![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#4870 closed defect (can't reproduce)
Segger: n is None
| 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: Linux-3.10.0-957.21.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > format session Log from Wed Jul 7 20:02:25 2021UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > format session Showing cryosparc_P1_J6_map_sharp.seg - 2517 regions, 2517 surfaces Log from Wed Jul 7 19:01:13 2021UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > format session Log from Wed Jul 7 18:40:22 2021UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > format session Showing cryosparc_P1_J6_map_sharp.seg - 2539 regions, 2539 surfaces Log from Wed Jul 7 16:44:50 2021UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > format session Showing cryosparc_P1_J6_map_sharp.seg - 2596 regions, 2596 surfaces Log from Wed Jul 7 14:50:38 2021UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/70S_GH_2/P1/J6/cryosparc_P1_J6_mask_fsc.mrc Opened cryosparc_P1_J6_mask_fsc.mrc, grid size 350,350,350, pixel 1.38, shown at level 0.0352, step 2, values float32 > volume #1 step 1 > open > /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/70S_GH_2/P1/J6/cryosparc_P1_J6_map_sharp.mrc Opened cryosparc_P1_J6_map_sharp.mrc, grid size 350,350,350, pixel 1.38, shown at level 0.0339, step 2, values float32 > volume #2 step 1 > close #1 > volume #2 level 0.02764 > set bgColor white > volume #2 color #babdb6 > volume #2 color #888a85 > ui tool show "Segment Map" Segmenting cryosparc_P1_J6_map_sharp.mrc, density threshold 0.027637 Showing cryosparc_P1_J6_map_sharp.seg - 0 regions, 0 surfaces Showing 124 region surfaces 7657 watershed regions, grouped to 124 regions > open > /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/MDFF/50S+H68_coot.pdb 50S+H68_coot.pdb title: Structure of the 50S large ribosomal subunit from mycobacterium smegmatis [more info...] Chain information for 50S+H68_coot.pdb #3 --- Chain | Description 2 | No description available 3 | BL37 A | 23S RRNA B | 5S RRNA C | UL2 D | UL3 E | UL4 F | UL5 G | UL6 H | BL9 I | UL10 J | UL11 K | UL13 L | UL14 M | UL15 N | UL16 O | BL17 P | UL18 Q | BL19 R | BL20 S | BL21 T | UL22 U | UL23 V | UL24 W | 50S ribosomal protein L25 X | 50S ribosomal protein L27 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 Non-standard residues in 50S+H68_coot.pdb #3 --- MG — magnesium ion ZN — zinc ion > show cartoons > hide surfaces > hide surfaces > style sphere Changed 98153 atom styles > style sphere Changed 98153 atom styles > style ball Changed 98153 atom styles > hide atoms > set bgColor black > select clear Grouped 5 regions Ungrouped to 3 regions Ungrouped to 9 regions Ungrouped to 33 regions Ungrouped to 93 regions Ungrouped to 0 regions Grouped 12 regions Grouped 4 regions Grouped 4 regions > hide #!1 models > show #!1 models > hide #!2 models Grouped 2 regions Grouped 12 regions Grouped 5 regions Grouped 4 regions > select clear Ungrouped to 3 regions Ungrouped to 8 regions Ungrouped to 50 regions Ungrouped to 78 regions Ungrouped to 0 regions Grouped 13 regions Grouped 5 regions Grouped 8 regions Grouped 6 regions Grouped 2 regions Showing 268 region surfaces Grouped 2 regions > select clear Ungrouped to 4 regions > select clear Ungrouped to 130 regions Ungrouped to 2 regions Ungrouped to 18 regions Ungrouped to 46 regions Ungrouped to 0 regions Grouped 6 regions Grouped 8 regions Grouped 4 regions > select clear > select clear