Color editor calling into dead color button

[semchonok@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110020016 (2021-10-02 00:16:37 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202110020016 (2021-10-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/daredevil/Downloads/poster/1_ses.cxs format session

Opened cryosparc_P12_J183_008_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.961, shown at level 0.852, step 1, values float32  
Opened bc1__emd_22189.map as #2, grid size 240,240,240, pixel 1.36, shown at
level 0.0606, step 1, values float32  
Opened ATP__emd_9333.map as #3, grid size 320,320,320, pixel 1.06, shown at
level 0.35, step 1, values float32  
Log from Wed Nov 10 15:07:54 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/daredevil/Documents/meeting___presentation/local/1a.mrc

Opened 1a.mrc as #1, grid size 256,256,256, pixel 1, shown at level 0.204,
step 1, values float32  

> pub preset

Unknown command: pub preset  

> preset pub

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> volume #1 color #ff9300

> open
> /Users/daredevil/Documents/meeting___presentation/local/1a__local__C2.mrc

Opened 1a__local__C2.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32  

> ui tool show "Show Volume Menu"

> ui tool show "Surface Color"

> help help:user/tools/surfacecolor.html

> color sample #1.1 map #2 palette
> 3,#ff0000:4,#ffffff:5,#0000ff:6,#808080:7,#808080:8,#808080:9,#808080:10,#808080

Map values for surface "surface": minimum 0, mean 7.432, maximum 12.72  

> color sample #1.1 map #2 palette
> 3,#0000ff:4,#0091ff:5,#00ffda:6,#00ff48:7,#48ff00:8,#daff00:9,#ff9100:10,#ff0000

Map values for surface "surface": minimum 0, mean 7.432, maximum 12.72  

> volume #1 level 0.1114

> volume #1 level 0.1279

> key blue:3 #0091ff:4 #00ffda:5 #00ff48:6 #48ff00:7 #daff00:8 #ff9100:9
> red:10 showTool true

> ui mousemode right "color key"

> key pos 0.296947,0.11985 size 0.390278,0.0320203

> scalebar

> key pos 0.298795,0.908281 size 0.391308,0.0327485

> volume #1 level 0.1204

> color single #1.1

> color sample #1.1 map #2 palette
> 3,#0000ff:4,#0091ff:5,#00ffda:6,#00ff48:7,#48ff00:8,#daff00:9,#ff9100:10,#ff0000

Map values for surface "surface": minimum 0, mean 6.832, maximum 16.88  

> color single #1.1

> color sample #2.1 map #1 palette
> 3,#0000ff:4,#0091ff:5,#00ffda:6,#00ff48:7,#48ff00:8,#daff00:9,#ff9100:10,#ff0000

Map values for surface "surface": minimum -0.1109, mean 0.02205, maximum
0.2739  

> color sample #1.1 map #2 palette
> 3,#0000ff:4,#0091ff:5,#00ffda:6,#00ff48:7,#48ff00:8,#daff00:9,#ff9100:10,#ff0000

Map values for surface "surface": minimum 0, mean 6.832, maximum 16.88  

> key red:10 #ff9100:9 #daff00:8 #48ff00:7 #00ff48:6 #00ffda:5 #0091ff:4
> blue:3

> key blue:3 #0091ff:4 #00ffda:5 #00ff48:6 #48ff00:7 #daff00:8 #ff9100:9
> red:10

> key red:10 #ff9100:9 #daff00:8 #48ff00:7 #00ff48:6 #00ffda:5 #0091ff:4
> blue:3

> key blue:3 #0091ff:4 #00ffda:5 #00ff48:6 #48ff00:7 #daff00:8 #ff9100:9
> red:10

> close session

> ui mousemode right translate

> open "/Users/daredevil/Downloads/output_volume (14).mrc"

Opened output_volume (14).mrc as #1, grid size 256,256,256, pixel 0.96, shown
at level 0.205, step 1, values float32  

> open
> /Users/daredevil/Documents/meeting___presentation/local/1a__local__C2.mrc

Opened 1a__local__C2.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32  

> volume #2 level 6.377

> ui tool show "Surface Color"

> color gradient #2.1 map #1 palette
> 4,#0000ff:5,#0091ff:6,#00ffda:7,#00ff48:8,#48ff00:9,#daff00:10,#ff9100:11,#ff0000

Map values for surface "surface": minimum 9.152e-05, mean 0.01337, maximum
0.1572  

> color sample #2.1 map #1 palette
> 4,#0000ff:5,#0091ff:6,#00ffda:7,#00ff48:8,#48ff00:9,#daff00:10,#ff9100:11,#ff0000

Map values for surface "surface": minimum -0.223, mean 0.008888, maximum
0.5257  

> color sample #1.1 map #2 palette
> 4,#0000ff:5,#0091ff:6,#00ffda:7,#00ff48:8,#48ff00:9,#daff00:10,#ff9100:11,#ff0000

Map values for surface "surface": minimum 0, mean 7.38, maximum 10.41  

> volume #1 level 0.177

> volume #1 level 0.1273

> key blue:4 #0091ff:5 #00ffda:6 #00ff48:7 #48ff00:8 #daff00:9 #ff9100:10
> red:11 showTool true

> ui mousemode right "color key"

> key pos 0.338595,0.84313 size 0.338814,0.0416132

> scalebar

> view

> key pos 0.31598,0.972219 size 0.429579,0.0197478

> select #4

2 models selected  

> key pos 0.311311,0.107143 size 0,0

> key pos 0.310056,0.0998282 size 0.00125535,0.00731494

> key pos 0.320805,0.963179 size 0.460388,0.0190224

> ui mousemode right translate

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,0.046577,0,1,0,-0.99706,0,0,1,0

> close #4

> scalebar

> select #5

2 models selected  

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,0.046577,0,1,0,-0.13972,0,0,1,0

> ~select #5

Nothing selected  

> select #3

1 model selected  

> view matrix models #3,1,0,0,-7.7616,0,1,0,0.62183,0,0,1,0

> view matrix models #3,1,0,0,31.846,0,1,0,-4.1064,0,0,1,0

> key blue:4 #0091ff:5 #00ffda:6 #00ff48:7 #48ff00:8 #daff00:9 #ff9100:10
> red:11 showTool true

> ui mousemode right "color key"

> key pos 0.253217,0.955337 size 0.238643,0.026666

> key pos 0.236957,0.955541 size 0.171055,0.00773501

> key blue:4 #0091ff:5 #00ffda:6 #00ff48:7 #48ff00:8 #daff00:9 #ff9100:10
> red:11 showTool true

[Repeated 2 time(s)]

> key pos 0.256621,0.932949 size 0.323542,0.0404531

> ui mousemode right select

> close #3

> key blue:4 #0091ff:5 #00ffda:6 #00ff48:7 #48ff00:8 #daff00:9 #ff9100:10
> red:11 showTool true

> ui mousemode right "color key"

> key pos 0.298672,0.963221 size 0.442506,0.0228399

> save /Users/daredevil/Documents/meeting___presentation/local/1a_top.jpg
> width 3000 height 1866 supersample 3

