Multiple layers of transparency

[bs15ml@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
I have three laers of membrane wihtin each other and would like o hsow the two outer membranes as semi-transparent enabling me to visualise all 3 at once. If the outer membrane is set at 20% opacity, the middle membrane is only viewable at 100%, blocking the view of the central membrane. Is there a way for the outer and second membranes to both be semi-transparent?

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/bs15ml/segmentations/ML-19A_TS_07_2/figure_full.cxs format
> session

Log from Wed Oct 14 16:55:17 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/bs15ml/segmentations/ML-19A_TS_07_2/figure_full.cxs format
> session

Log from Tue Oct 13 15:47:47 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/bs15ml/segmentations/ML-19A_TS_07_2/figure_full.cxs format
> session

Log from Wed Oct 7 20:11:24 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/bs15ml/segmentations/ML-19A_TS_07_2/figure.cxs format session

Log from Tue Oct 6 20:03:31 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/bs15ml/segmentations/ML-19A_TS_07_2/TS_07_figure.cxs format
> session

Log from Mon Oct 5 16:47:07 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/bs15ml/segmentations/ML-19A_TS_07_2/postsyn.cmm

Opened 1 marker sets containing 31225 markers  

> ui mousemode right select

Drag select of 31225 atoms  

> marker change sel radius 1

> select clear

Drag select of 6 atoms  

> delete sel

Drag select of 4 atoms  

> delete sel

> delete sel

Drag select of  
Drag select of 7 atoms  

> delete sel

> delete sel

Drag select of 6 atoms  

> delete sel

Drag select of 12 atoms  

> delete sel

Drag select of 14 atoms  

> delete sel

Drag select of 4 atoms  

> delete sel

Drag select of 36 atoms  

> delete sel

Drag select of 3 atoms  

> delete sel

> delete sel

> delete sel

> ui mousemode right "move markers"