Grouped 2 regions Grouped 20 regions Ungrouped to 20 regions Grouped 19 regions Showing 366 region surfaces Grouped 3 regions > select clear Grouped 4 regions Grouped 5 regions Grouped 5 regions Grouped 5 regions Ungrouped to 5 regions Grouped 5 regions Grouped 2 regions > select clear Ungrouped to 4 regions Ungrouped to 19 regions Ungrouped to 34 regions Ungrouped to 0 regions Grouped 2 regions Showing 387 region surfaces Grouped 3 regions > select clear Ungrouped to 0 regions Ungrouped to 3 regions Ungrouped to 14 regions Ungrouped to 0 regions Grouped 3 regions Showing 397 region surfaces Grouped 2 regions Grouped 3 regions Grouped 3 regions > select clear Ungrouped to 0 regions Ungrouped to 6 regions Ungrouped to 11 regions Ungrouped to 0 regions Showing 405 region surfaces Grouped 1 regions > select clear Ungrouped to 2 regions Ungrouped to 19 regions Ungrouped to 57 regions Ungrouped to 0 regions Showing 465 region surfaces Grouped 7 regions Grouped 2 regions Grouped 3 regions Grouped 2 regions Grouped 3 regions Grouped 2 regions > select clear Showing 452 region surfaces Grouped 2 regions > select clear > select clear Grouped 2 regions Ungrouped to 5 regions Ungrouped to 39 regions Ungrouped to 93 regions Ungrouped to 0 regions Grouped 6 regions Grouped 2 regions Grouped 5 regions Grouped 5 regions Grouped 3 regions Grouped 4 regions > select #1 534 models selected > ~select #1 Nothing selected Ungrouped to 0 regions Grouped 4 regions Grouped 2 regions Grouped 1 regions Ungrouped to 1 regions > select clear Showing 529 region surfaces Grouped 10 regions > select clear > select clear Grouped 7 regions Grouped 2 regions > select clear Ungrouped to 4 regions Ungrouped to 24 regions Ungrouped to 61 regions Ungrouped to 0 regions Showing 581 region surfaces Grouped 2 regions Grouped 2 regions > select clear Ungrouped to 21 regions Ungrouped to 52 regions Ungrouped to 0 regions > select clear Showing 636 region surfaces Grouped 4 regions Grouped 2 regions Grouped 2 regions Grouped 3 regions Grouped 2 regions Grouped 2 regions > select clear Ungrouped to 3 regions Ungrouped to 20 regions Ungrouped to 29 regions Ungrouped to 0 regions Ungrouped to 0 regions Ungrouped to 386 regions Grouped 3 regions Showing 938 region surfaces Grouped 2 regions Grouped 2 regions Grouped 5 regions Grouped 3 regions Grouped 7 regions Grouped 2 regions Showing 923 region surfaces Grouped 9 regions Ungrouped to 9 regions Grouped 7 regions > select clear > select clear Ungrouped to 7 regions Ungrouped to 2 regions Ungrouped to 7 regions Ungrouped to 3 regions Ungrouped to 5 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 5 regions Ungrouped to 2 regions Ungrouped to 3 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 7 regions Ungrouped to 10 regions > select clear > select clear > select clear Drag select of 1901, 6 of 968 triangles, 1624, 5 of 848 triangles, 1 residues Grouped 19 regions Grouped 8 regions Grouped 7 regions Grouped 5 regions Grouped 2 regions Grouped 2 regions Grouped 2 regions Drag select of 2 residues Grouped 8 regions Grouped 3 regions Grouped 3 regions > open /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/MDFF/L2.pdb Chain information for L2.pdb #4 --- Chain | Description C | No description available > hide #!3 models Showing 918 region surfaces > select clear > show #!3 models > hide #4 models > show #4 models > hide #4 models Grouped 5 regions Grouped 4 regions Grouped 2 regions Grouped 12 regions Grouped 