> turn #2 x 90

Expected an axis vector or a keyword  

> turn y 90 #2

Expected 'forever' or an integer >= 1 or a keyword  

> show #!2 models

> hide #!2 models

> select #1

2 models selected  

> hide #!1 models

> show #!1 models

> turn y 90 #1

Expected 'forever' or an integer >= 1 or a keyword  

> turn #1 y 90

Expected an axis vector or a keyword  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.15457,0.044237,0.98699,-22.829,0.057913,0.99687,-0.05375,-0.1275,-0.98628,0.065468,0.15152,217.41

> save /Users/daredevil/Documents/meeting___presentation/local/1a_side.jpg
> width 3000 height 1866 supersample 3

> key blue:4 #0091ff:5 #00ffda:6 #00ff48:7 #48ff00:8 #daff00:9 #ff9100:10
> red:11 showTool true

[Repeated 1 time(s)]

> view matrix models
> #1,0.15737,0.095958,0.98287,-29.022,0.049806,0.99323,-0.10494,7.6071,-0.98628,0.065468,0.15152,217.41

> select #6

1 model selected  

> view matrix models
> #6,0.78042,-0.0050471,-0.62523,0.013848,0.22458,0.9355,0.27277,0.050233,0.58353,-0.3533,0.73122,0.30218

> undo

> ui mousemode right select

> select clear

> close #6

> select clear

> key blue:4 #0091ff:5 #00ffda:6 #00ff48:7 #48ff00:8 #daff00:9 #ff9100:10
> red:11 showTool true

> ui mousemode right "color key"

> key pos 0.82558,0.107618 size 0.0449841,0.219696

> key pos 0.757398,0.0824909 size 0.0724261,0.725144

> save /Users/daredevil/Documents/meeting___presentation/local/1_color.jpg
> width 300 height 187 supersample 3

> save /Users/daredevil/Documents/meeting___presentation/local/1_color.jpg
> width 3000 height 1866 supersample 3

> open /Users/daredevil/Downloads/cryosparc_P30_J440_004_volume_map_half_A.mrc

Opened cryosparc_P30_J440_004_volume_map_half_A.mrc as #8, grid size
256,256,256, pixel 0.96, shown at level 0.438, step 1, values float32  

> open "/Users/daredevil/Downloads/cryosparc_P30_J440_004_volume_map_sharp
> (1).mrc"

Opened cryosparc_P30_J440_004_volume_map_sharp (1).mrc as #9, grid size
256,256,256, pixel 0.96, shown at level 0.525, step 1, values float32  

> close session

> ui mousemode right select

> open "/Volumes/Seagate Backup Plus Drive/for_paper_figures_4b/3a.mrc"

Opened 3a.mrc as #1, grid size 256,256,256, pixel 1, shown at level 0.202,
step 1, values float32  

> volume #1 level 0.1002

[Repeated 1 time(s)]

> open /Users/daredevil/Downloads/cryosparc_P30_J873_map_locres.mrc

Opened cryosparc_P30_J873_map_locres.mrc as #2, grid size 256,256,256, pixel
0.96, shown at level 13.5, step 1, values float32  

> close #1

> volume flip #2

Opened cryosparc_P30_J873_map_locres.mrc z flip as #1, grid size 256,256,256,
pixel 0.96, shown at step 1, values float32  

> close #2

> open "/Volumes/Seagate Backup Plus Drive/for_paper_figures_4b/3a.mrc"

Opened 3a.mrc as #2, grid size 256,256,256, pixel 1, shown at level 0.202,
step 1, values float32  

> volume #1 level 7.418

> ui tool show "Surface Color"

> color sample #2.1 map #1 palette
> #0000ff:#0091ff:#00ffda:#00ff48:#48ff00:#daff00:#ff9100:#ff0000

Map values for surface "surface": minimum 6.822, mean 8.195, maximum 15.46  

> color sample #2.1 map #1 palette
> 5,#0000ff:6,#0091ff:7,#00ffda:8,#00ff48:9,#48ff00:10,#daff00:11,#ff9100:12,#ff0000

Map values for surface "surface": minimum 6.822, mean 8.195, maximum 15.46  

> volume #2 level 0.155

> key blue:5 #0091ff:6 #00ffda:7 #00ff48:8 #48ff00:9 #daff00:10 #ff9100:11
> red:12 showTool true

> ui mousemode right "color key"

> key pos 0.8395,0.0190051 size 0.0970355,0.66508

> key pos 0.847813,0.932777 size 0.000536601,0.000316122

> ui mousemode right select

> view

> scalebar

> save /Users/daredevil/Documents/meeting___presentation/local/3a__top.jpg
> width 3000 height 1891 supersample 3

> turn y 90 map #2

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 90 #2

Expected 'forever' or an integer >= 1 or a keyword  

> map #2 turn y 90

Unknown command: map #2 turn y 90  

> turn y 90

> save /Users/daredevil/Documents/meeting___presentation/local/3a__side.jpg
> width 3000 height 1891 supersample 3

> hide #!2 models

> key blue:5 #0091ff:6 #00ffda:7 #00ff48:8 #48ff00:9 #daff00:10 #ff9100:11
> red:12 showTool true

> ui mousemode right "color key"

> key pos 0.703457,0.0164201 size 0.0848495,0.935009

> hide #!4 models

> save /Users/daredevil/Documents/meeting___presentation/local/3a_color.jpg
> width 3000 height 1891 supersample 3

> open /Users/daredevil/Downloads/cryosparc_P30_J874_map_locres.mrc

Opened cryosparc_P30_J874_map_locres.mrc as #5, grid size 256,256,256, pixel
0.96, shown at level 9.8, step 1, values float32  

> close session

> ui mousemode right select

> open /Users/daredevil/Downloads/cryosparc_P30_J874_map_locres.mrc

Opened cryosparc_P30_J874_map_locres.mrc as #1, grid size 256,256,256, pixel
0.96, shown at level 9.8, step 1, values float32  

> open "/Volumes/Seagate Backup Plus Drive/for_paper_figures_4b/4a.mrc"

Opened 4a.mrc as #2, grid size 256,256,256, pixel 1, shown at level 0.356,
step 1, values float32  

> volume flip #1

Opened cryosparc_P30_J874_map_locres.mrc z flip as #3, grid size 256,256,256,
pixel 0.96, shown at step 1, values float32  

> close #1

> ui tool show "Surface Color"

> color sample #2.1 map #3 palette
> 2,#0000ff:3,#0091ff:4,#00ffda:5,#00ff48:6,#48ff00:7,#daff00:8,#ff9100:9,#ff0000

Map values for surface "surface": minimum 4.011, mean 5.649, maximum 32.08  

> volume #2 level 0.2916

> view

> scalebar

> save /Users/daredevil/Documents/meeting___presentation/local/4a__top.jpg
> width 3000 height 1891 supersample 3

> turn y 90

> save /Users/daredevil/Documents/meeting___presentation/local/4a__side.jpg
> width 3000 height 1891 supersample 3

> open /Users/daredevil/Downloads/cryosparc_P30_J875_map_locres.mrc

Opened cryosparc_P30_J875_map_locres.mrc as #4, grid size 256,256,256, pixel
0.96, shown at level 10.2, step 1, values float32  

