Opened 16 months ago

Closed 16 months ago

#15566 closed defect (fixed)

Error in custom "lattice" command

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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:
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    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
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
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    ChimeraX-MDcrds: 2.7.1
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    ChimeraX-MMTF: 2.2
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    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
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    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
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    imagecodecs: 2024.1.1
    imagesize: 1.4.1
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    networkx: 3.3
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    numpy: 1.26.4
    openvr: 1.26.701
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    PyOpenGL: 3.1.7
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    pyopenxr: 1.0.3401
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Change History (6)

comment:1 by pett, 16 months ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Error in custom "lattice" command

comment:2 by pett, 16 months ago

Resolution: → can't reproduce
Status: accepted → closed

Maybe for light-sheet microscopy?

comment:3 by Tom Goddard, 16 months ago

Fixed.

This was a script I wrote and apparently I never tested the error handling since the import to report that the arguments were wrong was incorrect. I've fixed the script and sent it to Tobias Beck who should be the only one who has it, since the script is not online yet (awaiting Beck publication).

comment:4 by Tom Goddard, 16 months ago

Resolution: can't reproduce
Status: closed → reopened

comment:5 by Tom Goddard, 16 months ago

Component: Third Party → Volume Data
Owner: changed from pett to Tom Goddard
Status: reopened → assigned

comment:6 by Tom Goddard, 16 months ago

Resolution: → fixed
Status: assigned → closed
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