Mottled ribbons

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-13)
Description
Hi,

Ribbons look kind of odd and mottled when used with soft lighting. This is generally not an issue, except when ribbons and surfaces are combined - e.g. looking at a peptide binding in na groove, or havinf a single subunit in ribbon with the rest in surface. Is there any way to make ambient occlusion play nicer with ribbon models? 

Cheers
Oli

Log:
> camera ortho

> lighting soft

> set bgColor white

> lighting depthCueColor white

> cofr centerOfView

UCSF ChimeraX version: 0.9 (2019-03-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/oliverclarke/Dropbox/Documents/Work/Projects/RyR/Structures_and_maps/ryr_maps_paper2/paper2_maps/ca30/refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc

Opened
refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc,
grid size 400,400,400, pixel 1.25, shown at level 0.0284, step 2, values
float32  

> close all

> open 3ch3

3ch3 title:  
Crystal Structure Analysis of SERA5E from plasmodium falciparum [more info...]  
  
Chain information for 3ch3 #1  
---  
Chain | Description  
X | Serine-repeat antigen protein  
  
Non-standard residues in 3ch3 #1  
---  
2HP — dihydrogenphosphate ion  
  
  

> surface #1

> measure convexity #1

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> select up

Nothing selected  

> measure convexity #1 palette rdylbu-5

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> measure convexity #1 palette ylgnbu-5

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> close all

> open /Users/oliverclarke/Dropbox/best_new_4cmc_combined_pixcorr.mrc

Opened best_new_4cmc_combined_pixcorr.mrc, grid size 512,512,512, pixel 1.06,
shown at level 0.0133, step 2, values float32  

> measure convexity #1 palette ylgnbu-5

Convexity -4.85 - 6.28, mean 0.982, std deviation 1.33 at 2122386 vertices of
level 0.01326 1.1  

> surface dust #1 size 20

Unknown command: 100  

> surface dust #1 size 100

> surface dust #1 size 20

> measure convexity #1 palette ylgnbu-5

Convexity -4.42 - 5.05, mean 1.07, std deviation 0.856 at 1432972 vertices of
level 0.01879 1.1  

> set bgColor black

> measure convexity #1 palette ylgnbu-5

Convexity -4.42 - 5.05, mean 1.07, std deviation 0.856 at 1432972 vertices of
level 0.01879 1.1  

> help alias

> toolshed show '"Side View"'

> close all

> open 3ch3

3ch3 title:  
Crystal Structure Analysis of SERA5E from plasmodium falciparum [more info...]  
  
Chain information for 3ch3 #1  
---  
Chain | Description  
X | Serine-repeat antigen protein  
  
Non-standard residues in 3ch3 #1  
---  
2HP — dihydrogenphosphate ion  
  
  

> surface dust #1 size 20

No surfaces specified  

> surface #1

> measure convexity #1 palette ylgnbu-5

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> measure convexity #1 palette ylgnbu-5 smoothingIterations 10

Convexity -0.901 - 1.09, mean -0.0354, std deviation 0.328 at 159015 vertices
of 3ch3_X SES surface 1.3  

> measure convexity #1 palette ylgnbu-5 smoothingIterations 100

Convexity -0.78 - 0.561, mean -0.0105, std deviation 0.218 at 159015 vertices
of 3ch3_X SES surface 1.3  

> open 1bl8

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #2  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> close #1

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10

> surface #2

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 50

Convexity -0.555 - 0.612, mean 0.0398, std deviation 0.202 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.593 - 0.674, mean 0.0366, std deviation 0.204 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.577 - 0.64, mean 0.0408, std deviation 0.202 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.624 - 0.635, mean 0.038, std deviation 0.204 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 1

Convexity -1.32 - 2.13, mean -0.00213, std deviation 0.43 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -1.32 - 1.9, mean -0.00612, std deviation 0.435 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -1.37 - 2.16, mean -0.00135, std deviation 0.434 at 67241 vertices
of 1bl8_C SES surface 2.4  
Convexity -1.24 - 1.58, mean -0.00412, std deviation 0.433 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 5

Convexity -0.866 - 1.18, mean 0.00647, std deviation 0.355 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.923 - 1.24, mean 0.0028, std deviation 0.358 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.955 - 1.23, mean 0.0072, std deviation 0.356 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.967 - 1.2, mean 0.00433, std deviation 0.358 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 1,-1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 10,-10

