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#3838 closed defect (wontfix)

Multiple layers of transparency

Reported by:	Tom Goddard	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:	bs15ml@leeds.ac.uk	Platform:	all
Project:	ChimeraX

Description (last modified by pett)

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

Attachments (1)

emd1080_3_layers.png (753.9 KB ) - added by Tom Goddard 3 years ago.: 3 layers of transparency rendered in Chimera 1.16

Download all attachments as: .zip

Change History (5)

comment:1 by pett, 5 years ago

Component:	Unassigned → Graphics
Description:	modified (diff)
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Multiple layers of transparency

Reported by Megan Lovatt

comment:2 by Tom Goddard, 5 years ago

Resolution:	→ wontfix
Status:	assigned → closed

Unfortunately ChimeraX graphics is not able to correctly show 2 or more transparent layers. This is discussed on the ChimeraX mailing list

http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html

It is hard to render multiple transparent layers, requiring slow and complex code to depth sort all triangles or ray tracing, neither of which we have the resources to implement.

One solution is to use mesh style for the outer or middle layer and opaque for the innermost layer.

comment:3 by Tom Goddard, 3 years ago

Notify when closed:	→ bs15ml@leeds.ac.uk
Reporter:	changed from bs15ml@… to Tom Goddard

Chimera was able to display multiple layers of transparency within a single surface model by depth sorting the triangles. This was an option in Chimera Viewing Controls / Effects called "single-layer" transparency -- default on, but off meant multi-layer transparency

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects

It was slow to rotate large models because the triangles need to be sorted by depth for each view angle. And it can give incorrect appearance when it does not get the sort depth right (I think it uses the depth of the center of each triangle). It was not very difficult to implement but visually the appearance is so confusing that I have never seen a useful image made with it. It would probably help if back facing triangles were eliminated. I've attached an image of map emdb 1080 with 3 transparent layers at different thresholds as an example.

by Tom Goddard, 3 years ago

Attachment:	emd1080_3_layers.png added

3 layers of transparency rendered in Chimera 1.16

comment:4 by Tom Goddard, 3 years ago

Another more general way to handle multiple transparent layers is with "depth peeling" where multiple rendering passes are done for each successive layer. I think it is too complicated and too rarely useful to be worth the time to implement it and maintain it.

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