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#6502 closed defect (duplicate)

Problem saving blast table info in session

Reported by:	chimerax-bug-report@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.4.0-210-generic-x86_64-with-glibc2.23
ChimeraX Version: 1.3rc202112030319 (2021-12-03 03:19:12 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3rc202112030319 (2021-12-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/soto/Dropbox/GalanLab/OrgA/pod.cxs format session

Opened 8544 as #1, grid size 400,400,400, pixel 2.6, shown at level 4.67, step
2, values float32  
opened ChimeraX session  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #2.2,0.75251,-0.36858,-0.54578,-158.76,0.55107,0.80619,0.21536,128.18,0.36063,-0.46282,0.80978,-1.5127

> undo

> select #2.2/b

4758 atoms, 4810 bonds, 303 residues, 1 model selected  

> select #2.2/b:1-130

2059 atoms, 2089 bonds, 130 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2.2,0.75251,-0.36858,-0.54578,-185.61,0.55107,0.80619,0.21536,135.68,0.36063,-0.46282,0.80978,-4.2734

> undo

> ui mousemode right "translate selected atoms"

> undo

[Repeated 2 time(s)]

> ui mousemode right pivot

> ui mousemode right "color key"

> ui mousemode right pivot

> undo

> ui mousemode right "map eraser"

> undo

> close session

> open "/home/soto/Dropbox/GalanLab/OrgA/reconstruct map.cxs" format session

Opened 8544 as #1, grid size 400,400,400, pixel 2.6, shown at level 4.67, step
2, values float32  
opened ChimeraX session  

> open /home/soto/Dropbox/GalanLab/OrgA/Paper/PrgH-OrgA-SpaONter.pdb

Chain information for PrgH-OrgA-SpaONter.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select #3

6929 atoms, 7020 bonds, 434 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,90.916,0,1,0,-164.96,0,0,1,-196.72

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.14799,-0.27109,0.95111,96.493,-0.93878,0.26403,0.22133,-167.84,-0.31112,-0.92563,-0.21542,-211.74

> view matrix models
> #3,0.087406,-0.43797,0.89473,94.879,-0.9748,-0.22268,-0.013773,-173.25,0.20527,-0.87097,-0.44639,-213.69

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.087406,-0.43797,0.89473,-55.777,-0.9748,-0.22268,-0.013773,-102.68,0.20527,-0.87097,-0.44639,-238.38

> view matrix models
> #3,0.087406,-0.43797,0.89473,-64.58,-0.9748,-0.22268,-0.013773,-165.27,0.20527,-0.87097,-0.44639,-227.77

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.087406,-0.43797,0.89473,-46.591,-0.9748,-0.22268,-0.013773,-108.61,0.20527,-0.87097,-0.44639,-186.79

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.18201,0.19221,-0.96433,-54.126,0.96723,0.14159,0.21078,-107.36,0.17705,-0.97109,-0.16014,-185.64

> volume #1 style mesh

> view matrix models
> #3,0.18717,-0.0090524,-0.98229,-55.865,0.98042,-0.060658,0.18737,-109.15,-0.06128,-0.99812,-0.002478,-184.41

> view matrix models
> #3,0.19565,-0.009113,-0.98063,-55.869,0.97869,-0.061753,0.19584,-109.1,-0.062342,-0.99805,-0.0031635,-184.41

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.19565,-0.009113,-0.98063,-55.92,0.97869,-0.061753,0.19584,-115.23,-0.062342,-0.99805,-0.0031635,-189.36

> view matrix models
> #3,0.19565,-0.009113,-0.98063,-49.137,0.97869,-0.061753,0.19584,-123.43,-0.062342,-0.99805,-0.0031635,-185.05

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 6.949, steps = 228  
shifted from previous position = 35.9  
rotated from previous position = 77.1 degrees  
atoms outside contour = 1945, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.66511563 -0.65351929 -0.36129451 -39.79678356  
0.07914854 -0.41940708 0.90434130 -116.13471489  
-0.74253396 -0.63008748 -0.22722911 -148.58612182  
Axis -0.88054530 0.21877758 0.42044780  
Axis point 0.00000000 -104.95062499 -49.08833383  
Rotation angle (degrees) 119.39056493  
Shift along axis -52.83750916  
  

> view matrix models
> #3,0.66512,-0.65352,-0.36129,-49.038,0.079149,-0.41941,0.90434,-134.72,-0.74253,-0.63009,-0.22723,-209.87

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.48134,-0.098366,-0.871,-46.13,0.87188,0.048524,-0.48731,-141.57,0.090199,-0.99397,0.062407,-212.21

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #3,-0.48134,-0.098366,-0.871,-57.449,0.87188,0.048524,-0.48731,-129.48,0.090199,-0.99397,0.062407,-175.93

> view matrix models
> #3,-0.48134,-0.098366,-0.871,-58.659,0.87188,0.048524,-0.48731,-130.83,0.090199,-0.99397,0.062407,-184.19

> view matrix models
> #3,-0.48134,-0.098366,-0.871,-62.289,0.87188,0.048524,-0.48731,-127.14,0.090199,-0.99397,0.062407,-181.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.48134,-0.098366,-0.871,-60.343,0.87188,0.048524,-0.48731,-127.97,0.090199,-0.99397,0.062407,-177.72

