id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3390 Session save: cycle detected chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-5.3.0-51-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-05-09) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/mpillana/AD41_MARZO_2020/map_general/new_colors_fac4t.cxs format > session Log from Mon Jun 1 11:39:50 2020UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/mpillana/AD41_MARZO_2020/map_general/VI_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/H4_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/VII_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/IX_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/VIII_EXTRA_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/VIII_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/IIIA_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/PENTON_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/H3_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/H2_AD41_FACET.pdb > /home/mpillana/AD41_MARZO_2020/map_general/H1_AD41_FACET.pdb Chain information for VI_AD41_FACET.pdb #1 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e u | No description available Chain information for H4_AD41_FACET.pdb #2 --- Chain | Description A B J | No description available C D K | No description available E F L | No description available Chain information for VII_AD41_FACET.pdb #3 --- Chain | Description A B C D E W | No description available F G H I J w | No description available Chain information for IX_AD41_FACET.pdb #4 --- Chain | Description A B C D E F G H Q R S T | No description available Chain information for VIII_EXTRA_AD41_FACET.pdb #5 --- Chain | Description A B C D E O | No description available Chain information for VIII_AD41_FACET.pdb #6 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e | No description available Chain information for IIIA_AD41_FACET.pdb #7 --- Chain | Description A B C D E F G H N | No description available Chain information for PENTON_AD41_FACET.pdb #8 --- Chain | Description A B C D E F G H I J K L M N O | No description available Chain information for H3_AD41_FACET.pdb #9 --- Chain | Description A B G | No description available C D H | No description available E F I | No description available Chain information for H2_AD41_FACET.pdb #10 --- Chain | Description A B C D G H | No description available E I J K L M | No description available F N O P Q R | No description available Chain information for H1_AD41_FACET.pdb #11 --- Chain | Description A D E F G H | No description available B I J K L M | No description available C N O P Q R | No description available > view orient > toolshed show ""Side View"" > set bgColor white > lighting full > lighting soft > lighting simple > graphics silhouettes true > graphics silhouettes false > lighting shadows true > lighting shadows false > select #8 54135 atoms, 55425 bonds, 30 pseudobonds, 2 models selected > color (#!8 & sel) hot pink > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > select #5 8282 atoms, 8509 bonds, 12 pseudobonds, 2 models selected > color (#!5 & sel) yellow > select #6 42749 atoms, 43927 bonds, 62 pseudobonds, 2 models selected > color (#!6 & sel) yellow > split #4 Chain information for IX_AD41_FACET.pdb A #4.1 --- Chain | Description A | No description available Chain information for IX_AD41_FACET.pdb B #4.2 --- Chain | Description B | No description available Chain information for IX_AD41_FACET.pdb C #4.3 --- Chain | Description C | No description available Chain information for IX_AD41_FACET.pdb D #4.4 --- Chain | Description D | No description available Chain information for IX_AD41_FACET.pdb E #4.5 --- Chain | Description E | No description available Chain information for IX_AD41_FACET.pdb F #4.6 --- Chain | Description F | No description available Chain information for IX_AD41_FACET.pdb G #4.7 --- Chain | Description G | No description available Chain information for IX_AD41_FACET.pdb H #4.8 --- Chain | Description H | No description available Chain information for IX_AD41_FACET.pdb Q #4.9 --- Chain | Description Q | No description available Chain information for IX_AD41_FACET.pdb R #4.10 --- Chain | Description R | No description available Chain information for IX_AD41_FACET.pdb S #4.11 --- Chain | Description S | No description available Chain information for IX_AD41_FACET.pdb T #4.12 --- Chain | Description T | No description available Split IX_AD41_FACET.pdb (#4) into 12 models > hide #1 models > hide #!2 models > hide #3 models > hide #!5 models > hide #!6 models > hide #7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #4.1 models > show #4.1 models > select #4 4380 atoms, 4488 bonds, 13 models selected > color sel magenta > hide #4.1 models > show #4.1 models > hide #4.2 models > show #4.2 models > hide #4.3 models > show #4.3 models > hide #4.4 models > show #4.4 models > hide #4.5 models > show #4.5 models > hide #4.6 models > show #4.6 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > show #4.9 models > hide #4.10 models > show #4.10 models > hide #4.11 models > show #4.11 models > hide #4.12 models > show #4.12 models > hide #4.12 models > ~select #4 Nothing selected > select #4.7 365 atoms, 374 bonds, 1 model selected > show #4.7 models > color sel cyan > show #4.8 models > select #4.8 365 atoms, 374 bonds, 1 model selected > color sel cyan > show #4.12 models > select #4.12 365 atoms, 374 bonds, 1 model selected > color sel cyan > show #!8 models > show #7 models > sym #7 I,222r copies true > select #12 1250640 atoms, 1271160 bonds, 61 models selected > ~select #12 Nothing selected > select #12 1250640 atoms, 1271160 bonds, 61 models selected > select #3 732 atoms, 750 bonds, 1 model selected > ~select #3 Nothing selected > select #4 4380 atoms, 4488 bonds, 13 models selected > ~select #4 Nothing selected > select #12 1250640 atoms, 1271160 bonds, 61 models selected > hide #12.1 models > hide #12.2 models > hide #12.3 models > hide #12.4 models > hide #12.5 models > hide #12.6 models > hide #12.7 models > hide #12.8 models > hide #12.9 models > hide #12.10 models > hide #12.11 models > hide #12.12 models > hide #12.13 models > show #12.13 models > hide #12.13 models > hide #12.14 models > hide #12.15 models > hide #12.16 models > hide #12.17 models > hide #12.18 models > show #12.18 models > hide #12.18 models > show #12.18 models > hide #12.18 models > hide #12.19 models > show #12.19 models > hide #12.19 models > hide #12.20 models > hide #12.21 models > hide #12.22 models > hide #12.23 models > hide #12.24 models > show #12.24 models > hide #12.24 models > hide #12.25 models > hide #12.26 models > hide #12.27 models > hide #12.28 models > hide #12.29 models > hide #12.30 models > hide #12.31 models > hide #12.32 models > hide #12.33 models > hide #12.34 models > hide #12.35 models > hide #12.36 models > hide #12.37 models > show #12.37 models > hide #12.37 models > hide #12.38 models > hide #12.39 models > hide #12.40 models > hide #12.41 models > hide #12.42 models > hide #12.43 models > hide #12.44 models > hide #12.45 models > hide #12.46 models > hide #12.47 models > hide #12.48 models > hide #12.49 models > hide #12.50 models > hide #12.51 models > hide #12.52 models > hide #12.53 models > hide #12.54 models > hide #12.55 models > hide #12.56 models > show #12.56 models > hide #12.57 models > show #12.57 models > hide #12.58 models > show #12.58 models > hide #12.58 models > hide #12.59 models > show #12.59 models > hide #12.60 models > show #12.60 models > close #12.1-55 > close #12.58 > color sel orange > select clear > view orient > split #12 Chain information for IIIA_AD41_FACET.pdb A #12.56.1 --- Chain | Description A | No description available Chain information for IIIA_AD41_FACET.pdb B #12.56.2 --- Chain | Description B | No description available Chain information for IIIA_AD41_FACET.pdb C #12.56.3 --- Chain | Description C | No description available Chain information for IIIA_AD41_FACET.pdb D #12.56.4 --- Chain | Description D | No description available Chain information for IIIA_AD41_FACET.pdb E #12.56.5 --- Chain | Description E | No description available Chain information for IIIA_AD41_FACET.pdb F #12.56.6 --- Chain | Description F | No description available Chain information for IIIA_AD41_FACET.pdb G #12.56.7 --- Chain | Description G | No description available Chain information