Cap colors don't track surface colors

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-11)
Description
Color a molecular surface by chain, clip, and then change chain colors.  The cap colors don't change to the new colors.  This is hard to remedy by hand changing individual caps with a 20 chain structure.

Log:
UCSF ChimeraX version: 0.92 (2020-01-11)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6n2y

6n2y title:  
Bacillus PS3 ATP synthase class 1 [more info...]  
  
Chain information for 6n2y #1  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | ATP synthase subunit δ  
a | ATP synthase subunit a  
b1 | ATP synthase subunit b  
b2 | ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2y #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> select /A:2-501

3827 atoms, 3888 bonds, 1 model selected  

> select /B:2-501

3787 atoms, 3846 bonds, 1 model selected  

> sequence chain #1/A#1/B#1/C

Alignment identifier is 1  

> select ::name="ATP"

93 atoms, 99 bonds, 1 model selected  

> view sel

> view

> select clear

> log metadata #1

Metadata for 6n2y #1  
---  
Title | Bacillus PS3 ATP synthase class 1  
Citation | Guo, H., Suzuki, T., Rubinstein, J.L. (2019). Structure of a
bacterial ATP synthase. Elife, 8. PMID: 30724163. DOI: 10.7554/eLife.43128  
Non-standard residues | ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
Gene source | Bacillus sp. (strain PS3)  
Experimental method | Electron microscopy  
Resolution | 3.0Å  
  
> select clear

> select /D:112@OD2

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

132 atoms, 133 bonds, 1 model selected  

> select down

8 atoms, 7 bonds, 1 model selected  

> select up

132 atoms, 133 bonds, 1 model selected  

> select up

3622 atoms, 3685 bonds, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide atoms

> show cartoons

> select ::name="ATP"

93 atoms, 99 bonds, 1 model selected  

> show sel atoms

> style sel sphere

Changed 93 atom styles  

> select clear

> preset cartoons/nucleotides cylinders/stubs

Changed 34914 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> color bypolymer

> color /A,B,C pink

> select ligand

125 atoms, 132 bonds, 1 model selected  

> color sel orange

> show sel atoms

> style sel sphere

Changed 125 atom styles  

> color sel byhetero

> select clear

> set bgColor white

> graphics silhouettes true

> lighting soft

> show surfaces

> hide cartoons

> color bypolymer

> color /A,B,C pink

> save /Users/goddard/Desktop/image1.png supersample 3

> hide surfaces

> show cartoons

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> graphics silhouettes false

> set bgColor black

> lighting simple

> open 6n2z

6n2z title:  
Bacillus PS3 ATP synthase class 2 [more info...]  
  
Chain information for 6n2z #2  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | Bacillus PS3 ATP synthase subunit δ  
a | Bacillus PS3 ATP synthase subunit a  
b1 | Bacillus PS3 ATP synthase subunit b  
b2 | Bacillus PS3 ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2z #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> open 6n30

6n30 title:  
Bacillus PS3 ATP synthase class 3 [more info...]  
  
Chain information for 6n30 #3  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | Bacillus PS3 ATP synthase subunit δ  
a | Bacillus PS3 ATP synthase subunit a  
b1 | Bacillus PS3 ATP synthase subunit b  
b2 | Bacillus PS3 ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n30 #3  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> hide #!1 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> morph #1,2

Computed 21 frame morph #4  

> coordset #4 1,21

> show #!4 atoms

> hide #!4 cartoons

> style #!4 sphere

Changed 34728 atom styles  

> lighting simple

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> close #4

> show #!1 models

> morph #1,2,3 wrap true same true

Computed 61 frame morph #4  

> coordset #4 1,61

> lighting soft

> movie record

> movie encode /Users/goddard/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/goddard/Desktop/movie.mp4  
  

> close #4

> open 9333 fromDatabase emdb

Opened emd_9333.map, grid size 320,320,320, pixel 1.06, shown at level 0.321,
step 2, values float32  

