Opened 2 years ago

Closed 2 years ago

#10047 closed defect (fixed)

Dead volume model (self.session is None) in session.selection

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-165-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_Apo+Ribosome-
> tRNA/Refined_Apo+Ribosome-tRNA-head.mrc

Opened Refined_Apo+Ribosome-tRNA-head.mrc as #1, grid size 360,360,360, pixel
1.46, shown at level 0.00244, step 2, values float32  

> open "/home/yuanx0c/Documents/EM_Data/EM_density_map/From
> Article/Tomato_80S.map"

Opened Tomato_80S.map as #2, grid size 540,540,540, pixel 0.83, shown at level
0.0446, step 4, values float32  

> hide #!1 models

> volume #2 level 0.02847

> open /home/yuanx0c/Desktop/new_Ribosome_apo/apo-RNA.mrc

Opened apo-RNA.mrc as #3, grid size 360,360,360, pixel 1.46, shown at level
0.0199, step 2, values float32  

> ui mousemode right "rotate selected models"

> select add #3

2 models selected  

> view matrix models
> #3,0.33755,0.19289,-0.92133,372.64,-0.74462,-0.54405,-0.38671,694.18,-0.57584,0.81658,-0.040014,222.46

> view matrix models
> #3,-0.92528,-0.17125,-0.33842,649.62,-0.16669,0.98508,-0.042714,59.818,0.34069,0.01689,-0.94002,417.83

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.92528,-0.17125,-0.33842,599.64,-0.16669,0.98508,-0.042714,23.642,0.34069,0.01689,-0.94002,367.01

> volume #3 level 0.009591

> fitmap #3 inMap #2

Fit map apo-RNA.mrc in map Tomato_80S.map using 113230 points  
correlation = 0.2975, correlation about mean = 0.02816, overlap = 40.02  
steps = 112, shift = 4.47, angle = 3.03 degrees  
  
Position of apo-RNA.mrc (#3) relative to Tomato_80S.map (#2) coordinates:  
Matrix rotation and translation  
-0.90816330 -0.17767830 -0.37903804 606.75887005  
-0.16255169 0.98408196 -0.07183060 27.03537189  
0.38576723 -0.00362064 -0.92258904 352.99280558  
Axis 0.08881622 -0.99585327 0.01969636  
Axis point 269.26765781 0.00000000 237.28386407  
Rotation angle (degrees) 157.41863970  
Shift along axis 33.91943745  
  

> select up

6 models selected  

> select up

6 models selected  

> fitmap #3 inMap #2

Fit map apo-RNA.mrc in map Tomato_80S.map using 113230 points  
correlation = 0.2975, correlation about mean = 0.02818, overlap = 40.02  
steps = 60, shift = 0.00253, angle = 0.00222 degrees  
  
Position of apo-RNA.mrc (#3) relative to Tomato_80S.map (#2) coordinates:  
Matrix rotation and translation  
-0.90816561 -0.17767745 -0.37903290 606.75620341  
-0.16256570 0.98408225 -0.07179495 27.02788333  
0.38575589 -0.00358396 -0.92259392 352.98706394  
Axis 0.08881948 -0.99585335 0.01967744  
Axis point 269.26738089 0.00000000 237.27894006  
Rotation angle (degrees) 157.41915501  
Shift along axis 33.92184750  
  

> close #1

> volume #3 step 4

> open
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_Apo+Ribosome-
> tRNA/Refined_Apo+Ribosome-tRNA-head.mrc
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_Apo+Ribosome-
> tRNA/Refined_Apo+Ribosome-tRNA-60S.mrc
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_Apo+Ribosome-
> tRNA/Refined_Apo+Ribosome-tRNA-40S-body.mrc

Opened Refined_Apo+Ribosome-tRNA-head.mrc as #1.1, grid size 360,360,360,
pixel 1.46, shown at level 0.00244, step 2, values float32  
Opened Refined_Apo+Ribosome-tRNA-60S.mrc as #1.2, grid size 360,360,360, pixel
1.46, shown at level 0.0148, step 2, values float32  
Opened Refined_Apo+Ribosome-tRNA-40S-body.mrc as #1.3, grid size 360,360,360,
pixel 1.46, shown at level 0.00523, step 2, values float32  

> view matrix models
> #2,1,0,0,-55.637,0,1,0,95.65,0,0,1,-124.91,#3,-0.90817,-0.17768,-0.37903,551.12,-0.16257,0.98408,-0.071795,122.68,0.38576,-0.003584,-0.92259,228.07

