id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15566 "Error in custom ""lattice"" command" chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.6.6-x86_64-i386-64bit ChimeraX Version: 1.8rc202406072045 (2024-06-07 20:45:50 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_07_onlymodel.cxs Opened grid8_lam4_tomo4_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 Log from Sat Jun 22 22:01:06 2024UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_04_intermed_ferr.cxs Opened grid8_lam4_tomo4_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 Log from Thu Jun 20 11:42:33 2024UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_03.cxs Opened grid8_lam4_tomo4_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 Log from Thu Jun 20 11:16:46 2024UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_02.cxs Opened grid8_lam4_tomo4_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 Log from Tue Jun 11 16:49:25 2024UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_01.cxs Opened grid8_lam4_tomo4_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 Log from Wed May 29 21:27:29 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo5_rec.mrc > format mrc Opened grid8_lam4_tomo5_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 level -0.9991,0 level 3.999,0.8 level 9,1 > volume #1 level -1.339,0.4615 level 3.999,0.8 level 9,1 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 tiltedSlabAxis -0.1894,-0.03347,0.9813 tiltedSlabOffset -761.3 > close session > open > /Users/tbeck/owngroup/position_HH/projects/cryo_em_CSSB/FIB/2024-03-16/grid8_lam4_tomo1_rec.mrc Opened grid8_lam4_tomo1_rec.mrc as #1, grid size 1024,1440,302, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 tiltedSlabAxis -0.1894,-0.03347,0.9813 tiltedSlabOffset -761.3 > volume #1 level -0.9991,0 level 3.001,0.8 level 9,1 > volume #1 level -1.288,0.4923 level 3.001,0.8 level 9,1 > ui mousemode right ""move planes"" > volume #1 region 0,0,158,1023,1439,158 > volume #1 region 0,0,171,1023,1439,171 > volume #1 region 0,0,161,1023,1439,161 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.9397,-0.07134,-0.3345 tiltedSlabOffset -3783 > volume #1 tiltedSlabAxis -0.9397,-0.07134,-0.3345 tiltedSlabOffset -3687 > volume #1 tiltedSlabAxis -0.1894,-0.03347,0.9813 tiltedSlabOffset -761.3 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 region 0,0,145,1023,1439,145 > volume #1 region 0,0,151,1023,1439,151 > volume #1 region 0,0,148,1023,1439,148 > volume #1 region 0,0,181,1023,1439,181 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.7947,-0.1134,-0.5963 tiltedSlabOffset -3418 > volume #1 tiltedSlabAxis -0.7947,-0.1134,-0.5963 tiltedSlabOffset -3929 > volume #1 tiltedSlabAxis -0.7947,-0.1134,-0.5963 tiltedSlabOffset -3161 > volume #1 tiltedSlabAxis -0.7947,-0.1134,-0.5963 tiltedSlabOffset -4478 > volume #1 tiltedSlabAxis 0.1634,-0.07409,0.9838 tiltedSlabOffset 1235 > volume #1 tiltedSlabAxis -0.152,0.003057,0.9884 tiltedSlabOffset 31.55 > volume #1 tiltedSlabAxis 0.1618,0.002264,0.9868 tiltedSlabOffset 1136 > volume #1 tiltedSlabAxis 0.1724,0.003563,-0.985 tiltedSlabOffset 307.5 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 region 0,0,109,1023,1439,109 > volume #1 region 0,0,193,1023,1439,193 > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid3_lam1_tomo2_rec.mrc Opened grid3_lam1_tomo2_rec.mrc as #1, grid size 1024,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 region 0,0,239,1023,1439,239 > volume #1 region 0,0,145,1023,1439,145 > volume #1 level -1,0 level 0.9999,0.8 level 3,1 > volume #1 level -1,0 level 1.042,0.6615 level 3,1 > volume #1 level -0.9296,0.5077 level 1.042,0.6615 level 3,1 > volume #1 region 0,0,76,1023,1439,76 > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid3_lam1_tomo8_rec.mrc Opened grid3_lam1_tomo8_rec.mrc as #1, grid size 1023,1440,181, pixel 5.49,5.49,5.49, shown at level 7, step 4, values int16 > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid3_lam1_tomo8_rec.mrc