Opened 4 years ago

Closed 4 years ago

#5497 closed defect (fixed)

Graphics presets don't reset depthJump

Reported by: jrf296@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc: pett, Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Dear ChimeraX Team,

I've always had an issue where I get dark black shadows on the edges of models after using cetrain settings. I recently figured out this is due to the  silhouettes depthJump changing to .01 with the flat setting then that value persisting when switching back to other presets. Is this correct? It doesn't appear that there's a way to change that value back to defualt through the GUI presets. 

Best,

Ryan

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/rabinterface1.cxs"

Opened composite59_split2split1.mrc as #4, grid size 196,196,196, pixel 1.25,
shown at level 13, step 1, values float32  
Opened composite59_split2split2.mrc as #5, grid size 196,196,196, pixel 1.25,
shown at level 6.94, step 1, values float32  
Opened composite59_split1plus.mrc as #7, grid size 196,196,196, pixel 1.25,
shown at level 4.64, step 1, values float32  
Log from Thu Oct 28 11:48:52 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/density_coloringv7.cxs"

Opened composite59_split2split1.mrc as #4, grid size 196,196,196, pixel 1.25,
shown at level 13, step 1, values float32  
Opened composite59_split2split2.mrc as #5, grid size 196,196,196, pixel 1.25,
shown at level 6.94, step 1, values float32  
Opened composite59_split1plus.mrc as #7, grid size 196,196,196, pixel 1.25,
shown at level 4.64, step 1, values float32  
Log from Thu Oct 28 11:33:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/density_coloringv4.cxs"

Opened composite59_split2split1.mrc as #4, grid size 196,196,196, pixel 1.25,
shown at level 13, step 1, values float32  
Opened composite59_split2split2.mrc as #5, grid size 196,196,196, pixel 1.25,
shown at level 7.51, step 1, values float32  
Opened composite59_split1.mrc as #6, grid size 196,196,196, pixel 1.25, shown
at level 5.62, step 1, values float32  
Log from Thu Oct 14 12:07:02 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Volumes/GoogleDrive/My Drive/RRYfigs/density_coloringv3.cxs"

Opened composite59_split2split1.mrc as #4, grid size 196,196,196, pixel 1.25,
shown at level 11.5, step 1, values float32  
Opened composite59_split2split2.mrc as #5, grid size 196,196,196, pixel 1.25,
shown at level 5.48, step 1, values float32  
Opened composite59_split1.mrc as #6, grid size 196,196,196, pixel 1.25, shown
at level 4.68, step 1, values float32  
Log from Wed Oct 13 16:16:03 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/GoogleDrive/My Drive/Maps/Rgp1final.pdb"
> "/Volumes/GoogleDrive/My Drive/Maps/Ric1final.pdb" "/Volumes/GoogleDrive/My
> Drive/Maps/Ypt6final.pdb"

Summary of feedback from opening /Volumes/GoogleDrive/My
Drive/Maps/Rgp1final.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 MET A 106
GLU A 111 1 6  
Start residue of secondary structure not found: HELIX 2 2 ASN A 169 TYR A 176
1 8  
Start residue of secondary structure not found: HELIX 3 3 SER A 545 LEU A 547
1 3  
Start residue of secondary structure not found: HELIX 4 4 ILE A 709 VAL A 711
1 3  
Start residue of secondary structure not found: HELIX 5 5 PRO A 713 LYS A 715
1 3  
78 messages similar to the above omitted  
  
Summary of feedback from opening /Volumes/GoogleDrive/My
Drive/Maps/Ric1final.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 18 18 GLN B
44 GLU B 46 1 3  
Start residue of secondary structure not found: HELIX 19 19 TYR B 126 HIS B
128 1 3  
Start residue of secondary structure not found: HELIX 20 20 ARG B 380 VAL B
389 1 10  
Start residue of secondary structure not found: HELIX 21 21 ILE B 399 GLY B
408 1 10  
Start residue of secondary structure not found: HELIX 22 22 ARG B 454 SER B
458 1 5  
36 messages similar to the above omitted  
  
Summary of feedback from opening /Volumes/GoogleDrive/My
Drive/Maps/Ypt6final.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 MET A 106
GLU A 111 1 6  
Start residue of secondary structure not found: HELIX 2 2 ASN A 169 TYR A 176
1 8  
Start residue of secondary structure not found: HELIX 3 3 SER A 545 LEU A 547
1 3  
Start residue of secondary structure not found: HELIX 4 4 ILE A 709 VAL A 711
1 3  
Start residue of secondary structure not found: HELIX 5 5 PRO A 713 LYS A 715
1 3  
95 messages similar to the above omitted  
  
