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Opened 4 years ago
Closed 4 years ago
#5299 closed defect (duplicate)
Session code trying to take len() of 'SurfaceUpdaters'
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| 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: Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202109170828 (2021-09-17 08:28:14 UTC)
Description
trying to save the session as .cxs file. This has worked before also with this version
Log:
UCSF ChimeraX version: 1.3.dev202109170828 (2021-09-17)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Leonie Anton\Documents\Uni\Columbia
> university\research\Projects\Pf_api_mito_tomo\Ribosome_test\relion\ribosomes.cxs"
> format session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.18, step 1, values float32
Opened ini_model_refine25_M_4A.mrc z flip as #8, grid size 150,150,150, pixel
4, shown at level 0.903, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc z flip as #10, grid size 240,240,240,
pixel 2.5, shown at level 1.12, step 1, values float32
Opened EMD-2660.map gaussian as #13, grid size 360,360,360, pixel 1.34, shown
at level 0.0744, step 1, values float32
Opened run_class001.mrc z flip as #14, grid size 150,150,150, pixel 4, shown
at level 0.894, step 1, values float32
Opened run_class001.mrc as #21, grid size 240,240,240, pixel 2.5, shown at
level 0.783, step 1, values float32
Opened run_class001.mrc z flip as #22, grid size 240,240,240, pixel 2.5, shown
at level 0.498, step 1, values float32
Opened run_class001.mrc z flip as #34, grid size 240,240,240, pixel 2.5, shown
at level 0.769, step 1, values float32
Opened run_ct28_class001.mrc as #32, grid size 240,240,240, pixel 2.5, shown
at level 0.628, step 1, values float32
Opened run_ct28_class001.mrc z flip as #33, grid size 240,240,240, pixel 2.5,
shown at level 0.722, step 1, values float32
Opened RefineJ040_2.5Apix_240box_filtsharp.mrc z flip as #37, grid size
240,240,240, pixel 2.5, shown at level 0.00441, step 1, values float32
Opened RefineJ040_2.5Apix_240box_filt.mrc z flip as #39, grid size
240,240,240, pixel 2.5, shown at level 0.00363, step 1, values float32
Opened RefineJ038_2.5Apx_240box_filtsharp.mrc z flip as #41, grid size
240,240,240, pixel 2.5, shown at level 0.00356, step 1, values float32
Opened RefineJ038_2.5Apx_240box_mask.mrc as #36, grid size 240,240,240, pixel
2.5, shown at level 5e-05, step 1, values float32
Opened RefineJ038_2.5Apx_240box_mask.mrc z flip as #38, grid size 240,240,240,
pixel 2.5, shown at level 0.00519, step 1, values float32
Opened RefineJ038_2.5Apx_240box_denoised.mrc as #40, grid size 240,240,240,
pixel 2.5, shown at level 0.00318, step 1, values float32
Opened RefineJ038_2.5Apx_240box_denoised.mrc z flip as #42, grid size
240,240,240, pixel 2.5, shown at level 0.00143, step 1, values float32
Opened mask.mrc z flip as #44, grid size 240,240,240, pixel 2.5, shown at
level 0.995, step 1, values float32
Log from Thu Sep 23 17:22:34 2021UCSF ChimeraX version: 1.3.dev202109170828
(2021-09-17)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Opened run_ct22_it025_class002.mrc as #1, grid size 150,150,150, pixel 4,
shown at level 0.761, step 1, values float32
Opened run_ct22_it025_class002.mrc z flip as #2, grid size 150,150,150, pixel
4, shown at level 0.582, step 1, values float32
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.18, step 1, values float32
Opened run_ct2_class001.mrc as #4, grid size 150,150,150, pixel 4, shown at
level 0.908, step 1, values float32
Opened run_ct2_class001.mrc z flip as #5, grid size 150,150,150, pixel 4,
shown at level 0.586, step 1, values float32
Opened run_ct2_class001_invert.mrc as #6, grid size 150,150,150, pixel 4,
shown at level 0.597, step 1, values float32
Opened ini_model_refine25_M_4A.mrc as #7, grid size 150,150,150, pixel 4,
shown at level 0.863, step 1, values float32
Opened ini_model_refine25_M_4A.mrc z flip as #8, grid size 150,150,150, pixel
4, shown at level 0.903, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc as #9, grid size 240,240,240, pixel 2.5,
shown at level 0.996, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc z flip as #10, grid size 240,240,240,
pixel 2.5, shown at level 1.12, step 1, values float32
Opened run_class001.mrc as #11, grid size 150,150,150, pixel 4, shown at level
0.769, step 1, values float32
Opened EMD-2660.map gaussian as #12, grid size 360,360,360, pixel 1.34, shown
at level 0.0925, step 1, values float32
Opened EMD-2660.map gaussian as #13, grid size 360,360,360, pixel 1.34, shown
at level 0.0744, step 1, values float32
Opened run_class001.mrc z flip as #14, grid size 150,150,150, pixel 4, shown
at level 0.894, step 1, values float32
Opened run_it025_class001.mrc as #15.1, grid size 150,150,150, pixel 4, shown
at level 0.697, step 1, values float32
Opened run_it025_class002.mrc as #15.2, grid size 150,150,150, pixel 4, shown
at level 0.844, step 1, values float32
Opened run_it025_class003.mrc as #15.3, grid size 150,150,150, pixel 4, shown
at level 0.605, step 1, values float32
Opened run_it025_class001.mrc z flip as #16, grid size 150,150,150, pixel 4,
shown at level 0.717, step 1, values float32
Opened run_it025_class002.mrc z flip as #17, grid size 150,150,150, pixel 4,
shown at level 0.844, step 1, values float32
Opened run_it025_class003.mrc z flip as #18, grid size 150,150,150, pixel 4,
shown at level 0.616, step 1, values float32
Opened run_class001.mrc as #19, grid size 150,150,150, pixel 4, shown at level
0.559, step 1, values float32
Opened run_ct2_class001_invert.mrc as #20, grid size 150,150,150, pixel 4,
shown at level 0.734, step 1, values float32
Opened run_class001.mrc as #21, grid size 240,240,240, pixel 2.5, shown at
level 0.783, step 1, values float32
Opened run_class001.mrc z flip as #22, grid size 240,240,240, pixel 2.5, shown
at level 0.498, step 1, values float32
Log from Fri Sep 17 15:48:01 2021UCSF ChimeraX version: 1.3.dev202109170828
(2021-09-17)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Opened run_ct22_it025_class002.mrc as #1, grid size 150,150,150, pixel 4,
shown at level 0.761, step 1, values float32
Opened run_ct22_it025_class002.mrc z flip as #2, grid size 150,150,150, pixel
4, shown at level 0.582, step 1, values float32
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.18, step 1, values float32
Opened run_ct2_class001.mrc as #4, grid size 150,150,150, pixel 4, shown at
level 0.908, step 1, values float32
Opened run_ct2_class001.mrc z flip as #5, grid size 150,150,150, pixel 4,
shown at level 0.586, step 1, values float32
Opened run_ct2_class001_invert.mrc as #6, grid size 150,150,150, pixel 4,
shown at level 0.597, step 1, values float32
Opened ini_model_refine25_M_4A.mrc as #7, grid size 150,150,150, pixel 4,
shown at level 0.863, step 1, values float32
Opened ini_model_refine25_M_4A.mrc z flip as #8, grid size 150,150,150, pixel
4, shown at level 0.903, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc as #9, grid size 240,240,240, pixel 2.5,
shown at level 0.996, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc z flip as #10, grid size 240,240,240,
pixel 2.5, shown at level 1.12, step 1, values float32
Opened run_class001.mrc as #11, grid size 150,150,150, pixel 4, shown at level
0.769, step 1, values float32
Opened EMD-2660.map gaussian as #12, grid size 360,360,360, pixel 1.34, shown
at level 0.0925, step 1, values float32
Opened EMD-2660.map gaussian as #13, grid size 360,360,360, pixel 1.34, shown
at level 0.0744, step 1, values float32
Opened run_class001.mrc z flip as #14, grid size 150,150,150, pixel 4, shown
at level 0.894, step 1, values float32
Opened run_it025_class001.mrc as #15.1, grid size 150,150,150, pixel 4, shown
at level 0.697, step 1, values float32
Opened run_it025_class002.mrc as #15.2, grid size 150,150,150, pixel 4, shown
at level 0.844, step 1, values float32