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 2,-2

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> lighting soft

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 2,-1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 1,-1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -1,1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -2,2

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -1.5,1.5

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> set bgColor white

> lighting depthCueColor white

> select up

Nothing selected  

> select up

Nothing selected  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -1,1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> hide #!2.1 models

> show #!2.1 models

> hide #!2.2 models

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting gentle

> lighting soft

> lighting full

> show #!2.2 models

> lighting soft

> measure convexity #2 palette blues-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  
Fetching compressed palette YlOrRd-9 from
http://www.colourlovers.com/api/palettes?keywords=YlOrRd-9&format=json&numResults=100  

> measure convexity #2 palette ylorrd-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

Expected a keyword  

> measure convexity #2 palette ylorrd-6 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd-8 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd-3 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette blues-9 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette blues-3 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette blues-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-9 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-9 smoothingIterations 50 range -1,1

Convexity -0.555 - 0.612, mean 0.0398, std deviation 0.202 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.593 - 0.674, mean 0.0366, std deviation 0.204 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.577 - 0.64, mean 0.0408, std deviation 0.202 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.624 - 0.635, mean 0.038, std deviation 0.204 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-9 smoothingIterations 40 range -1,1

Convexity -0.59 - 0.674, mean 0.0367, std deviation 0.219 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.62 - 0.733, mean 0.0335, std deviation 0.222 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.603 - 0.699, mean 0.0377, std deviation 0.219 at 67241 vertices
of 1bl8_C SES surface 2.4  
Convexity -0.653 - 0.702, mean 0.035, std deviation 0.221 at 67443 vertices of
1bl8_D SES surface 2.5  

> lighting full

> close all

> open 1bl8

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> rainbow palette rdylbu-9

> surface #1

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.4 models

> lighting soft




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: Screen Shot 2019-03-14 at 11.33.49 AM.png

Screen Shot 2019-03-14 at 11.33.49 AM.png​

[olibclarke@…]

Added by email2trac

[Elaine Meng]

This may well be soft lighting.  The depth parameter is appropriate for big structures/surfaces and is not good for ribbons.  I’ve seen “smudgy”-looking ribbons and tube helices with soft lighting mode.  Try “light gentle” or light settings without ambient shadows.

[olibclarke@…]

Hi Elaine - yes it is soft lighting. That’s what I was wondering - soft lighting is great for surfaces, not so good for ribbons, I was wondering if there is a way to make it better for situations where you have both ribbons and surfaces displayed.

Cheers
Oli

[Elaine Meng]

As mentioned, you could try “light gentle” but there is no way to use different multishadow parameters on objects with detail at different scales (e.g. surfaces vs. ribbons.  You may be able to fiddle a compromise (see msDepthBias in the lighting manpage) but it wouldn’t give optimal appearance for all scales at the same time.  

[Tom Goddard]

ChimeraX ambient occlusion is an approximation. To compute ambient shadows correctly light needs to be cast from every direction (an infinity of directions). ChimeraX approximates this using typically 64 directions. With 64 directions you actually see smudgy shadows from the individual lights if your scene lets light filter through, ie is mostly open space, as with a ribbon depiction. For this reason I recommend not using ambient lighting with ribbons. If you really want to work hard to get a better depiction for say making a figure you can start fiddling with the ambient shadow parameters, the multiShadow option of the lighting command will let you increase the number of light directions (e.g to 128, 256, 512...) and two other parameters msMapSize controls the coarseness of individual shadows, and msDepthBias limit self-shadowing artifacts.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html

If you use more light directions rendering will of course be slower, 512 directions with render about 8 times slower than 64 directions. I spent hundreds of hours figuring out the best defaults for the ambient shadows, and can tell you that it ranges from hard to impossible to find settings that make sparse scenes look good.

[Tom Goddard]

An enhancement that would help your case of surface plus ribbon is to allow turning off ambient shadows for specific models. Since the surface is a submodel of the structure it would require being able to turn off ambient shadows for a parent model, while leaving it on for a child model. This should be possible, and has other uses such as ambient shadows on a surface, with no shadows on a bound ligand in a pocket shown as stick. Another ticket can be made asking per-model shadow disabling if desired.

[olibclarke@…]

Yes that is exactly the kind of case I am thinking of! Ok I will make another ticket for that, and in the meantime just use a vector graphics program to layer the images (with transparent backgrounds, different lighting and shadows on/off)

Oli