> surface dust #2 size 8.3

> surface dust #3 size 14.6

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1.3 models

> show #!1.1 models

> show #!1.2 models

> surface dust #3 size 14.6

> view matrix models
> #2,1,0,0,-62.153,0,1,0,114.76,0,0,1,-117.12,#3,-0.90817,-0.17768,-0.37903,544.6,-0.16257,0.98408,-0.071795,141.79,0.38576,-0.003584,-0.92259,235.87

> select subtract #3

2 models selected  

> select add #3

4 models selected  

> select subtract #2

2 models selected  

> view matrix models
> #3,-0.90817,-0.17768,-0.37903,531.07,-0.16257,0.98408,-0.071795,262.06,0.38576,-0.003584,-0.92259,379.87

> view matrix models
> #3,-0.90817,-0.17768,-0.37903,537.86,-0.16257,0.98408,-0.071795,255.68,0.38576,-0.003584,-0.92259,386.28

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.95648,-0.27882,0.086081,453.75,-0.26122,0.68668,-0.6784,515.46,0.13004,-0.67136,-0.72963,570.16

> view matrix models
> #3,-0.88708,-0.12549,-0.44424,536.36,-0.16493,0.98498,0.051109,223.8,0.43115,0.11861,-0.89445,336.33

> view matrix models
> #3,0.9093,0.40015,0.1143,-219.26,-0.41567,0.88647,0.20346,275.04,-0.01991,-0.23251,0.97239,53.452

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.9093,0.40015,0.1143,-98.072,-0.41567,0.88647,0.20346,90.347,-0.01991,-0.23251,0.97239,64.899

> surface dust #3 size 14.6

> select subtract #3

Nothing selected  

> hide #!3 models

> hide #!1.1 models

> hide #!1.2 models

> surface dust #1.3 size 14.6

> show #!1.2 models

> fitmap #1.2 inMap #1.3

Fit map Refined_Apo+Ribosome-tRNA-60S.mrc in map Refined_Apo+Ribosome-
tRNA-40S-body.mrc using 58290 points  
correlation = 0.4635, correlation about mean = 0.093, overlap = 13.61  
steps = 140, shift = 4.46, angle = 5.8 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-60S.mrc (#1.2) relative to
Refined_Apo+Ribosome-tRNA-40S-body.mrc (#1.3) coordinates:  
Matrix rotation and translation  
0.99488235 -0.00143782 -0.10102988 26.33902990  
0.00115460 0.99999524 -0.00286173 0.37380494  
0.10103351 0.00273044 0.99487928 -26.84106175  
Axis 0.02766245 -0.99953506 0.01282377  
Axis point 278.16544615 0.00000000 246.61199352  
Rotation angle (degrees) 5.80128960  
Shift along axis 0.01076729  
  

> undo

> show #!1.2 models

> show #!1.1 models

> show #!3 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> surface dust #3 size 14.6

> surface dust #1.1 size 14.6

> hide #!1.1 models

> show #!1.2 models

> fitmap #1.1 inMap #3

Fit map Refined_Apo+Ribosome-tRNA-head.mrc in map apo-RNA.mrc using 58174
points  
correlation = 0.7292, correlation about mean = 0.3718, overlap = 10.03  
steps = 424, shift = 19.6, angle = 28.4 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-head.mrc (#1.1) relative to apo-RNA.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.99815605 0.02553018 -0.05507018 8.21939778  
-0.02657937 0.99947728 -0.01840429 13.31188302  
0.05457153 0.01983409 0.99831286 -20.59218164  
Axis 0.30043941 -0.86145632 -0.40942542  
Axis point 385.90900023 0.00000000 139.42592314  
Rotation angle (degrees) 3.64862092  
Shift along axis -0.56721203  
  

> select add #1.2

2 models selected  

> view matrix models
> #1.2,0.99488,-0.0014378,-0.10103,49.488,0.0011546,1,-0.0028617,25.783,0.10103,0.0027304,0.99488,-35.227

> fitmap #1.1 inMap #3

Fit map Refined_Apo+Ribosome-tRNA-head.mrc in map apo-RNA.mrc using 58174
points  
correlation = 0.7293, correlation about mean = 0.372, overlap = 10.04  
steps = 48, shift = 0.0339, angle = 0.00685 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-head.mrc (#1.1) relative to apo-RNA.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.99815071 0.02554204 -0.05516140 8.21008199  
-0.02658886 0.99947843 -0.01832758 13.31738526  
0.05466450 0.01976037 0.99830923 -20.60129091  
Axis 0.29897002 -0.86207458 -0.40919964  
Axis point 385.63259140 0.00000000 139.13914766  
Rotation angle (degrees) 3.65213395  
Shift along axis -0.59597016  
  