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.87864,-0.15329,0.45221,-54.157,-0.47659,-0.22346,0.85025,-119.01,-0.029289,-0.96258,-0.2694,-179.49

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 4.673, steps = 72  
shifted from previous position = 13.9  
rotated from previous position = 11.9 degrees  
atoms outside contour = 3372, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.92730217 -0.12863039 0.35151798 -49.74763656  
-0.37276648 -0.40263863 0.83601870 -123.41066555  
0.03399730 -0.90627609 -0.42131678 -192.75540270  
Axis -0.97457973 0.17761013 -0.13656132  
Axis point 0.00000000 -124.98487473 -50.84178500  
Rotation angle (degrees) 116.63637198  
Shift along axis 52.88698593  
  

> volume #1 level 9.967

> volume #1 level 4.671

> view matrix models
> #3,0.91045,-0.12012,0.39578,-49.356,-0.41092,-0.37173,0.83244,-123.12,0.047133,-0.92053,-0.38781,-192.67

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.91045,-0.12012,0.39578,-46.647,-0.41092,-0.37173,0.83244,-122.53,0.047133,-0.92053,-0.38781,-186.53

> select #3/c

2031 atoms, 2065 bonds, 129 residues, 1 model selected  

> color #3/c red

> color #3/c firebrick

> color #3/a mediumblue

> color #3/a gray

> view matrix models
> #3,0.91045,-0.12012,0.39578,-46.647,-0.41092,-0.37173,0.83244,-122.53,0.047133,-0.92053,-0.38781,-186.53

> select #3

6929 atoms, 7020 bonds, 434 residues, 1 model selected  

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.47049,-0.022781,-0.88211,-52.156,0.85719,0.22546,-0.46302,-128.48,0.20943,-0.97399,-0.086549,-185.21

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.54629,-0.056314,-0.8357,-51.991,0.80627,0.23496,-0.54288,-128.85,0.22693,-0.97037,-0.082951,-185.18

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.54629,-0.056314,-0.8357,-58.82,0.80627,0.23496,-0.54288,-122.91,0.22693,-0.97037,-0.082951,-184.48

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 6.949, steps = 244  
shifted from previous position = 40.3  
rotated from previous position = 123 degrees  
atoms outside contour = 1951, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.66518718 -0.65353728 -0.36113020 -39.77932654  
0.07952866 -0.41888730 0.90454884 -116.09910866  
-0.74242925 -0.63041450 -0.22666352 -148.61370470  
Axis -0.88052304 0.21873004 0.42051913  
Axis point 0.00000000 -104.96711966 -49.08530437  
Rotation angle (degrees) 119.35253289  
Shift along axis -52.86265506  
  

> view matrix models
> #3,0.66519,-0.65354,-0.36113,-55.381,0.079529,-0.41889,0.90455,-119.53,-0.74243,-0.63041,-0.22666,-181.85

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.11019,-0.60538,0.78827,-46.049,-0.62198,-0.57661,-0.52977,-129.23,0.77524,-0.54867,-0.313,-184.24

> view matrix models
> #3,0.088681,0.70816,-0.70046,-45.807,0.98883,-0.14718,-0.023613,-125.04,-0.11982,-0.69054,-0.7133,-186.59

> view matrix models
> #3,-0.36318,-0.41354,0.83492,-43.788,-0.81856,-0.2864,-0.49792,-126.37,0.44503,-0.86427,-0.2345,-185.71

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 4.781, steps = 312  
shifted from previous position = 19.7  
rotated from previous position = 115 degrees  
atoms outside contour = 3156, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
-0.67272675 0.14014009 -0.72649808 -46.55530615  
0.72203098 0.33878124 -0.60324002 -127.45305151  
0.16158581 -0.93036982 -0.32909270 -205.40749631  
Axis -0.29444831 -0.79936097 0.52375780  
Axis point 39.96018117 0.00000000 -152.84363679  
Rotation angle (degrees) 146.25510458  
Shift along axis 8.00534830  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.67273,0.14014,-0.7265,-43.338,0.72203,0.33878,-0.60324,-123.99,0.16159,-0.93037,-0.32909,-190.92

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.68045,-0.41495,0.60399,-38.876,-0.52415,-0.30041,-0.79689,-128.37,0.51211,-0.85882,-0.013082,-188.81

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 4.781, steps = 284  
shifted from previous position = 16.7  
rotated from previous position = 94.4 degrees  
atoms outside contour = 3156, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
-0.67307949 0.14007886 -0.72618311 -46.55352541  
0.72172793 0.33878800 -0.60359877 -127.45594598  
0.16147070 -0.93037659 -0.32913008 -205.40166385  
Axis -0.29428355 -0.79938691 0.52381081  
Axis point 39.91965456 0.00000000 -152.83955170  
Rotation angle (degrees) 146.27488025  
Shift along axis 7.99493991  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.67308,0.14008,-0.72618,-44.409,0.72173,0.33879,-0.6036,-124.56,0.16147,-0.93038,-0.32913,-191.26