> close session

> open /Users/daredevil/Downloads/cryosparc_P30_J875_map_locres.mrc

Opened cryosparc_P30_J875_map_locres.mrc as #1, grid size 256,256,256, pixel
0.96, shown at level 10.2, step 1, values float32  

> volume #1 level 10.39

> volume #1 level 10.34

> open "/Volumes/Seagate Backup Plus Drive/for_paper_figures_4b/2a.mrc"

Opened 2a.mrc as #2, grid size 256,256,256, pixel 1, shown at level 0.0945,
step 1, values float32  

> volume flip #1

Opened cryosparc_P30_J875_map_locres.mrc z flip as #3, grid size 256,256,256,
pixel 0.96, shown at step 1, values float32  

> close #1

> ui tool show "Surface Color"

> color sample #2.1 map #3 palette
> #0000ff:#0091ff:#00ffda:#00ff48:#48ff00:#daff00:#ff9100:#ff0000

Map values for surface "surface": minimum 10.25, mean 10.25, maximum 10.29  

> close session

> open /Users/daredevil/Downloads/cryosparc_P30_J874_map_locres.mrc format mrc

Opened cryosparc_P30_J874_map_locres.mrc as #1, grid size 256,256,256, pixel
0.96, shown at level 9.8, step 1, values float32  

> open "/Volumes/Seagate Backup Plus Drive/for_paper_figures_4b/4a.mrc"

Opened 4a.mrc as #2, grid size 256,256,256, pixel 1, shown at level 0.356,
step 1, values float32  

> volume flip #1

Opened cryosparc_P30_J874_map_locres.mrc z flip as #3, grid size 256,256,256,
pixel 0.96, shown at step 1, values float32  

> close #1

> ui tool show "Surface Color"

> color sample #2.1 map #3 palette
> #0000ff:#0091ff:#00ffda:#00ff48:#48ff00:#daff00:#ff9100:#ff0000

Map values for surface "surface": minimum 4.011, mean 5.649, maximum 32.08  

> color sample #2.1 map #3 palette
> 2.5,#0000ff:3,#0091ff:3.5,#00ffda:4,#00ff48:4.5,#48ff00:5,#daff00:6,#ff9100:7,#ff0000

Map values for surface "surface": minimum 4.011, mean 5.649, maximum 32.08  

> ui tool show "Side View"

> volume #2 level 0.315

> surface dust #2 size 10

> volume #2 level 0.2715

> color sample #2.1 map #3 palette
> 3,#0000ff:3.5,#0091ff:4,#00ffda:5.5,#00ff48:5,#48ff00:6,#daff00:7,#ff9100:8,#ff0000

Map values for surface "surface": minimum 4.011, mean 5.715, maximum 38.89  

> view

> save /Users/daredevil/Documents/meeting___presentation/local/4a__top_new.jpg
> width 3000 height 1891 supersample 2

> turn y 90

> save
> /Users/daredevil/Documents/meeting___presentation/local/4a__side_new.jpg
> width 3000 height 1891 supersample 4

> key blue:3.0 #0091ff:3.5 #00ffda:4.0 #48ff00:5.0 #00ff48:5.5 #daff00:6.0
> #ff9100:7.0 red:8.0 showTool true

> ui mousemode right "color key"

> hide #!2 models

> key pos 0.82355,0.0308353 size 0.0536009,0.591759

> key bold true

> key blue:3.0 #0091ff:3.5 #00ffda:4.0 #48ff00:5.0 #00ff48:5.5 #daff00:6.0
> #ff9100:7.0 red:8.0 showTool true

> key bold false

> ui mousemode right select

> save /Users/daredevil/Documents/meeting___presentation/local/4__scale.tif
> width 3000 height 1891 supersample 4 transparentBackground true

> open
> /Users/daredevil/Documents/Invited__paper__/F4/After_D/4C/test_coord_pos.pdb

Chain information for test_coord_pos.pdb #4  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> hide #!4 models

> show #!4 models

> show #!3 models

> close #3

> close #2

> close #1

> open 2i5k

Summary of feedback from opening 2i5k fetched from pdb  
---  
warnings | Atom CD1 has no neighbors to form bonds with according to residue
template for LEU /A:170  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /B:170  
note | Fetching compressed mmCIF 2i5k from
http://files.rcsb.org/download/2i5k.cif  
  
2i5k title:  
Crystal structure of Ugp1p [more info...]  
  
Chain information for 2i5k #1  
---  
Chain | Description | UniProt  
A B | UTP--glucose-1-phosphate uridylyltransferase | UGPA1_YEAST  
  
2i5k mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open /Users/daredevil/Downloads/2i5k.pdb

2i5k.pdb title:  
Crystal structure of UGP1P [more info...]  
  
Chain information for 2i5k.pdb  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A | No description available  
2.1/B 2.2/B 2.3/B 2.4/B | No description available  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> close #1

Drag select of 93 residues  

> combine #2

Remapping chain ID 'A' in 2i5k.pdb #2.2 to 'C'  
Remapping chain ID 'B' in 2i5k.pdb #2.2 to 'D'  
Remapping chain ID 'A' in 2i5k.pdb #2.3 to 'E'  
Remapping chain ID 'B' in 2i5k.pdb #2.3 to 'F'  
Remapping chain ID 'A' in 2i5k.pdb #2.4 to 'G'  
Remapping chain ID 'B' in 2i5k.pdb #2.4 to 'H'  

> close #2#2.1-4

> select #4

13234 atoms, 13452 bonds, 8 pseudobonds, 1882 residues, 2 models selected  

> ~select #4

Nothing selected  

> select #1

26468 atoms, 26904 bonds, 16 pseudobonds, 3764 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,33.528,0,1,0,262.09,0,0,1,28.306

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,83.974,0,1,0,124.07,0,0,1,86.716

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.40505,0.83627,0.36957,116.75,-0.87991,0.24674,0.40605,172.55,0.24838,-0.48966,0.83578,73.031

> view matrix models
> #1,-0.82764,-0.49901,-0.25692,184.67,-0.51481,0.85728,-0.0066657,152.43,0.22358,0.12675,-0.96641,74.398

> view matrix models
> #1,0.30918,-0.40142,0.86213,122.03,-0.93294,-0.30387,0.19309,175.47,0.18447,-0.86401,-0.46846,76.553

> view matrix models
> #1,0.50849,-0.18502,0.84096,111.05,-0.82001,-0.40202,0.40738,169.25,0.26271,-0.89675,-0.35614,72.242

> view matrix models
> #1,0.30775,-0.36979,0.87667,122.11,-0.93918,-0.26564,0.21764,175.82,0.1524,-0.89033,-0.42905,78.32

> view matrix models
> #1,0.45687,-0.30435,0.83584,113.9,-0.87107,-0.34352,0.35104,172.06,0.18029,-0.88846,-0.42206,76.783

> view matrix models
> #1,-0.77649,0.44205,-0.44906,181.85,0.39615,-0.21176,-0.89344,102.25,-0.49004,-0.87164,-0.01069,113.71

> view matrix models
> #1,0.38266,0.91542,0.12477,117.99,0.07139,0.10535,-0.99187,120.14,-0.92112,0.38846,-0.025038,137.47