for IIIA_AD41_FACET.pdb H #12.56.8 --- Chain | Description H | No description available Chain information for IIIA_AD41_FACET.pdb N #12.56.9 --- Chain | Description N | No description available Split IIIA_AD41_FACET.pdb (#12.56) into 9 models Chain information for IIIA_AD41_FACET.pdb A #12.57.1 --- Chain | Description A | No description available Chain information for IIIA_AD41_FACET.pdb B #12.57.2 --- Chain | Description B | No description available Chain information for IIIA_AD41_FACET.pdb C #12.57.3 --- Chain | Description C | No description available Chain information for IIIA_AD41_FACET.pdb D #12.57.4 --- Chain | Description D | No description available Chain information for IIIA_AD41_FACET.pdb E #12.57.5 --- Chain | Description E | No description available Chain information for IIIA_AD41_FACET.pdb F #12.57.6 --- Chain | Description F | No description available Chain information for IIIA_AD41_FACET.pdb G #12.57.7 --- Chain | Description G | No description available Chain information for IIIA_AD41_FACET.pdb H #12.57.8 --- Chain | Description H | No description available Chain information for IIIA_AD41_FACET.pdb N #12.57.9 --- Chain | Description N | No description available Split IIIA_AD41_FACET.pdb (#12.57) into 9 models Chain information for IIIA_AD41_FACET.pdb A #12.59.1 --- Chain | Description A | No description available Chain information for IIIA_AD41_FACET.pdb B #12.59.2 --- Chain | Description B | No description available Chain information for IIIA_AD41_FACET.pdb C #12.59.3 --- Chain | Description C | No description available Chain information for IIIA_AD41_FACET.pdb D #12.59.4 --- Chain | Description D | No description available Chain information for IIIA_AD41_FACET.pdb E #12.59.5 --- Chain | Description E | No description available Chain information for IIIA_AD41_FACET.pdb F #12.59.6 --- Chain | Description F | No description available Chain information for IIIA_AD41_FACET.pdb G #12.59.7 --- Chain | Description G | No description available Chain information for IIIA_AD41_FACET.pdb H #12.59.8 --- Chain | Description H | No description available Chain information for IIIA_AD41_FACET.pdb N #12.59.9 --- Chain | Description N | No description available Split IIIA_AD41_FACET.pdb (#12.59) into 9 models Chain information for IIIA_AD41_FACET.pdb A #12.60.1 --- Chain | Description A | No description available Chain information for IIIA_AD41_FACET.pdb B #12.60.2 --- Chain | Description B | No description available Chain information for IIIA_AD41_FACET.pdb C #12.60.3 --- Chain | Description C | No description available Chain information for IIIA_AD41_FACET.pdb D #12.60.4 --- Chain | Description D | No description available Chain information for IIIA_AD41_FACET.pdb E #12.60.5 --- Chain | Description E | No description available Chain information for IIIA_AD41_FACET.pdb F #12.60.6 --- Chain | Description F | No description available Chain information for IIIA_AD41_FACET.pdb G #12.60.7 --- Chain | Description G | No description available Chain information for IIIA_AD41_FACET.pdb H #12.60.8 --- Chain | Description H | No description available Chain information for IIIA_AD41_FACET.pdb N #12.60.9 --- Chain | Description N | No description available Split IIIA_AD41_FACET.pdb (#12.60) into 9 models > hide #12.56.1 models > hide #12.56.2 models > hide #12.56.3 models > hide #12.56.4 models > hide #12.56.5 models > show #12.56.5 models > hide #12.56.6 models > show #12.56.6 models > hide #12.56.7 models > hide #12.56.8 models > show #12.56.8 models > hide #12.56.9 models > show #12.56.9 models > hide #12.57.1 models > show #12.57.1 models > hide #12.57.2 models > hide #12.57.3 models > show #12.57.3 models > hide #12.57.4 models > hide #12.57.5 models > show #12.57.5 models > hide #12.57.5 models > hide #12.57.6 models > show #12.57.6 models > hide #12.57.7 models > hide #12.57.8 models > show #12.57.8 models > hide #12.57.9 models > show #12.57.9 models > hide #12.59.1 models > hide #12.59.2 models > hide #12.59.3 models > show #12.59.3 models > hide #12.59.4 models > hide #12.59.5 models > hide #12.59.6 models > show #12.59.6 models > hide #12.59.7 models > hide #12.59.8 models > hide #12.60.1 models > show #12.60.1 models > hide #12.60.2 models > hide #12.60.3 models > hide #12.60.4 models > hide #12.60.5 models > show #12.60.5 models > hide #12.60.6 models > hide #12.60.7 models > hide #12.60.8 models > show #12.60.8 models > hide #12.60.9 models > show #!5 models > show #!6 models > graphics silhouettes true > lighting full > hide #!5 models > hide #!6 models > hide #!8 models > hide #12 models > hide #!4 models > show #!11 models > show #!10 models > show #!9 models > select #9 65115 atoms, 66918 bonds, 18 pseudobonds, 2 models selected > ~select #9 Nothing selected > color #9-11 light sea green > select #9 65115 atoms, 66918 bonds, 18 pseudobonds, 2 models selected > show #!4 models > hide #!4 models > show #!4 models > select clear > show #!2 models > select #2 65202 atoms, 67008 bonds, 24 pseudobonds, 2 models selected > select clear > show #!8 models > show #12 models > hide #12.56.1 models > hide #12.56.2 models > hide #12.56.3 models > hide #12.56.4 models > hide #12.56.5 models > show #12.56.5 models > hide #12.56.5 models > show #12.56.5 models > show #12.56.4 models > hide #12.56.4 models > hide #12.56.5 models > show #12.56.5 models > hide #12.56.6 models > show #12.56.6 models > hide #12.56.7 models > hide #12.56.8 models > show #12.56.8 models > hide #12.56.9 models > show #12.56.9 models > close #12.56.1-4,7 > hide #12.57.1 models > show #12.57.1 models > hide #12.57.2 models > hide #12.57.3 models > show #12.57.3 models > hide #12.57.4 models > hide #12.57.5 models > show #12.57.5 models > hide #12.57.5 models > hide #12.57.6 models > show #12.57.6 models > hide #12.57.7 models > hide #12.57.8 models > show #12.57.8 models > hide #12.57.8 models > show #12.57.8 models > hide #12.57.9 models > show #12.57.9 models > close #12.57.2,4-5,7 > hide #12.59.1 models > show #12.59.1 models > hide #12.59.1 models > hide #12.59.2 models > hide #12.59.3 models > show #12.59.3 models > hide #12.59.4 models > hide #12.59.5 models > hide #12.59.6 models > show #12.59.6 models > hide #12.59.7 models > hide #12.59.8 models > hide #12.59.9 models > show #12.59.9 models > close #12.59.1-2,4-5,7-8 > hide #12.60.1 models > show #12.60.1 models > hide #12.60.2 models > hide #12.60.3 models > hide #12.60.4 models > hide #12.60.5 models > show #12.60.5 models > hide #12.60.6 models > hide #12.60.7 models > hide #12.60.8 models > show #12.60.8 models > hide #12.60.9 models > close #12.60.2-4,6-7,9 > view orient > show #!5 models > show #!6 models > view orient > split #5 #6 Chain information for VIII_EXTRA_AD41_FACET.pdb A #5.1 --- Chain | Description A | No description available Chain information for VIII_EXTRA_AD41_FACET.pdb B #5.2 --- Chain | Description B | No description available Chain information for VIII_EXTRA_AD41_FACET.pdb C #5.3 --- Chain | Description C | No description available Chain information for VIII_EXTRA_AD41_FACET.pdb D #5.4 --- Chain | Description D | No description available Chain information for VIII_EXTRA_AD41_FACET.pdb E #5.5 --- Chain | Description E | No description available Chain information for VIII_EXTRA_AD41_FACET.pdb O #5.6 --- Chain | Description O | No description available Split VIII_EXTRA_AD41_FACET.pdb (#5) into 7 models Chain information for VIII_AD41_FACET.pdb A #6.1 --- Chain | Description A | No description available Chain information for VIII_AD41_FACET.pdb B #6.2 --- Chain | Description B | No description available Chain information for VIII_AD41_FACET.pdb C #6.3 --- Chain | Description C | No description available Chain information for VIII_AD41_FACET.pdb D #6.4 --- Chain | Description D | No description available Chain information for VIII_AD41_FACET.pdb E #6.5 --- Chain | Description E | No description available Chain information for VIII_AD41_FACET.pdb F #6.6 --- Chain | Description F | No description available Chain information for VIII_AD41_FACET.pdb G #6.7 --- Chain | Description G | No description available Chain information for VIII_AD41_FACET.pdb H #6.8 --- Chain | Description H | No description available Chain information for VIII_AD41_FACET.pdb I #6.9 --- Chain | Description I | No description available Chain information for VIII_AD41_FACET.pdb J #6.10 --- Chain | Description J | No description