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.37885,0.91119,-0.1619,-34.944,-0.36324,-0.30731,-0.87956,-129.81,-0.85119,-0.27441,0.4474,-179.16

> view matrix models
> #3,-0.33015,0.94372,0.019938,-33.548,0.036495,0.033869,-0.99876,-128.52,-0.94322,-0.32902,-0.045623,-182.75

> view matrix models
> #3,-0.41632,0.90892,0.023334,-33.663,-0.43563,-0.17688,-0.88257,-128.67,-0.79806,-0.3776,0.46959,-179.93

> view matrix models
> #3,-0.64438,0.75775,0.10286,-33.97,-0.36961,-0.19087,-0.90937,-129.06,-0.66945,-0.624,0.40307,-182.55

> view matrix models
> #3,-0.68413,0.72489,-0.080635,-35.394,-0.25774,-0.3437,-0.90302,-130.43,-0.6823,-0.597,0.42197,-182.19

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 3.209, steps = 256  
shifted from previous position = 6.82  
rotated from previous position = 40.4 degrees  
atoms outside contour = 4607, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
-0.27145304 0.89122217 -0.36336798 -36.77840587  
0.23386023 -0.30515204 -0.92314225 -137.27555093  
-0.93360732 -0.33556709 -0.12558697 -181.48908819  
Axis 0.55958468 0.54307470 -0.62604701  
Axis point -132.86991170 -136.68104893 -0.00000000  
Rotation angle (degrees) 148.33108032  
Shift along axis 18.48919044  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.27223,-0.49459,0.82539,-40.814,-0.92175,-0.38022,0.076181,-129.31,0.27615,-0.78155,-0.55939,-189.93

> view matrix models
> #3,0.073972,-0.45207,0.88891,-39.726,-0.87851,-0.45138,-0.15645,-131.51,0.47196,-0.76935,-0.43054,-189.29

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.073972,-0.45207,0.88891,59.774,-0.87851,-0.45138,-0.15645,-84.997,0.47196,-0.76935,-0.43054,-235.12

> view matrix models
> #3,0.073972,-0.45207,0.88891,74.83,-0.87851,-0.45138,-0.15645,-115.77,0.47196,-0.76935,-0.43054,-194.59

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.67737,0.19692,-0.70879,68.363,0.73006,-0.2984,0.61479,-112.01,-0.090438,-0.9339,-0.34589,-194.43

> fitmap #3 inMap #1

Fit molecule PrgH-OrgA-SpaONter.pdb (#3) to map 8544 (#1) using 6929 atoms  
average map value = 4.673, steps = 76  
shifted from previous position = 13.5  
rotated from previous position = 12.6 degrees  
atoms outside contour = 3385, contour level = 4.6711  
  
Position of PrgH-OrgA-SpaONter.pdb (#3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.78864652 0.28578452 -0.54439312 82.07999217  
0.61378988 -0.31404276 0.72431977 -104.85257395  
0.03603666 -0.90537525 -0.42308037 -192.78241845  
Axis -0.92554604 -0.32964111 0.18628275  
Axis point 0.00000000 -124.59069780 -46.08189187  
Rotation angle (degrees) 118.30976770  
Shift along axis -77.31713103  
  

> view matrix models
> #3,0.76031,0.30573,-0.57312,82.094,0.64874,-0.31305,0.69364,-105.11,0.032655,-0.89918,-0.43635,-192.82

> ui mousemode right translate

> select #2

30330 atoms, 30545 bonds, 20 pseudobonds, 3907 residues, 8 models selected  

> select #2.1

19607 atoms, 19905 bonds, 18 pseudobonds, 2563 residues, 3 models selected  

> select #2.2

5487 atoms, 5584 bonds, 2 pseudobonds, 714 residues, 2 models selected  

> select #2.3

3714 atoms, 3754 bonds, 226 residues, 1 model selected  

> view sel

> ui tool show "Blast Protein"

Cannot run BLAST without a chain.  

> select #2.3

3714 atoms, 3754 bonds, 226 residues, 1 model selected  

> select #2.3

3714 atoms, 3754 bonds, 226 residues, 1 model selected  

> select #2.1

19607 atoms, 19905 bonds, 18 pseudobonds, 2563 residues, 3 models selected  

> select #2.4

1522 atoms, 1302 bonds, 404 residues, 1 model selected  

> select #2.3

3714 atoms, 3754 bonds, 226 residues, 1 model selected  

> select #2.2

5487 atoms, 5584 bonds, 2 pseudobonds, 714 residues, 2 models selected  

> select #2.2/A

3418 atoms, 3481 bonds, 2 pseudobonds, 446 residues, 2 models selected  

> select #2.2/B

Nothing selected  

> select #2.2/c

Nothing selected  

> select #2.2/d

Nothing selected  

> select #2.2/a

3418 atoms, 3481 bonds, 2 pseudobonds, 446 residues, 2 models selected  

> select #2.2/e

1040 atoms, 1057 bonds, 135 residues, 1 model selected  

> select #2.2/i

1029 atoms, 1046 bonds, 133 residues, 1 model selected  

> select #2.2/e

1040 atoms, 1057 bonds, 135 residues, 1 model selected  

> blastprotein #2.2/E database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> name bp1

ChimeraX REST job id: 6RV5986TAZLU7ZD9  
BlastProtein finished.  
Parsing BLAST results.  