Opened grid3_lam1_tomo8_rec.mrc as #1, grid size 1023,1440,181, pixel 5.49,5.49,5.49, shown at level 7, step 4, values int16 > volume #1 region 0,0,0,1022,1439,180 [Repeated 2 time(s)] > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo1_rec.mrc Opened grid8_lam4_tomo1_rec.mrc as #1, grid size 1024,1440,302, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 level -0.9991,0 level 3.001,0.8 level 9,1 > volume #1 level -0.8136,0.4154 level 3.001,0.8 level 9,1 > volume #1 region 0,0,134,1023,1439,134 > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo2_rec.mrc Opened grid8_lam4_tomo2_rec.mrc as #1, grid size 1024,1440,285, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 level -1.001,0 level 3.999,0.8 level 10,1 > volume #1 level -0.9003,0.4923 level 3.999,0.8 level 10,1 > volume #1 region 0,0,186,1023,1439,186 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis 0.2401,0.01225,0.9707 tiltedSlabOffset 1010 > volume #1 tiltedSlabAxis 0.02475,0.1471,0.9888 tiltedSlabOffset 454.7 > volume #1 tiltedSlabAxis 0.1717,-0.1145,0.9785 tiltedSlabOffset 349.3 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset 316.4 tiltedSlabPlaneCount 14 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo3_rec.mrc Opened grid8_lam4_tomo3_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int8 > ui mousemode right ""rotate slab"" > volume #1 level 22.01,0 level 80,0.8 level 127,1 > volume #1 level 19.44,0.4 level 80,0.8 level 127,1 > volume #1 tiltedSlabAxis 0.1204,0.05662,0.9911 tiltedSlabOffset 740.8 > volume #1 tiltedSlabAxis -0.07779,0.04953,0.9957 tiltedSlabOffset -204.5 > volume #1 tiltedSlabAxis -0.07779,0.04953,0.9957 tiltedSlabOffset -209.2 > volume #1 tiltedSlabAxis -0.07779,0.05661,0.9954 tiltedSlabOffset -181.7 > volume #1 tiltedSlabAxis -0.09941,-0.02922,0.9946 tiltedSlabOffset -568.9 > volume #1 tiltedSlabAxis -0.04208,-0.01826,0.9989 tiltedSlabOffset -186.7 > volume #1 tiltedSlabAxis 0.09979,0.01713,0.9949 tiltedSlabOffset 538.7 > volume #1 tiltedSlabAxis -0.1332,-0.01943,0.9909 tiltedSlabOffset -503.8 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -481.8 tiltedSlabPlaneCount 15 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 region 0,0,182,1022,1439,182 > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo1_rec.mrc Opened grid8_lam4_tomo1_rec.mrc as #1, grid size 1024,1440,302, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.8296,0.1584,0.5355 tiltedSlabOffset -3397 > volume #1 tiltedSlabAxis -0.5563,0.07607,0.8275 tiltedSlabOffset -2666 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > ui mousemode right ""move planes"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > ui mousemode right ""move planes"" > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 region 0,0,148,1023,1439,148 step 1 imageMode ""full region"" > volume #1 region 0,0,0,1023,1439,301 step 4 > volume #1 region 0,0,0,1023,1439,301 step 4 imageMode ""tilted slab"" > tiltedSlabAxis -0.1435,-0.2236,0.9641 tiltedSlabOffset -1237 > tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1369 tiltedSlabPlaneCount 15 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 [Repeated 1 time(s)] > ui mousemode right ""crop volume"" > ui mousemode right ""move planes"" > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 [Repeated 9 time(s)] > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 orthoplanes xyz positionPlanes 512,720,151 style image region all > mousemode rightMode ""move planes"" > volume #1 orthoplanes xyz positionPlanes 512,720,151 style image region all > mousemode rightMode ""move planes"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume #1 orthoplanes xyz positionPlanes 512,720,151 style image region all > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1336 tiltedSlabPlaneCount 10 > ui mousemode right ""rotate slab"" > ui mousemode right ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 tiltedSlabAxis -0.2698,-0.2687,0.9247 tiltedSlabOffset -1740 