> fitmap #1.1 inMap #3

Fit map Refined_Apo+Ribosome-tRNA-head.mrc in map apo-RNA.mrc using 58174
points  
correlation = 0.7292, correlation about mean = 0.3718, overlap = 10.03  
steps = 44, shift = 0.0352, angle = 0.00669 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-head.mrc (#1.1) relative to apo-RNA.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.99815578 0.02553659 -0.05507203 8.21968743  
-0.02658573 0.99947714 -0.01840259 13.31299470  
0.05457329 0.01983279 0.99831279 -20.59153028  
Axis 0.30039830 -0.86143435 -0.40950179  
Axis point 385.88255493 0.00000000 139.42298220  
Rotation angle (degrees) 3.64883436  
Shift along axis -0.56682219  
  

> fitmap #1.1 inMap #3

Fit map Refined_Apo+Ribosome-tRNA-head.mrc in map apo-RNA.mrc using 58174
points  
correlation = 0.7293, correlation about mean = 0.372, overlap = 10.04  
steps = 48, shift = 0.0322, angle = 0.00535 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-head.mrc (#1.1) relative to apo-RNA.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.99815191 0.02553530 -0.05514277 8.20972112  
-0.02658253 0.99947834 -0.01834199 13.31676459  
0.05464563 0.01977393 0.99831000 -20.59993083  
Axis 0.29925840 -0.86197851 -0.40919122  
Axis point 385.71474705 0.00000000 139.17022975  
Rotation angle (degrees) 3.65129272  
Shift along axis -0.59262594  
  

> view matrix models
> #1.2,0.99488,-0.0014378,-0.10103,46.3,0.0011546,1,-0.0028617,13.441,0.10103,0.0027304,0.99488,-23.888

> view matrix models
> #1.2,0.99488,-0.0014378,-0.10103,50.898,0.0011546,1,-0.0028617,31.769,0.10103,0.0027304,0.99488,-40.048

> hide #!3 models

> show #!1.1 models

> show #!1.3 models

> open "/home/yuanx0c/Documents/EM_Data/EM_density_map/Not
> Refined/Ribosome_apo-tRNA.mrc"

Opened Ribosome_apo-tRNA.mrc as #4, grid size 360,360,360, pixel 1.46, shown
at level 0.0295, step 2, values float32  

> surface dust #1.2 size 14.6

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> select subtract #1.2

Nothing selected  

> surface dust #4 size 14.6

> show #!1.1 models

> show #!1.2 models

> show #!1.3 models

> volume #4 step 1

> volume #4 level 0.3

> volume #4 level 0.003

> volume #4 level 0.03

> fitmap #1.1 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-head.mrc in map Ribosome_apo-tRNA.mrc using
58174 points  
correlation = 0.5878, correlation about mean = 0.2603, overlap = 11.64  
steps = 480, shift = 19.2, angle = 30.2 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-head.mrc (#1.1) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99966926 -0.02566826 -0.00158259 6.88708671  
0.02563830 0.99953185 -0.01669587 -1.62859537  
0.00201040 0.01664977 0.99985936 -5.38902439  
Axis 0.54400971 -0.05861709 0.83702896  
Axis point 70.19228640 281.57859398 0.00000000  
Rotation angle (degrees) 1.75627688  
Shift along axis -0.66866390  
  

> fitmap #1.2 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-60S.mrc in map Ribosome_apo-tRNA.mrc using
58290 points  
correlation = 0.9609, correlation about mean = 0.8922, overlap = 99.43  
steps = 184, shift = 39.5, angle = 2.83 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-60S.mrc (#1.2) relative to Ribosome_apo-
tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99852606 0.01031986 -0.05328420 12.29887056  
-0.01060065 0.99993136 -0.00498974 4.27465760  
0.05322905 0.00554723 0.99856692 -16.41392572  
Axis 0.09661752 -0.97666113 -0.19182827  
Axis point 313.75273920 0.00000000 221.84365709  
Rotation angle (degrees) 3.12584767  
Shift along axis 0.16204939  
  