> lighting simple

> volume #4 level -0.1515

> volume #4 level 0.321

> volume #4 color #bb7aaf

> volume #4 color #b69cb0

> volume #4 color #aab484

> volume #4 color #93b598

> volume #4 color #a0b4aa

> volume #4 step 1

> volume #4 level 0.5379

> volume #4 style mesh

> volume #4 style surface

> show #!1 models

> style #!1 stick

Changed 35043 atom styles  

> volume #4 color #cae4d7

> volume #4 color #b6cec2

> volume #4 color #b6cec2fe

> volume #4 color #b6cec2fd

> volume #4 color #b6cec2fc

> volume #4 color #b6cec2fb

> volume #4 color #b6cec2fa

> volume #4 color #b6cec2f8

> volume #4 color #b6cec2f6

> volume #4 color #b6cec2f2

> volume #4 color #b6cec2ee

> volume #4 color #b6cec2e8

> volume #4 color #b6cec2e1

> volume #4 color #b6cec2da

> volume #4 color #b6cec2d4

> volume #4 color #b6cec2cd

> volume #4 color #b6cec2ca

> volume #4 color #b6cec2c0

> volume #4 color #b6cec2b9

> volume #4 color #b6cec2b1

> volume #4 color #b6cec2aa

> volume #4 color #b6cec29f

> volume #4 color #b6cec299

> volume #4 color #b6cec295

> volume #4 color #b6cec28c

> volume #4 color #b6cec280

> volume #4 color #b6cec275

> volume #4 color #b6cec273

> volume #4 color #b6cec26b

> volume #4 color #b6cec267

> volume #4 color #b6cec262

> volume #4 color #b6cec25f

> volume #4 color #b6cec25b

> volume #4 color #b6cec259

> volume #4 color #b6cec255

> volume #4 color #b6cec254

> volume #4 color #b6cec251

> volume #4 color #b6cec24f

> volume #4 color #b6cec24d

> volume #4 color #b6cec24c

> volume #4 color #b6cec24b

> volume #4 color #b6cec24a

> volume #4 color #b6cec24c

> volume #4 color #b6cec24f

> volume #4 color #b6cec251

> volume #4 color #b6cec253

> volume #4 color #b6cec254

> volume #4 color #b6cec255

> volume #4 color #b6cec256

> volume #4 color #b6cec257

> volume #4 color #b6cec259

> volume #4 color #b6cec25b

> volume #4 color #b6cec25c

> volume #4 color #b6cec25f

> volume #4 color #b6cec262

> volume #4 color #b6cec263

> volume #4 color #b6cec265

> volume #4 color #b6cec268

> volume #4 color #b6cec26b

> volume #4 color #b6cec26c

> volume #4 color #b6cec26f

> volume #4 color #b6cec271

> volume #4 color #b6cec272

> volume #4 color #b6cec273

> volume #4 color #b6cec274

> volume #4 color #b6cec275

> view :ADP

> close #2-3

> view :ADP

> volume #4 style mesh

> volume #4 level 1.561

> volume #4 level 3.792

> toolshed show "Side View"

> surface cap false

> volume #4 level 1.964

> hide #!1 models

> hide #!4 models

> show #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view :PO4

> volume #4 level 0.5999

> view :PO4

> view :ADP

> volume #4 level 2.521

> hide atoms

> show :404-441

> view :404-441

> show :ADP

> hide atoms

> show /A:404-441

Missing required "range" argument  

> volume zone #4 nearAtoms /A:404-441 range 5

> color byhetero

> volume #2 level 2.861

> view all

> view

> surface zone #4 nearAtoms /A:404-441

> show #!4 models

> volume #4 level 1.747

> set bgColor white

> volume #4 subdivideSurface true

> graphics silhouettes true

> volume #4 subdivideSurface false

> graphics silhouettes false

> volume #4 subdivideSurface true

> volume #4 subdivideSurface true subdivisionLevels 2

> volume #4 color #b6cec2b5

> volume #4 color #b6cec2f0

> volume #4 color #b6cec276

> volume #4 color #b6cec244

> volume #4 color #b6cec29f

> volume #4 color #b6cec29e

> volume #4 level 1.5

> volume #4 subdivideSurface false

> open 4xd7

4xd7 title:  
Structure of thermophilic F1-ATPase inhibited by ε subunit [more info...]  
  