available Chain information for VIII_AD41_FACET.pdb K #6.11 --- Chain | Description K | No description available Chain information for VIII_AD41_FACET.pdb L #6.12 --- Chain | Description L | No description available Chain information for VIII_AD41_FACET.pdb M #6.13 --- Chain | Description M | No description available Chain information for VIII_AD41_FACET.pdb N #6.14 --- Chain | Description N | No description available Chain information for VIII_AD41_FACET.pdb O #6.15 --- Chain | Description O | No description available Chain information for VIII_AD41_FACET.pdb P #6.16 --- Chain | Description P | No description available Chain information for VIII_AD41_FACET.pdb Q #6.17 --- Chain | Description Q | No description available Chain information for VIII_AD41_FACET.pdb R #6.18 --- Chain | Description R | No description available Chain information for VIII_AD41_FACET.pdb S #6.19 --- Chain | Description S | No description available Chain information for VIII_AD41_FACET.pdb T #6.20 --- Chain | Description T | No description available Chain information for VIII_AD41_FACET.pdb U #6.21 --- Chain | Description U | No description available Chain information for VIII_AD41_FACET.pdb V #6.22 --- Chain | Description V | No description available Chain information for VIII_AD41_FACET.pdb W #6.23 --- Chain | Description W | No description available Chain information for VIII_AD41_FACET.pdb X #6.24 --- Chain | Description X | No description available Chain information for VIII_AD41_FACET.pdb Y #6.25 --- Chain | Description Y | No description available Chain information for VIII_AD41_FACET.pdb Z #6.26 --- Chain | Description Z | No description available Chain information for VIII_AD41_FACET.pdb a #6.27 --- Chain | Description a | No description available Chain information for VIII_AD41_FACET.pdb b #6.28 --- Chain | Description b | No description available Chain information for VIII_AD41_FACET.pdb c #6.29 --- Chain | Description c | No description available Chain information for VIII_AD41_FACET.pdb d #6.30 --- Chain | Description d | No description available Chain information for VIII_AD41_FACET.pdb e #6.31 --- Chain | Description e | No description available Split VIII_AD41_FACET.pdb (#6) into 31 models > hide #!5.1 models > show #!5.1 models > hide #!5.1 models > show #!5.1 models > hide #!5.2 models > show #!5.2 models > hide #!5.3 models > show #!5.3 models > hide #!5.4 models > show #!5.4 models > hide #!5.5 models > show #!5.5 models > hide #!5.5 models > show #!5.5 models > hide #!5.6 models > show #!5.6 models > hide #5.7 models > show #5.7 models > hide #5.7 models > close #5.7 > hide #!6.31 models > hide #!6.30 models > hide #!6.29 models > hide #!6.28 models > hide #!6.27 models > show #!6.27 models > hide #!6.27 models > hide #!6.26 models > show #!6.26 models > hide #!6.25 models > hide #!6.24 models > hide #!6.23 models > hide #!6.22 models > show #!6.22 models > hide #!6.21 models > show #!6.21 models > hide #!6.20 models > show #!6.20 models > hide #!6.20 models > show #!6.20 models > hide #!6.19 models > show #!6.19 models > hide #!6.18 models > show #!6.18 models > hide #!6.17 models > show #!6.17 models > hide #!6.16 models > show #!6.16 models > hide #!6.15 models > show #!6.15 models > hide #!6.15 models > hide #!6.14 models > hide #!6.13 models > hide #!6.12 models > hide #!6.11 models > hide #!6.10 models > show #!6.10 models > hide #!6.9 models > show #!6.9 models > hide #!6.8 models > show #!6.8 models > hide #!6.7 models > hide #!6.6 models > hide #!6.5 models > show #!6.5 models > hide #!6.4 models > show #!6.4 models > hide #!6.3 models > show #!6.3 models > hide #!6.2 models > show #!6.2 models > hide #!6.1 models > show #!6.1 models > hide #!6.21 models > close #6.6-7,11-15,21,23-25,27-31 > save /home/mpillana/AD41_MARZO_2020/map_general/new_colors_fac4t.cxs opened ChimeraX session > lighting simple > graphics silhouettes false > open > /home/mpillana/AD41_MARZO_2020/MAPS/NEW_MAPS/AD41_PRE_2962_relion_class001.mrc Opened AD41_PRE_2962_relion_class001.mrc, grid size 780,780,780, pixel 1.38, shown at step 1, values float32 > toolshed show ""Map Coordinates"" > volume #13 region 0,0,0,779,779,779 step 4 > volume #13 