHGIDWDPEVTLANRWEWEKAHFDRIKRMVERDKNHPSIIFWSLGNEAGDGVNFEKAALWIKKRDNTRLIHYEGTTRRGESYYVDVFSLMYPKMDILLEYASKKREKPFIMCEYAHAMGNSVGNLKDYWDVIEKYPYLHGGCIWDWVDQGIRKKDENGREFWAYGGDFGDTPNDGNFCINGVVLPDRTPEPELYEVKKVY 2357 atoms, 2426 bonds, 1 model selected > color sel plum > select /u sequence QNVKIRQVSKDTYEVENRYLFTNLEMFDGAWKIRKDGEVIEEKTFKIFAEPGEKRLLKIPLPEMDDSEYFLEISFSLSEDTPWAEKGHVVAWEQFLLK 824 atoms, 844 bonds, 1 model selected > color sel palegoldenrod > select /u sequence APAFEKKSISDGVSLREDGKHLTVEAKDTVYVFSKLTGLLEQILHRRKKILKSPVVPNFWRVPTDNDIGNRMPQRLAIWKRASKERKLFKMHWKKEENRVSVHSVFQLPGNSWVYTTYTVFGNGDVLVDLSLIPAEDVPEIPRIGFQFTVPEEFGTVEWYGRGPHETYWDRKESGLFARYRKAVGEMMHRYVRPQETGNRSDVRWFALSDGETKLFVSGMPQIDFSVWPFSMEDLERVQHISELPERDFVTVNVDFRQMGLGGDDSWGAMPHLEYRLLPKPYRFSFRMRISEEIPSWRVLAAI 2501 atoms, 2574 bonds, 1 model selected > color sel skyblue > select /u sequence PETLHVEMSSEDVIREGDTLRVKFSLLNDTPLSKEKQVVLFVDGNEYSVRRVVIPPFKKEELVFKVEGLKKGEHLIHTNLNTRKTIYVR 728 atoms, 740 bonds, 1 model selected > color sel "peach puff" > ~select all Nothing selected > show all models > lighting full > select #1.1 9027 atoms, 9295 bonds, 1 model selected > hide selAtoms > show selAtoms surfaces > hide selAtoms ribbons > select #1.2 54163 atoms, 55770 bonds, 1 model selected > hide selAtoms > hide selAtoms surfaces > show selAtoms ribbons > select #1.3 9027 atoms, 9295 bonds, 1 model selected > hide selAtoms > show selAtoms surfaces > hide selAtoms ribbons > color zone #1.3 near #1.3 distance 3 > ~select all 1 model selected > lighting direction 1,-1,-1 > close #1.1 > close #1.2 > view matrix camera -0.41403,0.57423,-0.70628,18.19,-0.805,-0.59318,-0.010373,152.66,-0.42491,0.56426,0.70785,398.67 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > movie record > turn y 2 180 > wait 180 > movie encode /home/smiguez/Desktop/movie3.mp4 Movie saved to /home/smiguez/Desktop/movie3.mp4 > view matrix camera -0.41403,0.57423,-0.70628,18.19,-0.805,-0.59318,-0.010373,152.66,-0.42491,0.56426,0.70785,398.67 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > save /home/smiguez/Desktop/image1.png supersample 3 > close > open /home/smiguez/ccpem_project/Molrep_18/molrep.pdb Chain information for molrep.pdb #1 --- Chain | Description 3 B E I M Q U Y | No description available > preset cartoons/nucleotides ribbons/slabs Changed 72216 atom styles Preset expands to these ChimeraX commands: surf hide; style (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x rect; nucleotides tube/slab shape box > hide selAtoms > open /home/smiguez/emdata/TMBGAL/tmbgal3/final_things/postprocess_masked.mrc Opened postprocess_masked.mrc, grid size 512,512,512, pixel 0.67, shown at level 0.0211, step 2, values float32 > volume #2 level 0.021 step 1 > fitmap #1 inMap #2 Fit molecule molrep.pdb (#1) to map postprocess_masked.mrc (#2) using 72232 atoms average map value = 0.07463, steps = 40 shifted from previous position = 0.00497 rotated from previous position = 0.00291 degrees atoms outside contour = 3339, contour level = 0.021 Position of molrep.pdb (#1) relative to postprocess_masked.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00002254 0.00004361 -0.00429957 0.00002254 1.00000000 -0.00001307 -0.00591895 -0.00004361 0.00001307 1.00000000 0.00283017 Axis 0.25734315 0.85844465 0.44367476 Axis point 115.07913900 0.00000000 69.49579474 Rotation angle (degrees) 0.00291050 Shift along axis -0.00493188 > lighting full > color list all 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 . > show #2 models > surface dust #2.1 size 5 > color /3 palegreen > color /b aquamarine > color /e salmon > color /i palegoldenrod > color /m skyblue > color /q "peach puff" > color /u seashell > color /y khaki > color zone #2 near #1 distance 5 > lighting direction 1,-1,-1 > view matrix camera 0.99819,-0.055785,0.022588,182.51,0.025082,0.044425,-0.9987,-315.59,0.054709,0.99745,0.045743,193.83 models #1,1,-6.6527e-05,4.3276e-05,0.0033002,6.6527e-05,1,-1.3171e-05,-0.013487,-4.3275e-05,1.3173e-05,1,0.0024598,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > surface dust #2.1 size 5 > hide #!1 models > show #!1 models > hide #!2 models > movie record > turn y 2 180 > wait 180 > movie encode /home/smiguez/Desktop/movie3.mp4 Movie saved to /home/smiguez/Desktop/movie3.mp4 > show #!2 models > view matrix camera 0.99819,-0.055785,0.022588,182.51,0.025082,0.044425,-0.9987,-315.59,0.054709,0.99745,0.045743,193.83 models #1,1,-6.6527e-05,4.3276e-05,0.0033002,6.6527e-05,1,-1.3171e-05,-0.013487,-4.3275e-05,1.3173e-05,1,0.0024598,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > view cofr false > view cofr false > view matrix camera 0.99819,-0.055785,0.022588,182.51,0.025082,0.044425,-0.9987,-315.59,0.054709,0.99745,0.045743,193.83 models #1,1,-6.6527e-05,4.3276e-05,0.0033002,6.6527e-05,1,-1.3171e-05,-0.013487,-4.3275e-05,1.3173e-05,1,0.0024598,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > show selAtoms > hide selAtoms surfaces > hide selAtoms ribbons > style selAtoms stick Changed 72232 atom styles > hide #!2.1 models > show #!2.1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > close #1 > close Chain information for 1_colour.pdb #1.1 --- Chain | Description E | No description available Chain information for 6mer.pdb #1.2 --- Chain | Description 3 B I M Q Y | No description available Chain information for dif_colour.pdb #1.3 --- Chain | Description U | No description available > set bgColor white > lighting full > color /3 palegreen > color /b aquamarine > color /e salmon > color /i palegoldenrod > color /m skyblue > color /q "peach puff" > color /u seashell > color /y khaki > select /u sequence PYEWENPQLVSEGTEKSHASFIPYLDPFSGEWEYPEEFISLNGNWRFLFAKNPFEVPEDFFSEKFDDSNWDEIEVPSNWEMKGYGKPIYTNVVYPFEPNPPFVPKDDNPTGVYRRWIEIPEDWFKKEIFLHFEGVRSFFYLWVNGKKIGFSKDSCTPAEFRLTDVLRPGKNLITVEVLKWSDGSYLEDQDMWWFAGIYRDVYLYALPKF 1780 atoms, 1854 bonds, 1 model selected > color sel palegreen > select /u sequence HIRDVFVRTDLDENYRNGKIFLDVEMRNLGEEEEKDLEVTLITPDGDEKTLVKETVKPEDRVLSFAFDVKDPKKWSAETPHLYVLKLKLGEDEKKVNFGFR 837 atoms, 852 bonds, 1 model selected > color sel aquamarine > select /u sequence KIEIKDGTLLFNGKPLYIKGVNRHEFDPDRGHAVTVERMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYFGLYVIDEANIESHGIDWDPEVTLANRWEWEKAHFDRIKRMVERDKNHPSIIFWSLGNEAGDGVNFEKAALWIKKRDNTRLIHYEGTTRRGESYYVDVFSLMYPKMDILLEYASKKREKPFIMCEYAHAMGNSVGNLKDYWDVIEKYPYLHGGCIWDWVDQGIRKKDENGREFWAYGGDFGDTPNDGNFCINGVVLPDRTPEPELYEVKKVY 2357 atoms, 2426 bonds, 1 model selected > color sel plum > select /u sequence QNVKIRQVSKDTYEVENRYLFTNLEMFDGAWKIRKDGEVIEEKTFKIFAEPGEKRLLKIPLPEMDDSEYFLEISFSLSEDTPWAEKGHVVAWEQFLLK 824 atoms, 844 bonds, 1 model selected > color sel palegoldenrod > select /u sequence APAFEKKSISDGVSLREDGKHLTVEAKDTVYVFSKLTGLLEQILHRRKKILKSPVVPNFWRVPTDNDIGNRMPQRLAIWKRASKERKLFKMHWKKEENRVSVHSVFQLPGNSWVYTTYTVFGNGDVLVDLSLIPAEDVPEIPRIGFQFTVPEEFGTVEWYGRGPHETYWDRKESGLFARYRKAVGEMMHRYVRPQETGNRSDVRWFALSDGETKLFVSGMPQIDFSVWPFSMEDLERVQHISELPERDFVTVNVDFRQMGLGGDDSWGAMPHLEYRLLPKPYRFSFRMRISEEIPSWRVLAAI 2501 atoms, 2574 bonds, 1 model selected > color sel skyblue > select /u sequence PETLHVEMSSEDVIREGDTLRVKFSLLNDTPLSKEKQVVLFVDGNEYSVRRVVIPPFKKEELVFKVEGLKKGEHLIHTNLNTRKTIYVR 728 atoms, 740 bonds, 1 model selected > color sel "peach puff" > ~select all Nothing selected > show all models > lighting full > select #1.1 9027 atoms, 9295 bonds, 1 model selected > hide selAtoms > show selAtoms surfaces > hide selAtoms ribbons > select #1.2 54163 atoms, 55770 bonds, 1 model selected > hide selAtoms > hide selAtoms surfaces > show selAtoms ribbons > select #1.3 9027 atoms, 9295 bonds, 1 model selected > hide selAtoms > show selAtoms surfaces > hide selAtoms ribbons > color zone #1.3 near #1.3 distance 3 > ~select all 1 model selected > lighting direction 1,-1,-1 > close #1.2 > close #1.1 > view matrix camera -0.41403,0.57423,-0.70628,18.19,-0.805,-0.59318,-0.010373,152.66,-0.42491,0.56426,0.70785,398.67 models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0 > show selAtoms ribbons > hide selAtoms surfaces > movie record > turn y 2 180 > wait 180 > movie encode /home/smiguez/Desktop/movie1.mp4 Movie saved to /home/smiguez/Desktop/movie1.mp4 > save image /home/smiguez/Desktop/side1.1.tif width 4000 height 4000 supersample 4 transparentBackground true Missing or invalid "models" argument: empty atom specifier Missing or invalid "models" argument: empty atom specifier > smoothlines #1.3 Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. > close > open /home/smiguez/Documents/PymolImages/TmBGal/image1/coloredmonomer_smooth.pdb Chain information for coloredmonomer_smooth.pdb #1 --- Chain | Description U | No description available Expected a keyword Expected a keyword Missing or invalid "models" argument: empty atom specifier Missing "replace" keyword's argument Missing or invalid "models" argument: only initial part "#1.3" of atom specifier valid > smoothlines /u replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. > smoothlines /u stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. > close > open /home/smiguez/Documents/PymolImages/TmBGal/image1/coloredmonomer_smooth.pdb Chain information for coloredmonomer_smooth.pdb #1 --- Chain | Description U | No description available > smoothlines /u stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. > smoothlines /u stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. > hide selAtoms ribbons > style selAtoms stick Changed 9027 atom styles > style selAtoms stick Changed 9027 atom styles > hide selAtoms surfaces > hide selAtoms > show selAtoms ribbons > style selAtoms stick Changed 9027 atom styles > style selAtoms stick Changed 9027 atom styles > hide selAtoms ribbons > style selAtoms stick Changed 9027 atom styles > style selAtoms ball Changed 9027 atom styles > style selAtoms sphere Changed 9027 atom styles > show selAtoms surfaces > hide selAtoms > show selAtoms > hide selAtoms ribbons > hide selAtoms surfaces > hide selAtoms surfaces > style selAtoms stick Changed 9027 atom styles Invalid "replace" argument: Expected true or false (or 1 or 0) > smoothlines /u stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. Expected a keyword > smoothlines /u stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. Missing or invalid "models" argument: invalid models specifier > hide #!1 models > hide #!1.1 models > hide #!1.2 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > hide #!1 models > show #!1.1 models > show selAtoms ribbons > hide selAtoms ribbons > hide selAtoms > show selAtoms ribbons > show #!1.2 models > hide #!1.1 models > show #!1.1 models Unknown command: smoothlines~/Documents/PymolImages/TmBGal/image1/coloredmonomer_smooth.pdb stepFactor 0.1 iteration 10 replace true Missing or invalid "models" argument: only initial part "~/Documents/PymolImages/TmBGal/image1/coloredmonomer" of atom specifier valid Missing or invalid "models" argument: only initial part "~/Documents/PymolImages/TmBGal/image1/coloredmonomer" of atom specifier valid Missing or invalid "models" argument: only initial part "~/Documents/PymolImages/TmBGal/image1/coloredmonomer" of atom specifier valid Missing or invalid "models" argument: only initial part "~/Documents/PymolImages/TmBGal/image1/dif" of atom specifier valid Missing or invalid "models" argument: only initial part "~/Documents/PymolImages/TmBGal/image1/difcolour" of atom specifier valid > close #1.1 > close > open /home/smiguez/Documents/PymolImages/TmBGal/image1/coloredmonomer_smooth.pdb Chain information for coloredmonomer_smooth.pdb #1 --- Chain | Description U | No description available > smoothlines #1.1 stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. Unknown command: print #1.1 > smoothlines #1.1 stepFactor 0.1 iterations 10 replace true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 255, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2631, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: AttributeError: 'NoneType' object has no attribute 'shape' AttributeError: 'NoneType' object has no attribute 'shape' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/smooth_lines/smoothlines.py", line 37, in smoothlines if ta.shape[1] != 2: See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 410.48 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → smoothlines: 'NoneType' object has no attribute 'shape' |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
User tried to apply smoothlines to a molecule. It require a line model (which is a Surface). Added error handling with clear error message if model is not the right type.