Chain information for 4xd7 #2  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
  
Non-standard residues in 4xd7 #2  
---  
ADP — adenosine-5'-diphosphate  
SO4 — sulfate ion  
  
  

> hide #!4 models

> hide #!1 models

> view

> set bgColor black

> show #!4 models

> usage surface zone

surface zone surfaces nearAtoms an atoms specifier [distance a number]
[bondPointSpacing a number] [maxComponents an integer] [update true or false]  
— show surface near atoms  

> surface unzone #4

> volume #4 level 0.7872

> volume #4 style surface

> select #2/F:31@CE

1 atom, 1 model selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> volume #4 color #cf89d19e

> toolshed show "Fit in Map"

Fit molecule 4xd7 (#2) to map 9333 (#4) using 22656 atoms  
average map value = 0.288, steps = 112  
shifted from previous position = 2.47  
rotated from previous position = 4.21 degrees  
atoms outside contour = 17706, contour level = 0.78719  
  
Position of 4xd7 (#2) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.36744830 -0.68594901 0.62805709 113.60344424  
0.70364183 -0.23655016 -0.67002402 160.15520653  
0.60816932 0.68812643 0.39574246 187.38125706  
Axis 0.69893351 0.01023468 0.71511341  
Axis point -121.53547217 58.57983720 0.00000000  
Rotation angle (degrees) 103.69065586  
Shift along axis 215.03924172  
  
Fit molecule 4xd7 (#2) to map 9333 (#4) using 22656 atoms  
average map value = 0.2619, steps = 104  
shifted from previous position = 2.99  
rotated from previous position = 2.98 degrees  
atoms outside contour = 17970, contour level = 0.78719  
  
Position of 4xd7 (#2) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.89905806 -0.33988894 -0.27598932 139.01502110  
-0.20151107 0.23839684 -0.95003170 221.32242271  
0.38870025 0.90974857 0.14584122 212.71403567  
Axis 0.93936164 -0.33572992 0.06989367  
Axis point 0.00000000 7.97894440 251.70971345  
Rotation angle (degrees) 81.85677612  
Shift along axis 71.14818251  
  
Fit molecule 4xd7 (#2) to map 9333 (#4) using 22656 atoms  
average map value = 0.2678, steps = 108  
shifted from previous position = 5.3  
rotated from previous position = 2.72 degrees  
atoms outside contour = 17691, contour level = 0.78719  
  
Position of 4xd7 (#2) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
-0.58612075 -0.42265533 0.69124883 158.90521258  
0.68730472 -0.71114022 0.14795880 115.55188723  
0.42903927 0.56182031 0.70730704 175.22143068  
Axis 0.34110985 0.21611642 0.91484303  
Axis point 35.00185630 51.34233790 0.00000000  
Rotation angle (degrees) 142.65307975  
Shift along axis 239.47689744  
  

> help vol gauss

> volume gaussian #4 sDev 3

Fit molecule 4xd7 (#2) to map 9333 (#4) using 22656 atoms  
average map value = 0.3177, steps = 108  
shifted from previous position = 3.49  
rotated from previous position = 7.33 degrees  
atoms outside contour = 17076, contour level = 0.78719  
  
Position of 4xd7 (#2) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.45917590 -0.79956885 0.38710096 117.88392889  
0.57851895 -0.06153863 -0.81334422 176.06097949  
0.67414637 0.59741330 0.43430867 175.27308848  
Axis 0.70788220 -0.14403208 0.69148937  
Axis point 0.00000000 66.71758842 161.13847384  
Rotation angle (degrees) 94.82007779  
Shift along axis 179.28898367  
  

> ui mousemode rightMode "translate selected models"

Fit molecule 4xd7 (#2) to map 9333 (#4) using 22656 atoms  
average map value = 0.4631, steps = 80  
shifted from previous position = 2.01  
rotated from previous position = 3.83 degrees  
atoms outside contour = 15710, contour level = 0.78719  
  