> view matrix models
> #1,-0.81722,0.0051123,-0.5763,184.09,-0.44436,-0.64237,0.62443,148.55,-0.367,0.76638,0.52723,106.94

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> view matrix models
> #1,-0.78064,0.0028125,-0.62497,182.08,-0.43768,-0.71628,0.54348,148.19,-0.44613,0.6978,0.56039,111.3

> view matrix models
> #1,-0.7309,-0.055915,-0.68019,179.34,-0.43311,-0.73224,0.52559,147.93,-0.52745,0.67875,0.51097,115.78

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.7309,-0.055915,-0.68019,114.69,-0.43311,-0.73224,0.52559,254.25,-0.52745,0.67875,0.51097,92.759

> view matrix models
> #1,-0.7309,-0.055915,-0.68019,114.95,-0.43311,-0.73224,0.52559,249.24,-0.52745,0.67875,0.51097,94.402

> select #4

13234 atoms, 13452 bonds, 8 pseudobonds, 1882 residues, 2 models selected  

> view matrix models #4,1,0,0,5.2282,0,1,0,-2.4826,0,0,1,3.182

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.83253,-0.43188,0.34694,240.76,-0.46763,0.88365,-0.022134,71.896,-0.29702,-0.18067,-0.93763,298.55

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.83253,-0.43188,0.34694,184.85,-0.46763,0.88365,-0.022134,172.25,-0.29702,-0.18067,-0.93763,236.31

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.70009,-0.38576,0.60089,131.9,-0.53723,0.8389,-0.087372,194.28,-0.47038,-0.38399,-0.79454,265.18

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.70009,-0.38576,0.60089,135.38,-0.53723,0.8389,-0.087372,199.76,-0.47038,-0.38399,-0.79454,266.19

> view matrix models
> #4,-0.70009,-0.38576,0.60089,137.22,-0.53723,0.8389,-0.087372,189.58,-0.47038,-0.38399,-0.79454,270.52

> view matrix models
> #4,-0.70009,-0.38576,0.60089,133.77,-0.53723,0.8389,-0.087372,195.2,-0.47038,-0.38399,-0.79454,269.06

> fitmap #1 #4

Missing required "in_map" argument  

> fitmap #1 inmodel #4

Expected a keyword  

> fitmap #1 inmod #4

Expected a keyword  

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ~select #4

Nothing selected  

> select #1

26468 atoms, 26904 bonds, 16 pseudobonds, 3764 residues, 2 models selected  

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,108.19,-0.39386,-0.75852,0.51916,247.07,-0.68909,0.61745,0.37935,103.31

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,114.1,-0.39386,-0.75852,0.51916,248.69,-0.68909,0.61745,0.37935,101.8

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,113.46,-0.39386,-0.75852,0.51916,248.51,-0.68909,0.61745,0.37935,101.24

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,107.81,-0.39386,-0.75852,0.51916,245.86,-0.68909,0.61745,0.37935,95.681

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,116.89,-0.39386,-0.75852,0.51916,241.37,-0.68909,0.61745,0.37935,102.76

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,118.87,-0.39386,-0.75852,0.51916,245.83,-0.68909,0.61745,0.37935,104.97

> view matrix models
> #1,-0.6083,-0.20834,-0.76588,117.3,-0.39386,-0.75852,0.51916,244.33,-0.68909,0.61745,0.37935,103.26

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.53427,-0.76601,0.35747,113.22,-0.32435,0.57628,0.75013,240.5,-0.78061,0.28482,-0.55634,108.3

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.53427,-0.76601,0.35747,112.11,-0.32435,0.57628,0.75013,240.62,-0.78061,0.28482,-0.55634,107.15

> view matrix models
> #1,-0.53427,-0.76601,0.35747,109.39,-0.32435,0.57628,0.75013,240.14,-0.78061,0.28482,-0.55634,104.29

> view matrix models
> #1,-0.53427,-0.76601,0.35747,118.92,-0.32435,0.57628,0.75013,142.12,-0.78061,0.28482,-0.55634,104.82

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.76871,-0.60504,0.20742,131.84,-0.3499,0.66926,0.65548,143.53,-0.53541,0.4313,-0.72617,91.315

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.76871,-0.60504,0.20742,124.45,-0.3499,0.66926,0.65548,242.26,-0.53541,0.4313,-0.72617,87.289

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.76871,-0.60504,0.20742,128.73,-0.3499,0.66926,0.65548,242.95,-0.53541,0.4313,-0.72617,77.612

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.77238,-0.57602,0.26763,128.93,-0.32756,0.72225,0.60915,241.72,-0.54418,0.38283,-0.74653,78.095

> view matrix models
> #1,-0.7737,-0.56735,0.28197,129,-0.32881,0.74001,0.58675,241.79,-0.54155,0.36125,-0.75909,77.95

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.7737,-0.56735,0.28197,130.13,-0.32881,0.74001,0.58675,238.22,-0.54155,0.36125,-0.75909,78.546

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.7737,-0.56735,0.28197,129.06,-0.32881,0.74001,0.58675,237.81,-0.54155,0.36125,-0.75909,81.162

> view matrix models
> #1,-0.7737,-0.56735,0.28197,128.63,-0.32881,0.74001,0.58675,237.87,-0.54155,0.36125,-0.75909,80.817

> view matrix models
> #1,-0.7737,-0.56735,0.28197,129.3,-0.32881,0.74001,0.58675,237.63,-0.54155,0.36125,-0.75909,78.927

> view matrix models
> #1,-0.7737,-0.56735,0.28197,128.26,-0.32881,0.74001,0.58675,238.3,-0.54155,0.36125,-0.75909,79.806

> ~select #1

Nothing selected  

> select #4

13234 atoms, 13452 bonds, 8 pseudobonds, 1882 residues, 2 models selected  

> view matrix models
> #4,-0.70009,-0.38576,0.60089,118.57,-0.53723,0.8389,-0.087372,313.67,-0.47038,-0.38399,-0.79454,222.31

> view

> ui mousemode right select

> select clear

> scalebar

> movie record

> turn y 1 360

> wait

> movie encode

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

> close session

> open

Missing or invalid "fileNames" argument: Expected a file name  

> open 4R7P

Summary of feedback from opening 4R7P fetched from pdb  
---  
notes | Fetching compressed mmCIF 4r7p from
http://files.rcsb.org/download/4r7p.cif  
Fetching CCD UPG from http://ligand-expo.rcsb.org/reports/U/UPG/UPG.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
Fetching CCD ACT from http://ligand-expo.rcsb.org/reports/A/ACT/ACT.cif  
Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
  
4r7p title:  
Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose
[more info...]  
  