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 5.488 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo4_rec.mrc Opened grid8_lam4_tomo4_rec.mrc as #2, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #2 level -0.9989,0 level 4,0.8 level 12,1 [Repeated 1 time(s)] > volume #1 level -0.9991,0 level 3.001,0.8 level 9,1 > close #2 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo2_rec.mrc Opened grid8_lam4_tomo2_rec.mrc as #2, grid size 1024,1440,285, pixel 5.49,5.49,5.49, shown at step 1, values int16 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo3_rec.mrc Opened grid8_lam4_tomo3_rec.mrc as #3, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int8 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo4_rec.mrc Opened grid8_lam4_tomo4_rec.mrc as #4, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo5_rec.mrc Opened grid8_lam4_tomo5_rec.mrc as #5, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #5 level -0.9991,0 level 3.999,0.8 level 9,1 > volume #5 level -1.044,0.5231 level 3.999,0.8 level 9,1 > volume #4 level -0.9989,0 level 4,0.8 level 12,1 > volume #4 level -1.109,0.07692 level 4,0.8 level 12,1 > volume #4 level -1.054,0.4923 level 4,0.8 level 12,1 > volume #1 level -1.04,0 level 3.001,0.8 level 9,1 > volume #2 level -1.04,0 level 3.999,0.8 level 10,1 > volume #1 tiltedSlabAxis -0.3278,-0.2414,0.9133 tiltedSlabOffset -2120 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #2 tiltedSlabAxis -0.03907,0.1085,0.9933 tiltedSlabOffset 77.8 > volume #2 tiltedSlabAxis -0.07593,0.007305,0.9971 tiltedSlabOffset -319.1 > volume #3 level 22.01,0 level 80,0.8 level 127,1 > volume #3 level -1.04,0 level 80,0.8 level 127,1 > volume #3 tiltedSlabAxis -0.249,-0.07828,0.9653 tiltedSlabOffset -1266 > volume #3 region 0,0,148,1022,1439,148 step 1 imageMode ""full region"" > volume #3 region 0,0,172,1022,1439,172 > volume #3 tiltedSlabAxis -0.249,-0.07828,0.9653 tiltedSlabOffset -1266 > volume #3 region 0,0,299,1022,1439,299 > volume #3 region 0,0,37,1022,1439,37 > volume #3 region 0,0,48,1022,1439,48 > ui mousemode right ""rotate slab"" > volume #3 tiltedSlabAxis -0.2405,0.003133,0.9706 tiltedSlabOffset -1719 > volume #3 tiltedSlabAxis -0.249,-0.07828,0.9653 tiltedSlabOffset -1266 > volume #3 > volume #3 style image region 0,0,148,1022,1439,148 step 1 imageMode ""full > region"" > volume #3 region 0,0,140,1022,1439,140 > volume #3 color #feff3d color #b3b3ff color #b3b3ff > volume #3 level -1.04,0.3846 level 80,0.8 level 127,1 > volume #3 region 0,0,182,1022,1439,182 > volume #4 region 0,0,229,1022,1439,229 > volume #5 region 0,0,176,1022,1439,176 > volume #5 region 0,0,169,1022,1439,169 > volume #5 region 0,0,173,1022,1439,173 > volume #5 region 0,0,210,1022,1439,210 > volume #5 region 0,0,167,1022,1439,167 > volume #5 region 0,0,123,1022,1439,123 > volume #5 region 0,0,224,1022,1439,224 > volume #5 region 0,0,189,1022,1439,189 > volume #4 region 0,0,163,1022,1439,163 > volume #4 region 0,0,173,1022,1439,173 > volume #3 region 0,0,128,1022,1439,128 > volume #3 region 0,0,151,1022,1439,151 > volume #3 region 0,0,153,1022,1439,153 > volume #3 region 0,0,190,1022,1439,190 > volume #4 region 0,0,203,1022,1439,203 > volume #2 tiltedSlabOffset -330.1 tiltedSlabPlaneCount 14 > volume #2 region 0,0,140,1023,1439,140 step 1 imageMode ""full region"" > volume #2 region 0,0,160,1023,1439,160 > volume #2 color #7fff2b color #b3ffff color #b3ffff > volume #2 color #fff935 color #b3ffff color #b3ffff > volume #2 level -1.04,0.3538 level 3.999,0.8 level 10,1 > volume #2 region 0,0,147,1023,1439,147 > volume #1 region 0,0,0,1023,1439,301 step 1 colorMode opaque8 positionPlanes > 511,719,150 imageMode orthoplanes > volume #1 region 0,0,148,1023,1439,148 step 1 colorMode auto8 imageMode > ""full region"" > volume #1 region 0,0,104,1023,1439,104 > volume #1 level -1.083,0.4154 level 3.001,0.8 level 9,1 > volume #1 region 0,0,261,1023,1439,261 > volume #5 region 0,0,150,1022,1439,150 > volume #3 region 0,0,203,1022,1439,203 > volume #3 region 0,0,196,1022,1439,196 > volume #3 region 0,0,167,1022,1439,167 > volume #3 region 0,0,140,1022,1439,140 > volume #3 region 0,0,0,1022,1439,299 step 4 > volume #3 region 0,0,0,1022,1439,299 step 4 imageMode ""tilted slab"" > tiltedSlabAxis 0.07146,0.1878,0.9796 tiltedSlabOffset 755.1 > volume #3 tiltedSlabAxis 0.2152,0.02139,0.9763 tiltedSlabOffset 889.2 > volume #3 tiltedSlabAxis 0.1063,-0.0596,0.9925 tiltedSlabOffset 293.9 > volume #3 region 0,0,148,1022,1439,148 step 1 imageMode ""full region"" > volume #3 region 0,0,138,1022,1439,138 > select clear > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 [Repeated 1 time(s)] > ui mousemode right ""pick blobs"" > ui mousemode right ""map eraser"" > ui mousemode right ""pick blobs"" > ui mousemode right ""play map series"" > ui mousemode right ""map eraser"" > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo5_rec.mrc > format mrc Opened grid8_lam4_tomo5_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 level -0.9991,0 level 3.999,0.8 level 9,1 > volume #1 level -0.9991,0.5147 level 3.999,0.8 level 9,1 > volume #1 level -0.9991,0.5147 level 3.875,0.7559 level 9,1 > volume #1 level -0.9991,0.2647 level 3.875,0.7559 level 9,1 > volume #1 level -1.5,0.2647 level 3.875,0.7559 level 9,1 > volume #1 level -1.5,0.2647 level 4.495,1 level 9,1 > ui mousemode right ""rotate slab"" > select clear [Repeated 2 time(s)] > volume #1 tiltedSlabAxis 0.1033,0.03243,0.9941 tiltedSlabOffset 503.2 > volume #1 tiltedSlabAxis 0.2064,0.02993,0.978 tiltedSlabOffset 813.5 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset -1.137e-13 tiltedSlabSpacing 5.488 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1177 tiltedSlabPlaneCount 10 > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset -1.137e-13 tiltedSlabSpacing 5.488 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1039 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1039 tiltedSlabPlaneCount 10 > volume #1 tiltedSlabOffset -1105 tiltedSlabPlaneCount 10 > volume #1 region 0,0,148,1022,1439,148 step 1 imageMode ""full region"" > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset -1.137e-13 tiltedSlabSpacing 5.488 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1400 > ui tool show ""Selection Inspector"" > ui mousemode right zoom > ui mousemode right ""move planes"" > select clear > volume #1 tiltedSlabOffset -1647 tiltedSlabPlaneCount 10 [Repeated 1 time(s)] > volume #1 tiltedSlabOffset -1422 tiltedSlabPlaneCount 10 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 region 0,0,169,1022,1439,169 > volume #1 region 0,0,171,1022,1439,171 > select clear > volume #1 region 0,0,171,1022,1439,171 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2017,-0.01246,0.9794 tiltedSlabOffset -813.5 > volume #1 tiltedSlabAxis -0.2722,-0.04646,0.9611 tiltedSlabOffset -1369 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1501 tiltedSlabPlaneCount 15 > select clear > volume #1 step 1 > volume projectionMode 2d-xyz > volume #1 step 16 > volume #1 step 1 > volume #1 level -1.559,0.6618 level 4.495,1 level 9,1 > volume #1 level -1.737,0.07353 level 4.495,1 level 9,1 > volume step 1 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo1_01.cxs > volume #1 tiltedSlabOffset -1501 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1545 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1413 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1303 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1331 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1160 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1292 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1342 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1331 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1199 tiltedSlabPlaneCount 15 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo1_02.cxs > volume #1 tiltedSlabOffset -1007 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -940.9 