> fitmap #1.2 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-60S.mrc in map Ribosome_apo-tRNA.mrc using
58290 points  
correlation = 0.9608, correlation about mean = 0.8922, overlap = 99.45  
steps = 28, shift = 0.037, angle = 0.0176 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-60S.mrc (#1.2) relative to Ribosome_apo-
tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99851043 0.01028659 -0.05358279 12.41118464  
-0.01057243 0.99993134 -0.00505395 4.29157957  
0.05352713 0.00561293 0.99855062 -16.54360640  
Axis 0.09728808 -0.97690399 -0.19024623  
Axis point 314.51965145 0.00000000 222.58803931  
Rotation angle (degrees) 3.14259358  
Shift along axis 0.16235788  
  

> fitmap #1.3 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-40S-body.mrc in map Ribosome_apo-tRNA.mrc
using 58276 points  
correlation = 0.7585, correlation about mean = 0.4843, overlap = 32.63  
steps = 76, shift = 0.73, angle = 2.84 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-40S-body.mrc (#1.3) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99878154 0.01118766 0.04806533 -12.74472384  
-0.01102652 0.99993267 -0.00361625 3.92234921  
-0.04810255 0.00308185 0.99883765 11.56645994  
Axis 0.06770736 0.97210734 -0.22455074  
Axis point 235.53754122 0.00000000 271.62206190  
Rotation angle (degrees) 2.83521290  
Shift along axis 0.35277579  
  

> fitmap #1.1 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-head.mrc in map Ribosome_apo-tRNA.mrc using
58174 points  
correlation = 0.5879, correlation about mean = 0.2605, overlap = 11.64  
steps = 40, shift = 0.0271, angle = 0.00179 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-head.mrc (#1.1) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99966898 -0.02567769 -0.00161119 6.87565971  
0.02564727 0.99953176 -0.01668740 -1.61857023  
0.00203893 0.01664056 0.99985946 -5.40533701  
Axis 0.54363997 -0.05954000 0.83720402  
Axis point 69.85255541 281.49944313 0.00000000  
Rotation angle (degrees) 1.75653978  
Shift along axis -0.69111675  
  

> fitmap #1.2 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-60S.mrc in map Ribosome_apo-tRNA.mrc using
58290 points  
correlation = 0.9609, correlation about mean = 0.8922, overlap = 99.44  
steps = 40, shift = 0.0149, angle = 0.0123 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-60S.mrc (#1.2) relative to Ribosome_apo-
tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99851872 0.01037273 -0.05341129 12.32753952  
-0.01065238 0.99993099 -0.00495386 4.28350940  
0.05335622 0.00551548 0.99856031 -16.46008517  
Axis 0.09576738 -0.97664708 -0.19232547  
Axis point 313.89236333 0.00000000 221.80682069  
Rotation angle (degrees) 3.13336196  
Shift along axis 0.16279290  
  

> fitmap #1.3 inMap #4

Fit map Refined_Apo+Ribosome-tRNA-40S-body.mrc in map Ribosome_apo-tRNA.mrc
using 58276 points  
correlation = 0.7586, correlation about mean = 0.4845, overlap = 32.63  
steps = 40, shift = 0.008, angle = 0.00562 degrees  
  
Position of Refined_Apo+Ribosome-tRNA-40S-body.mrc (#1.3) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99878222 0.01121733 0.04804414 -12.75131097  
-0.01105184 0.99993205 -0.00370872 3.95036755  
-0.04808248 0.00317323 0.99883833 11.53375685  
Axis 0.06957635 0.97183879 -0.22514105  
Axis point 234.96906840 0.00000000 271.87840292  
Rotation angle (degrees) 2.83477951  
Shift along axis 0.35520873  
  

> fitmap #3 inMap #4

Fit map apo-RNA.mrc in map Ribosome_apo-tRNA.mrc using 14104 points  
correlation = 0.4066, correlation about mean = 0.08056, overlap = 4.297  
steps = 76, shift = 1.56, angle = 2.03 degrees  
  
Position of apo-RNA.mrc (#3) relative to Ribosome_apo-tRNA.mrc (#4)
coordinates:  
Matrix rotation and translation  
0.91793608 0.38808248 0.08237309 -88.38725150  
-0.39665770 0.89385519 0.20901089 82.01922957  
0.00748385 -0.22453256 0.97443785 56.46889621  
Axis -0.48189778 0.08324185 -0.87226448  
Axis point 138.03853269 256.73821539 0.00000000  
Rotation angle (degrees) 26.73273063  
Shift along axis 0.16524072  
  