Position of 4xd7 (#2) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.51628365 -0.77586506 0.36260805 119.26589126  
0.54947380 -0.02467759 -0.83514643 184.15524478  
0.65690923 0.63041607 0.41357689 175.86005083  
Axis 0.73360613 -0.14731624 0.66341539  
Axis point 0.00000000 66.08484876 170.65207917  
Rotation angle (degrees) 92.71732697  
Shift along axis 177.03339501  
  

> volume #3 level 0.1745

Fit map 4xd7 map 10 in map 9333 using 14570 points  
correlation = 0.2839, correlation about mean = 0.2339, overlap = 1838  
steps = 88, shift = 4.87, angle = 2.43 degrees  
  
Position of 4xd7 map 10 (#5) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.48412166 -0.79085873 0.37439109 120.99950312  
0.57628035 -0.03378670 -0.81655338 184.51453443  
0.65842781 0.61106540 0.43939948 170.38544637  
Axis 0.71489672 -0.14223470 0.68461081  
Axis point 0.00000000 71.68226239 166.03013207  
Rotation angle (degrees) 93.16047832  
Shift along axis 176.90549885  
  
Average map value = 2.318 for 22656 atoms, 5228 outside contour  

> hide #!3 models

> show #!3 models

Fit map 4xd7 map 10 in map 9333 using 14570 points  
correlation = 0.2839, correlation about mean = 0.2339, overlap = 1838  
steps = 60, shift = 0.00274, angle = 0.00186 degrees  
  
Position of 4xd7 map 10 (#5) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.48412563 -0.79086702 0.37436845 121.00220316  
0.57628418 -0.03375704 -0.81655190 184.51218162  
0.65842154 0.61105631 0.43942150 170.38495411  
Axis 0.71489034 -0.14224267 0.68461583  
Axis point 0.00000000 71.68209161 166.03219190  
Rotation angle (degrees) 93.15888164  
Shift along axis 176.90603564  
  
Average map value = 2.318 for 22656 atoms, 5231 outside contour  
Fit map 4xd7 map 10 in map 9333 gaussian using 14570 points  
correlation = 0.9625, correlation about mean = 0.711, overlap = 1292  
steps = 64, shift = 0.33, angle = 0.84 degrees  
  
Position of 4xd7 map 10 (#5) relative to 9333 gaussian (#3) coordinates:  
Matrix rotation and translation  
0.47932189 -0.78777118 0.38686832 120.40914851  
0.58592668 -0.04094622 -0.80932894 183.31686899  
0.65340681 0.61460555 0.44194973 170.54296801  
Axis 0.71324528 -0.13350847 0.68808187  
Axis point 0.00000000 71.53568966 163.98436615  
Rotation angle (degrees) 93.43047382  
Shift along axis 178.75442626  
  
Average map value = 0.3625 for 22656 atoms, 1231 outside contour  

> show #!4 models

> volume #4 level 0.6942

Fit map 4xd7 map 3 in map 9333 using 240777 points  
correlation = 0.6818, correlation about mean = 0.4752, overlap = 2.5e+05  
steps = 68, shift = 0.227, angle = 0.386 degrees  
  
Position of 4xd7 map 3 (#3) relative to 9333 (#4) coordinates:  
Matrix rotation and translation  
0.47776211 -0.79081786 0.38255782 120.91011341  
0.58208729 -0.04118434 -0.81208265 183.74712618  
0.65796486 0.61066436 0.44064871 170.27092599  
Axis 0.71271765 -0.13796371 0.68774963  
Axis point 0.00000000 71.97494048 164.21427848  
Rotation angle (degrees) 93.51941522  
Shift along axis 177.92810385  
  
Average map value = 2.444 for 22656 atoms, 4507 outside contour  

> close #3

Unknown command: colorzone #4 near #2 dist 8  

> color zone #4 near #2 distance 8

> hide #!2 models

> volume #4 level 0.6322

> lighting soft

> close #4

> close #2

> show #!1 models

> show atoms

> show surfaces

> color bychain

> color bfactor

35043 atoms, 4722 residues, 22 surfaces, atom bfactor range 0 to 144  

> mlp

Map values for surface "6n2y_A SES surface": minimum -30.04, mean -5.032,
maximum 23.52  
Map values for surface "6n2y_B SES surface": minimum -31.35, mean -5.231,
maximum 23.62  
Map values for surface "6n2y_C SES surface": minimum -30.16, mean -5.291,
maximum 24.33  
Map values for surface "6n2y_D SES surface": minimum -28.55, mean -4.971,
maximum 23.95  
Map values for surface "6n2y_E SES surface": minimum -28.65, mean -5.069,
maximum 23.94  
Map values for surface "6n2y_F SES surface": minimum -28.41, mean -5.084,
maximum 24.47  
Map values for surface "6n2y_G SES surface": minimum -27.27, mean -3.999,
maximum 22.86  
Map values for surface "6n2y_H SES surface": minimum -24.23, mean -3.949,
maximum 23.21  
Map values for surface "6n2y_I SES surface": minimum -25.84, mean -3.747,
maximum 24.87  
Map values for surface "6n2y_b2 SES surface": minimum -25.51, mean -4.746,
maximum 22.56  
Map values for surface "6n2y_b1 SES surface": minimum -24.64, mean -4.328,
maximum 22.18  
Map values for surface "6n2y_a SES surface": minimum -24.66, mean 0.2745,
maximum 23.4  
Map values for surface "6n2y_c0 SES surface": minimum -23.39, mean 0.4235,
maximum 22.32  
Map values for surface "6n2y_c1 SES surface": minimum -25.21, mean 0.5904,
maximum 21.82  
Map values for surface "6n2y_c2 SES surface": minimum -26.59, mean 0.4196,
maximum 22.54  
Map values for surface "6n2y_c3 SES surface": minimum -27.36, mean 0.4744,
maximum 22.18  
Map values for surface "6n2y_c4 SES surface": minimum -26, mean 0.2986,
maximum 22.05  
Map values for surface "6n2y_c5 SES surface": minimum -25.28, mean 0.2251,
maximum 22.47  
Map values for surface "6n2y_c6 SES surface": minimum -23.31, mean 0.2942,
maximum 22.26  
Map values for surface "6n2y_c7 SES surface": minimum -23.86, mean 0.4079,
maximum 22.05  
Map values for surface "6n2y_c8 SES surface": minimum -25.81, mean 0.435,
maximum 22.38  
Map values for surface "6n2y_c9 SES surface": minimum -24.84, mean 0.2815,
maximum 22.57  

> color bfactor

35043 atoms, 4722 residues, 22 surfaces, atom bfactor range 0 to 144  

> color bychain

> select /C*:56

5 atoms, 4 bonds, 1 model selected  

> select /c*:56

90 atoms, 80 bonds, 1 model selected  

> select /C

3798 atoms, 3859 bonds, 3 pseudobonds, 2 models selected  

> select /C*

3798 atoms, 3859 bonds, 3 pseudobonds, 2 models selected  

> select /C*:56

5 atoms, 4 bonds, 1 model selected  

> select /c*:56

90 atoms, 80 bonds, 1 model selected  

> select /C*:56

5 atoms, 4 bonds, 1 model selected  

> select clear

> hide surfaces

> select /C*:56

5 atoms, 4 bonds, 1 model selected  

> select /c*:56

90 atoms, 80 bonds, 1 model selected  

> select clear

> show surfaces

> select /c*:56

90 atoms, 80 bonds, 1 model selected  

> color sel red

> toolshed show "Side View"

> surface cap true

> lighting simple

> ui mousemode rightMode clip

> lighting soft

> lighting simple

> ui mousemode rightMode zoom

> clip off

> ui mousemode rightMode clip

> lighting soft

> lighting simple

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> color sel bychain

> color sel bychain

> color bfactor sel

90 atoms, 10 residues, 10 surfaces, atom bfactor range 74.1 to 83.5  

> select clear

> color bychain

> color bfactor

35043 atoms, 4722 residues, 22 surfaces, atom bfactor range 0 to 144  

> color bychain

> surface cap false

> surface cap true




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.