> blastprotein #2.2/E database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp2

ChimeraX REST job id: 6D4LIN5AHKPE5R48  

> select #2.2/i

1029 atoms, 1046 bonds, 133 residues, 1 model selected  

> select #2.2/a

3418 atoms, 3481 bonds, 2 pseudobonds, 446 residues, 2 models selected  

> select #2.3

3714 atoms, 3754 bonds, 226 residues, 1 model selected  

> select #2.4

1522 atoms, 1302 bonds, 404 residues, 1 model selected  

> select #2.4 and #2.3

Expected a keyword  

> select #2.3-4

5236 atoms, 5056 bonds, 630 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2.3,0.78653,0.22037,0.57689,-55.112,-0.53934,0.70014,0.46788,16.492,-0.3008,-0.67914,0.66954,95.585,#2.4,0.78653,0.22037,0.57689,-55.112,-0.53934,0.70014,0.46788,16.492,-0.3008,-0.67914,0.66954,95.585

> ui mousemode right "translate selected models"

> view matrix models
> #2.3,0.78653,0.22037,0.57689,-131.32,-0.53934,0.70014,0.46788,21.137,-0.3008,-0.67914,0.66954,113.64,#2.4,0.78653,0.22037,0.57689,-131.32,-0.53934,0.70014,0.46788,21.137,-0.3008,-0.67914,0.66954,113.64

> view matrix models
> #2.3,0.78653,0.22037,0.57689,-130.69,-0.53934,0.70014,0.46788,19.74,-0.3008,-0.67914,0.66954,113.71,#2.4,0.78653,0.22037,0.57689,-130.69,-0.53934,0.70014,0.46788,19.74,-0.3008,-0.67914,0.66954,113.71

> ui mousemode right "rotate selected models"

> view matrix models
> #2.3,0.63814,0.42987,0.63873,-129.8,-0.67959,0.70439,0.2049,69.641,-0.36184,-0.56484,0.74164,109.4,#2.4,0.63814,0.42987,0.63873,-129.8,-0.67959,0.70439,0.2049,69.641,-0.36184,-0.56484,0.74164,109.4

> ui mousemode right "translate selected models"

> view matrix models
> #2.3,0.63814,0.42987,0.63873,-80.664,-0.67959,0.70439,0.2049,63.061,-0.36184,-0.56484,0.74164,104.25,#2.4,0.63814,0.42987,0.63873,-80.664,-0.67959,0.70439,0.2049,63.061,-0.36184,-0.56484,0.74164,104.25

> view matrix models
> #2.3,0.63814,0.42987,0.63873,-118.35,-0.67959,0.70439,0.2049,79.76,-0.36184,-0.56484,0.74164,110.47,#2.4,0.63814,0.42987,0.63873,-118.35,-0.67959,0.70439,0.2049,79.76,-0.36184,-0.56484,0.74164,110.47

> view matrix models
> #2.3,0.63814,0.42987,0.63873,-115.65,-0.67959,0.70439,0.2049,81.841,-0.36184,-0.56484,0.74164,109.8,#2.4,0.63814,0.42987,0.63873,-115.65,-0.67959,0.70439,0.2049,81.841,-0.36184,-0.56484,0.74164,109.8

> ui mousemode right "rotate selected models"

> view matrix models
> #2.3,0.43761,0.32416,0.8387,-114.45,-0.81422,0.53861,0.21666,100.9,-0.3815,-0.7777,0.49964,147.97,#2.4,0.43761,0.32416,0.8387,-114.45,-0.81422,0.53861,0.21666,100.9,-0.3815,-0.7777,0.49964,147.97

> view matrix models
> #2.3,0.48066,0.25097,0.84023,-117.43,-0.81279,0.48715,0.31946,89.331,-0.32914,-0.83648,0.43814,151.18,#2.4,0.48066,0.25097,0.84023,-117.43,-0.81279,0.48715,0.31946,89.331,-0.32914,-0.83648,0.43814,151.18

> fitmap #2.3-4 inMap #1

Fit molecules reconstruct.pdb (#2.3), reconstruct.pdb (#2.4) to map 8544 (#1)
using 5236 atoms  
average map value = 3.552, steps = 280  
shifted from previous position = 12.9  
rotated from previous position = 45.6 degrees  
atoms outside contour = 3521, contour level = 4.6711  
  
Position of reconstruct.pdb (#2.3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.82834366 0.43931805 0.34762974 -109.39408423  
-0.50899402 0.84940582 0.13940885 58.56763105  
-0.23403390 -0.29241990 0.92721019 71.25522184  
Axis -0.36186004 0.48741736 -0.79465818  
Axis point 29.73811478 251.14899725 0.00000000  
Rotation angle (degrees) 36.63243394  
Shift along axis 11.50868343  
  
Position of reconstruct.pdb (#2.4) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.82834366 0.43931805 0.34762974 -109.39408423  
-0.50899402 0.84940582 0.13940885 58.56763105  
-0.23403390 -0.29241990 0.92721019 71.25522184  
Axis -0.36186004 0.48741736 -0.79465818  
Axis point 29.73811478 251.14899725 0.00000000  
Rotation angle (degrees) 36.63243394  
Shift along axis 11.50868343  
  