Chain information for 4r7p #1  
---  
Chain | Description | UniProt  
A B C D | UTP--glucose-1-phosphate uridylyltransferase | UGPA_HUMAN  
  
Non-standard residues in 4r7p #1  
---  
ACT — acetate ion  
EDO — 1,2-ethanediol (ethylene glycol)  
SO4 — sulfate ion  
UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl-
monophosphate ester)  
ZN — zinc ion  
  
4r7p mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open "/Volumes/Seagate Backup Plus Drive/for_paper_figures_4b/5a.vol"

Opened 5a.vol as #2, grid size 256,256,256, pixel 1, shown at level 0.215,
step 1, values float32  

> surface dust #2 size 10

> select #2

2 models selected  

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-94.676,0,1,0,-190.91,0,0,1,-76.865

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.67136,0.30489,-0.67552,-5.2618,-0.68991,0.59006,-0.41935,3.4879,0.27074,0.74758,0.60649,-156.89

> view matrix models
> #2,0.46499,0.49671,-0.73285,3.9329,-0.64451,0.75743,0.10442,-90.715,0.60695,0.42378,0.67233,-166.9

> view matrix models
> #2,0.55304,0.23231,-0.80011,35.104,-0.78597,0.46407,-0.40852,30.524,0.27641,0.85479,0.43924,-149.95

> view matrix models
> #2,0.44614,0.53991,-0.71376,-1.6267,-0.57962,0.78198,0.22922,-118.12,0.6819,0.31145,0.66182,-160.77

> view matrix models
> #2,0.54197,0.32719,-0.77409,21.049,-0.82779,0.36682,-0.42451,50.369,0.14506,0.87085,0.46965,-139.08

> view matrix models
> #2,0.45031,0.45144,-0.77034,16.399,-0.78225,0.61543,-0.096611,-29.206,0.43048,0.6461,0.63027,-167.39

> fitmap #1 inMap #2

Fit molecule 4r7p (#1) to map 5a.vol (#2) using 15591 atoms  
average map value = 0.1343, steps = 212  
shifted from previous position = 25.9  
rotated from previous position = 10.7 degrees  
atoms outside contour = 11307, contour level = 0.21528  
  
Position of 4r7p (#1) relative to 5a.vol (#2) coordinates:  
Matrix rotation and translation  
0.57144005 -0.67147851 0.47177631 52.85200551  
0.43059162 0.73472752 0.52418158 135.08587681  
-0.69860370 -0.09639542 0.70898575 132.40377057  
Axis -0.36012781 0.67918468 0.63954369  
Axis point 103.12966208 0.00000000 -138.48995414  
Rotation angle (degrees) 59.49745335  
Shift along axis 157.39277673  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open
> /Users/daredevil/Downloads/poster/mapS/cryosparc_P12_J183_008_volume_map_sharp.mrc

Opened cryosparc_P12_J183_008_volume_map_sharp.mrc as #3, grid size
384,384,384, pixel 0.961, shown at level 0.48, step 2, values float32  

> close #2

> close #1

> view

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.  

> surface dust #3 size 9.61

>

Incomplete command: segmentation  

> volume #3 step 1

> volume #3 level 0.9085

> ui tool show "Segment Map"

Segmenting cryosparc_P12_J183_008_volume_map_sharp.mrc, density threshold
0.908487  
Only showing 60 of 3370 regions.  
Showing 60 of 3370 region surfaces  
9932 watershed regions, grouped to 3370 regions  
Showing cryosparc_P12_J183_008_volume_map_sharp.seg - 3370 regions, 60
surfaces  
Drag select of 16490, 15996 of 446772 triangles, 16494, 13546 of 165688
triangles, 15620, 1410 of 3040 triangles, 3
cryosparc_P12_J183_008_volume_map_sharp.mrc  

> ui mousemode right select

> select clear

Grouped 3 regions  

> color #1.3 forest green

Grouped 3 regions  
Grouped 1 regions  
Grouped 3 regions  
Grouped 2 regions  
[Repeated 1 time(s)]Grouped 4 regions  
Grouped 2 regions  
Grouped 1 regions  
[Repeated 2 time(s)]Grouped 2 regions  
Grouped 1 regions  
[Repeated 6 time(s)]

> select clear

Grouped 1 regions  
[Repeated 1 time(s)]

> volume #3 level 1.206

Grouped 1 regions  
Grouped 2 regions  

> undo

[Repeated 2 time(s)]

> select clear

Ungrouped to 850 regions, but did not show all surfaces, see Options  
Got 3356 regions after grouping by connections  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #3 level 0.8342

Got 3353 regions after grouping by connections  

> hide #!3 models

> close #3

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> close session

> open
> /Users/daredevil/Downloads/poster/mapS/cryosparc_P12_J183_008_volume_map_sharp.mrc
> /Users/daredevil/Downloads/poster/mapS/bc1__emd_22189.map
> /Users/daredevil/Downloads/poster/mapS/atp_emd_8359.map

Opened cryosparc_P12_J183_008_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.961, shown at level 0.48, step 2, values float32  
Opened bc1__emd_22189.map as #2, grid size 240,240,240, pixel 1.36, shown at
level 0.00699, step 1, values float32  
Opened atp_emd_8359.map as #3, grid size 250,250,250, pixel 1.4, shown at
level 0.0522, step 1, values float32  

> select #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,211.08,0,1,0,155.17,0,0,1,18.712

> select #3

2 models selected  

> view matrix models #3,1,0,0,334.24,0,1,0,240.75,0,0,1,6.9361

> view

> select #2

2 models selected  

> select #3

2 models selected  

> view matrix models #3,1,0,0,330.81,0,1,0,238.1,0,0,1,5.6297

> surface dust #3 size 14

> select #1

2 models selected  

> surface dust #1 size 9.61

> select #2

2 models selected  

> view matrix models #2,1,0,0,211.56,0,1,0,159.52,0,0,1,38.687

> ui mousemode right select

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.45093,-0.883,-0.13024,466.84,0.85837,0.38903,0.33445,63.741,-0.24466,-0.26261,0.93337,132.51

> view matrix models
> #2,0.57038,-0.82131,0.011011,413.88,0.81879,0.56959,0.071699,84.255,-0.065159,-0.03188,0.99737,54.96

> view matrix models
> #2,0.69264,-0.70811,-0.13722,400.01,0.71238,0.6418,0.28391,54.686,-0.11297,-0.2944,0.94898,113.62

> view matrix models
> #2,0.74249,-0.66559,-0.075488,374.71,0.6653,0.71962,0.19882,63.764,-0.078012,-0.19785,0.97712,87.497

> view matrix models
> #2,0.66893,-0.6945,-0.26495,422.82,0.73108,0.55029,0.40335,46.782,-0.13433,-0.46352,0.87585,156.82

> view matrix models
> #2,0.67675,-0.73279,-0.070897,395.65,0.73561,0.66915,0.10545,75.992,-0.029834,-0.12352,0.99189,65.057

> view matrix models
> #2,0.53983,-0.84095,-0.03724,430.07,0.84177,0.53918,0.026486,92.957,-0.0021943,-0.045646,0.99896,46.668

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.53983,-0.84095,-0.03724,290.32,0.84177,0.53918,0.026486,-3.494,-0.0021943,-0.045646,0.99896,1.1403

> view matrix models
> #2,0.53983,-0.84095,-0.03724,271.31,0.84177,0.53918,0.026486,-12.52,-0.0021943,-0.045646,0.99896,38.627

> view matrix models
> #2,0.53983,-0.84095,-0.03724,273.85,0.84177,0.53918,0.026486,-15.75,-0.0021943,-0.045646,0.99896,40.067

> surface dust #2 size 13.6

> view matrix models
> #2,0.53983,-0.84095,-0.03724,372.54,0.84177,0.53918,0.026486,85.733,-0.0021943,-0.045646,0.99896,56.684

> select #3

2 models selected  

> view matrix models #3,1,0,0,330.29,0,1,0,236.48,0,0,1,-1.1437

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.23443,-0.8864,0.39917,636.25,-0.97002,0.24034,-0.035983,554.68,-0.06404,-0.39564,-0.91617,445.58

> volume #1 step 1

> volume #1 level 0.8517

> volume #2 level 0.06057

> open 6XI0

Summary of feedback from opening 6XI0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 6xi0 from
http://files.rcsb.org/download/6xi0.cif  
Fetching CCD FES from http://ligand-expo.rcsb.org/reports/F/FES/FES.cif  
Fetching CCD HEC from http://ligand-expo.rcsb.org/reports/H/HEC/HEC.cif  
  
6xi0 title:  
R. capsulatus cyt bc1 (CIII2) at 3.3A [more info...]  
  