> show #!3 models

> hide #!1.2 models

> show #!1.2 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!4 models

> volume #1.3 step 1

> volume #1.2 step 1

> open
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_SALTY2+Ribosome-
> tRNA/Refined_SALTY2+Ribosome-tRNA-60S.mrc
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_SALTY2+Ribosome-
> tRNA/Refined_SALTY2+Ribosome-tRNA-40S-head.mrc
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_SALTY2+Ribosome-
> tRNA/Refined_SALTY2+Ribosome-tRNA-40S-body.mrc

Opened Refined_SALTY2+Ribosome-tRNA-60S.mrc as #5.1, grid size 360,360,360,
pixel 1.46, shown at level 0.0136, step 2, values float32  
Opened Refined_SALTY2+Ribosome-tRNA-40S-head.mrc as #5.2, grid size
360,360,360, pixel 1.46, shown at level 0.00325, step 2, values float32  
Opened Refined_SALTY2+Ribosome-tRNA-40S-body.mrc as #5.3, grid size
360,360,360, pixel 1.46, shown at level 0.00511, step 2, values float32  

> surface dust #1.1 size 14.6

> surface dust #1.2 size 14.6

> surface dust #1.3 size 14.6

> surface dust #4 size 14.6

> surface dust #5.1 size 14.6

> surface dust #5.2 size 14.6

> surface dust #5.3 size 14.6

> fitmap #5.1 inMap #4

Fit map Refined_SALTY2+Ribosome-tRNA-60S.mrc in map Ribosome_apo-tRNA.mrc
using 58296 points  
correlation = 0.96, correlation about mean = 0.88, overlap = 103.8  
steps = 84, shift = 1.36, angle = 5.53 degrees  
  
Position of Refined_SALTY2+Ribosome-tRNA-60S.mrc (#5.1) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99534587 -0.07121907 0.06491872 1.59982009  
0.07125507 0.99745657 0.00176355 -20.49670575  
-0.06487921 0.00287045 0.99788900 18.04369756  
Axis 0.00574302 0.67344530 0.73921474  
Axis point 283.48418588 3.97459902 0.00000000  
Rotation angle (degrees) 5.53009495  
Shift along axis -0.45605516  
  

> fitmap #5.2 inMap #4

Fit map Refined_SALTY2+Ribosome-tRNA-40S-head.mrc in map Ribosome_apo-tRNA.mrc
using 58228 points  
correlation = 0.5749, correlation about mean = 0.2493, overlap = 14.34  
steps = 104, shift = 2.31, angle = 3.34 degrees  
  
Position of Refined_SALTY2+Ribosome-tRNA-40S-head.mrc (#5.2) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99863292 -0.02385554 0.04651027 -4.14312685  
0.02265895 0.99940284 0.02608706 -11.94779138  
-0.04710482 -0.02499752 0.99857712 18.35832583  
Axis -0.43906455 0.80460801 0.39978528  
Axis point 390.42631473 0.00000000 104.84904775  
Rotation angle (degrees) 3.33502737  
Shift along axis -0.45479995  
  

> fitmap #5.3 inMap #4

Fit map Refined_SALTY2+Ribosome-tRNA-40S-body.mrc in map Ribosome_apo-tRNA.mrc
using 58199 points  
correlation = 0.7484, correlation about mean = 0.4553, overlap = 33.89  
steps = 56, shift = 0.967, angle = 0.772 degrees  
  
Position of Refined_SALTY2+Ribosome-tRNA-40S-body.mrc (#5.3) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99991152 0.00833387 -0.01036823 -0.15695128  
-0.00835567 0.99996297 -0.00206170 1.97266975  
0.01035067 0.00214815 0.99994412 -2.74524490  
Axis 0.15629180 -0.76919609 -0.61960491  
Axis point 255.59559619 0.00000000 -19.71671445  
Rotation angle (degrees) 0.77167656  
Shift along axis 0.15906715  
  