> marker change #1:23060 position 572.9,250,184.3

> marker change #1:24581 position 576.5,260.5,190.7

> marker change #1:23554 position 578.9,249.2,186.5

> marker change #1:24510 position 578.6,248.2,189.7

> marker change #1:25175 position 578.6,249.5,192.4

> marker change #1:23060 position 576.1,252,185.2

> marker change #1:22760 position 575.2,254.5,182.2

> marker change #1:22200 position 573.1,255.5,179.3

> marker change #1:21872 position 570.5,253.8,176.1

> marker change #1:21661 position 568.2,253.4,174.1

> marker change #1:21839 position 570,255.5,175.8

> marker change #1:21268 position 566.4,253.2,171.6

> marker change #1:21285 position 566.2,254.4,173.4

> marker change #1:21614 position 567.3,254.6,174.3

> marker change #1:21024 position 565.3,252.2,170.4

> marker change #1:21040 position 565.8,254.5,170.6

> marker change #1:21024 position 566,253.3,169.8

> marker change #1:20448 position 563.4,255.2,169.4

> marker change #1:20712 position 564.8,254.3,170.6

> marker change #1:20785 position 562.9,256.1,170.6

> marker change #1:20513 position 562.2,256.5,168.8

> marker change #1:20233 position 561.1,256.1,167.4

> marker change #1:20351 position 560.3,255.3,167.8

> marker change #1:20077 position 559.4,255.9,166.5

> marker change #1:19949 position 559.7,255.7,165

> marker change #1:19806 position 559.5,255.4,164.5

> marker change #1:19573 position 558.3,255.8,163.5

> marker change #1:19646 position 559.6,256.1,163.5

> marker change #1:19478 position 558,255.2,162.7

> marker change #1:19203 position 556.7,255.3,161.7

> marker change #1:19426 position 560.1,255.3,161.4

> marker change #1:19511 position 560.5,257,162.8

> marker change #1:19646 position 562,256.1,162.9

> marker change #1:19806 position 562.5,255.7,162.9

> marker change #1:18968 position 559.4,255.8,158.1

> marker change #1:18731 position 557.2,257.2,159.1

> marker change #1:18581 position 555.3,257.3,157

> marker change #1:18555 position 556,256.8,157.8

> marker change #1:18281 position 555.4,255.6,156

> marker change #1:18302 position 556,256.5,158.1

> marker change #1:18018 position 554.1,256.4,155.2

> marker change #1:19203 position 557.4,256.6,161.6

> marker change #1:19478 position 559.1,256.7,162.9

> marker change #1:19949 position 560.8,257.4,165

> marker change #1:20351 position 561.1,256.5,167.8

> marker change #1:20581 position 561.7,256,170

> marker change #1:20813 position 562.3,255.7,170.9

> marker change #1:21024 position 566.4,253.9,169.8

> marker change #1:20063 position 571.5,251.7,167

> marker change #1:20366 position 572.5,250.8,169

> marker change #1:20420 position 573.6,250.1,168.8

> marker change #1:20716 position 575.3,249.9,169.7

> marker change #1:20920 position 572.4,251.2,171.6

> marker change #1:20988 position 574.2,250.5,171.8

> marker change #1:21872 position 571.8,254.3,174.4

> marker change #1:22128 position 571.3,255.9,175.5

> marker change #1:22037 position 571.1,257.3,175

> marker change #1:21661 position 570.4,253.7,173.4

> marker change #1:21268 position 569,253.4,170.6

> marker change #1:20448 position 566,255.7,168.8

> marker change #1:20813 position 567,256.3,169.3

> marker change #1:21318 position 566.8,256.5,173.2

> marker change #1:21580 position 568.9,254.7,173.4

> marker change #1:21803 position 569.5,256,174.8

> marker change #1:21726 position 569.3,257.6,174.2

> marker change #1:21830 position 570.6,259.6,174

> marker change #1:21567 position 569.5,259.7,173.2

> marker change #1:21491 position 566.9,258.2,174.3

> marker change #1:21343 position 567.1,260.1,172.8

> marker change #1:21289 position 567.8,261.9,172.6

> marker change #1:21570 position 567.6,262,174.3