Chain information for 6xi0 #4  
---  
Chain | Description | UniProt  
C P | Cytochrome b | CYB_RHOCB  
D Q | Cytochrome c1 | CY1_RHOCB  
E R | Ubiquinol-cytochrome c reductase iron-sulfur subunit | UCRI_RHOCB  
  
Non-standard residues in 6xi0 #4  
---  
FES — FE2/S2 (inorganic) cluster  
HEC — heme C  
  

> show cartoons

> hide atoms

> select #4

13079 atoms, 13491 bonds, 48 pseudobonds, 1686 residues, 3 models selected  

> view matrix models
> #4,-0.77471,0.46149,-0.43226,286.1,-0.5964,-0.76041,0.25706,341.76,-0.21006,0.45694,0.86433,-17.724

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.77471,0.46149,-0.43226,401.77,-0.5964,-0.76041,0.25706,497.49,-0.21006,0.45694,0.86433,132.46

> ui mousemode right select

> select clear

> select /D/Q

3681 atoms, 3781 bonds, 14 pseudobonds, 472 residues, 3 models selected  

> select ::name="FES"

8 atoms, 8 bonds, 2 residues, 1 model selected  
Drag select of 57 residues  

> select clear

> select ::name="FES"

8 atoms, 8 bonds, 2 residues, 1 model selected  

> show sel target ab

> select #2

2 models selected  

> select clear

> ui mousemode right "rotate selected models"

> select #3

2 models selected  

> ~select #3

Nothing selected  

> select #2

2 models selected  

> view matrix models
> #2,0.58265,-0.81252,-0.018121,357.71,0.81272,0.58244,0.015906,85.184,-0.00237,-0.023995,0.99971,53.053

> view matrix models
> #2,0.68312,-0.72792,-0.05889,334.32,0.7272,0.67058,0.14667,62.886,-0.067277,-0.14302,0.98743,85.124

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.68312,-0.72792,-0.05889,335.85,0.7272,0.67058,0.14667,64.006,-0.067277,-0.14302,0.98743,88.895

> view matrix models
> #2,0.68312,-0.72792,-0.05889,335.15,0.7272,0.67058,0.14667,63.195,-0.067277,-0.14302,0.98743,81.098

> view matrix models
> #2,0.68312,-0.72792,-0.05889,334.97,0.7272,0.67058,0.14667,63.282,-0.067277,-0.14302,0.98743,89.07

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.84024,-0.54214,-0.0089087,270.65,0.54009,0.83538,0.10215,74.367,-0.047939,-0.090643,0.99473,76.145

> view matrix models
> #2,0.56588,-0.75086,-0.34057,404.96,0.81876,0.46314,0.33932,49.971,-0.097053,-0.47086,0.87685,165.93

> view matrix models
> #2,0.13933,-0.97779,0.15658,428.45,0.97848,0.11165,-0.17352,167.04,0.15218,0.17739,0.9723,3.4933

> view matrix models
> #2,0.95768,-0.27652,-0.079915,220.01,0.2752,0.961,-0.027397,118.77,0.084374,0.0042446,0.99643,38.782

> view matrix models
> #2,0.38326,-0.78377,-0.48869,464.9,0.92161,0.35956,0.14612,82.403,0.06119,-0.50638,0.86014,148.7

> view matrix models
> #2,0.84749,-0.50566,-0.16143,289.02,0.51759,0.85469,0.040103,85.267,0.11769,-0.11754,0.98607,54.952

> view matrix models
> #2,0.23645,-0.8447,-0.48018,497.38,0.9708,0.22592,0.080619,107.14,0.040385,-0.48522,0.87346,146.41

> view matrix models
> #2,0.7783,-0.62687,0.03574,287.11,0.59373,0.71625,-0.36671,163.48,0.20428,0.30663,0.92965,-18.967

> view matrix models
> #2,0.048056,-0.95472,-0.29359,514.88,0.98269,0.097838,-0.15731,165.9,0.17891,-0.28095,0.9429,78.85

> view matrix models
> #2,0.73652,-0.63022,-0.24568,341.55,0.60676,0.77609,-0.17184,118.99,0.29896,-0.0225,0.954,15.222

> select #4

13079 atoms, 13491 bonds, 48 pseudobonds, 1686 residues, 3 models selected  

> view matrix models
> #4,-0.6795,0.59331,-0.43158,364.61,-0.70572,-0.6894,0.16337,519.32,-0.2006,0.41558,0.88716,133.87

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.6795,0.59331,-0.43158,401.64,-0.70572,-0.6894,0.16337,520.52,-0.2006,0.41558,0.88716,40.382

> fitmap #4 inMap #2

Fit molecule 6xi0 (#4) to map bc1__emd_22189.map (#2) using 13079 atoms  
average map value = 0.06723, steps = 148  
shifted from previous position = 4.85  
rotated from previous position = 23.7 degrees  
atoms outside contour = 6107, contour level = 0.060574  
  
Position of 6xi0 (#4) relative to bc1__emd_22189.map (#2) coordinates:  
Matrix rotation and translation  
-0.99999973 -0.00024111 0.00068813 326.32083409  
0.00024088 -0.99999992 -0.00032905 326.41319594  
0.00068821 -0.00032888 0.99999971 -0.08005212  
Axis 0.00034390 -0.00016463 0.99999993  
Axis point 163.14076467 163.22625196 0.00000000  
Rotation angle (degrees) 179.98619190  
Shift along axis -0.02156633  
  

> view matrix models
> #4,-0.73684,0.63012,-0.24496,376.76,-0.60669,-0.77618,-0.17168,570.32,-0.29831,0.022114,0.95421,103.92

> ui mousemode right select

> select clear

> select #2

2 models selected  

> turn z 180

[Repeated 1 time(s)]

> ui mousemode right select

> select clear

> select #2

2 models selected  

> hide #!4 models

> turn z 180

[Repeated 1 time(s)]

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.6454,0.75164,0.13596,67.068,0.74334,-0.65901,0.11467,282.99,0.17579,0.027053,-0.98406,351.39

> view matrix models
> #2,0.63591,0.73468,0.23637,54.591,0.76976,-0.62586,-0.12561,313.45,0.055658,0.26182,-0.96351,329.24

> view matrix models
> #2,0.78565,0.52125,0.33323,48.783,0.61433,-0.72097,-0.32062,386.96,0.073128,0.45661,-0.88666,281.75