region 0,0,0,779,779,779 step 4 > set bgColor black > toolshed show ""Map Eraser"" > volume #13 change image level -0.004528,0 level 0.02895,0.8 level 0.04107,1 > volume copy #13 subregion 149,224,346,633,708,779 > volume erase #15 center 2.4454,104.22,270.25 radius 328.15 outside true > hide #!4 models > volume zone #16 nearAtoms #1-3 #5-11 range 3 invert true minimalBounds true > newMap true > volume zone #15 nearAtoms #1-3 #5-11 range 3 invert true minimalBounds true > newMap true > hide #!2 models > hide #!5 models > hide #!6 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #12 models > volume #16 level 0.01668 > volume #16 level 0.008712 > volume #16 level 0.007654 > volume #16 level 0.005255 > volume #16 level 0.003492 > close #16 > volume zone #15 nearAtoms #1-11 range 3 invert true minimalBounds true > newMap true > volume #16 level 0.009346 > vop scale #16 factor 146.97 > volume #16 step 1 > close #17 > vop scale #16 factor 146.97 > volume #17 level 2.103 > volume #17 level 0.796 > volume #17 level 1.077 > volume #17 level 1.25 > volume #17 level 0.7636 > volume zone #17 nearAtoms #4 range 20 invert false minimalBounds true newMap > true > volume #18 level 0.102 > show #!4 models > volume #18 level 0.2085 > volume #18 level 0.4595 > volume #18 level 0.4214 > surface dust #18 size 10 > surface undust #18 size 5 Expected fewer arguments > surface dust #18 size 5 > surface undust #18 > volume #18 level 0.1857 > surface dust #18 size 5 > volume zone #15 nearAtoms #1-11 range 4 invert true minimalBounds true > newMap true > volume #19 level 0.007229 > volume zone #19 nearAtoms #4 range 20 invert false minimalBounds true newMap > true > volume #20 level 0.0005589 > vop scale #20 factor 146.97 > surface dust #21 size 5 > surface dust #21 size 8 > surface dust #21 size 10 > volume #21 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.5 > subdivideSurface true subdivisionLevels 1 smoothLines true > volume #21 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8 > subdivideSurface true subdivisionLevels 1 smoothLines true > volume #21 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.8 > subdivideSurface true subdivisionLevels 1 smoothLines true > volume #21 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.8 > subdivideSurface true subdivisionLevels 2 smoothLines true > volume #21 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.8 > subdivideSurface true subdivisionLevels 5 smoothLines true > graphics silhouettes true > graphics silhouettes false > volume #21 surfaceSmoothing true smoothingIterations 2 smoothingFactor 0.8 > subdivideSurface true subdivisionLevels 5 smoothLines true > volume #21 surfaceSmoothing false smoothingIterations 2 smoothingFactor 0.8 > subdivideSurface false subdivisionLevels 5 smoothLines true > ui mousemode right ""pick blobs"" > measure blob #!21.1 triangleNumber 28731 color #8ae234ff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 3336.3 area = 2905.6 size = 52.02 47.932 11.863 > transparency #21.1-2 50 > measure blob #!21.1 triangleNumber 21195 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 13997 area = 9485 size = 105.03 79.219 31.845 > measure blob #!21.1 triangleNumber 51766 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 13654 area = 9313.1 size = 95.864 85.401 33.592 > measure blob #!21.1 triangleNumber 28560 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 13948 area = 9326.2 size = 91.272 87.753 33.15 > transparency #21.1-5 0 > transparency #21.1-5 50 > set bgColor white > graphics silhouettes true > view orient > show #!2 models > select #2 65202 atoms, 67008 bonds, 24 pseudobonds, 2 models selected > ~select #2 Nothing selected > hide #4.1-12#!2 atoms > show #4.1-12#!2 cartoons > graphics silhouettes false > view orient > show #!9 models > hide #4.1-12#!2,9 atoms > show #4.1-12#!2,9 cartoons > show #4.1-12#!2,9 cartoons > show #!10 models > show #4.1-12#!2,9-10 cartoons > hide #4.1-12#!2,9-10 atoms > show #!11 models > hide #4.1-12#!2,9-11 atoms > show #4.1-12#!2,9-11 cartoons > show #!8 models > select #8 54135 atoms, 55425 bonds, 30 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > select clear > view orient > select #4 4380 atoms, 