Chain information for Rgp1final.pdb #1  
---  
Chain | Description  
B | No description available  
  
Chain information for Ric1final.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for Ypt6final.pdb #3  
---  
Chain | Description  
C | No description available  
  

> open "/Volumes/GoogleDrive/My Drive/Maps/ref1426composite_split1.mrc"

Opened ref1426composite_split1.mrc as #4, grid size 196,196,196, pixel 1.25,
shown at level 2.36, step 1, values float32  

> open "/Volumes/GoogleDrive/My Drive/Maps/ref1426composite_split2.mrc"

Opened ref1426composite_split2.mrc as #5, grid size 196,196,196, pixel 1.25,
shown at level 0.0021, step 1, values float32  

> volume #5 level 3.946

> volume #4 level 7.867

> open /Users/jfeath6971/Downloads/composite59_split2.mrc

Opened composite59_split2.mrc as #6, grid size 196,196,196, pixel 1.25, shown
at level 0.00763, step 1, values float32  

> open /Users/jfeath6971/Downloads/composite59_split1.mrc

Opened composite59_split1.mrc as #7, grid size 196,196,196, pixel 1.25, shown
at level 0.763, step 1, values float32  

> close #4

> close #5

> volume #6 level 4.366

> volume #7 level 5.387

> volume #6 level 13.98

> volume #6 level 11.43

> volume #7 level 3.075

> ui tool show "Surface Zone"

> surface zone #7 nearAtoms #1 distance 5.24

> surface zone #7 nearAtoms #1 distance 5.24

> surface unzone #7

> surface zone #7 nearAtoms 1,2,3 distance 5

Invalid "nearAtoms" argument: invalid atoms specifier  

> surface zone #7 nearAtoms #1,2,3 distance 5

> surface zone #7 nearAtoms #1,2,3 distance 4

> surface zone #7 nearAtoms #1,2,3 distance 3.5

> volume #7 level 3.775

> color zone #1 near #1,2,3 distance 4

> color zone #6,7 near #1,2,3 distance 4

> color zone #6,7 near #1,2,3 distance 4

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting simple

> lighting soft

> lighting full

> lighting soft

> ui tool show "Hide Dust"

> surface dust #6 size 1.61

> surface dust #6 size 1.53

> surface dust #6 size 2.14

> surface dust #6 size 2.14

> surface dust #6 size 2.18

> surface dust #6 size 2.45

> surface dust #6 size 4

> surface dust #7 size 3.67

> surface dust #7 size 3.43

> surface dust #7 size 4.06

> surface zone #7 nearAtoms #1,2,3 distance 3.5

> surface dust #7 size 3.1

> surface dust #7 size 40.19

> surface dust #7 size 41.57

> surface dust #7 size 2.49

> color zone #6,7 near #1,2,3 distance 4

> surface zone #7 nearAtoms #1,2,3 distance 3.5

> surface zone #7 nearAtoms #1,2,3 distance 3

> surface zone #7 nearAtoms #1,2,3 distance 3.5

> hide #!1 models

> hide #!2 models

> hide #!3 models

> volume #7 level 5.316

> volume #7 level 5.036

> volume #6 level 13.9

> volume #6 level 7.406

> volume #6 level 14.06

> close #6

> close #7

> open "/Volumes/GoogleDrive/My Drive/Maps/composite59_split2split1.mrc"

Opened composite59_split2split1.mrc as #4, grid size 196,196,196, pixel 1.25,
shown at level 0.00763, step 1, values float32  

> open "/Volumes/GoogleDrive/My Drive/Maps/composite59_split2split2.mrc"

Opened composite59_split2split2.mrc as #5, grid size 196,196,196, pixel 1.25,
shown at level 0.00262, step 1, values float32  

> open /Users/jfeath6971/Downloads/composite59_split1.mrc

Opened composite59_split1.mrc as #6, grid size 196,196,196, pixel 1.25, shown
at level 0.763, step 1, values float32  

> volume #6 level 10.57

> volume #5 level -0.2255

> volume #4 level 3.721

> volume #5 level 1.143

> volume #4 level 16.1

> volume #5 level 5.763

> volume #4 level 12.39

> volume #4 level 16.1

> volume #6 level 8.466

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> volume #5 level 7.816

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> volume #6 level 7.205

> color zone #5,6,7 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> volume #6 level 5.244