> view matrix models
> #2.3,0.68467,0.27403,0.67538,-129.45,-0.65678,0.63374,0.40867,47.901,-0.31603,-0.72338,0.61388,131.66,#2.4,0.68467,0.27403,0.67538,-129.45,-0.65678,0.63374,0.40867,47.901,-0.31603,-0.72338,0.61388,131.66

> ui mousemode right "translate selected models"

> view matrix models
> #2.3,0.68467,0.27403,0.67538,-85.268,-0.65678,0.63374,0.40867,39.814,-0.31603,-0.72338,0.61388,112.79,#2.4,0.68467,0.27403,0.67538,-85.268,-0.65678,0.63374,0.40867,39.814,-0.31603,-0.72338,0.61388,112.79

> fitmap #2.3-4 inMap #1

Fit molecules reconstruct.pdb (#2.3), reconstruct.pdb (#2.4) to map 8544 (#1)
using 5236 atoms  
average map value = 5.171, steps = 120  
shifted from previous position = 4.01  
rotated from previous position = 21.9 degrees  
atoms outside contour = 2730, contour level = 4.6711  
  
Position of reconstruct.pdb (#2.3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.63678605 0.44625335 0.62877776 -79.67805765  
-0.77042144 0.33558224 0.54206582 47.19014882  
0.03089204 -0.82960383 0.55749724 85.31907845  
Axis -0.71125000 0.31002087 -0.63088073  
Axis point -0.00000000 95.07655056 39.47481574  
Rotation angle (degrees) 74.63704203  
Shift along axis 17.47478728  
  
Position of reconstruct.pdb (#2.4) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.63678605 0.44625335 0.62877776 -79.67805765  
-0.77042144 0.33558224 0.54206582 47.19014882  
0.03089204 -0.82960383 0.55749724 85.31907845  
Axis -0.71125000 0.31002087 -0.63088073  
Axis point -0.00000000 95.07655056 39.47481574  
Rotation angle (degrees) 74.63704203  
Shift along axis 17.47478728  
  

> view matrix models
> #2.3,0.63679,0.44625,0.62878,-81.91,-0.77042,0.33558,0.54207,43.95,0.030892,-0.8296,0.5575,87.737,#2.4,0.63679,0.44625,0.62878,-81.91,-0.77042,0.33558,0.54207,43.95,0.030892,-0.8296,0.5575,87.737

> fitmap #2.3-4 inMap #1

Fit molecules reconstruct.pdb (#2.3), reconstruct.pdb (#2.4) to map 8544 (#1)
using 5236 atoms  
average map value = 5.171, steps = 48  
shifted from previous position = 4.63  
rotated from previous position = 0.0246 degrees  
atoms outside contour = 2728, contour level = 4.6711  
  
Position of reconstruct.pdb (#2.3) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.63655285 0.44612748 0.62910312 -79.68517861  
-0.77061846 0.33536773 0.54191851 47.26593807  
0.03078385 -0.82975825 0.55727336 85.37552103  
Axis -0.71118569 0.31021602 -0.63085731  
Axis point 0.00000000 95.12745126 39.45150450  
Rotation angle (degrees) 74.65699382  
Shift along axis 17.47383843  
  
Position of reconstruct.pdb (#2.4) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.63655285 0.44612748 0.62910312 -79.68517861  
-0.77061846 0.33536773 0.54191851 47.26593807  
0.03078385 -0.82975825 0.55727336 85.37552103  
Axis -0.71118569 0.31021602 -0.63085731  
Axis point 0.00000000 95.12745126 39.45150450  
Rotation angle (degrees) 74.65699382  
Shift along axis 17.47383843  
  

> view matrix models
> #2.3,0.63655,0.44613,0.6291,-81.416,-0.77062,0.33537,0.54192,47.148,0.030784,-0.82976,0.55727,84.7,#2.4,0.63655,0.44613,0.6291,-81.416,-0.77062,0.33537,0.54192,47.148,0.030784,-0.82976,0.55727,84.7

> ui mousemode right translate

> select

37259 atoms, 37565 bonds, 20 pseudobonds, 4341 residues, 11 models selected  

> view sel

> ui mousemode right translate

BlastProtein finished.  
BlastProtein failed:  
BlastProtein failed: 'results.json: (400)\nReason: Bad Request\nHTTP response
headers: HTTPHeaderDict({\'Date\': \'Wed, 30 Mar 2022 14:10:17 GMT\',
\'Server\': \'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-
age=63072000; includeSubdomains; preload\', \'Content-Length\': \'107\',
\'vary\': \'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "Invalid parameter",
"description": "The \\\\\\\"6D4LIN5AHKPE5R48\\\\\\\" parameter is invalid. No
such job"}\'\n'  
Parsing BLAST results.  
Parsing BlastProtein results failed: the JSON object must be str, bytes or
bytearray, not NoneType  