4488 bonds, 13 models selected > show sel atoms > select clear > transparency #21.1 0 > turn x 20 > view orient > toolshed show ""Side View"" > turn x 20 > shape icosahedron radius 450 orientation 222r mesh true d2 Expected a keyword > shape icosahedron radius 450 orientation 222r mesh true divisions 2 > view orient > lighting simple > lighting soft > lighting full > lighting full > view orient > turn x 20 > hide #!22 models > turn x -45 > volume #21 level 0.1043 > volume #21 level 0.4519 > volume #21 level 0.3477 > volume #21 level 0.299 > volume #21 level 0.2225 > volume #21 level 0.2 > view orient > hide #!2 models > hide #!8 models > hide #!10 models > hide #!11 models > hide #!9 models > surface undust #21 > surface dust #21 size 5 > measure blob #!21.1 triangleNumber 29464 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 8501.5 area = 6750 size = 90.853 80.865 28.448 > measure blob #!21.1 triangleNumber 16020 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 8487.1 area = 6702.1 size = 97.149 78.124 28.658 > measure blob #!21.1 triangleNumber 35523 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 7998.3 area = 6181.2 size = 84.562 73.231 30.14 > measure blob #!21.1 triangleNumber 26168 color #8ae234ff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 2299.7 area = 2137.4 size = 46.17 40.355 10.996 > view orient > turn x 20 > show #!2 models > show #!9 models > show #!10 models > show #!11 models > show #!8 models > measure blob #!21.1 triangleNumber 10912 color #8ae234ff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 8501.5 area = 6750 size = 90.853 80.865 28.448 > measure blob #!21.1 triangleNumber 32774 color #fce94fff outline true Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob: volume = 8501.5 area = 6750 size = 90.853 80.865 28.448 > save /home/mpillana/AD41_MARZO_2020/IX/2020.06.12/IX_facet.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 817, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 571, in save for name, data in mgr.walk(): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 300, in walk key = next(odg) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 69, in order_dag yield from _postorder_traversal(path, d, node) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1> from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>] chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models', , , ] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1543, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 106, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 117, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 48, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2849, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2849, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 817, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 571, in save for name, data in mgr.walk(): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py"", line 300, in walk key = next(odg) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 69, in order_dag yield from _postorder_traversal(path, d, node) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 82, in _postorder_traversal yield from _postorder_traversal(path, d, dnode) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1> from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>] chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models', , , ] File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/order_dag.py"", line 80, in _postorder_traversal raise OrderDAGError(""cycle detected, reached %s from %s"" % (repr(dnode), repr(path)), path) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.82 OpenGL renderer: GeForce MX130/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: HP Model: HP Pavilion Laptop 14-ce0xxx OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz Cache Size: 6144 KB Memory: total used free shared buff/cache available Mem: 15G 9.6G 5.3G 112M 618M 5.5G Swap: 2.0G 135M 1.9G Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07) Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:84ba] Kernel driver in use: i915 }}} " defect assigned normal Sessions Tom Goddard all ChimeraX