4 regions Showing 896 region surfaces > select clear Grouped 3 regions Grouped 2 regions Grouped 3 regions Grouped 3 regions > select clear > show #4 models > select #4 2110 atoms, 2153 bonds, 1 model selected > show sel atoms > hide #!3 models > hide #!1 models > show #!1 models > select clear Showing 889 region surfaces Grouped 2 regions > select clear Ungrouped to 3 regions Ungrouped to 3 regions Ungrouped to 3 regions Ungrouped to 4 regions Ungrouped to 12 regions Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 5 regions Ungrouped to 0 regions > 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 clear > hide #4 models Drag select of 2069, 2155, 1828, 2245, 1486, 1495, 1496, 1376, 1439, 1565, 1700, 2086, 1827, 1441, 2327, 1839, 1906, 2546, 1562, 1917, 1992, 1988, 1687, 2151, 1558, 1899, 1908, 2247, 1768 Grouped 26 regions > show #!3 models Showing 891 region surfaces > show #4 models Grouped 4 regions Ungrouped to 4 regions Grouped 2 regions > select clear Showing 890 region surfaces Grouped 3 regions Grouped 2 regions Grouped 2 regions Grouped 2 regions Grouped 2 regions Grouped 2 regions > select clear Ungrouped to 0 regions Ungrouped to 0 regions Ungrouped to 2106 regions Showing 2608 region surfaces Grouped 2 regions > select clear Grouped 2 regions Grouped 2 regions Grouped 2 regions > select #4 2110 atoms, 2153 bonds, 1 model selected > hide sel atoms Grouped 4 regions > select clear Showing 2601 region surfaces Grouped 2 regions > select clear Ungrouped to 0 regions Grouped 2 regions Grouped 1 regions Ungrouped to 1 regions Showing 2599 region surfaces Grouped 2 regions > select #4 2110 atoms, 2153 bonds, 1 model selected > show sel atoms Grouped 2 regions Showing 2597 region surfaces Grouped 2 regions > select clear Showing 2596 region surfaces > hide #!3 models Showing 2596 region surfaces > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs opened ChimeraX session > select clear > show #!3 models > hide #!3 models > show #!3 models Showing 2596 region surfaces > select clear > hide #!3 models Grouped 6 regions Ungrouped to 6 regions > select clear > select clear Grouped 3 regions Grouped 2 regions > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models Grouped 5 regions > select clear Ungrouped to 4 regions Ungrouped to 0 regions > show #!3 models > hide #!3 models Ungrouped to 7 regions Ungrouped to 0 regions > select clear > show #!3 models > hide #!3 models > show #!3 models Grouped 6 regions Grouped 10 regions Grouped 3 regions > select clear > hide #!3 models Ungrouped to 3 regions Ungrouped to 0 regions > show #!3 models > hide #!3 models Ungrouped to 0 regions > show #!3 models > hide #!3 models Showing 2584 region surfaces Grouped 4 regions > select clear > select clear Grouped 15 regions Grouped 2 regions Grouped 2 regions Grouped 6 regions Grouped 2 regions Ungrouped to 2 regions Ungrouped to 9 regions Ungrouped to 12 regions Ungrouped to 2 regions Ungrouped to 18 regions Ungrouped to 16 regions Ungrouped to 35 regions Ungrouped to 12 regions Ungrouped to 0 regions > hide #4 models Drag select of 3353, 3508, 3683, 3588, 1819, 3261, 3430, 2995, 3967, 4237, 3177, 3587, 2648, 2757, 2834, 1197, 978, 1085, 1612, 926, 1256, 1428, 923, 1024, 880, 791, 1892, 979, 1430, 2454, 1670, 1739, 1741, 1429, 1481, 2716, 2977, 2397, 2547, 1422, 1479, 1537, 1542, 1478, 1482, 1539, 2062, 2325, 1611, 1682, 1749, 1821, 1488, 1967, 2050, 2052, 2138, 2225, 1613, 1755, 1763, 1979, 2145, 2149, 2237, 2316, 2331, 