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78565,0.52125,0.33323,49.282,0.61433,-0.72097,-0.32062,388.66,0.073128,0.45661,-0.88666,284.88

> view matrix models
> #2,0.78565,0.52125,0.33323,40.909,0.61433,-0.72097,-0.32062,376.52,0.073128,0.45661,-0.88666,270.83

> view matrix models
> #2,0.78565,0.52125,0.33323,43.273,0.61433,-0.72097,-0.32062,384.59,0.073128,0.45661,-0.88666,285.75

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.73191,0.50247,0.46025,33.864,0.64132,-0.73621,-0.21612,365.2,0.23025,0.45334,-0.86108,256.36

> view matrix models
> #2,0.59574,0.79044,0.14246,62.243,0.79353,-0.60666,0.047651,275.09,0.12409,0.084657,-0.98865,355.19

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.59574,0.79044,0.14246,-27.035,0.79353,-0.60666,0.047651,176.71,0.12409,0.084657,-0.98865,346.06

> view matrix models
> #2,0.59574,0.79044,0.14246,-28.836,0.79353,-0.60666,0.047651,172.35,0.12409,0.084657,-0.98865,322.35

> view matrix models
> #2,0.59574,0.79044,0.14246,100.3,0.79353,-0.60666,0.047651,274.51,0.12409,0.084657,-0.98865,349.94

> ui mousemode right select

> select clear

> select #3

2 models selected  

> close #3

> open /Users/daredevil/Downloads/poster/mapS/ATP__emd_9333.map.gz

File reader requires uncompressed file;
'/Users/daredevil/Downloads/poster/mapS/ATP__emd_9333.map.gz' is compressed  

> open /Users/daredevil/Downloads/poster/mapS/ATP__emd_9333.map

Opened ATP__emd_9333.map as #3, grid size 320,320,320, pixel 1.06, shown at
level 0.321, step 2, values float32  
Drag select of 3 ATP__emd_9333.map  
[Repeated 1 time(s)]

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,256.85,0,1,0,220.54,0,0,1,24

> view matrix models #3,1,0,0,258.81,0,1,0,221.95,0,0,1,27.115

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.69706,0.71007,0.09952,400.1,0.71375,0.67396,0.19062,122.18,0.068284,0.20391,-0.97661,363.74

> view matrix models
> #3,0.81379,-0.5754,0.081606,368.54,-0.58067,-0.8108,0.073684,601.77,0.023768,-0.10735,-0.99394,425.77

> view matrix models
> #3,0.81382,-0.57383,0.091693,366.33,-0.57967,-0.81274,0.058615,604.83,0.040887,-0.10085,-0.99406,421.92

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.81382,-0.57383,0.091693,402.93,-0.57967,-0.81274,0.058615,632.88,0.040887,-0.10085,-0.99406,367.14

> view matrix models
> #3,0.81382,-0.57383,0.091693,442.38,-0.57967,-0.81274,0.058615,661.19,0.040887,-0.10085,-0.99406,378.18

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.81114,-0.56962,0.13263,434.23,-0.58207,-0.80835,0.088107,655.16,0.057025,-0.14867,-0.98724,382.12

> volume #3 color silver

> volume #3 color #d6d6d6

> volume #3 color silver

> volume #3 color darkgrey

> volume #3 color silver

> volume #3 step 1

> surface dust #3 size 10.6

> volume #3 level 0.7

> volume #3 level 0.3501

> ui mousemode right select

> select clear

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.5359,0.82239,0.19103,96.725,0.83744,-0.54652,0.003498,264.91,0.10728,0.1581,-0.98158,339.52

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.5359,0.82239,0.19103,96.545,0.83744,-0.54652,0.003498,264.71,0.10728,0.1581,-0.98158,341.2

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.50158,0.81098,0.30121,85.579,0.82822,-0.55073,0.10363,250.15,0.24992,0.19749,-0.94791,305.86

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.50158,0.81098,0.30121,66.389,0.82822,-0.55073,0.10363,270.99,0.24992,0.19749,-0.94791,299.79

> select #3

2 models selected  

> select #2

2 models selected  

> view matrix models
> #2,0.50158,0.81098,0.30121,67.846,0.82822,-0.55073,0.10363,269.66,0.24992,0.19749,-0.94791,299.91

> select #3

2 models selected  

> view matrix models
> #3,0.81114,-0.56962,0.13263,391.48,-0.58207,-0.80835,0.088107,685.23,0.057025,-0.14867,-0.98724,378.35

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.80355,-0.56138,0.19787,378.77,-0.59126,-0.79116,0.15649,670.72,0.068695,-0.24274,-0.96766,388

> ui mousemode right select

> select clear

> select #3

2 models selected  
Drag select of 3 ATP__emd_9333.map  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.80134,-0.55058,0.23393,370.41,-0.59285,-0.78316,0.18758,663.67,0.079928,-0.289,-0.95399,391.08

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.80134,-0.55058,0.23393,379.85,-0.59285,-0.78316,0.18758,671.91,0.079928,-0.289,-0.95399,398.42

> view matrix models
> #3,0.80134,-0.55058,0.23393,380.1,-0.59285,-0.78316,0.18758,672.12,0.079928,-0.289,-0.95399,398.32

> ui mousemode right select

> select clear

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right select

> select #3

2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.80134,-0.55058,0.23393,379.01,-0.59285,-0.78316,0.18758,671.26,0.079928,-0.289,-0.95399,400.95

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.62617,-0.73658,0.25567,433.64,-0.77874,-0.60702,0.15842,678.42,0.038506,-0.2983,-0.95369,409.15

> view matrix models
> #3,0.62552,-0.72411,0.29049,424.99,-0.77932,-0.5976,0.1885,671.17,0.037099,-0.34429,-0.93813,413.87

> save /Users/daredevil/Downloads/poster/1_ses.cxs includeMaps true

> ui mousemode right select

> select clear

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> select #3

2 models selected  

> view matrix models
> #3,0.62656,-0.74305,0.23514,438.6,-0.77838,-0.61182,0.14072,682.56,0.039305,-0.2712,-0.96172,406.15

> view matrix models
> #3,0.62621,-0.7373,0.25349,434.18,-0.7787,-0.60755,0.15654,678.87,0.038592,-0.29542,-0.95459,408.84

> view matrix models
> #3,0.62639,-0.74029,0.24417,436.43,-0.77854,-0.60978,0.1485,680.75,0.038957,-0.28311,-0.9583,407.49

> ui mousemode right select

> select clear

> save /Users/daredevil/Downloads/poster/1_ses.cxs includeMaps true

——— End of log from Wed Nov 10 15:07:54 2021 ———

opened ChimeraX session  

> open 1cxc

Summary of feedback from opening 1cxc fetched from pdb  
---  
note | Fetching compressed mmCIF 1cxc from
http://files.rcsb.org/download/1cxc.cif  
  
files.rcsb.org failed to respond  

> open /Users/daredevil/Downloads/1cxc.pdb1

1cxc.pdb1 title:  
Crystallization and X-ray structure determination of cytochrome C2 from
rhodobacter sphaeroides In three crystal forms [more info...]  
  