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/density_coloring.cxs"
> includeMaps true

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 dust #4,5,6 size 3

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 surface dust #4,5,6 size 3

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> surface zone,dust #4,5,6 near #1,2,3 distance 3.5

Expected an atoms specifier or a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 dust

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> ui tool show "Hide Dust"

> surface dust #4 size 3.16

> surface dust #5 size 3.55

> surface dust #6 size 7.5

> surface dust #6 size 7.45

> surface dust #6 size 3.1

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> surface dust #6 size 3.1

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/density_coloringv2.cxs"
> includeMaps true

> volume #4 level 13.01

> volume #5 level 5.021

> volume #4 level 11.92

> volume #5 level 4.337

> volume #5 level 5.478

> volume #4 level 11.46

> volume #6 level 6.225

> volume #6 level 4.684

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> color chain #1 #fdcdac

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color bychain #1 #fdcdac

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1 #fdcdac

> color #3 #b3e2cd

> color #2 #cbd5e8

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> color zone #5,6,4 near #1,2,3 distance 4

> color #2 cornflowerblue

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> color zone #5,6,4 near #1,2,3 distance 4

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 newmap true

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 Newmap true

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 NewMap true

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 New Map true

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 newmap

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 new

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 map

Expected a keyword  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update false

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/density_coloringv3.cxs"
> includeMaps true

——— End of log from Wed Oct 13 16:16:03 2021 ———

opened ChimeraX session  

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update true

> volume #4 level 14.56

> volume #5 level 6.24

> volume #6 level 7.648

> volume #6 level 6.4

> volume #6 level 4.84

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.4 update true

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.5 update true

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.4 update true

> color zone #5,6,4 near #1,2,3 distance 3.4

> color zone #5,6,4 near #1,2,3 distance 3.6

> color zone #5,6,4 near #1,2,3 distance 3.8

> color zone #5,6,4 near #1,2,3 distance 3

> color zone #5,6,4 near #1,2,3 distance 3.5

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> show #!2 models

> show #!6 models

> hide #!4 models

> show #!4 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> volume #6 level 7.18

> hide #!4 models

> show #!4 models

> hide #!2 models

> volume #6 level 5.62

> volume #4 level 12.84

> volume #4 level 13.01

> volume #5 level 7.51

> surface zone #4,5,6 nearAtoms #1,2,3 distance 3.4 update true

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/density_coloringv4.cxs"
> includeMaps true

——— End of log from Thu Oct 14 12:07:02 2021 ———

opened ChimeraX session  

> open "/Volumes/GoogleDrive/My Drive/Maps/composite59_split1plus.mrc"

Opened composite59_split1plus.mrc as #7, grid size 196,196,196, pixel 1.25,
shown at level 0.000295, step 1, values float32  

> volume #7 level 5.182

> volume #7 level 5.042

> volume #7 level 5.602

> volume #7 level 5.62

> close #6

> color zone #5,7,4 near #1,2,3 distance 3.5

> volume #7 level 4.5

> volume #7 level 5.06

> volume #4 level 15.95

> volume #4 level 13.32

> volume #5 level 6.54

> ui tool show "Hide Dust"

> surface dust #4 size 7.5

> surface dust #4,5,7 update false size 5

> surface dust #4,5,7 update false size 3

> surface dust #4,5,7 update false size 4

> surface dust #4,5,7 update false size 3

> color zone #5,7,4 near #1,2,3 distance 3.6

> color zone #5,7,4 near #1,2,3 distance 3.7

> color zone #5,7,4 near #1,2,3 distance 4

> volume #4 color #336699

> volume #4 color #003366

> volume #4 color #6699cc

> color zone #5,7,4 near #1,2,3 distance 4

> surface dust #4,5,7 update false size 5

> surface dust #4,5,7 update false size 4

> surface dust #4,5,7 update false size 5

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color #1 #91c8e8

> color #1 #91c8e8

> color #2 #e8b0b9

> color #3 #b8d7ad

> color zone #5,7,4 near #1,2,3 distance 4

> color #2 #cfbcd5

> color #1 #d6cdae

> color #3 #a3d5d3

> color zone #5,7,4 near #1,2,3 distance 4

> color #2 #b9c3e1

> color #1 #e3c0b1

> color #3 #b4d7c1

> color zone #5,7,4 near #1,2,3 distance 4

> color #3 #a3cf6a

> color #1 #df9b8d

> color #2 #a3cf6a

> color #2 #a3b5d5

> color zone #5,7,4 near #1,2,3 distance 4

> color #3 #92be60

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> volume #5 level 6.94

> volume #4 level 13.01

> volume #7 level 3.099

> volume #7 level 4.64

> surface dust #4,5,7 update false size 4

> surface dust #4,5,7 update false size 4

> surface dust #4,5,7 update false size 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/density_coloringv5.cxs"
> includeMaps true