1911, 713 of 1068 triangles, 1692, 877 of 940 triangles, 1902, 1982, 1985, 1832, 237 of 396 triangles, 1994, 298 of 424 triangles, 2083, 1830, 1091 of 1152 triangles, 1909, 2398, 2549, 2243 Grouped 79 regions Showing 2560 region surfaces > select clear > select clear > show #!3 models > hide #!3 models Grouped 2 regions > show #4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models Grouped 4 regions > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models Grouped 5 regions > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models Grouped 2 regions > select clear > select clear Ungrouped to 0 regions > show #!3 models > hide #!3 models Grouped 3 regions Showing 2549 region surfaces Grouped 2 regions Showing 2548 region surfaces > select clear Ungrouped to 0 regions > hide #4 models Grouped 3 regions > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models Grouped 7 regions Ungrouped to 7 regions Grouped 6 regions > show #4 models Grouped 3 regions Grouped 3 regions Ungrouped to 3 regions Ungrouped to 3 regions Ungrouped to 6 regions Ungrouped to 0 regions > show #!3 models > hide #!3 models > show #!3 models Grouped 5 regions Grouped 3 regions > hide #!3 models > select clear > select clear Ungrouped to 7 regions Ungrouped to 0 regions Ungrouped to 2 regions Ungrouped to 0 regions > select clear Grouped 4 regions > show #!3 models > hide #!3 models Grouped 5 regions > select clear Showing 2540 region surfaces Grouped 2 regions Showing 2539 region surfaces > select clear > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs opened ChimeraX session > select clear > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models Grouped 5 regions Grouped 2 regions Grouped 2 regions Grouped 2 regions Showing 2532 region surfaces Grouped 2 regions Showing 2531 region surfaces > select clear > select #4 2110 atoms, 2153 bonds, 1 model selected > hide sel atoms > ~select #4 Nothing selected Grouped 3 regions Grouped 4 regions > select #4 2110 atoms, 2153 bonds, 1 model selected Grouped 6 regions Grouped 5 regions Showing 2517 region surfaces Grouped 2 regions > show sel atoms > show sel atoms > hide sel atoms Showing 2516 region surfaces Grouped 5 regions Ungrouped to 5 regions > select clear > select clear Showing 2516 region surfaces Grouped 2 regions > select #4 2110 atoms, 2153 bonds, 1 model selected > show sel atoms > hide sel atoms > hide sel atoms Showing 2515 region surfaces > select clear Ungrouped to 5 regions Grouped 4 regions > select #4 2110 atoms, 2153 bonds, 1 model selected > show sel atoms Ungrouped to 4 regions Grouped 4 regions > select clear Showing 2516 region surfaces Grouped 2 regions > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs Showing 2515 region surfaces > select clear > select clear > show #!3 models > hide #!3 models Grouped 2 regions Drag select of 10194, 39984 of 43320 triangles, 1208 atoms, 268 residues, 1026 bonds > color (#4 & sel) red > hide #4 models > show #4 models > select #4 2110 atoms, 2153 bonds, 1 model selected > ~select #4 Nothing selected > ui tool show "Color Actions" > color sel lime Showing 2514 region surfaces > select clear > select clear Showing 2514 region surfaces Grouped 3 regions Ungrouped to 3 regions Ungrouped to 2 regions Ungrouped to 7 regions Ungrouped to 2 regions Ungrouped to 6 regions Ungrouped to 10 regions Ungrouped to 10 regions Ungrouped to 9 regions Ungrouped to 7 regions Ungrouped to 10 regions Ungrouped to 21 regions Ungrouped to 2 regions