> color #5 #729fcfff models

> color #1 #888a85ff models

> volume #4 level 0.02697

> hide #!4 models

> show #!4 models

> hide #!4 models

> volume #5.1 style mesh

> volume #5.2 style mesh

> volume #5.3 style mesh

> volume #5.1 level 0.013

> close #2

> volume #1.1 step 1

> volume #5.1 step 1

> volume #5.2 step 1

> volume #5.3 step 1

> volume #1.1 level 0.0024

> volume #5.1 level 0.0024

> volume #5.1 level 0.013

> volume #1.2 level 0.016

> volume #5.2 level 0.006361

> volume #5.3 level 0.00763

> volume #1.3 level 0.004

> volume #1.3 level 0.0055

> volume #5.3 level 0.0055

> volume #1.3 level 0.006

> volume #5.3 level 0.006

> volume #1.1 level 0.003

> volume #1.1 level 0.004

> volume #1.2 level 0.02

> volume #1.2 level 0.002

> volume #1.2 level 0.08

> volume #1.2 level 0.008

> volume #1.2 level 0.012

> volume #5.2 level 0.012

> open
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_SALTY2+Ribosome-
> tRNA/Coordinated_60S_SALTY2+Ribosome-tRNA.pdb
> /home/yuanx0c/Documents/EM_Data/EM_density_map/Separately_Refined_Maps/Refined_SALTY2+Ribosome-
> tRNA/Coordinated_40Sbody_SALTY2+Ribosome-tRNA.pdb

Chain information for Coordinated_60S_SALTY2+Ribosome-tRNA.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  
Chain information for Coordinated_40Sbody_SALTY2+Ribosome-tRNA.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
h | No description available  
k | No description available  
l | No description available  
  

> fitmap #2 inMap #4

Fit molecule Coordinated_60S_SALTY2+Ribosome-tRNA.pdb (#2) to map
Ribosome_apo-tRNA.mrc (#4) using 223261 atoms  
average map value = 0.04289, steps = 80  
shifted from previous position = 1.28  
rotated from previous position = 5.54 degrees  
atoms outside contour = 84062, contour level = 0.026972  
  
Position of Coordinated_60S_SALTY2+Ribosome-tRNA.pdb (#2) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99532444 -0.07165591 0.06476649 1.80235466  
0.07169234 0.99742523 0.00176445 -20.64391601  
-0.06472616 0.00288706 0.99789889 18.00249245  
Axis 0.00581122 0.67032287 0.74204682  
Axis point 283.80670403 6.67248764 0.00000000  
Rotation angle (degrees) 5.54282727  
Shift along axis -0.46892283  
  

> fitmap #6 inMap #4

Fit molecule Coordinated_40Sbody_SALTY2+Ribosome-tRNA.pdb (#6) to map
Ribosome_apo-tRNA.mrc (#4) using 132938 atoms  
average map value = 0.02012, steps = 72  
shifted from previous position = 0.582  
rotated from previous position = 0.973 degrees  
atoms outside contour = 93910, contour level = 0.026972  
  
Position of Coordinated_40Sbody_SALTY2+Ribosome-tRNA.pdb (#6) relative to
Ribosome_apo-tRNA.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99985699 0.01417873 -0.00921744 -1.93914484  
-0.01416371 0.99989826 0.00169263 2.79638491  
0.00924050 -0.00156184 0.99995609 -1.52917552  
Axis -0.09577857 -0.54321412 -0.83411323  
Axis point 194.21695847 139.11374151 0.00000000  
Rotation angle (degrees) 0.97347698  
Shift along axis -0.05780172  
  

> select down

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 297, in forward_keystroke  
run(self.session, 'select down')  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/select.py", line 138, in select_down  
session.selection.demote(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/selection.py", line 64, in demote  
self._promotion.demote_selection()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/selection.py", line 200, in demote_selection  
p.demote()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/selection.py", line 229, in demote  
m.selected = False # This may clear child drawing selections.  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1138, in _set_selected  
Model.set_selected(self, sel, fire_trigger=fire_trigger)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 215, in set_selected  
self._selection_changed()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 218, in _selection_changed  
self.session.selection.trigger_fire_needed = True  
AttributeError: 'NoneType' object has no attribute 'selection'  
  
AttributeError: 'NoneType' object has no attribute 'selection'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 218, in _selection_changed  
self.session.selection.trigger_fire_needed = True  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 525.125.06
OpenGL renderer: Quadro P2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: SYS-5039A-I
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) W-2145 CPU @ 3.70GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       8.0Gi        47Gi       180Mi       6.9Gi        53Gi
	Swap:          15Gi          0B        15Gi

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106GL [Quadro P2000] [10de:1c30] (rev a1)	
	Subsystem: NVIDIA Corporation GP106GL [Quadro P2000] [10de:11b3]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 2 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Dead volume model (self.session is None) in session.selection

comment:2 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made the code that remembers selection promotions and demotions (up/down arrow key) check to make sure selected models were not deleted.

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