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color #3 #fabb4a

> color #2 #2553aba

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #2 #553aba

> color #1 #fabb4a

> color zone #5,7,4 near #1,2,3 distance 4

> color #1 #ed2f40

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> lighting simple

> lighting soft

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting simple

> lighting soft

> lighting soft

> lighting full

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting soft

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> save /Users/jfeath6971/Desktop/image304.png supersample 3

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> save /Users/jfeath6971/Desktop/image305.png supersample 3

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 4

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/density_coloringv6.cxs"
> includeMaps true

> save /Users/jfeath6971/Desktop/image306.png supersample 3

> save /Users/jfeath6971/Desktop/image307.png supersample 3

> save /Users/jfeath6971/Desktop/image308.png supersample 3

> save /Users/jfeath6971/Desktop/image309.png supersample 3

> hide #!4 models

> hide #!5 models

> hide #!7 models

> show #!3 models

> show #!2 models

> show #!1 models

> cartoon style #1-3 modeHelix tube sides 20

> style sphere

Changed 23634 atom styles  

> surface #1-3

> hide #!1 models

> show #!1 models

> save /Users/jfeath6971/Desktop/image310.png supersample 3

> save /Users/jfeath6971/Desktop/image311.png supersample 3

> save /Users/jfeath6971/Desktop/image312.png supersample 3

> hide #1.2 models

> hide #2.2 models

> hide #3.2 models

> save /Users/jfeath6971/Desktop/image313.png supersample 3

> dssp #1,2,3 energyCutoff -.8

> dssp #1,2,3 energyCutoff -.3

> dssp #1,2,3 energyCutoff -.1

> dssp #1,2,3 energyCutoff -.4

> dssp #1,2,3 energyCutoff -.3

> dssp #1,2,3 energyCutoff 0

> dssp #1,2,3 energyCutoff -.4

> dssp #1,2,3 energyCutoff -.3

> save /Users/jfeath6971/Desktop/image314.png supersample 3

> lighting simple

> lighting simple

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> lighting simple

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> dssp #1,2,3 energyCutoff -.2

> dssp #1,2,3 energyCutoff -.5

> ui tool show "Side View"

> graphics silhouettes false

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting soft

> lighting full

> lighting flat

> lighting full

> graphics silhouettes false

> lighting soft

> save /Users/jfeath6971/Desktop/image315.png supersample 3

> graphics silhouettes true

> save /Users/jfeath6971/Desktop/image316.png supersample 3

> lighting full

> lighting soft

> lighting full

> save /Users/jfeath6971/Desktop/image317.png supersample 3

> save /Users/jfeath6971/Desktop/image318.png supersample 3

> save /Users/jfeath6971/Desktop/image319.png supersample 3

> lighting intensity 2

> lighting intensity 1.5

> lighting intensity 1.5

> lighting intensity .5

> lighting intensity .1

> lighting intensity .1

> lighting intensity 1

> lighting intensity 1.1

> lighting intensity 1

> lighting depthCueEnd 1

> lighting depthCueEnd .5

> lighting depthCueEnd .8

> lighting depthCueEnd .7

> lighting depthCueEnd .5

> lighting depthCueEnd .6

> lighting depthCueEnd .7

> lighting depthCueEnd .8

> lighting depthCueEnd .7

> lighting depthCueEnd .6

> lighting depthCueEnd .5

> lighting depthCueEnd .6

> graphics silhouettes false

> lighting depthCueEnd .7

> show #1.2 models

> hide #!1.2 models

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting intensity .1

> lighting intensity 1

> lighting soft

> graphics silhouettes true

> set depthcueend .5

Expected a keyword  

> lighting simple

> lighting soft

> lighting soft

> set depthcue start .3

Expected a keyword  

> lighting depthCue start .3

Invalid "depthCue" argument: Expected true or false (or 1 or 0)  

> lighting depthCueStart .3

> lighting depthCueEnd .9

> lighting depthCueEnd .8

> graphics silhouettes false

> color zone #5,7,4 near #1,2,3 distance 4

> show #!4 models

> show #!5 models

> show #!7 models

> close #1.2

> close #2.2

> close #3.2

> hide #!5 models

> hide #!4 models

> hide #!7 models

> show #!4 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> color zone #5,7,4 near #1,2,3 distance 4

> lighting depthCueStart .2

> lighting depthCueStart .0

> lighting depthCueStart .5

> graphics silhouettes true

> save /Users/jfeath6971/Desktop/image320.png supersample 3

> show #!4 models

> show #!5 models

> show #!7 models

> hide #!3 models

> hide #3.1 models

> hide #!1 models

> hide #!2 models

> color zone #5,7,4 near #1,2,3 distance 3.5

> save /Users/jfeath6971/Desktop/image321.png supersample 3

> ui tool show "Side View"

> save /Users/jfeath6971/Desktop/image322.png supersample 3

> show #!3 models

> show #!2 models

> show #!1 models

> hide #!4 models

> hide #!5 models

> hide #!7 models

> save /Users/jfeath6971/Desktop/image323.png supersample 3

> lighting msDepthBias .05

> lighting msDepthBias .01

> lighting qualityOfShadows fine

> lighting qualityOfShadows normal

> lighting msDepthBias 1

> lighting msDepthBias .001

> lighting msDepthBias .01

> lighting depthBias .01

> lighting depthBias .0005

> lighting depthBias .1

> lighting depthBias .005

> save /Users/jfeath6971/Desktop/image324.png supersample 3

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!7 models

> show #!5 models

> show #!4 models

> save /Users/jfeath6971/Desktop/image325.png supersample 3

> hide #!4 models

> hide #!5 models

> hide #!7 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!7 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> color zone #5,7,4 near #1,2,3 distance 4

> color zone #5,7,4 near #1,2,3 distance 3.5

> turn

> turn

> turn

> turn

> turn

> turn

> turn

> turn

> turn

> turn

> turn

> turn

> turn x

> turn x

> turn x

> turn x

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> save /Users/jfeath6971/Desktop/image326.png supersample 3

> turn

> turn

> turn

> save /Users/jfeath6971/Desktop/image327.png supersample 3

> turn

> turn y

> turn y

> turn y

> turn y

> turn x

> turn x

> turn x

> save /Users/jfeath6971/Desktop/image328.png supersample 3

> hide #!4 models

> hide #!5 models

> hide #!7 models

> show #!1 models

> show #!2 models

> show #!3 models

> hide #!1 models

> quality of shadows finer

Unknown command: quality of shadows finer  

> qualityofshadows finer

Unknown command: qualityofshadows finer  

> qualityOfShadows finer

Unknown command: qualityOfShadows finer  

> qualityOfShadows

Unknown command: qualityOfShadows  

> QualityOfShadows

Unknown command: QualityOfShadows  

> lighting qualityOfShadows finer

> lighting msDepthBias .1

> lighting msDepthBias 1

> lighting msDepthBias .01

> lighting DepthBias .01

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> lighting depthBias .01

> lighting depthBias .1

> lighting depthBias .005

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/density_coloringv7.cxs"

——— End of log from Thu Oct 28 11:33:00 2021 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> graphics silhouettes depthJump .01

> graphics silhouettes depthJump .04

> save /Users/jfeath6971/Desktop/image329.png supersample 3

> save "/Volumes/GoogleDrive/My Drive/RRYfigs/fig1/rabinterface1.cxs"
> includeMaps true

——— End of log from Thu Oct 28 11:48:52 2021 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-12.10.25
OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro9,2
      Processor Name: Intel Core i7
      Processor Speed: 2.9 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 230.0.0.0.0
      SMC Version (system): 2.2f44
      Sudden Motion Sensor:
          State: Enabled

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G8022)
      Kernel Version: Darwin 18.7.0
      Time since boot: 12 days 4:26

Graphics/Displays:

    Intel HD Graphics 4000:

      Chipset Model: Intel HD Graphics 4000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0166
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1280 x 800
          UI Looks like: 1280 x 800
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Cc: pett Elaine Meng added
Component: Unassigned → Depiction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics presets don't reset depthJump

Reported by Ryan Feathers

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Thanks for catching that. I made the lighting presets simple, default, full, soft, gentle all restore the silhouette depth jump to its default 0.03 so that the flat value of 0.01 which shows more edges does not persist.

Fixed in 1.3 release candidate and 1.4 daily builds.

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