> select clear

> select #2.4

1522 atoms, 1302 bonds, 404 residues, 1 model selected  

> select #2.2

5487 atoms, 5584 bonds, 2 pseudobonds, 714 residues, 2 models selected  

> transparency 100 #2.2

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

> transparency #2.2 100 target c

> select clear

> hide #!1 models

> show #!1 models

> volume #1 style surface

> volume #1 style image

> volume #1 maximumIntensityProjection true

> volume #1 level -0.108,0 level 4.669,0.8 level 25.11,1

> volume #1 level -0.108,0 level 5.134,0.6481 level 25.11,1

> volume #1 region 0,0,198,399,399,198 step 1 maximumIntensityProjection false
> showOutlineBox true

> volume #1 region 0,0,0,399,399,399 step 2

> volume #1 style mesh region 0,0,0,399,399,399 step 2

> open "/home/soto/Downloads/2PrgHOrgA feb22/selected_prediction.pdb"

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

> select #4

7264 atoms, 7345 bonds, 459 residues, 1 model selected  

> mmaker #4 to #3

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 PrgH-OrgA-SpaONter.pdb, chain B (#3) with selected_prediction.pdb,
chain C (#4), sequence alignment score = 1022.5  
RMSD between 187 pruned atom pairs is 0.503 angstroms; (across all 199 pairs:
3.749)  
  

> ui mousemode right translate

> hide #!1 models

> show #!1 models

> delete #4

> delete #3

> open "/home/soto/Downloads/2PrgHOrgA feb22/2PrgH-OrgA-SpaONter.pdb"

Summary of feedback from opening /home/soto/Downloads/2PrgHOrgA feb22/2PrgH-
OrgA-SpaONter.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 2 2 ILE B 2
ARG B 10 1 9  
Start residue of secondary structure not found: HELIX 3 3 LEU B 13 PHE B 22 1
10  
Start residue of secondary structure not found: HELIX 4 4 PRO B 24 SER B 26 1
3  
Start residue of secondary structure not found: HELIX 5 5 PRO B 37 ILE B 40 1
4  
Start residue of secondary structure not found: HELIX 6 6 PRO B 43 ALA B 56 1
14  
19 messages similar to the above omitted  
  
Chain information for 2PrgH-OrgA-SpaONter.pdb  
---  
Chain | Description  
3.1/A | No description available  
3.2/A | No description available  
3.1/B | No description available  
3.1/C | No description available  
  

> select #3

8465 atoms, 8569 bonds, 534 residues, 3 models selected  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-35.159,0,1,0,-205.35,0,0,1,-293.27

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.54925,0.20687,-0.80965,-39.745,0.79672,-0.42194,0.43267,-214.69,-0.25211,-0.88271,-0.39657,-310.62

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.54925,0.20687,-0.80965,36.833,0.79672,-0.42194,0.43267,-96.849,-0.25211,-0.88271,-0.39657,-213.5

> view matrix models
> #3,0.54925,0.20687,-0.80965,57.627,0.79672,-0.42194,0.43267,-69.193,-0.25211,-0.88271,-0.39657,-174.5

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.54925,0.20687,-0.80965,73.83,0.79672,-0.42194,0.43267,-106,-0.25211,-0.88271,-0.39657,-179.18

> fitmap #3 inMap #1

Fit molecules 2PrgH-OrgA-SpaONter.pdb (#3.1), 2PrgH-OrgA-SpaONter.pdb (#3.2)
to map 8544 (#1) using 8465 atoms  
average map value = 6.349, steps = 144  
shifted from previous position = 30.6  
rotated from previous position = 24.4 degrees  
atoms outside contour = 2866, contour level = 4.6711  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.1) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.92102940 -0.30829346 -0.23803357 9.14351012  
0.33982476 0.93468546 0.10431795 -23.66933022  
0.19032597 -0.17696960 0.96563854 -12.97523171  
Axis -0.34044309 -0.51844472 0.78441926  
Axis point 73.09254837 9.80955895 0.00000000  
Rotation angle (degrees) 24.40096567  
Shift along axis -1.01962705  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.2) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.92102940 -0.30829346 -0.23803357 9.14351012  
0.33982476 0.93468546 0.10431795 -23.66933022  
0.19032597 -0.17696960 0.96563854 -12.97523171  
Axis -0.34044309 -0.51844472 0.78441926  
Axis point 73.09254837 9.80955895 0.00000000  
Rotation angle (degrees) 24.40096567  
Shift along axis -1.01962705  
  

> view matrix models
> #3,0.54925,0.20687,-0.80965,65.932,0.79672,-0.42194,0.43267,-114.36,-0.25211,-0.88271,-0.39657,-200.13

> select #3.1

6929 atoms, 7020 bonds, 434 residues, 1 model selected  

> select #3.1/b

3266 atoms, 3307 bonds, 199 residues, 1 model selected  

> select #3.1/c

2031 atoms, 2065 bonds, 129 residues, 1 model selected  

> select #3.1/a

1632 atoms, 1648 bonds, 106 residues, 1 model selected  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color #3.1/a skyblue

> color #3.2 skyblue

> color #3.1/b violet

> color #3.1/c green

> select #3

8465 atoms, 8569 bonds, 534 residues, 3 models selected  

> view matrix models
> #3,0.54925,0.20687,-0.80965,59.011,0.79672,-0.42194,0.43267,-122.14,-0.25211,-0.88271,-0.39657,-207.49