Ungrouped to 4 regions Drag select of 3073, 2982, 2474, 2706, 2712, 2787, 2791, 2964, 2719, 2324, 2467, 2621, 2544, 1978, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2556, 2558, 2627, 2634, 2635, 2640, 2642, 2734, 2822, 2900, 2259, 3070, 2549, 2461, 2402, 10152, 31273 of 31276 triangles, 2551, 1265 atoms, 275 residues, 1073 bonds > select clear Grouped 4 regions Grouped 4 regions Grouped 4 regions > select clear Drag select of 3073, 2982, 2474, 2706, 2712, 2787, 2791, 2964, 2719, 2324, 2467, 2621, 2544, 1978, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2549, 391 of 432 triangles, 2461, 2402, 10152, 30916 of 31276 triangles, 2551, 10198, 1258 atoms, 274 residues, 1065 bonds Drag select of 3073, 2982, 2474, 2706, 332 of 356 triangles, 2712, 2787, 317 of 396 triangles, 2791, 746 of 752 triangles, 2964, 2719, 2324, 2467, 2621, 2544, 1978, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2549, 2461, 2402, 10152, 31154 of 31276 triangles, 2551, 1261 atoms, 275 residues, 1069 bonds Drag select of 3073, 2982, 2474, 2706, 2712, 2787, 2791, 2964, 2719, 2324, 2467, 2621, 2544, 1978, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2549, 2461, 2402, 10152, 2551, 1262 atoms, 275 residues, 1071 bonds Ungrouped to 5 regions Ungrouped to 5 regions Ungrouped to 3 regions Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 4 regions Ungrouped to 6 regions Ungrouped to 2 regions > select clear Drag select of 3073, 2982, 2474, 2706, 2712, 2787, 2791, 2964, 2719, 2324, 2467, 2621, 2544, 1978, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2549, 2461, 2402, 2551, 2476, 1769, 2071, 2236, 2557, 2735, 2985, 1825, 1691, 2746, 2837, 3077, 3082, 2561, 2412, 2647, 2563, 3083, 10139, 25931 of 26104 triangles, 8443, 1183 of 1200 triangles, 1261 atoms, 275 residues, 1069 bonds > select clear Grouped 4 regions > select clear Drag select of 3073, 2982, 2474, 2706, 2712, 2787, 2791, 2964, 2719, 2324, 2467, 2621, 2544, 1978, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2461, 2402, 2551, 2476, 1769, 414 of 572 triangles, 2071, 2236, 2557, 1825, 1691, 548 of 660 triangles, 2746, 2837, 3082, 2561, 2412, 2647, 2563, 3083, 10139, 26076 of 26104 triangles, 8443, 10199, 1258 atoms, 275 residues, 1067 bonds > select clear Grouped 6 regions Drag select of 3073, 2982, 2474, 2719, 2324, 2467, 2621, 2544, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2461, 2402, 2551, 2476, 1769, 2071, 2236, 2557, 1825, 1691, 2746, 2837, 3082, 2561, 2412, 2647, 2563, 3083, 10139, 8443, 10200, 1265 atoms, 275 residues, 1073 bonds > select clear Drag select of 3073, 2982, 2474, 2719, 2324, 2467, 2621, 2544, 2827, 2820, 2825, 2980, 2727, 2968, 2730, 2821, 2725, 2814, 2804, 2531, 2971, 2978, 3060, 3065, 3067, 2632, 2816, 2465, 2797, 2625, 2828, 2639, 2903, 2638, 2630, 2157, 2330, 2390, 2710, 2392, 2396, 2070, 2540, 2403, 2552, 2627, 2734, 2461, 2402, 2551, 2476, 1769, 2071, 2236, 2557, 1825, 1691, 2746, 2837, 337 of 368 triangles, 3082, 2561, 2412, 2647, 2563, 3083, 10139, 8443, 1166 of 1200 triangles, 10200, 1265 atoms, 275 residues, 1073 bonds Grouped 67 regions > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs Showing cryosparc_P1_J6_map_sharp.seg - 2515 regions, 2515 surfaces opened ChimeraX session Ungrouped to 67 regions Ungrouped to 4 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 3 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 2 regions Ungrouped to 3 regions > select clear Grouped 3 regions > select clear Drag select of 2330, 