> marker change #1:20529 position 565.6,267.8,168.1

> marker change #1:21064 position 565.7,262,171.2

> marker change #1:20826 position 566.2,263,169.5

> marker change #1:21094 position 565.3,260,171.4

> marker change #1:20859 position 566.1,260.1,169.7

> marker change #1:20972 position 565.5,257.2,171

> marker change #1:20797 position 565,258.3,169.9

> marker change #1:20593 position 564.2,260.3,169.3

> marker change #1:20785 position 563.8,257.6,171.2

> marker change #1:20581 position 563.7,258.4,170.9

> marker change #1:20565 position 562.6,259.5,170.2

> marker change #1:19982 position 562.4,259.8,166.3

> marker change #1:20513 position 564,257.2,169.1

> marker change #1:20351 position 562.6,257.2,168.1

> marker change #1:20077 position 561.9,256.5,166.8

> marker change #1:19937 position 561.7,257.2,166.5

> marker change #1:19687 position 560,256.8,165.3

> marker change #1:19573 position 561.3,257.5,164.1

> marker change #1:19183 position 559.7,257.6,162.6

> marker change #1:18915 position 559.3,257.5,160.6

> marker change #1:18281 position 557.4,257.1,156.2

> marker change #1:17649 position 555.6,258.2,153.1

> marker change #1:20431 position 559.9,258.4,169.2

> marker change #1:17384 position 553.5,258.5,151.7

> marker change #1:16942 position 553.2,257.8,149.4

> marker change #1:16643 position 552.7,259.3,147.7

> marker change #1:20091 position 560.8,258.5,167.3

> marker change #1:20431 position 561.2,259.2,169.2

> marker change #1:20578 position 562.9,261.4,169.8

> marker change #1:20811 position 564,262.2,170.8

> marker change #1:21036 position 565.6,262.7,171.8

> marker change #1:20233 position 563.4,255.3,166.1

> marker change #1:21285 position 569.5,254,172.5

> marker change #1:20529 position 563.9,267.4,170.7

> marker change #1:20563 position 563.6,264.9,170.6

> marker change #1:20162 position 561.4,264.9,167.9

> marker change #1:19660 position 563.8,256.6,164.9

> marker change #1:19989 position 564.3,258.9,167.2

> marker change #1:20258 position 565.6,260,168.6

> marker change #1:18286 position 556.5,260.4,156.2

> marker change #1:18519 position 562.5,252.8,160.2

> marker change #1:18915 position 550.6,265.6,162.4

> marker change #1:18915 position 563.5,267.4,161.8

> marker change #1:18915 position 562.5,264.3,163.6

> marker change #1:18915 position 562,262.8,165.9

> marker change #1:23285 position 573.1,255,187.7

> marker change #1:23285 position 574.9,256.1,188.1

> marker change #1:23930 position 576.1,253.4,189.2

> marker change #1:24581 position 574.6,258.8,191.3

> marker change #1:25231 position 575,257.6,194.4

> marker change #1:23465 position 573.6,257.5,185.8

> marker change #1:26428 position 572.8,251.7,199.7

> marker change #1:26428 position 575.4,253.4,200.2

> marker change #1:23148 position 575.2,254.8,185.9

> marker change #1:23251 position 575.1,252.3,186.9

> marker change #1:22739 position 571.9,258.1,186.7

> marker change #1:22739 position 573.9,258.9,187.1

> marker change #1:25235 position 576.9,250.7,190.6

> marker change #1:25425 position 574.9,255.7,193

> marker change #1:20972 position 567.9,244,180

> marker change #1:21614 position 569.8,246.2,178.7

> marker change #1:21614 position 578.8,250.4,187.4

> marker change #1:20972 position 578.8,247.5,191

> marker change #1:23903 position 580.3,248.3,188.4

> marker change #1:20712 position 568.9,263.7,172.2

> marker change #1:20712 position 578.6,240.7,189.6

> marker change #1:20712 position 580,244.9,191.8

> marker change #1:25004 position 420.2,281.3,201.4

> marker change #1:25288 position 421.9,280,205.1


[had to cut out a bunch of these to get the ticket to fit within the length limit]

> marker change #116:13949 position 699,385.7,104.1

> marker change #116:13238 position 699,387.9,102.1

> marker change #116:13030 position 697.2,383,101.1

> marker change #116:13391 position 697.7,383.1,102.2

> marker change #116:14430 position 697.2,383.9,105.1

> marker change #116:14936 position 695.4,381,106

> marker change #116:11126 position 700.2,391.5,96.18

> marker change #116:10058 position 699.5,393.8,93.15

> marker change #116:9111 position 700.4,394.2,90.31

> marker change #116:7972 position 700.8,395.3,87.38

> marker change #116:7491 position 703.2,396,86.25

> marker change #116:8165 position 703,395.8,87.19

> marker change #116:8691 position 701.2,396.8,89.23

> marker change #116:9300 position 701.1,395.8,91.22

> marker change #116:9775 position 701.3,394.8,92.24

> marker change #116:10295 position 702.6,396.2,94.21

> marker change #116:10616 position 700.8,394.7,95.32

> marker change #116:11051 position 701.6,394.8,96.3

> marker change #116:11102 position 702.6,394.8,96.17

> marker change #116:11388 position 699.6,392.8,97.03

> marker change #116:10058 position 700.8,393.1,93.21

> marker change #116:11908 position 700.7,392.8,98.19

> marker change #116:12098 position 699.1,391.1,99.14

> marker change #116:11779 position 700.6,390.3,98.36

> marker change #116:8359 position 702.2,398,88.14

> marker change #116:8909 position 701.7,398.5,89.14

> marker change #116:9376 position 701.4,397.9,91.16

> marker change #116:8691 position 702.2,395.7,89.21

> marker change #116:7972 position 701.8,394.6,87.41

> marker change #116:10661 position 701.4,396.1,95.04

> marker change #116:12557 position 699.8,390.8,100.1

> marker change #116:7940 position 702.9,400.1,87.26

> marker change #116:876 position 702.9,399.7,67.48

> marker change #116:1692 position 703.2,401,70.13

> marker change #116:7493 position 704.1,399.4,83.17

> marker change #116:7442 position 703.8,401.1,83.37

> marker change #116:8280 position 702.6,400.2,86.56

> marker change #116:8359 position 703.5,397.4,87.01

> marker change #116:8692 position 702.6,400.3,87.69

> marker change #116:8880 position 703.5,400.2,87.62

> marker change #116:7783 position 703.9,401.3,84.52

> marker change #116:7154 position 703.9,402.5,84.16

> marker change #116:8053 position 703.5,401.1,85.56

> marker change #116:9026 position 702.9,398.8,88.13

> marker change #116:9407 position 702.5,399.3,89.73

> marker change #116:9807 position 702.6,398.5,90.75

> marker change #116:7933 position 703.5,401.7,86.49

> marker change #116:5547 position 702,394.7,80.02

> marker change #116:6067 position 702.1,396.7,80.85

> marker change #116:5005 position 701.9,397.7,77.46

> marker change #116:7160 position 703.6,387.5,84.01

> marker change #116:8621 position 695,376.9,88.61

> marker change #116:10880 position 688.5,372.8,94.44

> marker change #116:11838 position 687.8,373.3,97.75

> marker change #116:12853 position 691.4,376.4,101

> marker change #116:14965 position 686.2,374.4,106

> marker change #116:14320 position 686.8,373.6,101.6

> marker change #116:14965 position 686.8,374.4,104.9

> marker change #116:15333 position 690.2,377,104.8

> marker change #116:14806 position 693.3,379,105

> marker change #116:10010 position 700,392.2,92.69

> marker change #116:10616 position 700.5,393.5,93.16

> marker change #116:11263 position 698.2,389.9,94.43

> marker change #116:11388 position 701.2,392.9,94.62

> marker change #116:5046 position 700.8,391.3,77.02

> show #!12 models

> marker change #116:14222 position 696,372.6,101.9

> marker change #116:15806 position 693.7,374.2,106.1

> marker change #116:15057 position 695.9,375.4,105.3

> marker change #116:15763 position 697.2,375.7,106.9

> marker change #116:17299 position 696.5,377.7,110.8

> marker change #116:15748 position 699.1,378.7,105.7

> marker change #116:15748 position 698.9,378.8,105.5

> marker change #116:17758 position 701.5,378.6,111.9

> marker change #116:18160 position 695.1,377,109

> ui tool show "Side View"