> view matrix models
> #3,0.54925,0.20687,-0.80965,59.032,0.79672,-0.42194,0.43267,-117.46,-0.25211,-0.88271,-0.39657,-209.28

> view matrix models
> #3,0.54925,0.20687,-0.80965,66.746,0.79672,-0.42194,0.43267,-115.51,-0.25211,-0.88271,-0.39657,-208.06

> view matrix models
> #3,0.54925,0.20687,-0.80965,76.471,0.79672,-0.42194,0.43267,-113.07,-0.25211,-0.88271,-0.39657,-206.56

> fitmap #3 inMap #1

Fit molecules 2PrgH-OrgA-SpaONter.pdb (#3.1), 2PrgH-OrgA-SpaONter.pdb (#3.2)
to map 8544 (#1) using 8465 atoms  
average map value = 6.349, steps = 124  
shifted from previous position = 28.4  
rotated from previous position = 0.0606 degrees  
atoms outside contour = 2867, contour level = 4.6711  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.1) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.92086416 -0.30873927 -0.23809507 6.42745528  
0.34008637 0.93470417 0.10329265 -51.37261425  
0.19065796 -0.17609139 0.96573359 -18.57207485  
Axis -0.33809285 -0.51884971 0.78516763  
Axis point 135.37109493 -3.03924561 0.00000000  
Rotation angle (degrees) 24.40453503  
Shift along axis 9.89939737  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.2) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.92086416 -0.30873927 -0.23809507 6.42745528  
0.34008637 0.93470417 0.10329265 -51.37261425  
0.19065796 -0.17609139 0.96573359 -18.57207485  
Axis -0.33809285 -0.51884971 0.78516763  
Axis point 135.37109493 -3.03924561 0.00000000  
Rotation angle (degrees) 24.40453503  
Shift along axis 9.89939737  
  

> view matrix models
> #3,0.54925,0.20687,-0.80965,78.863,0.79672,-0.42194,0.43267,-130.24,-0.25211,-0.88271,-0.39657,-244.49

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.55629,-0.061138,0.82874,113.79,-0.66881,-0.55895,-0.49017,-142.7,0.49319,-0.82694,0.27005,-234.45

> view matrix models
> #3,-0.40589,-0.25333,0.87811,101.81,-0.85986,-0.21969,-0.46084,-119.77,0.30966,-0.9421,-0.12866,-248.45

> fitmap #3 inMap #1

Fit molecules 2PrgH-OrgA-SpaONter.pdb (#3.1), 2PrgH-OrgA-SpaONter.pdb (#3.2)
to map 8544 (#1) using 8465 atoms  
average map value = 4.321, steps = 120  
shifted from previous position = 17.8  
rotated from previous position = 33.8 degrees  
atoms outside contour = 4369, contour level = 4.6711  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.1) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.80771537 -0.51463330 0.28766029 5.80356908  
0.48138835 0.85736655 0.18217533 -36.44230918  
-0.34038380 -0.00866950 0.94024662 -25.56278885  
Axis -0.15998900 0.52650179 0.83498466  
Axis point 26.90133023 -11.66322618 0.00000000  
Rotation angle (degrees) 36.61471972  
Shift along axis -41.45998474  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.2) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.80771537 -0.51463330 0.28766029 5.80356908  
0.48138835 0.85736655 0.18217533 -36.44230918  
-0.34038380 -0.00866950 0.94024662 -25.56278885  
Axis -0.15998900 0.52650179 0.83498466  
Axis point 26.90133023 -11.66322618 0.00000000  
Rotation angle (degrees) 36.61471972  
Shift along axis -41.45998474  
  

> view matrix models
> #3,-0.36154,-0.15001,0.92021,107.29,-0.86471,-0.31515,-0.39111,-121.77,0.34867,-0.93711,-0.015778,-245.18

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.36154,-0.15001,0.92021,114.48,-0.86471,-0.31515,-0.39111,-109.65,0.34867,-0.93711,-0.015778,-221.69

> view matrix models
> #3,-0.36154,-0.15001,0.92021,113.71,-0.86471,-0.31515,-0.39111,-107.69,0.34867,-0.93711,-0.015778,-212.01

> fitmap #3 inMap #1

Fit molecules 2PrgH-OrgA-SpaONter.pdb (#3.1), 2PrgH-OrgA-SpaONter.pdb (#3.2)
to map 8544 (#1) using 8465 atoms  
average map value = 4.941, steps = 120  
shifted from previous position = 14.7  
rotated from previous position = 35.9 degrees  
atoms outside contour = 4052, contour level = 4.6711  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.1) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.98908649 -0.03370432 0.14342920 18.72193349  
0.06807378 0.96788702 -0.24199313 -51.45221208  
-0.13066705 0.24911590 0.95961836 -23.61976971  
Axis 0.85925004 0.47956197 0.17807212  
Axis point 0.00000000 54.14880815 -194.45059241  
Rotation angle (degrees) 16.60534224  
Shift along axis -12.79372474  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.2) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.98908649 -0.03370432 0.14342920 18.72193349  
0.06807378 0.96788702 -0.24199313 -51.45221208  
-0.13066705 0.24911590 0.95961836 -23.61976971  
Axis 0.85925004 0.47956197 0.17807212  
Axis point 0.00000000 54.14880815 -194.45059241  
Rotation angle (degrees) 16.60534224  
Shift along axis -12.79372474  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.36154,-0.15001,0.92021,116.18,-0.86471,-0.31515,-0.39111,-112.88,0.34867,-0.93711,-0.015778,-236.16