2621, 2465, 2820, 2630, 2978, 2727, 2980, 2638, 2825, 2828, 2746, 2396, 2531, 2324, 3073, 2403, 2827, 2625, 2412, 2968, 2390, 2461, 1691, 303 of 660 triangles, 2814, 2474, 2971, 3067, 2157, 2903, 2551, 2797, 2402, 2982, 2821, 2719, 2734, 2627, 2804, 2561, 2710, 1769, 169 of 572 triangles, 2552, 2557, 2725, 2236, 2392, 2476, 2837, 2540, 2632, 2544, 3082, 2467, 2639, 2647, 2070, 2816, 3083, 2071, 605 of 716 triangles, 2730, 1825, 908 of 960 triangles, 2563, 3171, 2911, 2478, 2753, 2410, 2486, 2624, 2815, 2733, 2546, 1439, 1372, 1262, 96 of 136 triangles, 1625, 10117, 21223 of 22960 triangles, 1775, 10202, 1205 atoms, 271 residues, 1019 bonds Grouped 79 regions Ungrouped to 79 regions Grouped 78 regions Showing 2517 region surfaces > select #4 2110 atoms, 2153 bonds, 1 model selected > ~select #4 Nothing selected > hide #4 models > close #4 > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs opened ChimeraX session > open > /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/Msm_23SrRNA.pdb Chain information for Msm_23SrRNA.pdb #4 --- Chain | Description A | No description available > select #4 66981 atoms, 75001 bonds, 1 model selected > hide sel atoms > open > /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/Msm_L_Protein.pdb Chain information for Msm_L_Protein.pdb #5 --- Chain | Description 3 | 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 > style sel ball Changed 66981 atom styles > select #5 28177 atoms, 28567 bonds, 2 pseudobonds, 2 models selected > style sel ball Changed 28177 atom styles > style sel stick Changed 28177 atom styles > hide sel atoms > show sel cartoons > ~select #5 Nothing selected > select clear Ungrouped to 4 regions Ungrouped to 4 regions Ungrouped to 8 regions Ungrouped to 0 regions Grouped 9 regions > hide #4 models > show #4 models > hide #4 models Grouped 10 regions Ungrouped to 10 regions Ungrouped to 27 regions Grouped 27 regions Grouped 22 regions > select clear Showing 2497 region surfaces Grouped 2 regions > select clear > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs Grouped 19 regions Grouped 24 regions Grouped 15 regions Grouped 7 regions > select clear Grouped 24 regions Grouped 14 regions Grouped 3 regions Grouped 7 regions Grouped 12 regions Grouped 12 regions Grouped 5 regions Grouped 6 regions Showing 2360 region surfaces Grouped 2 regions Grouped 3 regions Grouped 2 regions > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > select clear Grouped 4 regions > select clear Grouped 10 regions Grouped 18 regions Grouped 12 regions Grouped 10 regions > select clear Grouped 3 regions Grouped 6 regions Grouped 5 regions Grouped 7 regions Grouped 3 regions Grouped 3 regions Showing 2286 region surfaces > select clear > select clear Grouped 3 regions > select clear > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs Showing cryosparc_P1_J6_map_sharp.seg - 2284 regions, 2284 surfaces opened ChimeraX session > select clear > select clear Grouped 27 regions Grouped 5 regions Grouped 3 regions Grouped 5 regions Grouped 2 regions > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > select clear Ungrouped to 2 regions Ungrouped to 0 regions Ungrouped to 5 regions Ungrouped to 0 regions Grouped 4 regions > select clear Ungrouped to 0 regions Ungrouped to 2 regions Ungrouped to 0 regions Ungrouped to 5 regions Ungrouped to 0 regions > select clear Grouped 5 regions Showing 2250 region surfaces Grouped 3 regions > select clear Grouped 4 regions Grouped 2 regions > select clear Ungrouped to 8 regions Ungrouped to 0 regions Ungrouped to 2 regions Ungrouped to 0 regions Grouped 2 regions Grouped 4 regions Grouped 2 regions > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 10 regions Ungrouped to 2 regions Ungrouped to 4 regions Grouped 4 regions Grouped 2 regions Grouped 3 regions Grouped 3 regions Ungrouped to 0 regions Grouped 4 regions Grouped 2 regions Grouped 2 regions Showing 2249 region surfaces > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs Grouped 13 regions Grouped 1 regions Ungrouped to 1 regions Ungrouped to 13 regions > select clear Grouped 8 regions > select clear Ungrouped to 4 regions Ungrouped to 0 regions Ungrouped to 2 regions Grouped 10 regions Grouped 3 regions > hide #!1 models > show #!1 models Grouped 4 regions Grouped 2 regions Grouped 2 regions Grouped 6 regions Grouped 4 regions > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > select clear > hide #!5 models > show #4 models > show #!5 models Grouped 9 regions Grouped 9 regions > select clear Ungrouped to 0 regions Showing 2206 region surfaces Grouped 3 regions > hide #4 models Showing 2204 region surfaces Grouped 4 regions Showing 2201 region surfaces Grouped 4 regions Ungrouped to 4 regions > select clear > select clear Grouped 3 regions Showing 2199 region surfaces > select clear Grouped 2 regions Ungrouped to 2 regions Ungrouped to 7 regions Ungrouped to 7 regions Ungrouped to 9 regions Ungrouped to 4 regions Ungrouped to 12 regions Ungrouped to 10 regions Ungrouped to 2 regions Ungrouped to 4 regions Ungrouped to 9 regions Ungrouped to 14 regions Ungrouped to 5 regions Ungrouped to 0 regions > hide #!5 models Drag select of 5395, 5405, 5503, 5582, 5774, 4991, 5189, 5191, 5965, 5870, 5973, 5577, 5766, 6068, 6170, 6173, 5759, 5501, 6070, 5872, 5575, 5678, 5583, 5681, 5770, 5873, 5399, 5401, 5498, 5769, 6178, 6180, 5496, 5676, 6633, 5089, 4866, 5483, 5491, 5865, 5675, 5764, 5970, 6455, 6556, 6370, 6636, 6697, 6704, 6460, 6558, 6269, 6362, 6176, 5972, 6554, 6555, 6629, 6361, 6366 > show #!5 models Grouped 57 regions Ungrouped to 57 regions Grouped 55 regions Ungrouped to 55 regions Grouped 54 regions Ungrouped to 54 regions Grouped 53 regions Grouped 2 regions Ungrouped to 2 regions Ungrouped to 53 regions Grouped 52 regions Grouped 3 regions Ungrouped to 3 regions Ungrouped to 52 regions Grouped 51 regions Grouped 2 regions Grouped 3 regions Ungrouped to 3 regions Ungrouped to 53 regions Ungrouped to 0 regions > hide #!5 models Drag select of 5089, 6370, 6704, 6697, 6556, 5973, 5577, 5770, 5972, 4991, 6362, 6173, 5678, 6554, 6070, 5582, 6068, 5865, 5873, 5501, 6361, 6555, 5583, 5191, 5189, 6633, 6176, 5575, 6460, 5399, 5491, 6629, 5395, 6170, 5970, 5675, 5759, 6366, 6455, 6636, 6180, 5872, 6558, 5483, 4866, 5764, 5496, 6178, 5870, 5498, 5681, 5401, 5766, 6269 Grouped 54 regions > show #4 models > show #!5 models > hide #4 models Showing 2204 region surfaces > select clear > select clear > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs Grouped 13 regions Grouped 11 regions Grouped 2 regions Grouped 14 regions > select clear > select clear Grouped 5 regions Grouped 2 regions Grouped 4 regions Grouped 5 regions Grouped 5 regions Grouped 2 regions > select clear Ungrouped to 4 regions Ungrouped to 0 regions Ungrouped to 7 regions Ungrouped to 0 regions Ungrouped to 6 regions Ungrouped to 0 regions Showing 2165 region surfaces > select clear Grouped 3 regions Grouped 3 regions > select