> marker change #116:10801 position 683.1,368.9,94.18

> marker change #116:10801 position 683,367.8,93.89

> marker change #116:10390 position 679.8,367.6,92.68

> marker change #116:9589 position 679.5,367.5,90.14

> marker change #116:9007 position 679.6,367.5,88.62

> marker change #116:9086 position 679,367.4,89.28

> marker change #116:8809 position 678.1,366.7,88.27

> marker change #116:9914 position 678.4,368.7,91.02

> marker change #116:9914 position 678.6,368.2,90.88

> marker change #116:9914 position 678.3,367.2,90.62

> marker change #116:9641 position 677.1,367,91.35

> marker change #116:9641 position 677.2,366.5,91.21

> marker change #116:9914 position 678.4,366.3,90.37

> marker change #116:10463 position 678.1,367.9,93.18

> marker change #116:11216 position 681.3,368.4,95.44

> marker change #116:11216 position 681.4,368,95.33

> marker change #116:11636 position 683.9,369.5,96.34

> marker change #116:10598 position 685.9,369.7,93.32

> marker change #116:10036 position 687,371,90.19

> marker change #116:11244 position 686.4,371.1,95.23

> marker change #116:10880 position 689,372.3,94.27

> marker change #116:9846 position 689.5,372.1,89.19

> select #116

49661 atoms, 1 model selected  

> marker change sel radius 1

> ui mousemode right select

> select clear

Drag select of 1312 atoms  

> delete sel

Drag select of 301 atoms  

> delete sel

Drag select of 32 atoms  

> delete sel

Drag select of 88 atoms  

> delete sel

Drag select of 15 atoms  

> delete sel

Drag select of 451 atoms  

> delete sel

Drag select of 283 atoms  

> delete sel

Drag select of 21 atoms  

> delete sel

Drag select of 177 atoms  

> delete sel

Drag select of 647 atoms  

> delete sel

Drag select of 179 atoms  

> delete sel

Drag select of 70 othermem19.cmp , 123 atoms  

> select clear

Drag select of 145 atoms  

> delete sel

Drag select of 44 atoms  

> delete sel

Drag select of 442 atoms  

> delete sel

Drag select of 42 atoms  

> delete sel

Drag select of 204 atoms  

> delete sel

Drag select of 74 atoms  

> delete sel

Drag select of 527 atoms  

> delete sel

Drag select of 163 atoms  

> delete sel

Drag select of 234 atoms  

> delete sel

Drag select of 315 atoms  

> delete sel

Drag select of 217 atoms  

> delete sel

Drag select of 64 atoms  

> delete sel

Drag select of 548 atoms  

> delete sel

Drag select of 17 atoms  

> delete sel

Drag select of 5 atoms  

> delete sel

Drag select of 32 atoms  

> delete sel

Drag select of 49 atoms  
Drag select of  

> delete sel

Drag select of 33 atoms  

> delete sel

Drag select of 5 atoms  

> delete sel

Drag select of 14 atoms  

> delete sel

Drag select of 754 atoms  

> delete sel

Drag select of 246 atoms  

> delete sel

Drag select of 64 atoms  

> delete sel

Drag select of 19 atoms  

> delete sel

Drag select of 150 atoms  

> delete sel

Drag select of 368 atoms  

> delete sel

Drag select of 424 atoms  

> delete sel

Drag select of 149 atoms  

> delete sel

Drag select of 68 atoms  

> delete sel

Drag select of 96 atoms  

> delete sel

Drag select of 62 atoms  

> delete sel

Drag select of 86 atoms  

> delete sel

Drag select of 28 atoms  

> delete sel

Drag select of 28 atoms  

> delete sel

Drag select of 32 atoms  

> delete sel

Drag select of 538 atoms  

> delete sel

Drag select of 26 atoms  

> delete sel

Drag select of 18 atoms  

> delete sel

Drag select of 13 atoms  

> delete sel

Drag select of 313 atoms  

> delete sel

Drag select of 179 atoms  

> delete sel

Drag select of 129 atoms  

> delete sel

Drag select of 64 atoms  

> delete sel

Drag select of 32 atoms  

> delete sel

Drag select of 29 atoms  

> delete sel

Drag select of 114 atoms  

> delete sel

Drag select of 116 atoms  

> delete sel

Drag select of 114 atoms  

> delete sel

Drag select of 24 atoms  

> delete sel

Drag select of 33 atoms  

> delete sel

Drag select of 13 atoms  

> delete sel

Drag select of 48 atoms  

> delete sel

Drag select of 7 atoms  

> delete sel

Drag select of 10 atoms  

> delete sel

Drag select of 11 atoms  

> delete sel

Drag select of 13 atoms  

> delete sel

Drag select of 7 atoms  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 4 atoms  

> delete sel

Drag select of 14 atoms  

> delete sel

Drag select of 2 atoms  
Drag select of 5 atoms  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 13 atoms  