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -869.6 tiltedSlabPlaneCount 15 [Repeated 1 time(s)] > volume #1 tiltedSlabOffset -913.5 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -765.3 tiltedSlabPlaneCount 15 > ui mousemode right zoom > ui mousemode right ""rotate slab"" > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1018 tiltedSlabPlaneCount 15 > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo2_rec.mrc Opened grid8_lam4_tomo2_rec.mrc as #1, grid size 1024,1440,285, pixel 5.49,5.49,5.49, shown at step 1, values int16 > volume #1 level -1.001,0 level 3.999,0.8 level 10,1 > volume #1 level -1.091,0.4412 level 3.999,0.8 level 10,1 > ui mousemode right zoom > ui mousemode right rotate > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.0005388,0.08406,0.9965 tiltedSlabOffset 127.2 > ui mousemode right zoom > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis 0.1512,0.08054,0.9852 tiltedSlabOffset 823.5 > volume #1 tiltedSlabAxis 0.1687,0.07579,0.9827 tiltedSlabOffset 886 > ui mousemode right rotate > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis 0.1016,0.05572,0.9933 tiltedSlabOffset 553.5 [Repeated 1 time(s)] > volume #1 tiltedSlabAxis 0.1213,0.1113,0.9864 tiltedSlabOffset 784.3 > volume #1 step 1 > volume #1 tiltedSlabAxis 0.09456,0.1199,0.9883 tiltedSlabOffset 698.3 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo2_01_neworien.cxs > volume #1 tiltedSlabAxis 0.04237,0.1414,0.989 tiltedSlabOffset 513 > volume #1 tiltedSlabAxis -0.01648,0.09219,0.9956 tiltedSlabOffset 94.67 > volume #1 tiltedSlabAxis 0.09303,0.09487,0.9911 tiltedSlabOffset 650.2 > volume #1 tiltedSlabAxis 0.07678,0.08002,0.9938 tiltedSlabOffset 522.9 > volume #1 tiltedSlabAxis 0.07144,0.05529,0.9959 tiltedSlabOffset 441.4 > volume #1 tiltedSlabAxis 0.07562,0.08292,0.9937 tiltedSlabOffset 524.6 > volume #1 tiltedSlabAxis 0.05437,0.07828,0.9954 tiltedSlabOffset 425.4 > volume #1 tiltedSlabAxis -0.05874,0.03356,0.9977 tiltedSlabOffset -149.7 > volume #1 tiltedSlabAxis -0.1854,-0.01252,0.9826 tiltedSlabOffset -908.2 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo2_02_maybeplane.cxs > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo3_rec.mrc Opened grid8_lam4_tomo3_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int8 > volume #1 level 22.01,0 level 80,0.8 level 127,1 > volume #1 level 5.525,0.3529 level 80,0.8 level 127,1 > ui mousemode right rotate > ui mousemode right zoom > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis 0.05184,0.02522,0.9983 tiltedSlabOffset 241.2 > volume #1 step 1 > volume #1 tiltedSlabAxis -0.2447,-0.02509,0.9693 tiltedSlabOffset -1131 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo3_01.cxs > volume #1 level 5.525,0.5294 level 80,0.8 level 127,1 > volume #1 level 8.73,0.2353 level 80,0.8 level 127,1 > volume #1 level 1.405,0.5588 level 80,0.8 level 127,1 > volume #1 level 10.56,0.2353 level 80,0.8 level 127,1 > volume #1 level 10.56,0.2353 level 80,0.4029 level 127,1 > volume #1 level 10.56,0.2353 level 80,0.8147 level 127,1 > volume #1 level 10.56,0.2353 level 79.08,0.8882 level 127,1 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo3_01.cxs > close session > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/grid8_lam4_tomo4_rec.mrc Opened grid8_lam4_tomo4_rec.mrc as #1, grid size 1023,1440,300, pixel 5.49,5.49,5.49, shown at step 1, values int16 > ui mousemode right rotate > ui mousemode right zoom > volume #1 level -0.9989,0 level 4,0.8 level 12,1 > volume #1 level -4.266,0.25 level 4,0.8 level 12,1 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.2137,0.06892,0.9745 tiltedSlabOffset -734.7 > volume #1 step 1 > volume #1 tiltedSlabAxis -0.1305,0.01852,0.9913 tiltedSlabOffset -510.9 [Repeated 1 time(s)] > volume #1 tiltedSlabAxis 0.06162,-0.06018,0.9963 tiltedSlabOffset 21 > volume #1 tiltedSlabAxis 0.07005,0.0394,0.9968 tiltedSlabOffset 372.3 [Repeated 1 time(s)] > ui mousemode right translate > ui mousemode right rotate > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis 0.06346,0.1272,0.9898 tiltedSlabOffset 599.4 > volume #1 tiltedSlabAxis -0.01938,0.06542,0.9977 tiltedSlabOffset 81.05 [Repeated 1 time(s)] > volume #1 tiltedSlabAxis 0.1106,0.03647,0.9932 tiltedSlabOffset 588.1 > volume #1 tiltedSlabAxis -0.2534,-0.01611,0.9672 tiltedSlabOffset -1217 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1042 tiltedSlabPlaneCount 15 [Repeated 1 time(s)] > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_01.cxs ——— End of log from Wed May 29 21:27:29 2024 ——— opened ChimeraX session > volume #1 tiltedSlabOffset -1097 tiltedSlabPlaneCount 15 > ui mousemode right ""rotate slab"" > volume #1 tiltedSlabAxis -0.317,-0.04159,0.9475 tiltedSlabOffset -1443 > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1580 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1718 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1520 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1405 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1443 tiltedSlabPlaneCount 15 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_02.cxs ——— End of log from Tue Jun 11 16:49:25 2024 ——— opened ChimeraX session > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1575 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1454 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1575 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1328 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1580 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1311 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1427 tiltedSlabPlaneCount 15 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_03.cxs ——— End of log from Thu Jun 20 11:16:46 2024 ——— opened ChimeraX session > volume #1 level -4.148,0.7577 level 4,0.8 level 12,1 > volume #1 level -4.207,0.2038 level 4,0.8 level 12,1 > volume #1 level -4.207,0.2038 level 4,0.4 level 12,1 > volume #1 level -4.207,0.2038 level 3.822,1 level 12,1 > volume #1 level -4.207,0.2038 level 3.822,0.8154 level 12,1 > volume #1 tiltedSlabOffset -1580 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1685 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1564 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1586 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1564 tiltedSlabPlaneCount 15 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py executed lattice.py > ui mousemode right ""mark plane"" > marker #2 position 4435,5857,131.2 color #29eeff radius 5.488 > ui mousemode right ""delete markers"" > marker delete #2:1 > ui mousemode right ""mark plane"" > marker #2 position 4231,6304,82.49 color #29eeff radius 60 > ui mousemode right ""delete markers"" > marker delete #2:1 > ui mousemode right ""mark plane"" > marker #2 position 4191,5018,12.73 color #29eeff radius 60 > marker #2 position 4535,6197,179.5 color #29eeff radius 60 > marker #2 position 3230,5356,-294.1 color #29eeff radius 60 > lattice #2:1,2,3 spacing 6,7 extent -3,10,-3,5 > hide #3 models > lattice #2:1,2,3 spacing 6,7 extent -10,10,-10,10 > hide #4 models > delete #2 > delete #3 > delete #4 > marker #2 position 4850,4771,222.4 color #29eeff radius 60 > delete #2 > marker #2 position 4518,4906,117.2 color #29eeff radius 60 > marker #2 position 4741,5747,228.7 color #29eeff radius 60 > marker #2 position 3406,5288,-238 color #29eeff radius 60 > lattice #2:1,2,3 spacing 5,7 extent -10,10,-10,10 > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_04_intermed_ferr.cxs ——— End of log from Thu Jun 20 11:42:33 2024 ——— opened ChimeraX session > 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 > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1492 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1328 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1449 tiltedSlabPlaneCount 15 > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > volume #1 tiltedSlabOffset -1443 tiltedSlabPlaneCount 15 > show #3 models > hide #3 models > show #3 models > hide #3 models > volume #1 tiltedSlabOffset -1399 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1514 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1457 tiltedSlabPlaneCount 15 > ui mousemode right ""mark plane"" > marker change #2:3 radius 120 [Repeated 1 time(s)] > marker change #2:3 color #ff436e > marker change #2:3 color #ff3047 > marker change #2:3 color #ff2f46 > marker change #2:3 color #ff1732 > marker change #2:3 color #ff1631 > marker change #2:3 color #b71023 > marker change #2:3 color #c21125 > marker change #2:3 color #1caac2 > marker change #2:3 color #0996c2 > marker change #2:3 color #0995c2 > marker change #2:3 color #0895c2 > marker change #2:3 color #1ec29a > marker change #2:3 color #1fc29a > marker change #2:3 radius 60 > marker #2 position 4477,4619,203.6 color #1fc29a radius 5.488 > marker #2 position 4473,4622,202.5 color #1fc29a radius 5.488 > marker #2 position 4482,4619,205.4 color #1fc29a radius 5.488 > hide #2 models > show #2 models > ui mousemode right ""delete markers"" > marker delete #2:4 > marker delete #2:5 > marker delete #2:6 > ui mousemode right ""mark plane"" > marker #2 position 4483,4615,205.4 color #c22533 radius 120 > marker #2 position 2887,5156,-304.6 color #c22533 radius 120 > marker #2 position 4891,5981,401.9 color #c22533 radius 120 > lattice #2:7,8,9 spacing 4,7 extent -10,10,-10,10 Unknown command: lattice #2:7,8,9 spacing 4,7 extent -10,10,-10,10 > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py executed lattice.py > lattice #2:7,8,9 spacing 4,7 extent -10,10,-10,10 > delete #4 > lattice #2:7,8,9 spacing 5,4 extent -10,10,-10,10 > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #3 models > ui mousemode right ""delete markers"" > marker delete #2:9 > marker delete #2:7 > ui mousemode right ""mark plane"" > hide #3 models > marker #2 position 4570,6095,299.5 color #c22533 radius 120 > hide #!1 models > show #!1 models > marker #2 position 3648,3579,-119.3 color #c22533 radius 120 > hide #!1 models > show #!1 models > lattice #2:8,10,11 spacing 8,7 extent -10,10,-10,10 > delete #4 > delete #5 > lattice #2:8,10,11 spacing 8,7 extent -10,10,-10,10 > hide #2 models > hide #4 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > marker #2 position 2940,5328,-279.4 color #c22533 radius 120 > marker change #2:12 radius 60 > marker change #2:12 color #1b1bcf > marker change #2:12 color #1637cf > marker change #2:12 color #1242cf > marker #2 position 3803,3529,-69.73 color #1242cf radius 60 > ui mousemode right ""delete markers"" > ui mousemode right ""resize markers"" > ui mousemode right ""delete markers"" > hide #2 models > show #2 models > ui mousemode right ""mark surface"" > ui mousemode right ""delete markers"" > ui mousemode right ""mark plane"" > marker #2 position 4195,6033,171.3 color #1242cf radius 60 > show #4 models > hide #4 models > ui mousemode right ""delete markers"" > hide #!1 models > marker delete #2:13 > show #!1 models > ui mousemode right ""mark plane"" > marker #2 position 3914,3303,-42.58 color #1242cf radius 60 > ui mousemode right ""delete markers"" > marker delete #2:15 > ui mousemode right ""mark plane"" > marker #2 position 3920,3309,-40.11 color #1242cf radius 60 > hide #!1 models > show #!1 models > lattice #2:12,16,14 spacing 9,6 extent -10,10,-10,10 > show #4 models > show #3 models > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_06_encaps.cxs > hide #!1 models > hide #2 models > show #!1 models > hide #3 models > show #2 models > hide #5 models > hide #4 models > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1452 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1671 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1441 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1671 tiltedSlabPlaneCount 15 > ui mousemode right ""mark plane"" > marker #2 position 5118,4995,209 color #1242cf radius 60 > ui mousemode right ""delete markers"" > hide #!1 models > marker delete #2:17 > show #!1 models > ui mousemode