clear Grouped 4 regions Showing 2158 region surfaces Grouped 2 regions Ungrouped to 2 regions Ungrouped to 7 regions Ungrouped to 5 regions Ungrouped to 2 regions Ungrouped to 5 regions Ungrouped to 16 regions Ungrouped to 7 regions Ungrouped to 9 regions Ungrouped to 11 regions Ungrouped to 6 regions Ungrouped to 0 regions > hide #!5 models Drag select of 6346, 6435, 7036, 6156, 7394, 6755, 6437, 7323, 6973, 6688, 6825, 6971, 7146, 6751, 6162, 6256, 6258, 6534, 7037, 7097, 7194, 7232, 7321, 7098, 7276, 7147, 7192, 6753, 6750, 6901, 6827, 6341, 6344, 6434, 6620, 6622, 6754, 6160, 6432, 6822, 6153, 6821, 6900, 6970, 6527, 6685, 6686, 6155, 6157, 5663, 5746, 5845, 5953 > show #!5 models Grouped 48 regions Ungrouped to 48 regions Grouped 48 regions Ungrouped to 48 regions Grouped 47 regions Grouped 2 regions Ungrouped to 2 regions Ungrouped to 47 regions Grouped 47 regions Grouped 2 regions Showing 2162 region surfaces > color #1.540 cyan > select clear > hide #!1 models > show #!1 models Grouped 19 regions Grouped 2 regions Showing 2143 region surfaces Grouped 2 regions Grouped 2 regions > select clear Grouped 29 regions Grouped 17 regions Grouped 10 regions Grouped 7 regions Grouped 7 regions Grouped 10 regions Grouped 10 regions Grouped 12 regions Grouped 16 regions Grouped 8 regions Grouped 8 regions Grouped 4 regions Grouped 8 regions Grouped 6 regions Grouped 8 regions Grouped 5 regions Grouped 2 regions Grouped 2 regions Grouped 18 regions Showing 1973 region surfaces Grouped 2 regions > save /home/priya/Priya_Projects/Msmegmatis_Ribosome_GH/50S+H68/50S+H68.cxs > select clear Traceback (most recent call last): File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py", line 958, in ColorDensity smod.color_density() File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/segger/regions.py", line 851, in color_density color_surface_pieces(d.surfaces, m, ijk_to_xyz, offset, cmap) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/segger/regions.py", line 1886, in color_surface_pieces xyz = v - offset*n TypeError: unsupported operand type(s) for *: 'float' and 'NoneType' TypeError: unsupported operand type(s) for *: 'float' and 'NoneType' File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/segger/regions.py", line 1886, in color_surface_pieces xyz = v - offset*n See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 390.132 OpenGL renderer: Quadro 2000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision WorkStation T7500 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 12 Intel(R) Xeon(R) CPU X5690 @ 3.47GHz Cache Size: 12288 KB Memory: total used free shared buff/cache available Mem: 94G 5.7G 1.1G 115M 87G 87G Swap: 4.0G 733M 3.3G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF106GL [Quadro 2000] [10de:0dd8] (rev a1) Subsystem: NVIDIA Corporation Device [10de:084a] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Segger: n is None |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
User tried Segger menu Regions / Color Density Map and it was trying to color a volume surface but the normal vectors array was None. I don't see any way a volume surface can have normals array that is None. It could be the volume was closed but the current segger code checks for that. Not sure if the ChimeraX 1.0 Segger code checked that. I tried to reproduce this error with an empty volume surface with threshold level above highest map value. Did not cause an error, normals array is zero length but not None.