> delete sel

> select #116

38518 atoms, 1 model selected  

> molmap sel 5 gridSpacing 3

> hide #116 models

> ~select #116

Nothing selected  

> volume #117 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8

> volume #117 level 0.0119

> volume #117 level 0.007234

> volume #117 color #20ffff

> hide #!101 models

> show #!101 models

> volume #101 level 0.001711

> volume #101 level 0.006845

> volume #101 level 0.003423

> show #103 models

> hide #103 models

> show #!2 models

> hide #!2 models

> show #1 models

> close #101

> hide #!4 models

> hide #!14 models

> show #!14 models

> show #!16 models

> hide #!16 models

> close #16

> hide #!14 models

> show #!14 models

> hide #!109 models

> hide #!10 models

> show #!10 models

> hide #!8 models

> show #!8 models

> hide #!22 models

> hide #!34 models

> hide #!36 models

> show #!36 models

> hide #!46 models

Drag select of 231 atoms  

> delete sel

Drag select of 77 atoms  

> delete sel

Drag select of 10 atoms  

> delete sel

> show #!46 models

> hide #!110 models

> hide #!111 models

> show #!111 models

> hide #!113 models

> show #!113 models

> hide #!94 models

Drag select of 41 atoms  

> delete sel

> show #!94 models

> show #!96 models

> show #!102 models

> show #!110 models

> show #!109 models

> show #!34 models

> show #!22 models

> select #1

31115 atoms, 1 model selected  

> molmap sel 5 gridSpacing 3

> volume #16 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8

> ~select #1

Nothing selected  

> hide #1 models

> volume #16 level 0.003678

> volume #16 color #b4a1de

> volume #16 color #7d7099

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/postsyn_final_no_overlap.cmp
> format cmap models #16

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/postsyn_final_no_overlap.cmm
> format markers models #1

Wrote 1 marker sets containing 31115 markers  

> show #!6 models

> hide #!6 models

> close #6

> save /Users/bs15ml/segmentations/ML-19A_TS_07/circularmem_final_1.cmp format
> cmap models #115

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 157, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3910, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 313, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/cmap/write_cmap.py", line 81, in
write_grid_as_chimera_map  
h5file = tables.open_file(path, mode = mode)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tables/file.py", line 315, in open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tables/file.py", line 778, in __init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 374, in tables.hdf5extension.File._g_new  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tables/utils.py", line 172, in check_file_access  
raise IOError("``%s`` does not exist" % (parentname,))  
OSError: ``/Users/bs15ml/segmentations/ML-19A_TS_07`` does not exist  
  
OSError: ``/Users/bs15ml/segmentations/ML-19A_TS_07`` does not exist  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/tables/utils.py", line 172, in check_file_access  
raise IOError("``%s`` does not exist" % (parentname,))  
  
See log for complete Python traceback.  
  

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/circularmem_final_1.cmp
> format cmap models #115

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/circularmem_final_2.cmp
> format cmap models #113

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/circularmem_final_2.cmp
> format markers models #112

Wrote 1 marker sets containing 296126 markers  

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/circularmem_final_1.cmp
> format markers models #114

Wrote 1 marker sets containing 117938 markers  

> hide #!117 models

> show #!117 models

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/possiblemem_final.cmm format
> markers models #116

Wrote 1 marker sets containing 38518 markers  

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/possiblemem_final.cmp format
> cmap models #117

> show #!2 models

> hide #!2 models

> close #2

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!14 models

> show #!14 models

> hide #!16 models

> show #!16 models

> hide #!117 models

> show #!117 models

No known data format for file suffix '.csx'  

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/figure_full.cxs includeMaps
> true

> save /Users/bs15ml/segmentations/ML-19A_TS_07_2/figure_full.cxs includeMaps
> true

opened ChimeraX session  

> hide #!113 models

> show #!113 models

> hide #!113 models

> show #!113 models

> hide #!113 models

> show #!113 models

> hide #!113 models

> show #!113 models

> hide #!113 models

> hide #!115 models

> show #!115 models

> show #!113 models




OpenGL version: 4.1 INTEL-12.10.14
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini8,1
      Processor Name: Intel Core i3
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 8 GB
      Boot ROM Version: 1037.40.124.0.0 (iBridge: 17.16.11081.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G1012)
      Kernel Version: Darwin 18.7.0
      Time since boot: 3:06

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        PL2483H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1156292263700
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No
          Adapter Firmware Version:  2.0a

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

Reported by Megan Lovatt