Chain information for 1cxc.pdb1 #5  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 1cxc.pdb1 #5  
---  
HEC — heme C  
  

> select #5

986 atoms, 987 bonds, 6 pseudobonds, 149 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,265.04,0,1,0,233.88,0,0,1,304.79

> undo

> view matrix models #5,1,0,0,232.7,0,1,0,210.56,0,0,1,268.1

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.024807,0.91959,-0.3921,300.84,0.92462,-0.12801,-0.35873,165.06,-0.38007,-0.37144,-0.8471,331.52

> view matrix models
> #5,0.65338,0.53323,-0.53737,256.52,0.58196,-0.80777,-0.093952,203.4,-0.48417,-0.25134,-0.8381,337.21

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.65338,0.53323,-0.53737,302.73,0.58196,-0.80777,-0.093952,246.61,-0.48417,-0.25134,-0.8381,341.7

> view matrix models
> #5,0.65338,0.53323,-0.53737,302.17,0.58196,-0.80777,-0.093952,246.09,-0.48417,-0.25134,-0.8381,341.69

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.60029,0.77342,-0.20367,296.83,0.60108,-0.60426,-0.52304,246.05,-0.5276,0.19155,-0.82761,335.65

> view matrix models
> #5,-0.025872,-0.83797,0.54511,371.14,-0.51483,0.47858,0.71127,296.02,-0.8569,-0.26223,-0.44379,366.52

> view matrix models
> #5,-0.084069,-0.91012,0.40573,379.23,-0.39991,0.40376,0.82283,286.87,-0.91269,-0.093082,-0.39791,366.79

> view matrix models
> #5,0.91172,0.40809,0.047181,276.16,0.27738,-0.52681,-0.80345,274.21,-0.30303,0.7456,-0.59351,302.69

> view matrix models
> #5,0.56412,0.81462,-0.13482,297.93,-0.033699,-0.14043,-0.98952,293.53,-0.82501,0.56275,-0.051765,341.16

> view matrix models
> #5,0.83161,0.55331,-0.0477,280.8,0.20829,-0.39037,-0.89678,278.13,-0.51482,0.73584,-0.43989,317.83

> view matrix models
> #5,0.040951,0.74232,-0.6688,348.72,0.99909,-0.022645,0.036041,194.18,0.011608,-0.66967,-0.74257,309.43

> view matrix models
> #5,0.89789,-0.42807,-0.10273,297.02,0.073463,0.3758,-0.92379,273.09,0.43405,0.82191,0.36887,228.83

> view matrix models
> #5,0.96272,0.26485,0.055086,274.99,0.20129,-0.56529,-0.79996,281.09,-0.18073,0.78122,-0.59752,292.17

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.96272,0.26485,0.055086,291.38,0.20129,-0.56529,-0.79996,297.59,-0.18073,0.78122,-0.59752,252.43

> view matrix models
> #5,0.96272,0.26485,0.055086,240.8,0.20129,-0.56529,-0.79996,337.53,-0.18073,0.78122,-0.59752,244.57

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 3 maps.  

> volume style surface

> close #5

> show #!4 models

> hide #!4 models

> open /Users/daredevil/Downloads/poster/mapS/bc1__emd_22189.map

Opened bc1__emd_22189.map as #5, grid size 240,240,240, pixel 1.36, shown at
level 0.00699, step 1, values float32  

> hide #!5 models

> show #!5 models

> close #5

> open /Users/daredevil/Downloads/poster/mapS/c2_cytochrome__1cxc.mrc

Opened c2_cytochrome__1cxc.mrc as #5, grid size 58,57,53, pixel 1, shown at
level 1.08, step 1, values float32  

> select #5

2 models selected  

> view matrix models #5,1,0,0,268.79,0,1,0,273.7,0,0,1,263.03

> volume #5 color silver

[Repeated 1 time(s)]

> view matrix models #5,1,0,0,278.8,0,1,0,274.2,0,0,1,205.27

> view matrix models #5,1,0,0,262.63,0,1,0,301.08,0,0,1,183.45

> view matrix models #5,1,0,0,258,0,1,0,305.63,0,0,1,190.57

> view matrix models #5,1,0,0,236.61,0,1,0,293.82,0,0,1,276.24

> volume #5 level 0.3716

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.98231,0.099885,0.15838,233.64,0.16051,-0.013596,-0.98694,316.42,-0.096427,0.99491,-0.029388,278.29

> view matrix models
> #5,0.91626,0.35085,0.19331,233.21,0.11218,0.23852,-0.96464,314.72,-0.38455,0.90554,0.17919,300.24

> view matrix models
> #5,0.92001,0.34337,0.18889,233.13,0.10598,0.24602,-0.96345,315.05,-0.37729,0.9064,0.18995,299.48

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.92001,0.34337,0.18889,235.92,0.10598,0.24602,-0.96345,318.44,-0.37729,0.9064,0.18995,288.21

> view matrix models
> #5,0.92001,0.34337,0.18889,235.31,0.10598,0.24602,-0.96345,317.81,-0.37729,0.9064,0.18995,288.8

> view matrix models
> #5,0.92001,0.34337,0.18889,235.9,0.10598,0.24602,-0.96345,318.47,-0.37729,0.9064,0.18995,287.32

> view matrix models
> #5,0.92001,0.34337,0.18889,233.24,0.10598,0.24602,-0.96345,323.69,-0.37729,0.9064,0.18995,289.74

> view matrix models
> #5,0.92001,0.34337,0.18889,231.27,0.10598,0.24602,-0.96345,318.48,-0.37729,0.9064,0.18995,287.52

> ui mousemode right select

> select clear

> save /Users/daredevil/Downloads/poster/1c_map.cxs includeMaps true

> view

> save /Users/daredevil/Downloads/poster/etc.tif width 3000 height 1868
> supersample 4 transparentBackground true

> open /Users/daredevil/Downloads/UQ8.cif

> save /Users/daredevil/Downloads/poster/etc_all.cxs includeMaps true

> close session

> open /Users/daredevil/Downloads/UQ8.cif

> open /Users/daredevil/Downloads/UQ8_model.sdf

> hide target a

> hide #* target a

> show target ab

> cartoon hide

> surface hidePatches

> style ball

Changed 127 atom styles  

> style sphere

Changed 127 atom styles  

> style ringFill thin

Changed 1 residue ring style  

> hide #* target a

> show target ab

> style ball

Changed 127 atom styles  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback  
_color_callback(*args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 128, in _color_changed_cb  
self.set_color(color)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
RuntimeError: wrapped C/C++ object of type ColorButton has been deleted  
  
RuntimeError: wrapped C/C++ object of type ColorButton has been deleted  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback  
_color_callback(*args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 128, in _color_changed_cb  
self.set_color(color)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
RuntimeError: wrapped C/C++ object of type ColorButton has been deleted  
  
RuntimeError: wrapped C/C++ object of type ColorButton has been deleted  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3,8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 447.40.12.0.0
      OS Loader Version: 540.40.4~45
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 5 days 15:30

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, '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: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110020016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2
    ChimeraX-ModelPanel: 1.2
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    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: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Hi Dmitry,

Thanks for reporting this problem. We believe we fixed it near the end of last month, so if you get the latest release you shouldn't run into it again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab