Opened 5 years ago

Closed 5 years ago

#4509 closed defect (fixed)

Toolshed reporting obsolete command

Reported by: sergei.pourmal@… Owned by: Greg Couch
Priority: normal Milestone: 1.3
Component: Tool Shed Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Installed SEQCROW via "toolshed install SEQCROW" to run angle command. Seems to be installed per log. Run "angle #2:281 #2:342 #2:916 short" and receive the response "angel is provided by the unstalled bundle SEQCROW"

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210415.cxs format
> session

Log from Wed Apr 14 14:16:55 2021UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210414.cxs

Log from Wed Apr 14 01:34:40 2021 Startup Messages  
---  
note | Updating list of available bundles failed: Internal Server Error  
  
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P9_J643_009_volume_map_filtered.mrc

Opened cryosparc_P9_J643_009_volume_map_filtered.mrc, grid size 200,200,200,
pixel 1.28, shown at level 0.402, step 1, values float32  

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp.mrc

Opened cryosparc_P10_J41_005_volume_map_sharp.mrc, grid size 300,300,300,
pixel 0.834, shown at level 0.231, step 2, values float32  

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_apo_210402_final.pdb

Chain information for MRP4_apo_210402_final.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_ATP_bound.pdb

Chain information for MRP4_ATP_bound.pdb #4  
---  
Chain | Description  
A | No description available  
  

> matchmaker #4 to #3 bring #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker MRP4_apo_210402_final.pdb, chain A (#3) with MRP4_ATP_bound.pdb,
chain A (#4), sequence alignment score = 5507.9  
RMSD between 494 pruned atom pairs is 1.064 angstroms; (across all 1125 pairs:
13.102)  
  

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!3 models

> hide #!4 models

> hide #!2 models

> show #!3 models

> volume #1 level 0.854

> hide #!3 models

> show #!3 models

> hide #!1 models

> select #3:start-80

530 atoms, 535 bonds, 1 model selected  

> hide #!3 models

> show #!3 models

> select #3:start-80

530 atoms, 535 bonds, 1 model selected  

> color sel red

> color sel #FEE440

> select #3:80-390

5045 atoms, 5095 bonds, 1 model selected  

> view sel

> view sel

> set bgColor white

> select #3:80-390

5045 atoms, 5095 bonds, 1 model selected  

> select #3:start-90

714 atoms, 722 bonds, 1 model selected  

> color sel #FEE440

> undo

> select #3:start-89

692 atoms, 700 bonds, 1 model selected  

> color sel #FEE440

> select up

18454 atoms, 18642 bonds, 1 model selected  

> select up

27630 atoms, 28008 bonds, 6 models selected  

> select down

18454 atoms, 18642 bonds, 1 model selected  

> select down

692 atoms, 700 bonds, 1 model selected  

> select down

692 atoms, 700 bonds, 1 model selected  

> select down

692 atoms, 700 bonds, 1 model selected  

> select down

692 atoms, 700 bonds, 1 model selected  

> select #3:89-390

4888 atoms, 4937 bonds, 1 model selected  

> color sel #00bbf9

> select #3:89-391

4907 atoms, 4956 bonds, 1 model selected  

> color sel #00bbf9

> undo

> undo

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> volume #1 level 0.9007

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> select #3:391-615

3212 atoms, 3235 bonds, 4 pseudobonds, 2 models selected  

> color sel #00F5D4

> select #3:692-1018

5154 atoms, 5221 bonds, 2 pseudobonds, 2 models selected  

> color sel #9B5DE5

> select #3:1019-end

4532 atoms, 4572 bonds, 1 model selected  

> select up

18454 atoms, 18642 bonds, 1 model selected  

> select down

4532 atoms, 4572 bonds, 1 model selected  

> color sel #F15BB5

> select clear

> show #!3 atoms

> hide #!3 atoms

> show #!1 models

> volume #1 level 0.7916

> surface dust #1 size 5 update true

> surface dust #1 size 10 update true

> undo

> show #!1 models

> surface dust #1 size 15 update true

> volume #1 level 0.9475

> volume #1 level 0.854

> surface dust #1 size 12 update true

> surface dust #1 size 20 update true

> surface dust #1 size 12 update true

> undo

> show #!1 models

> surface dust #1 size 20 update true

> color zone #1 near #3 distance 1

> color zone #1 near #3 distance 2

> color zone #1 near #3 distance 3

> color zone #1 near #3 distance 2

> hide #!3 models

> show #!3 models

> color zone #1 near #3 distance 4

> color zone #1 near #3 distance 3

> surface dust #1 size 25 update true

> surface dust #1 size 20 update true

> surface dust #1 size 25 update true

> surface dust #1 size 30 update true

> surface dust #1 size 25 update true

> hide #!3 models

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> select #3:89-390

4888 atoms, 4937 bonds, 1 model selected  

> select #3:89-391

4907 atoms, 4956 bonds, 1 model selected  

> select #3:1019-end

4532 atoms, 4572 bonds, 1 model selected  

> select #3:89-391

4907 atoms, 4956 bonds, 1 model selected  

> hide #!1 models

> color sel #9B5DE5

> select #3:391-615

3212 atoms, 3235 bonds, 4 pseudobonds, 2 models selected  

> select #3:392-615

3193 atoms, 3216 bonds, 4 pseudobonds, 2 models selected  

> color sel #F15BB5

> select clear

> select #3:692-1018

5154 atoms, 5221 bonds, 2 pseudobonds, 2 models selected  

> color sel #00BBF9

> select #3:1019-end

4532 atoms, 4572 bonds, 1 model selected  

> color sel #00F5D4

> show #!1 models

> select clear

> color zone #1 near #3 distance 3

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> lighting full

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc

Opened cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc, grid size
300,300,300, pixel 0.834, shown at level 0.205, step 2, values float32  

> close #5

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P9_J643_009_volume_map_filtered_gaussian.mrc

Opened cryosparc_P9_J643_009_volume_map_filtered_gaussian.mrc, grid size
200,200,200, pixel 1.28, shown at level 0.386, step 1, values float32  

> volume #5 level 0.1531

> volume #5 color #bcb1ff

> volume #5 color #bfb3ff

> volume #5 color #c1b5ff

> volume #5 color #c4baff

> volume #5 color #c7c2fe

> volume #5 color #c7c5fe

> volume #5 color #cccafe

> volume #5 color #d1d0fd

> volume #5 color #d3d2fd

> volume #5 color #d4d5fd

> volume #5 color #d8dafd

> volume #5 color #d9dbfc

> volume #5 color #d9dcfc

> volume #5 color #dce0fc

> volume #5 color #dee3fc

> volume #5 color #e1e8fb

> volume #5 color #e3ecfb

> volume #5 color #e3eefb

> volume #5 color #e4f0fb

> volume #5 color #e4f1fb

> volume #5 color #e4f2fb

> volume #5 color #e3f3fb

> volume #5 color #e1f5fb

> volume #5 color #e0f4fb

> volume #5 color #def2fb

> volume #5 color #ddf1fb

> volume #5 color #ddf0fb

> volume #5 color #dceffb

> volume #5 color #dbeefb

> volume #5 color #dbedfb

> volume #5 color #daecfb

> volume #5 color #d8eafb

> volume #5 color #d8e8fc

> volume #5 color #d6e7fc

> volume #5 color #d5e6fc

> volume #5 color #d5e5fc

> volume #5 color #d2e3fc

> volume #5 color #d0e3fc

> volume #5 color #cee2fc

> volume #5 color #cde2fc

> volume #5 color #cce1fc

> volume #5 color #cbe1fc

> volume #5 color #cae1fc

> volume #5 color #c8e1fc

> volume #5 color #c7e1fc

> volume #5 color #c5e1fc

> volume #5 color #c5e2fc

> volume #5 color #c3e2fc

> volume #5 color #c2e3fc

> volume #5 color #c1e3fc

> volume #5 color #c0e4fc

> volume #5 color #c1e6fc

> volume #5 color #c2e8fc

> volume #5 color #c2e9fc

> volume #5 color #c4eafc

> volume #5 color #c6ebfc

> volume #5 color #c8ebfc

> volume #5 color #cdecfc

> volume #5 color #d0edfb

> volume #5 color #d1edfb

> volume #5 color #d3edfb

> volume #5 color #d4edfb

> volume #5 color #d6eefb

> volume #5 color #d8effb

> volume #5 color #d9effb

> volume #5 color #e0f1fb

> volume #5 color #e1f1fb

> volume #5 color #e0f1fb

> volume #5 color #dcf1fb

> volume #5 color #daf2fb

> volume #5 color #d9f2fb

> volume #5 color #d7f2fb

> volume #5 color #d7f3fb

> volume #5 color #dcf7fb

> volume #5 color #dff9fa

> volume #5 color #e0fafa

> volume #5 color #e4fbfa

> volume #5 color #e5fbf9

> volume #5 color #eafbf8

> volume #5 color #edfbf8

> volume #5 color #eefbf8

> volume #5 color #f0faf7

> volume #5 color #f0faf7fa

> volume #5 color #f0faf7e9

> volume #5 color #f0faf7c0

> volume #5 color #f0faf780

> volume #5 color #f0faf737

> volume #5 color #f0faf711

> volume #5 color #f0faf700

> volume #5 color #f0faf709

> volume #5 color #f0faf711

> volume #5 color #f0faf713

> volume #5 color #f0faf719

> volume #5 color #f0faf71c

> volume #5 color #f0faf71f

> volume #5 color #f0faf722

> volume #5 color #f0faf723

> volume #5 color #f0faf726

> volume #5 color #f0faf727

> volume #5 color #f0faf723

> volume #5 color #f0faf722

> volume #5 color #f0faf721

> volume #5 color #f0faf720

> volume #5 color #f0faf71d

> volume #5 color #f0faf71c

> volume #5 color #f0faf71b

> volume #5 color #f0faf71a

> volume #5 color #f0faf718

> volume #5 color #f0faf715

> volume #5 color #f0faf713

> volume #5 color #f0faf711

> volume #5 color #f0faf708

> volume #5 color #f0faf707

> volume #5 color #f0faf706

> volume #5 color #f0faf705

> volume #5 color #f0faf704

> volume #5 color #f0faf702

> volume #5 color #f0faf700

> volume #5 color #f0faf709

> volume #5 color #f0faf70a

> volume #5 color #f0faf70c

> volume #5 color #f0faf70d

> volume #5 color #f0faf70e

> volume #5 color #f0faf70f

> volume #5 color #f0faf70e

> volume #5 color #f0faf70d

> volume #5 color #f0faf70c

> volume #5 color #f0faf70b

> volume #5 color #f0faf70a

> volume #5 color #f0faf70b

> volume #5 color #f0faf70c

> graphics silhouettes true

> set silhouettes depthJump 1

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

> set silhouettes true depthJump 1

Expected a keyword  

> graphics silhouettes true depthJump 1

> graphics silhouettes true depthJump 0.1

> graphics silhouettes true depthJump 0.01

> graphics silhouettes true depthJump 0.03

> graphics silhouettes true depthJump 0.5

> graphics silhouettes true depthJump 0.1

> graphics silhouettes true depthJump 1

> graphics silhouettes true depthJump .9

> graphics silhouettes true depthJump .8

> graphics silhouettes true depthJump .1

> graphics silhouettes true depthJump .2

> graphics silhouettes true depthJump .3

> graphics silhouettes true depthJump .4

> graphics silhouettes true depthJump .4

> graphics silhouettes true depthJump .3

> graphics silhouettes true width 1 depthJump .3

> graphics silhouettes true width .9 depthJump .3

> graphics silhouettes true width 2 depthJump .3

> volume #5 color #f1fbf80c

> volume #5 color #f5fffc0c

> volume #5 color #f0fff60c

> volume #5 color #f0fff50c

> volume #5 color #f0fff30c

> volume #5 color #f0fff20c

> volume #5 color #f0fff10c

> volume #5 color #f1ffef0c

> volume #5 color #f0ffee0c

> volume #5 color #f1ffef0c

> volume #5 color #f2fff00c

> volume #5 color #f3fff20c

> volume #5 color #f4fff30c

> volume #5 color #f4fff40c

> volume #5 color #f5fff40c

> volume #5 color #f5fff50c

> volume #5 color #f7fff60c

> volume #5 color #f8fff60c

> volume #5 color #f9fff60c

> volume #5 color #fafff70c

> volume #5 color #fafff80c

> volume #5 color #f9fff90c

> volume #5 color #f8fff90c

> volume #5 color #f7fff90c

> volume #5 color #f7fff90d

> volume #5 color #f7fff90c

> volume #5 color #f7fff90a

> volume #5 color #f7fff904

> volume #5 color #f7fff900

> volume #5 color #f7fff909

> volume #5 color #f7fff90a

> volume #5 color #f7fff90b

> volume #5 color #f7fff90c

> volume #5 color #f7fff90d

> volume #5 color #f7fff90e

> volume #5 color #f7fff90f

> volume #5 color #f7fff910

> volume #5 color #f7fff911

> volume #5 color #f7fff912

> volume #5 color #f7fff913

> volume #5 color #f7fff914

> volume #5 color #f7fff915

> volume #5 color #f7fff916

> volume #5 color #f7fff917

> volume #5 color #f7fff918

> volume #5 color #f7fff919

> volume #5 color #f7fff91a

> volume #5 color #f7fff91b

> volume #5 color #f7fff91c

> volume #5 color #f7fff91d

> volume #5 color #f7fff91e

> volume #5 color #f7fff91f

> volume #5 color #f7fff920

> volume #5 color #f7fff921

> volume #5 color #f7fff923

> volume #5 color #f7fff924

> volume #5 color #f7fff926

> volume #5 color #f7fff927

> volume #5 color #f7fff929

> volume #5 color #f7fff92c

> volume #5 color #f7fff92d

> volume #5 color #f7fff92f

> volume #5 color #f7fff930

> volume #5 color #f7fff931

> volume #5 color #f7fff932

> volume #5 color #f7fff933

> volume #5 color #f7fff935

> volume #5 color #f7fff934

> volume #5 color #f7fff92f

> volume #5 color #f7fff928

> volume #5 color #f7fff922

> volume #5 color #f7fff91f

> volume #5 color #f7fff91c

> volume #5 color #f7fff918

> volume #5 color #f7fff916

> volume #5 color #f7fff918

> volume #5 color #f7fff91a

> volume #5 color #f7fff91c

> volume #5 color #f7fff91d

> volume #5 color #f7fff920

> volume #5 color #f7fff922

> volume #5 color #f7fff924

> volume #5 color #f7fff925

> volume #5 color #f7fff924

> volume #5 color #f7fff923

> volume #5 color #f7fff922

> volume #5 color #f7fff921

> volume #5 color #f7fff91e

> volume #5 color #f7fff91b

> volume #5 color #f7fff918

> volume #5 color #f7fff916

> volume #5 color #f7fff915

> volume #5 color #f7fff914

> volume #5 color #f7fff913

> volume #5 color #f7fff912

> volume #5 color #f7fff911

> volume #5 color #f7fff90f

> volume #5 color #f7fff90d

> volume #5 color #f7fff90b

> volume #5 color #f7fff908

> volume #5 color #f7fff907

> volume #5 color #f7fff906

> volume #5 color #f7fff905

> volume #5 color #f7fff902

> volume #5 color #f7fff900

> volume #5 color #f7fff909

> volume #5 color #f7fff90a

> volume #5 color #f7fff90b

Unknown data format: 'tiff'  
Unknown data format: '.tiff'  
Unknown data format: 'tif'  

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff supersample 3
> transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff 2400 2400
> supersample 3 transparentBackground true

Expected a keyword  

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a2.tiff width 800
> height 800 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a2.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> hide #!1 models

> show #!3 models

> hide #!5 models

> lighting soft

> lighting simple

> lighting full

> lighting full

> lighting flat

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting soft

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2b.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> show #!5 models

> hide #!5 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

> view matrix

camera position:
-0.17269,0.019211,0.98479,521.56,-0.98139,-0.088602,-0.17037,56.059,0.083981,-0.99588,0.034155,148.7  
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99244,0.031635,0.11859,-14.991,0.021502,-0.99608,0.085774,234.19,0.12084,-0.082575,-0.98923,249.89,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.99244,0.031635,0.11859,-14.991,0.021502,-0.99608,0.085774,234.19,0.12084,-0.082575,-0.98923,249.89,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> show #!2 models

> hide #!3 models

> hide #3.1 models

> volume #2 step 1

> volume #2 level 0.5642

> show #!4 models

> volume #2 level 0.436

> select #4:start-88

341 atoms, 347 bonds, 1 model selected  

> color sel #FEE440

> select #4:89-391

2396 atoms, 2445 bonds, 1 model selected  

> color sel #9B5DE5

> select #4:392-615

1665 atoms, 1690 bonds, 2 pseudobonds, 2 models selected  

> color sel #F15BB5

> select #4:692-1018

2422 atoms, 2488 bonds, 4 pseudobonds, 2 models selected  

> color sel #00BBF9

> select #4:1019-end

2352 atoms, 2393 bonds, 1 model selected  

> color sel #00F5D4

> select #4

9176 atoms, 9366 bonds, 8 pseudobonds, 2 models selected  

> hide sel atoms

> color zone #2 near #4 distance 3

> volume #1 color #b2b2b3

> color #2 #b2b2b3

> color zone #2 near #4 distance 3

> surface dust #2 size 25 update true

> surface dust #2 size 30 update true

> surface dust #2 size 40 update true

> surface dust #2 size 50 update true

> volume #2 level 0.6069

> surface dust #2 size 25 update true

> volume #2 level 0.4531

> volume #2 level 0.5215

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc

Opened cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc, grid size
300,300,300, pixel 0.834, shown at level 0.205, step 2, values float32  

> volume #6 step 1

> volume #6 level 0.2345

> save /Users/Hoodwinked/Data/For_Publication/Final_Models/figure_2.cxs

> close

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc
> /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_ATP_bound.pdb
> /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp.mrc

Chain information for MRP4_ATP_bound.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc, grid size
300,300,300, pixel 0.834, shown at level 0.205, step 2, values float32  
Opened cryosparc_P10_J41_005_volume_map_sharp.mrc, grid size 300,300,300,
pixel 0.834, shown at level 0.231, step 2, values float32  

> select #2:start-88

341 atoms, 347 bonds, 1 model selected  

> color sel #FEE440

> select #2:89-391

2396 atoms, 2445 bonds, 1 model selected  

> color sel #9B5DE5

> select #2:392-615

1665 atoms, 1690 bonds, 2 pseudobonds, 2 models selected  

> color sel #F15BB5

> select #2:692-1018

2422 atoms, 2488 bonds, 4 pseudobonds, 2 models selected  

> color sel #00BBF9

> select #2:1019-end

2352 atoms, 2393 bonds, 1 model selected  

> color sel #00F5D4

> select #2

9176 atoms, 9366 bonds, 8 pseudobonds, 2 models selected  

> hide sel atoms

> lighting soft

> graphics silhouettes true width 2 depthJump .3

> volume #3 color #f7fff90b

> show #!3 models

> volume #3 step 1

> volume #3 level 0.2652

> undo

> undo

> hide sel atoms

> volume #1 color #f7fff90b

> volume #1 color #f7fff90a

> volume #3 color #cdcdcd

> volume #3 level 0.4873

> surface dust #3 size 25 update true

> color zone #3 near #2 distance 3

> volume #3 level 0.5898

> surface dust #3 size 15 update true

> surface dust #3 size 10 update true

> surface dust #3 size 12 update true

> surface dust #3 size 13 update true

> 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

> show #!2 models

> hide #!2 models

> volume #3 level 0.4617

> surface dust #3 size 15 update true

> surface dust #3 size 20 update true

> surface dust #3 size 25 update true

> surface dust #3 size 20 update true

> volume #1 level 0.08724

> volume #1 level 0.06653

> volume #1 step 1

> volume #1 level 0.06537

> volume #3 level 0.4617

> volume #3 level 0.5044

> surface dust #3 size 25 update true

> surface dust #3 size 15 update true

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> lighting soft

> lighting full

> lighting full

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> volume #1 level 0.05143

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> color zone #3 near #2 distance 4

> color zone #3 near #2 distance 5

> color zone #3 near #2 distance 6

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

> hide #!3 models

> select clear

> hide #!2 models

> show #!3 models

> show #!1 models

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> hide #!1 models

> hide #!3 models

> show #!2 models

> select ::name="ATP"

62 atoms, 66 bonds, 1 model selected  

> select ATP

Expected an objects specifier or a keyword  

> select ::name="ATP","Mg"

Expected an objects specifier or a keyword  

> select ::name="ATP"

62 atoms, 66 bonds, 1 model selected  

> select ::name="ATP" and sel ::name="Mg"

Expected a keyword  

> select ::name="ATP" sel ::name="Mg"

Expected a keyword  

> select ::name="ATP,""Mg"

Expected an objects specifier or a keyword  

> select ::name="ATP"

62 atoms, 66 bonds, 1 model selected  

> style sel sphere

Changed 62 atom styles  

> show sel atoms

> color sel byhetero

> color sel grey

> color sel byhetero

> select clear

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2d.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> hide #!2 models

> show #!1 models

> show #!3 models

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> undo

> show #!3 models

> hide #!1 models

> hide #!3 models

> show #!2 models

> select up

Nothing selected  

> select ::name="ATP"

62 atoms, 66 bonds, 1 model selected  

> lighting grey

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

> select light grey

Expected an objects specifier or a keyword  

> color light grey

> undo

> color sel light grey

> color sel byhetero

> select clear

> select ::name="ATP"

62 atoms, 66 bonds, 1 model selected  

> color sel grey

> color sel byhetero

> select clear

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2d.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> select ::name="ATP"

62 atoms, 66 bonds, 1 model selected  

> color sel #FEE440

> color sel byhetero

> select clear

> save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2d_v2.tiff width 2400
> height 2400 supersample 3 transparentBackground true

> select #2:757

9 atoms, 8 bonds, 1 model selected  

> volume #3 level 0.3848

> volume #3 level 0.4531

> open /Users/Hoodwinked/Desktop/cynthia/2o1v_lpf.mrc

Opened 2o1v_lpf.mrc, grid size 256,256,256, pixel 1.44, shown at level 130,
step 1, values float32  

> volume #4 level 310.1

> close #4

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #3

> close #1

> open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/aligned_MRP4_apo.pdb

Chain information for aligned_MRP4_apo.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close #1

> close

> open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/aligned_MRP4_apo.pdb

Chain information for aligned_MRP4_apo.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/MRP4_ATP_bound.pdb

Chain information for MRP4_ATP_bound.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> show #!1 models

> hide atoms

> hide atoms

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting flat

> lighting soft

> lighting full

> lighting soft

> modeHelix tube

Unknown command: modeHelix tube  

> modehelix

Unknown command: modehelix  

> cartoon style protein cylinders

Expected a keyword  

> cartoon style protein cylinders

Expected a keyword  

> cartoon style protein cylinder

Expected a keyword  

> cartoon style protein modeHelix tube

> cartoon style protein modeHelix cylinder

Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'  

> cartoon style protein modeHelix cylinders

Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'  

> cartoon style protein modeHelix wrap

> cartoon style protein modeHelix default

> cartoon style protein modeHelix wrap

> cartoon style protein modeHelix tube

> cartoon style protein modeHelix default

> open
> /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_apo_210402_final.pdb

Chain information for MRP4_apo_210402_final.pdb #3  
---  
Chain | Description  
A | No description available  
  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker aligned_MRP4_apo.pdb, chain A (#1) with MRP4_apo_210402_final.pdb,
chain A (#3), sequence alignment score = 5847.8  
RMSD between 1139 pruned atom pairs is 0.156 angstroms; (across all 1144
pairs: 0.719)  
  

> hide #!2 models

> hide #!3 models

> show #!3 models

> close #1

> show #!2 models

Cannot determine format for '#3'  
Cannot determine format for '#3'  

> save #3 /Data/For_Publication/Figure_4/A/apo_aligned_use.pdb format pdb

Expected a models specifier or a keyword  

> save /Data/For_Publication/Figure_4/A/apo_aligned_use.pdb pdb #3

Expected a models specifier or a keyword  

> save /Data/For_Publication/Figure_4/A/apo_aligned_use.pdb format pdb models
> #3

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pdb/__init__.py", line 70, in save  
pdb.save_pdb(session, path, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pdb/pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
OSError: Unable to open file
'/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb' for writing  
  
OSError: Unable to open file
'/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb' for writing  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pdb/pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  

> save /Users/Hoodwinked/Data/For_Publication/Figure_4/Aapo_aligned_use.pdb
> format pdb models #3

> save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb
> format pdb models #3

> save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb
> format pdb models #3

> select #:391

Expected an objects specifier or a keyword  

> select :391

27 atoms, 25 bonds, 2 models selected  

> select :390-696

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> hide sel cartoons

> select :1018-end

6904 atoms, 6985 bonds, 2 models selected  

> hide sel cartoons

> select up

6939 atoms, 7021 bonds, 2 models selected  

> select up

27630 atoms, 28008 bonds, 2 models selected  

> select up

27630 atoms, 28008 bonds, 2 models selected  

> select down

6939 atoms, 7021 bonds, 2 models selected  

> select down

6904 atoms, 6985 bonds, 2 models selected  

> select down

6904 atoms, 6985 bonds, 2 models selected  

> select down

6904 atoms, 6985 bonds, 2 models selected  

> view sel

> ui tool show "Side View"

> cartoon style protein modeHelix tube

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> cartoon style protein modeHelix default

> select #:697-860

Expected an objects specifier or a keyword  

> select :697-860

3768 atoms, 3836 bonds, 4 pseudobonds, 4 models selected  

> color sel grey

> color sel light grey

> color sel stone

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

> color sel grey

> select :974-1017

1028 atoms, 1036 bonds, 2 models selected  

> color sel grey

> select up

1105 atoms, 1113 bonds, 2 models selected  

> select up

27630 atoms, 28008 bonds, 2 models selected  

> select :233-345

2745 atoms, 2771 bonds, 2 models selected  

> color sel grey

> select #3/A:1017

14 atoms, 13 bonds, 1 model selected  

> select clear

> select grey and #1

Expected an objects specifier or a keyword  

> select grey and #2

Expected an objects specifier or a keyword  

> hide cartoons

> hide cartoons

> show cartoons

> show cartoons

> select :390-696

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> hide sel cartoons

> select up

5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected  

> select down

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> select :1018-end

6904 atoms, 6985 bonds, 2 models selected  

> hide sel cartoons

> select :233-345

2745 atoms, 2771 bonds, 2 models selected  

> transperancy sel 50

Unknown command: transperancy sel 50  

> transparancy sel 50

Unknown command: transparancy sel 50  

> select transparency 50

Expected an objects specifier or a keyword  

> transparency 50

> transparency 50 target r

> transparency 0 target r

> transparency 0 sel

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

> select transparency 0

Expected an objects specifier or a keyword  

> transparency 0

> transparency 50

> transparency 50 target sel

Invalid "target" argument: Character 'e' is not an allowed target, must be one
of acrsbpfl  

> transparency sel 50 target cartoon

Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbpfl  

> transparency sel 50 cartoons

> select clear

> select :390-696

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> select up

5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected  

> select up

27630 atoms, 28008 bonds, 10 pseudobonds, 4 models selected  

> select down

5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected  

> select down

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> select up

5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected  

> select up

27630 atoms, 28008 bonds, 10 pseudobonds, 4 models selected  

> select down

5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected  

> select down

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> select down

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> transparency 50

> select :390-696

4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected  

> select :233-345

2745 atoms, 2771 bonds, 2 models selected  

> transparency sel 100 cartoons

> transparency sel 0 cartoons

> select :233-345

2745 atoms, 2771 bonds, 2 models selected  

> select :233-345

2745 atoms, 2771 bonds, 2 models selected  

> select :974-1017

1028 atoms, 1036 bonds, 2 models selected  

> select :697-860

3768 atoms, 3836 bonds, 4 pseudobonds, 4 models selected  

> select :233-345,697-860,974-1017

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> transparency sel 50 cartoons

> select clear

> transparency sel 25 cartoons

> select :233-345,697-860,974-1017

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> transparency sel 25 cartoons

> select clear

> transparency sel 75 cartoons

> select :233-345,697-860,974-1017

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> transparency sel 25 cartoons

> transparency sel 80 cartoons

> transparency sel 75 cartoons

> select clear

> select :48-232

4445 atoms, 4515 bonds, 2 models selected  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> show sel cartoons

> show sel cartoons

> select :346-398

1218 atoms, 1230 bonds, 2 models selected  

> select :861-973

2682 atoms, 2735 bonds, 2 pseudobonds, 3 models selected  

> select #2:233-345,974-1017,861-973

2042 atoms, 2086 bonds, 2 pseudobonds, 2 models selected  

> select #2:233-345,974-1017

1236 atoms, 1253 bonds, 1 model selected  

> select #2:233-345,974-1017,697-860

2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected  

> transparency sel 0 cartoons

> color sel grey

> color sel light grey

> select clear

> select :233-345,974-1017,697-860

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> transparency sel 0 cartoons

> select clear

> ui mousemode right select

Drag select of 6 pseudobonds, 1293 residues  

> cartoon style protein modeHelix tube

> cartoon style protein modeHelix licorice

Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'  

> cartoon style protein modeHelix default

> cartoon style protein modeHelix tube

> select clear

> select clear

> undo

> cartoon style protein modeHelix default

> select :47-390,617-1018

15861 atoms, 16106 bonds, 6 pseudobonds, 4 models selected  

> select :47-390

8285 atoms, 8397 bonds, 2 models selected  

> select clear

> select :47-232

4452 atoms, 4522 bonds, 2 models selected  

> select clear

> select :346-389

1061 atoms, 1073 bonds, 2 models selected  

> select :47-232,346-389,861-973

8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected  

> select :47-232

4452 atoms, 4522 bonds, 2 models selected  

> select :47-79

780 atoms, 790 bonds, 2 models selected  

> color sel #FEE440

> sel:80-232,346-389,861-973

Unknown command: sel:80-232,346-389,861-973  

> select :80-232,346-389,861-973

7415 atoms, 7538 bonds, 2 pseudobonds, 3 models selected  

> color sel #9B5DE5

> select :46-232,346-389,861-973

8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 50 cartoons

> transparency sel 90 cartoons

> select clear

> transparency sel 75 cartoons

> transparency sel 65 cartoons

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 65 cartoons

> select clear

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 70 cartoons

> select clear

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select :47-232,346-389,861-973

8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select :47-232,346-389,861-973

8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected  

> select :47-232,346-389,861-973

8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected  

> select :47-232,346-389,861-973

8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select #2:233-345,974-1017,697-860

2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected  

> select #:233-345,974-1017,697-860

Expected an objects specifier or a keyword  

> select :233-345,974-1017,697-860

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> color sel grey

> select clear

> select :233-345,974-1017,697-860

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> select :233-345,974-1017,697-860

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> color sel #e3dac9

> select clear

> select clear

> select :233-345,974-1017,697-860

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> select #2:233-345,974-1017,697-860

2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected  

> select clear

> transparency sel 70 cartoons

> select #2:233-345,974-1017,697-860

2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected  

> select :233-345,974-1017,697-860

7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected  

> select #2:46-232,346-389,861-973

2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected  

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 80 cartoons

> select clear

> select clear

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> select :1018-end

6904 atoms, 6985 bonds, 2 models selected  

> show sel cartoons

> color sel bone

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

> color sel #e3dac9

> select clear

> select :389-600

4586 atoms, 4636 bonds, 6 pseudobonds, 4 models selected  

> show sel cartoons

> select :390-600

4555 atoms, 4603 bonds, 6 pseudobonds, 4 models selected  

> color sel #F15BB5

> select #3:390-600

2989 atoms, 3012 bonds, 4 pseudobonds, 2 models selected  

> transparency sel 80 cartoons

> select clear

> save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210414.cxs

> select up

Nothing selected  

> select :1018-end

6904 atoms, 6985 bonds, 2 models selected  

> hide sel cartoons

> select :391-600

4528 atoms, 4576 bonds, 6 pseudobonds, 4 models selected  

> hide sel cartoons

> select #2/A:390

8 atoms, 7 bonds, 1 model selected  

> hide sel atoms

> hide sel cartoons

> save /Users/Hoodwinked/Desktop/image22.png supersample 3

> save /Users/Hoodwinked/Desktop/image22.png supersample 3
> transparentBackground true

> save /Users/Hoodwinked/Desktop/image22.png supersample 3
> transparentBackground true

> save /Users/Hoodwinked/Desktop/image22.png supersample 3
> transparentBackground true

> save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210414.cxs

opened ChimeraX session  

> select up

625 atoms, 632 bonds, 2 models selected  

> select clear

> save /Users/Hoodwinked/Desktop/image22.tiff supersample 3
> transparentBackground true

> save /Users/Hoodwinked/Desktop/image22.tiff 2400 2400 supersample 3
> transparentBackground true

Expected a keyword  

> save /Users/Hoodwinked/Desktop/image22.tiff 2400 supersample 3
> transparentBackground true

Expected a keyword  

> save /Users/Hoodwinked/Desktop/image22.tiff supersample 3 2400 2400
> transparentBackground true

Expected a keyword  

> save /Users/Hoodwinked/Desktop/image22.tiff supersample 3 width 2400 height
> 2400 transparentBackground true

> save /Users/Hoodwinked/Desktop/image222.tiff supersample 3 width 2400 height
> 2400 transparentBackground true

> select #3:390-600

2989 atoms, 3012 bonds, 4 pseudobonds, 2 models selected  

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 60 cartoons

> select clear

> select clear

> save /Users/Hoodwinked/Desktop/image22260.tiff supersample 3 width 2400
> height 2400 transparentBackground true

> transparency sel 70 cartoons

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 70 cartoons

> save /Users/Hoodwinked/Desktop/image22270.tiff supersample 3 width 2400
> height 2400 transparentBackground true

> select clear

> select #3:46-232,346-389,861-973

5561 atoms, 5629 bonds, 1 model selected  

> transparency sel 80 cartoons

> save /Users/Hoodwinked/Desktop/image22280.tiff supersample 3 width 2400
> height 2400 transparentBackground true

> select clear

> save /Users/Hoodwinked/Desktop/image22280.tiff supersample 3 width 2400
> height 2400 transparentBackground true

> angle #2.281;342;916 short

Unknown command: angle #2.281;342;916 short  

> angle #2.281 #2.342 #2.916 short

Unknown command: angle #2.281 #2.342 #2.916 short  

> angle #2:281 #2:342 #2:916 short

Unknown command: angle #2:281 #2:342 #2:916 short  

> save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210415.cxs

opened ChimeraX session  

> angle #2:281 #2:342 #2:916 short

angle is provided by the uninstalled bundle SEQCROW  
Downloading bundle SEQCROW-0.25.2-py3-none-any.whl  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.100.359.0.0 (iBridge: 17.16.14263.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E266)
      Kernel Version: Darwin 19.4.0
      Time since boot: 49 days 3 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.01.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LED Cinema Display:
          Display Type: LCD
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2A0292VN0K0 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StrudelScore: 0.1.3
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    mrcfile: 1.3.0
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    pandas: 1.2.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    recordtype: 1.3
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.25.2
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    threed-strudel: 0.6
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Toolshed reporting obsolete command

Hi Sergei,

The problem is that only older versions of SEQCROW provide the 'angle' command and the toolshed is installing the latest version. The reason SEQCROW dropped the command is because 'angle' is now a builtin command to ChimeraX, but you have to get the daily build. So getting the daily build would be the easiest way for you to resolve this problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Greg Couch, 5 years ago

Milestone: → 1.3
Resolution: → fixed
Status: assigned → closed

Changed message to show which versions of a bundle to install, This will show up in the 1.2 release.

Note: See TracTickets for help on using tickets.