> view matrix models
> #3,-0.36154,-0.15001,0.92021,107.04,-0.86471,-0.31515,-0.39111,-122.73,0.34867,-0.93711,-0.015778,-235.96

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.69197,-0.27762,-0.66641,28.154,0.45211,-0.55302,0.69983,-123.46,-0.56283,-0.78555,-0.25716,-217.52

> view matrix models
> #3,0.53171,0.023846,-0.84659,42.861,0.73162,-0.51648,0.44496,-135.05,-0.42663,-0.85597,-0.29206,-225.43

> view matrix models
> #3,0.54234,0.029885,-0.83963,43.224,0.7217,-0.52821,0.44737,-135.45,-0.43013,-0.84859,-0.30804,-225.45

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.54234,0.029885,-0.83963,42.345,0.7217,-0.52821,0.44737,-133.47,-0.43013,-0.84859,-0.30804,-216.42

> view matrix models
> #3,0.54234,0.029885,-0.83963,48.091,0.7217,-0.52821,0.44737,-132.49,-0.43013,-0.84859,-0.30804,-227.25

> fitmap #3 inMap #1

Fit molecules 2PrgH-OrgA-SpaONter.pdb (#3.1), 2PrgH-OrgA-SpaONter.pdb (#3.2)
to map 8544 (#1) using 8465 atoms  
average map value = 6.349, steps = 148  
shifted from previous position = 31.6  
rotated from previous position = 33.5 degrees  
atoms outside contour = 2864, contour level = 4.6711  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.1) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.97577377 -0.13516670 -0.17203348 16.35683322  
0.17293767 0.95816210 0.22807445 -79.98524717  
0.13400789 -0.25230014 0.95832485 -35.59976438  
Axis -0.74180888 -0.47259829 0.47578403  
Axis point 0.00000000 -206.25379530 294.77435508  
Rotation angle (degrees) 18.89203846  
Shift along axis 8.72944794  
  
Position of 2PrgH-OrgA-SpaONter.pdb (#3.2) relative to 8544 (#1) coordinates:  
Matrix rotation and translation  
0.97577377 -0.13516670 -0.17203348 16.35683322  
0.17293767 0.95816210 0.22807445 -79.98524717  
0.13400789 -0.25230014 0.95832485 -35.59976438  
Axis -0.74180888 -0.47259829 0.47578403  
Axis point 0.00000000 -206.25379530 294.77435508  
Rotation angle (degrees) 18.89203846  
Shift along axis 8.72944794  
  

> view matrix models
> #3,0.54234,0.029885,-0.83963,37.155,0.7217,-0.52821,0.44737,-143.3,-0.43013,-0.84859,-0.30804,-260.52

> view matrix models
> #3,0.54234,0.029885,-0.83963,36.539,0.7217,-0.52821,0.44737,-143.44,-0.43013,-0.84859,-0.30804,-257.85

> view matrix models
> #3,0.54234,0.029885,-0.83963,38.088,0.7217,-0.52821,0.44737,-146.59,-0.43013,-0.84859,-0.30804,-249.56

> view matrix models
> #3,0.54234,0.029885,-0.83963,31.489,0.7217,-0.52821,0.44737,-151.96,-0.43013,-0.84859,-0.30804,-253.35

> view matrix models
> #3,0.54234,0.029885,-0.83963,31.603,0.7217,-0.52821,0.44737,-138.68,-0.43013,-0.84859,-0.30804,-259.41

> view matrix models
> #3,0.54234,0.029885,-0.83963,31.785,0.7217,-0.52821,0.44737,-145.64,-0.43013,-0.84859,-0.30804,-267.69

> hide #!1 models

> select clear

> show #!1 models

> save "/home/soto/Dropbox/GalanLab/OrgA/Paper/Modelling of the pod.cxs"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 147, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8e96133250> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f8e552d3c70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 147, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8e96133250> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f8e552d3c70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /home/soto/Dropbox/GalanLab/OrgA/Paper/Sortingplatform.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 147, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8e96133250> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f8e552d3c70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 147, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8e96133250> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f8e552d3c70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8e96133250> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f8e552d3c70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 18.0.5
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Dell Inc.
Model: XPS 13 9370
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           7.5G        5.8G        150M        799M        1.6G        587M
	Swap:           15G         10G        4.5G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell Device [1028:07e6]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.8
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    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: 1.3rc202112030319
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    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: 2.1.2
    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-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    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: 2.0.4
    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: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    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: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    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: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    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: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    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: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    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: 3.0.6
    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: 2.2.0
    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
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Sessions
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Problem saving blast table info in session

comment:2 by Eric Pettersen, 4 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Duplicate of #5453

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