right ""delete markers"" > ui mousemode right ""move planes"" > volume #1 tiltedSlabOffset -1797 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1550 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1397 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1468 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1539 tiltedSlabPlaneCount 15 > volume #1 tiltedSlabOffset -1671 tiltedSlabPlaneCount 15 > ui mousemode right ""mark plane"" > marker #2 position 5293,6456,331.5 color #1242cf radius 60 > ui mousemode right ""delete markers"" > hide #!1 models > marker delete #2:18 > show #!1 models > ui mousemode right ""mark plane"" > marker #2 position 5276,6456,325.8 color #1242cf radius 60 > marker change #2:19 color #d83580 > marker change #2:19 color #d8560f > marker change #2:19 radius 120 > marker #2 position 3389,5428,-350.7 color #d8560f radius 120 > marker #2 position 5946,5101,490.5 color #d8560f radius 120 > hide #!1 models > show #!1 models > select ~sel & ##selected 11 atoms, 11 residues, 1 model selected > select ~sel & ##selected 1 atom, 1 residue, 1 model selected > select ~sel & ##selected 11 atoms, 11 residues, 1 model selected > select ~sel & ##selected 1 atom, 1 residue, 1 model selected > lattice #2:19,20,21 spacing 9,6 extent -10,10,-10,10 > hide #!1 models > show #3 models > show #4 models > show #5 models > save > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/crystal_tomos/tomo4_07_onlymodel.cxs ——— End of log from Sat Jun 22 22:01:06 2024 ——— opened ChimeraX session > show #!1 models > hide #2 models > show #2 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > open > /Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py FYI: command is replacing existing command: ""lattice"" executed lattice.py > lattice #7:7,8,9 spacing 5,4 extent 3,10,3,10 Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.06.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8-rc2024.06.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py"", line 30, in lattice from chimerax.users.core import UserError ModuleNotFoundError: No module named 'chimerax.users' ModuleNotFoundError: No module named 'chimerax.users' File ""/Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py"", line 30, in lattice from chimerax.users.core import UserError See log for complete Python traceback. > lattice #2:7,8,9 spacing 5,4 extent -10,10,-10,10 Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.06.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8-rc2024.06.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py"", line 30, in lattice from chimerax.users.core import UserError ModuleNotFoundError: No module named 'chimerax.users' ModuleNotFoundError: No module named 'chimerax.users' File ""/Users/tbeck/owngroup/mypapers/drafts/27_michael_heterbinary/data_uli/2024-05-13/tom_analysis/lattice.py"", line 30, in lattice from chimerax.users.core import UserError See log for complete Python traceback. OpenGL version: 4.1 INTEL-20.7.2 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 1.7 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 577.140.2~22 Software: System Software Overview: System Version: macOS 13.6.6 (22G630) Kernel Version: Darwin 22.6.0 Time since boot: 6 days, 19 hours, 33 minutes Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP Z24n: Resolution: 1200 x 1920 UI Looks like: 1200 x 1920 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CN461515LD Mirror: Off Online: Yes Rotation: 270 Adapter Type: DVI or HDMI Adapter Firmware Version: ff.c8 HP Z24n: Resolution: 1200 x 1920 UI Looks like: 1200 x 1920 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CN461515M1 Main Display: Yes Mirror: Off Online: Yes Rotation: 90 Adapter Type: DVI or HDMI Adapter Firmware Version: ff.c8 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202406072045 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.46 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Volume Data fixed Tom Goddard all ChimeraX