Opened run_it025_class003.mrc as #15.3, grid size 150,150,150, pixel 4, shown
at level 0.605, step 1, values float32
Opened run_it025_class001.mrc z flip as #16, grid size 150,150,150, pixel 4,
shown at level 0.717, step 1, values float32
Opened run_it025_class002.mrc z flip as #17, grid size 150,150,150, pixel 4,
shown at level 0.844, step 1, values float32
Opened run_it025_class003.mrc z flip as #18, grid size 150,150,150, pixel 4,
shown at level 0.616, step 1, values float32
Opened run_class001.mrc as #19, grid size 150,150,150, pixel 4, shown at level
0.559, step 1, values float32
Opened run_ct2_class001_invert.mrc as #20, grid size 150,150,150, pixel 4,
shown at level 0.734, step 1, values float32
Opened run_class001.mrc as #21, grid size 240,240,240, pixel 2.5, shown at
level 0.783, step 1, values float32
Opened run_class001.mrc z flip as #22, grid size 240,240,240, pixel 2.5, shown
at level 0.498, step 1, values float32
Log from Fri Sep 17 15:20:44 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Leonie Anton\Documents\Uni\Columbia
> university\research\Projects\Pf_api_mito_tomo\Ribosome_test\relion\ribosomes.cxs"
> format session
Opened run_ct22_it025_class002.mrc as #1, grid size 150,150,150, pixel 4,
shown at level 0.761, step 1, values float32
Opened run_ct22_it025_class002.mrc z flip as #2, grid size 150,150,150, pixel
4, shown at level 0.582, step 1, values float32
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.141, step 1, values float32
Opened run_ct2_class001.mrc as #4, grid size 150,150,150, pixel 4, shown at
level 0.908, step 1, values float32
Opened run_ct2_class001.mrc z flip as #5, grid size 150,150,150, pixel 4,
shown at level 0.586, step 1, values float32
Opened run_ct2_class001_invert.mrc as #6, grid size 150,150,150, pixel 4,
shown at level 0.597, step 1, values float32
Opened ini_model_refine25_M_4A.mrc as #7, grid size 150,150,150, pixel 4,
shown at level 0.863, step 1, values float32
Opened ini_model_refine25_M_4A.mrc z flip as #8, grid size 150,150,150, pixel
4, shown at level 0.903, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc as #9, grid size 240,240,240, pixel 2.5,
shown at level 0.996, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc z flip as #10, grid size 240,240,240,
pixel 2.5, shown at level 1.12, step 1, values float32
Opened run_class001.mrc as #11, grid size 150,150,150, pixel 4, shown at level
0.769, step 1, values float32
Opened EMD-2660.map gaussian as #12, grid size 360,360,360, pixel 1.34, shown
at level 0.0925, step 1, values float32
Opened EMD-2660.map gaussian as #13, grid size 360,360,360, pixel 1.34, shown
at level 0.086, step 1, values float32
Opened run_class001.mrc z flip as #14, grid size 150,150,150, pixel 4, shown
at level 0.769, step 1, values float32
Log from Fri Sep 17 07:49:28 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Leonie Anton\Documents\Uni\Columbia
> university\research\Projects\Pf_api_mito_tomo\Ribosome_test\relion\ribosomes.cxs"
> format session
Opened run_ct22_it025_class002.mrc as #1, grid size 150,150,150, pixel 4,
shown at level 0.761, step 1, values float32
Opened run_ct22_it025_class002.mrc z flip as #2, grid size 150,150,150, pixel
4, shown at level 0.582, step 1, values float32
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.141, step 1, values float32
Opened run_ct2_class001.mrc as #4, grid size 150,150,150, pixel 4, shown at
level 0.908, step 1, values float32
Opened run_ct2_class001.mrc z flip as #5, grid size 150,150,150, pixel 4,
shown at level 0.586, step 1, values float32
Opened run_ct2_class001_invert.mrc as #6, grid size 150,150,150, pixel 4,
shown at level 0.597, step 1, values float32
Opened ini_model_refine25_M_4A.mrc as #7, grid size 150,150,150, pixel 4,
shown at level 0.863, step 1, values float32
Opened ini_model_refine25_M_4A.mrc z flip as #8, grid size 150,150,150, pixel
4, shown at level 0.903, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc as #9, grid size 240,240,240, pixel 2.5,
shown at level 0.996, step 1, values float32
Opened ini_model_refine25_M_2.5A.mrc z flip as #10, grid size 240,240,240,
pixel 2.5, shown at level 1.12, step 1, values float32
Log from Thu Sep 16 23:37:56 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Opened run_ct22_it025_class002.mrc as #1, grid size 150,150,150, pixel 4,
shown at level 0.761, step 1, values float32
Opened run_ct22_it025_class002.mrc z flip as #2, grid size 150,150,150, pixel
4, shown at level 0.671, step 1, values float32
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.21, step 1, values float32
Log from Mon Sep 13 15:54:21 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/009/run_ct22_it025_class002.mrc"
Opened run_ct22_it025_class002.mrc as #1, grid size 150,150,150, pixel 4,
shown at level 0.761, step 1, values float32
> set bgColor white
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\Leonie Anton\Desktop\movie1.mp4"
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> volume flip #1
Opened run_ct22_it025_class002.mrc z flip as #2, grid size 150,150,150, pixel
4, shown at step 1, values float32
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/EMD-2660.map"
Opened EMD-2660.map as #3, grid size 360,360,360, pixel 1.34, shown at level
0.129, step 2, values float32
> hide #!3 models
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\Leonie Anton\Desktop\movie1.mp4"
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> show #!3 models
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.83123,-0.36641,-0.41809,229.81,0.095745,0.83518,-0.54158,147.27,0.54762,0.41015,0.7293,-165.52
> view matrix models
> #3,0.70429,-0.52179,-0.48136,313.11,0.047545,0.7112,-0.70138,227.3,0.70832,0.47109,0.5257,-169.83
> view matrix models
> #3,0.49522,-0.29387,-0.81756,389.62,0.81889,-0.15637,0.55223,-51.736,-0.29012,-0.94297,0.16321,499
> view matrix models
> #3,0.41546,0.22079,-0.88241,300.42,0.83491,0.29245,0.46627,-143.05,0.36101,-0.93044,-0.062839,393.62
> view matrix models
> #3,0.52704,-0.04014,-0.84889,328.35,0.68294,0.6145,0.39495,-166.87,0.50579,-0.7879,0.35128,224.51
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.52704,-0.04014,-0.84889,398.01,0.68294,0.6145,0.39495,-102.32,0.50579,-0.7879,0.35128,255.14
> view matrix models
> #3,0.52704,-0.04014,-0.84889,400.13,0.68294,0.6145,0.39495,-101,0.50579,-0.7879,0.35128,251.17
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.19037,-0.44556,-0.87478,585.22,0.78879,0.5999,-0.1339,4.5573,0.58444,-0.66452,0.46566,174.9
> view matrix models
> #3,0.099552,-0.37457,-0.92184,601.33,0.72289,0.66385,-0.19167,18.953,0.68375,-0.64731,0.33686,177.88
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.099552,-0.37457,-0.92184,579.3,0.72289,0.66385,-0.19167,0.72417,0.68375,-0.64731,0.33686,184.9
> ui tool show "Fit in Map"
Fit map EMD-2660.map in map run_ct22_it025_class002.mrc z flip using 58311
points
correlation = 0.9057, correlation about mean = 0.4517, overlap = 1.001e+04
steps = 148, shift = 17.9, angle = 24.3 degrees
Position of EMD-2660.map (#3) relative to run_ct22_it025_class002.mrc z flip
(#2) coordinates:
Matrix rotation and translation
0.01516156 0.02453815 -0.99958392 533.85057168
0.65943527 0.75122306 0.02844353 -41.73067380
0.75160844 -0.65959214 -0.00479161 254.01871114
Axis -0.34648835 -0.88188415 0.31972827
Axis point 136.59231461 0.00000000 376.28685047
Rotation angle (degrees) 96.84613604
Shift along axis -66.95441894
> ~select #3
Nothing selected
> volume #3 step 1
> volume #3 level 0.2103
> transparency #2
Missing or invalid "percent" argument: Expected a number
> transparency #2 40
> volume #2 level 0.6711
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
——— End of log from Mon Sep 13 15:54:21 2021 ———
opened ChimeraX session
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/025/run_ct2_class001.mrc"
Opened run_ct2_class001.mrc as #4, grid size 150,150,150, pixel 4, shown at
level 0.908, step 1, values float32
> volume flip #4
Opened run_ct2_class001.mrc z flip as #5, grid size 150,150,150, pixel 4,
shown at step 1, values float32
> ui tool show "Fit in Map"
Fit map run_ct2_class001.mrc z flip in map run_ct22_it025_class002.mrc z flip
using 33742 points
correlation = 0.9946, correlation about mean = 0.6887, overlap = 3.132e+04
steps = 92, shift = 16.8, angle = 22.9 degrees
Position of run_ct2_class001.mrc z flip (#5) relative to
run_ct22_it025_class002.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.92124407 0.36322967 -0.13918897 -29.04026199
-0.36090282 0.93163389 0.04251407 115.89603354
0.14511553 0.01106785 0.98935281 -44.55704862
Axis -0.04038923 -0.36515804 -0.93006898
Axis point 294.20271873 143.70689854 0.00000000
Rotation angle (degrees) 22.91030746
Shift along axis 0.29367389
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #5 level 0.6978
> show #!2 models
> volume #2 level 0.5816
> hide #!2 models
> hide #!5 models
> volume #3 level 0.2297
> volume #3 level 0.141
> show #!5 models
> hide #!3 models
> volume #5 level 0.5819
> volume #5 level 0.638
> volume #5 level 0.5862
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/025/run_ct2_class001_invert.mrc"
Opened run_ct2_class001_invert.mrc as #6, grid size 150,150,150, pixel 4,
shown at level 0.908, step 1, values float32
> hide #!5 models
> show #!5 models
> volume #6 level 0.5972
> select #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.48697,-0.81611,0.31116,294.46,-0.80052,-0.55952,-0.2147,765.76,0.34932,-0.14454,-0.92579,549.18
> view matrix models
> #6,0.40099,-0.84167,0.36166,311.71,-0.84001,-0.49533,-0.22141,760.9,0.36549,-0.21502,-0.90564,558.6
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.40099,-0.84167,0.36166,298.66,-0.84001,-0.49533,-0.22141,765.86,0.36549,-0.21502,-0.90564,532.78
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.03876,0.47008,-0.88177,440.65,0.60794,-0.68923,-0.39416,443.28,-0.79303,-0.55135,-0.25907,773.61
> ui tool show "Fit in Map"
> ui tool show "Fit in Map"
Fit map run_ct2_class001_invert.mrc in map run_ct2_class001.mrc z flip using
73010 points
correlation = 0.9476, correlation about mean = 0.4447, overlap = 5.236e+04
steps = 304, shift = 22.1, angle = 80.2 degrees
Position of run_ct2_class001_invert.mrc (#6) relative to run_ct2_class001.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.78126345 0.11938979 -0.61267733 211.91714460
0.04003842 -0.98910155 -0.14168644 626.40876320
-0.62291601 0.08616380 -0.77752907 689.91146204
Axis 0.94352009 0.04239803 -0.32859130
Axis point 0.00000000 286.29156137 401.97161876
Rotation angle (degrees) 173.06491232
Shift along axis -0.19232328
Fit map run_ct2_class001_invert.mrc in map run_ct2_class001.mrc z flip using
73010 points
correlation = 0.9476, correlation about mean = 0.4447, overlap = 5.236e+04
steps = 36, shift = 0.00695, angle = 0.0186 degrees
Position of run_ct2_class001_invert.mrc (#6) relative to run_ct2_class001.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.78144978 0.11944063 -0.61242974 211.76095549
0.04015114 -0.98909942 -0.14166941 626.37164906
-0.62267498 0.08611778 -0.77772720 689.91615489
Axis 0.94356978 0.04243919 -0.32844327
Axis point 0.00000000 286.28063692 401.91930715
Rotation angle (degrees) 173.06720768
Shift along axis -0.20437147
> hide #!5 models
> show #!5 models
> view matrix models
> #6,-0.86688,0.35256,0.35246,350.75,0.36873,0.92926,-0.02263,-69.054,-0.33551,0.11035,-0.93555,644.2
Fit map run_ct2_class001_invert.mrc in map run_ct2_class001.mrc z flip using
73010 points
correlation = 1, correlation about mean = 1, overlap = 6.026e+04
steps = 92, shift = 16.8, angle = 12.7 degrees
Position of run_ct2_class001_invert.mrc (#6) relative to run_ct2_class001.mrc
z flip (#5) coordinates:
Matrix rotation and translation
-1.00000000 -0.00010131 -0.00002214 600.01095632
-0.00010132 0.99999997 0.00024389 -0.04846470
0.00002211 0.00024389 -0.99999997 595.93466584
Axis 0.00005116 -0.99999999 -0.00012085
Axis point 300.00218030 0.00000000 297.97065502
Rotation angle (degrees) 179.99873219
Shift along axis 0.00714253
> hide #!5 models
> ~select #6
Nothing selected
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ini_model_refine25_M_4A.mrc"
Opened ini_model_refine25_M_4A.mrc as #7, grid size 150,150,150, pixel 4,
shown at level 0.983, step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 2560x1630+0+34 (frame:
2582x1686-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1346+0+34 (frame: 2582x1402-11-11) margins: 11, 45,
11, 11 minimum size: 432x815 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=886,1686 maxtrack=0,0)
> hide #!5 models
> hide #!6 models
> volume #7 level 0.5755
> volume #7 level 0.5813
> volume #7 level 0.6272
> volume #7 level 0.6502
> volume #7 level 0.6616
> volume #7 level 0.6674
> volume #7 level 0.6789
> volume #7 level 0.6903
> volume #7 level 0.6961
> volume #7 level 0.7133
> volume #7 level 0.742
> volume #7 level 0.7707
> volume #7 level 0.7994
> volume #7 level 0.8224
> volume #7 level 0.8396
> volume #7 level 0.8568
> volume #7 level 0.8855
> volume #7 level 0.9028
> volume #7 level 0.9085
> volume #7 level 0.9142
> volume #7 level 0.9315
> volume #7 level 0.9544
> volume #7 level 0.9716
> volume #7 level 0.9946
> volume #7 level 1
> volume #7 level 1.012
> volume #7 level 1.035
> volume #7 level 1.041
> volume #7 level 1.058
> volume #7 level 1.069
> volume #7 level 1.086
> volume #7 level 1.109
> volume #7 level 1.121
> volume #7 level 1.132
> volume #7 level 1.144
> volume #7 level 1.15
> volume #7 level 1.161
> volume #7 level 1.178
> volume #7 level 1.184
> volume #7 level 1.19
> volume #7 level 1.196
> volume #7 level 1.201
> volume #7 level 1.207
> volume #7 level 1.213
> volume #7 level 1.23
> volume #7 level 1.241
> volume #7 level 1.27
> volume #7 level 1.299
> volume #7 level 1.305
> volume #7 level 1.305
> volume #7 level 1.276
> volume #7 level 1.201
> volume #7 level 1.155
> volume #7 level 1.15
> volume #7 level 1.115
> volume #7 level 1.058
> volume #7 level 1.029
> volume #7 level 1.012
> volume #7 level 0.9544
> volume #7 level 0.9429
> volume #7 level 0.9315
> volume #7 level 0.897
> volume #7 level 0.8913
> volume #7 level 0.8855
> volume #7 level 0.874
> volume #7 level 0.8511
> volume #7 level 0.8453
> volume #7 level 0.8396
> volume #7 level 0.8281
> volume #7 level 0.8052
> volume #7 level 0.7879
> volume #7 level 0.7765
> volume #7 level 0.7707
> volume #7 level 0.765
> volume #7 level 0.742
> volume #7 level 0.7477
> volume #7 level 0.7592
> volume #7 level 0.7879
> volume #7 level 0.7937
> volume #7 level 0.8109
> volume #7 level 0.8396
> volume #7 level 0.8453
> volume #7 level 0.8511
> volume #7 level 0.8568
> volume #7 level 0.8626
> show #!3 models
> hide #!3 models
> volume flip #7
Opened ini_model_refine25_M_4A.mrc z flip as #8, grid size 150,150,150, pixel
4, shown at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 2560x1630+0+34 (frame:
2582x1686-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1346+0+34 (frame: 2582x1402-11-11) margins: 11, 45,
11, 11 minimum size: 432x815 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=886,1686 maxtrack=0,0)
> show #!3 models
Fit map ini_model_refine25_M_4A.mrc z flip in map EMD-2660.map using 46697
points
correlation = 0.3888, correlation about mean = 0.04324, overlap = 2277
steps = 96, shift = 4.84, angle = 4.26 degrees
Position of ini_model_refine25_M_4A.mrc z flip (#8) relative to EMD-2660.map
(#3) coordinates:
Matrix rotation and translation
-0.00949237 0.64157788 0.76699916 -161.65583595
-0.04152849 0.76611902 -0.64135562 197.89154625
-0.99909223 -0.03794031 0.01937147 544.94566285
Axis 0.30361799 0.88863691 -0.34371581
Axis point 148.90515103 0.00000000 382.78417108
Rotation angle (degrees) 96.43067386
Shift along axis -60.53432783
> hide #!8 models
> select #7
2 models selected
> ~select #7
Nothing selected
> show #!8 models
> select #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.80366,-0.59048,-0.073929,259,0.58979,0.80688,-0.033199,-112.38,0.079255,-0.016922,0.99671,-18.229
Fit map ini_model_refine25_M_4A.mrc z flip in map EMD-2660.map using 46697
points
correlation = 0.336, correlation about mean = 0.04957, overlap = 1871
steps = 88, shift = 2.08, angle = 0.949 degrees
Position of ini_model_refine25_M_4A.mrc z flip (#8) relative to EMD-2660.map
(#3) coordinates:
Matrix rotation and translation
0.45443808 0.52376459 0.72052529 -255.83906048
0.41024187 0.59492613 -0.69120512 124.34166215
-0.79068808 0.60969957 0.05548692 281.84904931
Axis 0.65134805 0.75664720 -0.05683952
Axis point 11.33821062 -0.00000000 283.58458469
Rotation angle (degrees) 86.99485885
Shift along axis -88.57766855
> ~select #8
Nothing selected
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!6 models
> select #8
2 models selected
> view matrix models
> #8,0.93487,0.32,-0.15368,-30.477,-0.22886,0.87423,0.42818,-8.9501,0.27137,-0.36512,0.89053,55.139
> view matrix models
> #8,0.96529,0.1991,-0.16906,0.21284,-0.12549,0.92117,0.36837,-37.942,0.22908,-0.33436,0.91418,52.454
> view matrix models
> #8,0.95248,0.22723,-0.20285,5.134,-0.13313,0.90954,0.39371,-39.157,0.27396,-0.348,0.89657,47.615
Fit map ini_model_refine25_M_4A.mrc z flip in map run_ct2_class001_invert.mrc
using 46697 points
correlation = 0.9808, correlation about mean = 0.4679, overlap = 5.008e+04
steps = 112, shift = 16, angle = 24.4 degrees
Position of ini_model_refine25_M_4A.mrc z flip (#8) relative to
run_ct2_class001_invert.mrc (#6) coordinates:
Matrix rotation and translation
-0.99999868 -0.00007725 -0.00162103 600.74982197
-0.00007458 0.99999863 -0.00165130 0.23103087
0.00162115 -0.00165118 -0.99999732 596.01979085
Axis 0.00003796 -0.99999966 0.00082563
Axis point 300.13336488 0.00000000 298.25345833
Rotation angle (degrees) 179.90711838
Shift along axis 0.28386889
> hide #!6 models
> ~select #8
Nothing selected
> show #!7 models
> hide #!7 models
> show #!3 models
> volume #8 level 0.9028
> hide #!3 models
> show #!3 models
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ini_model_refine25_M_2.5A.mrc"
Opened ini_model_refine25_M_2.5A.mrc as #9, grid size 240,240,240, pixel 2.5,
shown at level 0.996, step 1, values float32
> volume flip #9
Opened ini_model_refine25_M_2.5A.mrc z flip as #10, grid size 240,240,240,
pixel 2.5, shown at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 2560x1630+0+34 (frame:
2582x1686-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1346+0+34 (frame: 2582x1402-11-11) margins: 11, 45,
11, 11 minimum size: 473x815 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=968,1686 maxtrack=0,0)
Fit map ini_model_refine25_M_2.5A.mrc z flip in map EMD-2660.map using 138196
points
correlation = 0.4195, correlation about mean = 0.1548, overlap = 7797
steps = 496, shift = 19.2, angle = 22.9 degrees
Position of ini_model_refine25_M_2.5A.mrc z flip (#10) relative to
EMD-2660.map (#3) coordinates:
Matrix rotation and translation
-0.10882350 0.63532228 0.76454107 -133.73581719
-0.34577073 0.69688951 -0.62832127 305.32708323
-0.93198715 -0.33273204 0.14383790 564.72395004
Axis 0.14914063 0.85598956 -0.49501409
Axis point 185.14749110 0.00000000 436.00566068
Rotation angle (degrees) 97.70357668
Shift along axis -38.13496206
> hide #!10 models
> show #!10 models
> hide #!3 models
> volume #10 level 1.119
> volume #10 step 2
> volume #10 step 1
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
——— End of log from Thu Sep 16 23:37:56 2021 ———
opened ChimeraX session
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/027/run_class001.mrc"
Opened run_class001.mrc as #11, grid size 150,150,150, pixel 4, shown at level
0.999, step 1, values float32
> hide #!10 models
> show #!10 models
> vop gaussian #3
Opened EMD-2660.map gaussian as #12, grid size 360,360,360, pixel 1.34, shown
at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 2560x1410+0+34 (frame:
2582x1466-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1346+0+34 (frame: 2582x1402-11-11) margins: 11, 45,
11, 11 minimum size: 399x705 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=820,1466 maxtrack=0,0)
> hide #!10 models
> hide #!11 models
> show #!11 models
> select #12
2 models selected
> ~select #12
Nothing selected
> hide #!12 models
> volume #11 level 0.7686
> vop gaussian #12
Opened EMD-2660.map gaussian as #13, grid size 360,360,360, pixel 1.34, shown
at step 1, values float32
> show #!11 models
> volume flip #11
Opened run_class001.mrc z flip as #14, grid size 150,150,150, pixel 4, shown
at step 1, values float32
> ui tool show "Fit in Map"
Fit map run_class001.mrc z flip in map EMD-2660.map gaussian using 62448
points
correlation = 0.8191, correlation about mean = 0.3974, overlap = 3969
steps = 232, shift = 16.4, angle = 22.6 degrees
Position of run_class001.mrc z flip (#14) relative to EMD-2660.map gaussian
(#13) coordinates:
Matrix rotation and translation
-0.10341279 0.63530165 0.76530883 -133.99126703
-0.34246662 0.69964443 -0.62706801 302.35870435
-0.93382140 -0.32693959 0.14521743 564.33848149
Axis 0.15133410 0.85675438 -0.49302122
Axis point 185.52770261 0.00000000 434.76969790
Rotation angle (degrees) 97.42772635
Shift along axis -39.46114783
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
——— End of log from Fri Sep 17 07:49:28 2021 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> hide #!13 models
> hide #!14 models
> show #!2 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/023/run_it025_class001.mrc"
> "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/023/run_it025_class002.mrc"
> "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/023/run_it025_class003.mrc"
Opened run_it025_class001.mrc as #15.1, grid size 150,150,150, pixel 4, shown
at level 0.891, step 1, values float32
Opened run_it025_class002.mrc as #15.2, grid size 150,150,150, pixel 4, shown
at level 0.844, step 1, values float32
Opened run_it025_class003.mrc as #15.3, grid size 150,150,150, pixel 4, shown
at level 0.605, step 1, values float32
> hide #!2 models
> hide #!15.2 models
> hide #!15.3 models
> volume #15.1 level 0.6966
> volume flip #15
Opened run_it025_class001.mrc z flip as #16, grid size 150,150,150, pixel 4,
shown at step 1, values float32
Opened run_it025_class002.mrc z flip as #17, grid size 150,150,150, pixel 4,
shown at step 1, values float32
Opened run_it025_class003.mrc z flip as #18, grid size 150,150,150, pixel 4,
shown at step 1, values float32
> hide #!17 models
> hide #!18 models
> show #!7 models
> hide #!7 models
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> hide #!16 models
> show #!17 models
> save "C:\Users\Leonie Anton\Desktop\image6.png" supersample 3
> hide #!17 models
> show #!18 models
> save "C:\Users\Leonie Anton\Desktop\image7.png" supersample 3
> show #!16 models
> hide #!16 models
> hide #!18 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/022/run_class001.mrc"
Opened run_class001.mrc as #19, grid size 150,150,150, pixel 4, shown at level
0.741, step 1, values float32
> volume #19 level 0.5663
> volume #19 level 0.5587
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> show #!6 models
> hide #!6 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/025/run_ct2_class001_invert.mrc"
Opened run_ct2_class001_invert.mrc as #20, grid size 150,150,150, pixel 4,
shown at level 0.908, step 1, values float32
> hide #!19 models
> volume #20 level 0.7344
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> save "C:\Users\Leonie Anton\Desktop\image6.png" supersample 3
> hide #!20 models
> show #!16 models
> hide #!16 models
> show #!14 models
> show #!13 models
> hide #!15 models
> hide #!13 models
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> save "C:\Users\Leonie Anton\Desktop\image6.png" supersample 3
> save "C:\Users\Leonie Anton\Desktop\image7.png" supersample 3
> show #!13 models
> transparency #14 40
> save "C:\Users\Leonie Anton\Desktop\image8.png" supersample 3
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/028/run_class001.mrc"
Opened run_class001.mrc as #21, grid size 240,240,240, pixel 2.5, shown at
level 0.783, step 1, values float32
> volume flip #21
Opened run_class001.mrc z flip as #22, grid size 240,240,240, pixel 2.5, shown
at step 1, values float32
> ui tool show "Fit in Map"
Fit map run_class001.mrc z flip in map run_class001.mrc z flip using 138168
points
correlation = 0.9992, correlation about mean = 0.949, overlap = 1.578e+05
steps = 104, shift = 15.9, angle = 22.5 degrees
Position of run_class001.mrc z flip (#22) relative to run_class001.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.99999791 0.00051267 0.00197832 -0.97924641
-0.00050348 0.99998910 -0.00464198 1.46709599
-0.00198068 0.00464097 0.99998727 -2.19826366
Axis 0.91521222 0.39032020 -0.10018348
Axis point 0.00000000 476.78327313 323.62043469
Rotation angle (degrees) 0.29057529
Shift along axis -0.10335137
> hide #!14 models
> hide #!13 models
> show #!14 models
> volume #16 level 0.7169
> volume #14 level 0.9445
> transparency #14 0
> hide #!14 models
> show #!14 models
> hide #!22 models
> show #!22 models
> hide #!14 models
> volume #22 level 0.735
> volume #14 level 0.8943
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> save "C:\Users\Leonie Anton\Desktop\image6.png" supersample 3
> save "C:\Users\Leonie Anton\Desktop\image7.png" supersample 3
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!13 models
Fit map run_class001.mrc z flip in map EMD-2660.map gaussian using 167791
points
correlation = 0.8392, correlation about mean = 0.347, overlap = 1.03e+04
steps = 44, shift = 0.314, angle = 0.0784 degrees
Position of run_class001.mrc z flip (#22) relative to EMD-2660.map gaussian
(#13) coordinates:
Matrix rotation and translation
-0.10421065 0.63831354 0.76268995 -135.18019548
-0.34119880 0.69737967 -0.63027373 304.75881766
-0.93419672 -0.32591013 0.14511743 564.18906917
Axis 0.15350172 0.85580214 -0.49400397
Axis point 184.27593254 0.00000000 436.25458558
Rotation angle (degrees) 97.51910499
Shift along axis -38.64878639
> transparency #22 40
> select #13
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.015162,0.024538,-0.99958,534.48,0.65944,0.75122,0.028444,-40.916,0.75161,-0.65959,-0.0047916,257.42
Fit map run_class001.mrc z flip in map EMD-2660.map gaussian using 167791
points
correlation = 0.8392, correlation about mean = 0.3469, overlap = 1.03e+04
steps = 72, shift = 3.57, angle = 0.00742 degrees
Position of run_class001.mrc z flip (#22) relative to EMD-2660.map gaussian
(#13) coordinates:
Matrix rotation and translation
-0.10430918 0.63837086 0.76262851 -135.13645005
-0.34118550 0.69730853 -0.63035963 304.79543188
-0.93419058 -0.32595008 0.14506720 564.21719531
Axis 0.15352714 0.85578058 -0.49403341
Axis point 184.27830728 0.00000000 436.25783477
Rotation angle (degrees) 97.52545897
Shift along axis -38.65124350
> view matrix models
> #13,0.015162,0.024538,-0.99958,535.91,0.65944,0.75122,0.028444,-40.76,0.75161,-0.65959,-0.0047916,260.68
> ~select #13
Nothing selected
> save "C:\Users\Leonie Anton\Desktop\image8.png" supersample 3
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
> volume #22 level 0.7486
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!3 models
> volume #3 level 0.1798
> hide #!3 models
> show #!13 models
> select #22
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.92385,0.3526,-0.14891,-21.447,-0.35166,0.93553,0.03349,111.95,0.15112,0.021428,0.98828,-40.143
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.91486,0.34939,-0.20238,-2.9036,-0.34351,0.93692,0.064698,100.39,0.21222,0.01033,0.97717,-52.131
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.91486,0.34939,-0.20238,0.41998,-0.34351,0.93692,0.064698,97.964,0.21222,0.01033,0.97717,-62.04
Fit map run_class001.mrc z flip in map EMD-2660.map gaussian using 158895
points
correlation = 0.8416, correlation about mean = 0.3424, overlap = 9990
steps = 92, shift = 8.95, angle = 3.61 degrees
Position of run_class001.mrc z flip (#22) relative to EMD-2660.map gaussian
(#13) coordinates:
Matrix rotation and translation
-0.10418457 0.63802086 0.76293837 -135.15548890
-0.34124123 0.69761416 -0.62999120 304.62657562
-0.93418413 -0.32598139 0.14503839 564.25537353
Axis 0.15332143 0.85591074 -0.49387179
Axis point 184.36007089 0.00000000 436.20272703
Rotation angle (degrees) 97.51385929
Shift along axis -38.65889077
> ~select #22
Nothing selected
> hide #!13 models
> show #!13 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> volume #22 level 0.6163
> volume #22 level 0.7283
> volume #22 level 0.4297
> volume #13 level 0.07054
> volume #18 level 0.6159
> volume #13 level 0.08215
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> hide #!13 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
> bundle1.pdb" "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
> bundle2.pdb" "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
> bundle3.pdb" "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
> bundle4.pdb" "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
> bundle5.pdb"
Summary of feedback from opening C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
bundle1.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER RIBOSOME 2011-10-11 XXXX
Summary of feedback from opening C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
bundle2.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER RIBOSOME 2011-10-11 XXXX
Summary of feedback from opening C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
bundle3.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER RIBOSOME 2011-10-11 XXXX
Summary of feedback from opening C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
bundle4.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER RIBOSOME 2011-10-11 XXXX
Summary of feedback from opening C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/4v88-pdb-
bundle5.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER RIBOSOME 2011-10-11 XXXX
Chain information for 4v88-pdb-bundle1.pdb #23
---
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
i | No description available
Chain information for 4v88-pdb-bundle2.pdb #24
---
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
Chain information for 4v88-pdb-bundle3.pdb #25
---
Chain | Description
0 | No description available
1 | 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
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
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
Chain information for 4v88-pdb-bundle4.pdb #26
---
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
Chain information for 4v88-pdb-bundle5.pdb #27
---
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
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
> hide #27.1 models
> show #27.1 models
> hide #27.2 models
> hide #27.1 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!23 models
> show #!24 models
> select #23
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> select #24
99326 atoms, 104549 bonds, 2705 pseudobonds, 7462 residues, 3 models selected
> select #25
98224 atoms, 101807 bonds, 1336 pseudobonds, 9732 residues, 3 models selected
> select #26
98621 atoms, 103674 bonds, 2766 pseudobonds, 7473 residues, 3 models selected
> hide #!23-24 atoms
> show #!23-24 cartoons
> ~select #26
Nothing selected
> show #!26 models
> show #!25 models
> hide #!24 models
> hide #!23 models
> select #26
98621 atoms, 103674 bonds, 2766 pseudobonds, 7473 residues, 3 models selected
> select #25
98224 atoms, 101807 bonds, 1336 pseudobonds, 9732 residues, 3 models selected
> ~select #25
Nothing selected
> select #25
98224 atoms, 101807 bonds, 1336 pseudobonds, 9732 residues, 3 models selected
> select #26
98621 atoms, 103674 bonds, 2766 pseudobonds, 7473 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> hide #!25 models
> hide #!26 models
> show #!23 models
> show #!24 models
> select #23
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> select #24
99326 atoms, 104549 bonds, 2705 pseudobonds, 7462 residues, 3 models selected
> select #23
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> select #24
99326 atoms, 104549 bonds, 2705 pseudobonds, 7462 residues, 3 models selected
> select #23
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> select #25
98224 atoms, 101807 bonds, 1336 pseudobonds, 9732 residues, 3 models selected
> select #24
99326 atoms, 104549 bonds, 2705 pseudobonds, 7462 residues, 3 models selected
> select
413905 atoms, 431757 bonds, 8093 pseudobonds, 36945 residues, 64 models
selected
> select #23,24
177731 atoms, 186508 bonds, 3879 pseudobonds, 14639 residues, 6 models
selected
> view matrix models
> #23,1,0,0,217.58,0,1,0,41.995,0,0,1,67.215,#24,1,0,0,217.58,0,1,0,41.995,0,0,1,67.215
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.99211,-0.082378,-0.094464,225.61,0.11106,0.9271,0.35797,17.878,0.058088,-0.36564,0.92894,78.227,#24,0.99211,-0.082378,-0.094464,225.61,0.11106,0.9271,0.35797,17.878,0.058088,-0.36564,0.92894,78.227
> view matrix models
> #23,0.87265,0.47814,-0.099316,220.7,-0.01488,-0.17724,-0.98405,114.43,-0.48812,0.86021,-0.14755,136,#24,0.87265,0.47814,-0.099316,220.7,-0.01488,-0.17724,-0.98405,114.43,-0.48812,0.86021,-0.14755,136
> view matrix models
> #23,0.94999,0.30734,0.055304,211.9,-0.12543,0.53771,-0.83375,95.74,-0.28598,0.78511,0.54937,88.353,#24,0.94999,0.30734,0.055304,211.9,-0.12543,0.53771,-0.83375,95.74,-0.28598,0.78511,0.54937,88.353
> view matrix models
> #23,-0.06712,0.70072,-0.71028,241.91,0.70255,0.53867,0.46503,14.564,0.70846,-0.46779,-0.52845,197.76,#24,-0.06712,0.70072,-0.71028,241.91,0.70255,0.53867,0.46503,14.564,0.70846,-0.46779,-0.52845,197.76
> view matrix models
> #23,-0.10022,0.54101,-0.83502,250.24,0.6725,0.65535,0.34389,22.228,0.73328,-0.52709,-0.42951,191.41,#24,-0.10022,0.54101,-0.83502,250.24,0.6725,0.65535,0.34389,22.228,0.73328,-0.52709,-0.42951,191.41
> view matrix models
> #23,-0.074467,0.39731,-0.91466,256.37,0.66104,0.7064,0.25303,28.467,0.74664,-0.58579,-0.31524,183.44,#24,-0.074467,0.39731,-0.91466,256.37,0.66104,0.7064,0.25303,28.467,0.74664,-0.58579,-0.31524,183.44
> view matrix models
> #23,0.059425,0.44791,-0.8921,257.43,0.29027,0.84731,0.44476,7.3314,0.9551,-0.28538,-0.079664,170.7,#24,0.059425,0.44791,-0.8921,257.43,0.29027,0.84731,0.44476,7.3314,0.9551,-0.28538,-0.079664,170.7
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.059425,0.44791,-0.8921,248.82,0.29027,0.84731,0.44476,242.16,0.9551,-0.28538,-0.079664,323.72,#24,0.059425,0.44791,-0.8921,248.82,0.29027,0.84731,0.44476,242.16,0.9551,-0.28538,-0.079664,323.72
> view matrix models
> #23,0.059425,0.44791,-0.8921,373.07,0.29027,0.84731,0.44476,240.67,0.9551,-0.28538,-0.079664,289.68,#24,0.059425,0.44791,-0.8921,373.07,0.29027,0.84731,0.44476,240.67,0.9551,-0.28538,-0.079664,289.68
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.1246,0.43417,-0.89217,373.49,0.29074,0.84373,0.45121,240.23,0.94865,-0.31561,-0.021108,285.65,#24,0.1246,0.43417,-0.89217,373.49,0.29074,0.84373,0.45121,240.23,0.94865,-0.31561,-0.021108,285.65
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.1246,0.43417,-0.89217,376.71,0.29074,0.84373,0.45121,265.64,0.94865,-0.31561,-0.021108,276.34,#24,0.1246,0.43417,-0.89217,376.71,0.29074,0.84373,0.45121,265.64,0.94865,-0.31561,-0.021108,276.34
Fit molecule 4v88-pdb-bundle1.pdb (#23) to map run_class001.mrc z flip (#22)
using 78405 atoms
average map value = 0.7008, steps = 152
shifted from previous position = 22.2
rotated from previous position = 25.2 degrees
atoms outside contour = 9815, contour level = 0.42968
Position of 4v88-pdb-bundle1.pdb (#23) relative to run_class001.mrc z flip
(#22) coordinates:
Matrix rotation and translation
0.43170733 -0.20180213 -0.87914997 360.08682733
0.21218215 0.97002259 -0.11846902 308.66740566
0.87670263 -0.13539599 0.46158467 237.58443456
Axis -0.00938263 -0.97327010 0.22947172
Axis point -61.80227821 0.00000000 446.87454007
Rotation angle (degrees) 64.42721746
Shift along axis -249.27640954
Fit molecule 4v88-pdb-bundle2.pdb (#24) to map run_class001.mrc z flip (#22)
using 99326 atoms
average map value = 0.8759, steps = 128
shifted from previous position = 9.39
rotated from previous position = 18.6 degrees
atoms outside contour = 2705, contour level = 0.42968
Position of 4v88-pdb-bundle2.pdb (#24) relative to run_class001.mrc z flip
(#22) coordinates:
Matrix rotation and translation
0.34987252 -0.10359767 -0.93105142 360.37105888
0.17793702 0.98312255 -0.04252604 301.12481418
0.91974324 -0.15078982 0.36240142 250.46718090
Axis -0.05773412 -0.98697838 0.15013478
Axis point -41.66019329 0.00000000 398.76049658
Rotation angle (degrees) 69.65340602
Shift along axis -280.40555317
> ~select #24
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> ~select #23
Nothing selected
> transparency #22 60
> volume #22 level 0.3449
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
> show #!13 models
> hide #!24 models
> hide #!23 models
> volume #22 level 0.5756
> volume #22 level 0.562
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> transparency #22 0
> transparency #22 40
> show #!23 models
> hide #!23 models
> volume #22 level 0.5586
> volume #13 level 0.06538
> volume #22 level 0.6842
> volume #22 level 0.4908
> volume #22 level 0.2499
> show #!23 models
> show #!24 models
> volume #22 level 0.5756
> volume #22 level 0.3041
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> volume #22 level 0.5145
> volume #22 level 0.3754
> volume #22 level 0.562
> volume #22 level 0.4297
> volume #22 level 0.6706
> volume #22 level 0.5518
> hide #!22 models
> hide #!13 models
> select #23,24
177731 atoms, 186508 bonds, 3879 pseudobonds, 14639 residues, 6 models
selected
> nucleotides sel ladder
> ~select #24
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> ~select #23
Nothing selected
> show #!22 models
> volume #22 level 0.7249
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/3j79-assembly1.cif"
Summary of feedback from opening C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/3j79-assembly1.cif
---
notes | Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
3j79-assembly1.cif title:
Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-
protozoan drug emetine, large subunit [more info...]
Chain information for 3j79-assembly1.cif #28
---
Chain | Description
0 | 60S ribosomal protein eL24
1 | 60S ribosomal protein eL27
2 | 60S ribosomal protein eL28
3 | 60S ribosomal protein uL29
4 | 60S ribosomal protein eL29
5 | 60S ribosomal protein uL30
6 | 60S ribosomal protein eL30
7 | 60S ribosomal protein eL31
8 | 60S ribosomal protein eL32
9 | 60S ribosomal protein eL33
A | 28S ribosomal RNA
B | 5S ribosomal RNA
C | 5.8S ribosomal RNA
D | 60S ribosomal protein uL2
E | 60S ribosomal protein uL3
F | 60S ribosomal protein uL4
G | 60S ribosomal protein uL5
H | 60S ribosomal protein uL6
I | 60S ribosomal protein eL6
J | 60S ribosomal protein eL8
K | 60S ribosomal protein uL13
L | 60S ribosomal protein eL13
M | 60S ribosomal protein uL14
N | 60S ribosomal protein eL14
O | 60S ribosomal protein uL15
P | 60S ribosomal protein eL15
Q | 60S ribosomal protein uL16
R | 60S ribosomal protein uL18
S | 60S ribosomal protein eL18
T | 60S ribosomal protein eL19
U | 60S ribosomal protein eL20
V | 60S ribosomal protein eL21
W | 60S ribosomal protein uL22
X | 60S ribosomal protein eL22
Y | 60S ribosomal protein uL23
Z | 60S ribosomal protein uL24
a | 60S ribosomal protein eL34
b | 60S ribosomal protein eL36
c | 60S ribosomal protein eL37
d | 60S ribosomal protein eL38
e | 60S ribosomal protein eL39
f | 60S ribosomal protein eL40
g | 60S ribosomal protein eL41
h | 60S ribosomal protein eL43
i | 60S ribosomal protein eL44
Non-standard residues in 3j79-assembly1.cif #28
---
MG — (MG)
ZN — (ZN)
> select #28
124514 atoms, 133933 bonds, 3376 pseudobonds, 9872 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> hide #!24 models
> hide #!23 models
> view matrix models #28,1,0,0,268.36,0,1,0,2.2498,0,0,1,192.5
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.19325,0.71693,-0.66983,563.46,0.97856,0.091264,-0.18464,-3.9306,-0.07124,-0.69115,-0.71919,749.66
> view matrix models
> #28,-0.70976,0.56456,-0.42133,671.53,0.6996,0.49487,-0.51542,52.457,-0.08248,-0.66059,-0.7462,751.87
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.70976,0.56456,-0.42133,470.88,0.6996,0.49487,-0.51542,159.18,-0.08248,-0.66059,-0.7462,607.58
Fit molecule 3j79-assembly1.cif (#28) to map run_class001.mrc z flip (#22)
using 124514 atoms
average map value = 0.7363, steps = 276
shifted from previous position = 46.6
rotated from previous position = 40.2 degrees
atoms outside contour = 55333, contour level = 0.72487
Position of 3j79-assembly1.cif (#28) relative to run_class001.mrc z flip (#22)
coordinates:
Matrix rotation and translation
-0.68378701 0.16817001 -0.71003813 603.93406798
0.39173548 0.90556522 -0.16277256 38.07849429
0.61561238 -0.38944890 -0.68509191 376.53944622
Axis -0.16626469 -0.97235059 0.16398290
Axis point 219.97839916 0.00000000 311.18370844
Rotation angle (degrees) 137.02547442
Shift along axis -75.69252646
> undo
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.62788,0.55726,-0.54335,679.92,0.7274,0.66849,-0.15497,-73.916,0.27686,-0.49253,-0.82508,641.87
> view matrix models
> #28,-0.72552,0.57378,-0.38001,664.18,0.66192,0.43065,-0.61351,98.189,-0.18837,-0.69665,-0.69224,774.41
> view matrix models
> #28,-0.30268,-0.90431,-0.30101,864.18,0.94983,-0.31231,-0.016854,54.187,-0.078767,-0.29101,0.95347,286.83
> view matrix models
> #28,0.010562,-0.98883,-0.14868,769.23,0.9772,0.041741,-0.20818,12.597,0.21207,-0.14309,0.96672,177.82
> view matrix models
> #28,-0.21919,-0.048366,-0.97448,806.77,0.81212,0.5445,-0.20969,-55.771,0.54075,-0.83736,-0.080069,483.06
> view matrix models
> #28,-0.63633,0.031396,-0.77078,848.81,0.75815,0.20999,-0.61734,123.2,0.14248,-0.9772,-0.15743,631.9
> view matrix models
> #28,-0.7127,0.067499,-0.69821,843.84,0.6946,0.20687,-0.68901,156.09,0.097935,-0.97604,-0.19432,651.22
> hide #!22 models
> show #!13 models
> volume #13 level 0.08086
> volume #13 level 0.08601
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.7127,0.067499,-0.69821,823.32,0.6946,0.20687,-0.68901,241.75,0.097935,-0.97604,-0.19432,757.47
> view matrix models
> #28,-0.7127,0.067499,-0.69821,792.54,0.6946,0.20687,-0.68901,227.22,0.097935,-0.97604,-0.19432,785
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.80921,0.2164,-0.54621,749.98,0.54623,-0.065234,-0.83509,357.42,-0.21634,-0.97412,-0.065417,835
> view matrix models
> #28,-0.82534,0.28643,-0.48659,725.25,0.45848,-0.16303,-0.87362,409.77,-0.32956,-0.94413,0.0032305,841.56
> view matrix models
> #28,-0.73576,0.62157,-0.26889,579.93,-0.063957,-0.45904,-0.88611,609.69,-0.67422,-0.63477,0.3775,776.43
> view matrix models
> #28,-0.76007,0.12096,-0.63848,779.31,0.64915,0.096057,-0.75457,277.83,-0.029941,-0.988,-0.15153,810.32
> view matrix models
> #28,-0.77085,0.1367,-0.62218,774.91,0.63382,0.066703,-0.7706,291.76,-0.063839,-0.98836,-0.13806,815.93
> view matrix models
> #28,-0.40612,-0.77174,0.48937,631.84,0.54226,-0.63457,-0.55071,419.42,0.73554,0.041712,0.67619,204.11
> view matrix models
> #28,0.38326,0.2348,0.8933,120.15,0.92333,-0.072397,-0.37712,160.48,-0.023878,0.96934,-0.24455,399.77
> show sel surfaces
> view matrix models
> #28,0.45398,0.52197,0.72211,77.442,0.80627,0.1043,-0.58228,197.57,-0.37925,0.84656,-0.3735,546.31
> view matrix models
> #28,0.40251,0.14569,0.90375,132.17,0.78003,-0.57129,-0.25531,279.65,0.4791,0.80772,-0.34359,330.11
> hide sel surfaces
> view matrix models
> #28,-0.63161,0.41469,-0.65506,685.71,0.54955,0.83546,-0.0009715,-28.408,0.54687,-0.3606,-0.75558,662.43
> view matrix models
> #28,-0.21534,0.5405,-0.81332,588.49,0.65041,0.70063,0.2934,-90.609,0.72842,-0.46581,-0.50242,582.61
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.21534,0.5405,-0.81332,556.5,0.65041,0.70063,0.2934,-68.578,0.72842,-0.46581,-0.50242,488.91
> view matrix models
> #28,-0.21534,0.5405,-0.81332,501.18,0.65041,0.70063,0.2934,-72.57,0.72842,-0.46581,-0.50242,311.65
> view matrix models
> #28,-0.21534,0.5405,-0.81332,450.7,0.65041,0.70063,0.2934,-73.216,0.72842,-0.46581,-0.50242,326.73
> view matrix models
> #28,-0.21534,0.5405,-0.81332,449.78,0.65041,0.70063,0.2934,-73.271,0.72842,-0.46581,-0.50242,328.34
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.16271,0.49071,-0.856,457.02,0.66529,0.69524,0.27209,-71.048,0.72864,-0.52522,-0.43958,327.18
> view matrix models
> #28,-0.41836,0.15446,-0.89505,604.32,0.41168,0.91064,-0.035276,14.998,0.80963,-0.38323,-0.44457,276.64
> view matrix models
> #28,-0.49917,0.2669,-0.82438,584.13,0.43517,0.89992,0.027863,-2.8084,0.74931,-0.34484,-0.56536,310.67
> view matrix models
> #28,-0.41494,0.21707,-0.88358,587.12,0.45521,0.89037,0.0049635,-0.61877,0.78779,-0.40015,-0.46826,291.22
> view matrix models
> #28,-0.43801,0.17598,-0.88158,601.53,0.41713,0.90848,-0.025905,11.985,0.79634,-0.37908,-0.47132,285.12
Fit molecule 3j79-assembly1.cif (#28) to map EMD-2660.map gaussian (#13) using
124514 atoms
average map value = 0.1033, steps = 280
shifted from previous position = 12.9
rotated from previous position = 32.5 degrees
atoms outside contour = 41622, contour level = 0.086014
Position of 3j79-assembly1.cif (#28) relative to EMD-2660.map gaussian (#13)
coordinates:
Matrix rotation and translation
0.99999475 -0.00307755 -0.00099332 0.26149757
0.00307886 0.99999437 0.00132302 -0.87335632
0.00098924 -0.00132608 0.99999861 0.10073243
Axis -0.37902550 -0.28365765 0.88083938
Axis point 262.00257695 113.75583618 -0.00000000
Rotation angle (degrees) 0.20022766
Shift along axis 0.23734904
> ~select #28
45 models selected
> hide #!13 models
> show #!22 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/3j7a.pdb1"
3j7a.pdb1 title:
Cryo-em structure of the plasmodium falciparum 80S ribosome bound to the ANTI-
protozoan drug emetine, small subunit [more info...]
Chain information for 3j7a.pdb1 #29
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | 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
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
Non-standard residues in 3j7a.pdb1 #29
---
34G — emetine ((3Β,14Β)-6',7',10,11-tetramethoxyemetan)
MG — magnesium ion
ZN — zinc ion
> select #29
68866 atoms, 73566 bonds, 115 pseudobonds, 5857 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #29,1,0,0,-10.644,0,1,0,-281.06,0,0,1,51.199
> view matrix models #29,1,0,0,-27.996,0,1,0,-261.67,0,0,1,16.371
> view matrix models #29,1,0,0,-10.077,0,1,0,-282.4,0,0,1,52.624
> view matrix models #29,1,0,0,21.715,0,1,0,-297.27,0,0,1,108.08
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.23604,0.41052,-0.88077,272.13,0.27756,0.84014,0.46597,-421.91,0.93126,-0.35445,0.084361,261.47
> view matrix models
> #29,0.40641,0.48323,-0.77545,193.15,-0.36401,0.86407,0.34767,-277.78,0.83805,0.14097,0.52707,29.123
> view matrix models
> #29,-0.64963,0.15131,-0.74504,477.87,-0.40176,-0.9003,0.16747,268.83,-0.64542,0.40812,0.64566,204.59
> ui mousemode right "translate selected models"
> view matrix models
> #29,-0.64963,0.15131,-0.74504,464.43,-0.40176,-0.9003,0.16747,315.61,-0.64542,0.40812,0.64566,165.93
> view matrix models
> #29,-0.64963,0.15131,-0.74504,475,-0.40176,-0.9003,0.16747,316.02,-0.64542,0.40812,0.64566,180.76
> ui mousemode right "rotate selected models"
> view matrix models
> #29,-0.9316,-0.15263,-0.32989,509.12,-0.17129,-0.61614,0.76879,41.902,-0.3206,0.77271,0.54785,41.866
> view matrix models
> #29,-0.42677,0.46184,0.77754,-36.412,0.8441,0.51202,0.15917,-312.73,-0.32461,0.72425,-0.60835,346.54
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #29,-0.42677,0.46184,0.77754,-39.625,0.8441,0.51202,0.15917,-311.21,-0.32461,0.72425,-0.60835,321.87
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.56111,0.30754,0.76849,-180.64,0.2147,0.84257,-0.49394,-120.96,-0.79942,0.44215,0.40674,235.62
> view matrix models
> #29,-0.85017,0.16006,-0.50158,446.06,-0.45043,-0.71438,0.53551,182.23,-0.2726,0.68121,0.67944,0.71671
> view matrix models
> #29,-0.84443,0.10417,-0.52545,466.62,-0.43967,-0.69513,0.56876,166.46,-0.30601,0.7113,0.63279,10.312
> view matrix models
> #29,0.46464,0.17662,-0.86771,285.12,0.8021,0.33121,0.49693,-337.45,0.37516,-0.92688,0.012225,496.42
> view matrix models
> #29,0.53088,-0.047135,-0.84614,329.88,0.83113,0.22398,0.50898,-315.92,0.16553,-0.97345,0.15808,512.42
> view matrix models
> #29,0.65904,0.066502,-0.74916,249.49,0.48718,0.72112,0.49259,-386.12,0.57299,-0.68962,0.44285,284.47
> view matrix models
> #29,0.78609,-0.12311,-0.60573,242.6,0.5242,0.65206,0.54776,-387.62,0.32754,-0.74811,0.57711,313.48
> view matrix models
> #29,0.58178,-0.3903,-0.71358,383.1,0.73155,0.63456,0.24935,-346.93,0.35549,-0.66708,0.6547,266.02
> view matrix models
> #29,-0.068581,0.33955,-0.93809,357.83,0.91542,0.39524,0.076137,-271.11,0.39662,-0.85352,-0.33793,559.75
> ui mousemode right "translate selected models"
> view matrix models
> #29,-0.068581,0.33955,-0.93809,476.39,0.91542,0.39524,0.076137,-17.726,0.39662,-0.85352,-0.33793,444.49
> view matrix models
> #29,-0.068581,0.33955,-0.93809,424.73,0.91542,0.39524,0.076137,8.392,0.39662,-0.85352,-0.33793,463
> ui mousemode right "rotate selected models"
> view matrix models
> #29,-0.095427,0.32513,-0.94084,434.53,0.91138,0.40866,0.048785,12.264,0.40035,-0.85281,-0.33532,461.44
> view matrix models
> #29,-0.29956,0.29843,-0.9062,471.85,0.86586,0.48393,-0.12685,43.879,0.40069,-0.82265,-0.40336,470.02
> view matrix models
> #29,-0.30187,0.079533,-0.95003,544.61,0.81279,0.54227,-0.21287,59.157,0.49824,-0.83643,-0.22834,411.51
> view matrix models
> #29,0.15345,-0.091574,-0.9839,515.08,0.82945,0.55313,0.077882,-20.041,0.5371,-0.82805,0.16083,304.09
> view matrix models
> #29,-0.19064,0.28479,-0.93944,463.45,0.86801,0.49588,-0.025822,14.757,0.4585,-0.82037,-0.34173,442.98
> view matrix models
> #29,-0.15826,0.16675,-0.97322,498.88,0.85129,0.5224,-0.048927,16.285,0.50025,-0.83624,-0.22463,410.14
> hide #!22 models
> show #!13 models
Fit molecule 3j7a.pdb1 (#29) to map EMD-2660.map gaussian (#13) using 68866
atoms
average map value = 0.0879, steps = 212
shifted from previous position = 24.8
rotated from previous position = 22 degrees
atoms outside contour = 33899, contour level = 0.086014
Position of 3j7a.pdb1 (#29) relative to EMD-2660.map gaussian (#13)
coordinates:
Matrix rotation and translation
0.99996080 -0.00579866 0.00669334 0.82305492
0.00585585 0.99994626 -0.00855639 0.31140586
-0.00664337 0.00859525 0.99994100 -1.48676105
Axis 0.69566281 0.54093109 0.47270161
Axis point 0.00000000 175.30258937 32.87678906
Rotation angle (degrees) 0.70633454
Shift along axis 0.03822346
> ~select #29
Nothing selected
> volume #13 level 0.07441
> hide #!13 models
> show #!22 models
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!22 models
> show #!22 models
> hide #!28 models
> show #!28 models
> hide #!29 models
> volume #22 level 0.7384
> show #!29 models
> show #!23 models
> hide #!24 models
> hide #!23 models
> hide #!29 models
> hide #!22 models
> show #!29 models
> show #!22 models
> hide #!22 models
> show #!22 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> volume #22 level 0.5552
> volume #22 level 0.5552
> volume #22 level 0.657
> transparency #22 0
> hide #!28 models
> hide #!29 models
> volume #22 level 0.7079
> show #!29 models
> show #!28 models
> transparency #22 40
> volume #22 level 0.5043
> volume #22 level 0.6536
> volume #22 level 0.4975
> transparency #22 0
> transparency #22 20
> show #!23 models
> hide #!28 models
> hide #!29 models
> select #23/h
2444 atoms, 2490 bonds, 6 pseudobonds, 319 residues, 2 models selected
> hide #!22 models
> show #!22 models
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.34314,0.17579,-0.92269,385.08,0.076485,0.97384,0.21398,277.38,0.93617,-0.144,0.32072,258.53
> view matrix models
> #23,0.34314,0.17579,-0.92269,380.85,0.076485,0.97384,0.21398,278.03,0.93617,-0.144,0.32072,258.44
> undo
> undo
> undo
> redo
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
——— End of log from Fri Sep 17 15:20:44 2021 ———
opened ChimeraX session
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/PfRack1_fromAlphafold.pdb"
Chain information for PfRack1_fromAlphafold.pdb #30
---
Chain | Description
A | No description available
> select #23
78405 atoms, 81959 bonds, 1174 pseudobonds, 7177 residues, 3 models selected
> ~select #23
Nothing selected
> select #30
2510 atoms, 2566 bonds, 323 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #30,1,0,0,15.618,0,1,0,103.5,0,0,1,-74.931
> view matrix models #30,1,0,0,167.56,0,1,0,327.85,0,0,1,114.78
> view matrix models #30,1,0,0,240.68,0,1,0,223.68,0,0,1,174.49
> hide #!23 models
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.52887,0.78729,-0.31697,246.84,-0.67106,0.15927,-0.7241,228.6,-0.51959,0.59565,0.61255,180.75
> view matrix models
> #30,0.49375,0.79529,-0.35175,247.2,-0.66798,0.087861,-0.73898,228.44,-0.55679,0.59983,0.57462,181.13
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.49375,0.79529,-0.35175,248.1,-0.66798,0.087861,-0.73898,233.27,-0.55679,0.59983,0.57462,177.28
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.48097,0.77691,-0.4063,248.25,-0.69409,0.054291,-0.71784,233.39,-0.53564,0.62727,0.56536,177.17
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.48097,0.77691,-0.4063,244,-0.69409,0.054291,-0.71784,228.91,-0.53564,0.62727,0.56536,172.55
> view matrix models
> #30,0.48097,0.77691,-0.4063,243.78,-0.69409,0.054291,-0.71784,227.74,-0.53564,0.62727,0.56536,171.38
> view matrix models
> #30,0.48097,0.77691,-0.4063,241.87,-0.69409,0.054291,-0.71784,229.79,-0.53564,0.62727,0.56536,171.12
> view matrix models
> #30,0.48097,0.77691,-0.4063,243.35,-0.69409,0.054291,-0.71784,229.53,-0.53564,0.62727,0.56536,171.41
> show #!23 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> ~select #30
Nothing selected
> hide #!23 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!22 models
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
——— End of log from Fri Sep 17 15:48:01 2021 ———
opened ChimeraX session
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/032/run_class001.mrc"
Opened run_class001.mrc as #31, grid size 240,240,240, pixel 2.5, shown at
level 0.783, step 1, values float32
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/038/run_class001.mrc"
Opened run_class001.mrc as #32, grid size 240,240,240, pixel 2.5, shown at
level 0.792, step 1, values float32
> select #31,32
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #31,1,0,0,-112.75,0,1,0,225.06,0,0,1,-85.889,#32,1,0,0,-112.75,0,1,0,225.06,0,0,1,-85.889
> view matrix models
> #31,1,0,0,-6.0088,0,1,0,92.263,0,0,1,196.13,#32,1,0,0,-6.0088,0,1,0,92.263,0,0,1,196.13
> ui mousemode right "rotate selected models"
> view matrix models
> #31,-0.40575,0.9113,0.069911,126.01,-0.913,-0.40768,0.015301,779.12,0.042445,-0.05762,0.99744,200.62,#32,-0.40575,0.9113,0.069911,126.01,-0.913,-0.40768,0.015301,779.12,0.042445,-0.05762,0.99744,200.62
> view matrix models
> #31,0.67404,0.28597,0.6811,-207.61,-0.38275,0.92381,-0.0090878,232.69,-0.6318,-0.25457,0.73213,545.92,#32,0.67404,0.28597,0.6811,-207.61,-0.38275,0.92381,-0.0090878,232.69,-0.6318,-0.25457,0.73213,545.92
> view matrix models
> #31,0.88715,-0.21016,0.41084,-38.959,0.3021,0.93749,-0.17278,74.311,-0.34885,0.27739,0.89519,251.69,#32,0.88715,-0.21016,0.41084,-38.959,0.3021,0.93749,-0.17278,74.311,-0.34885,0.27739,0.89519,251.69
> view matrix models
> #31,0.61841,0.09614,0.77995,-166.13,-0.014237,0.9937,-0.1112,133.06,-0.78572,0.057663,0.61588,536.81,#32,0.61841,0.09614,0.77995,-166.13,-0.014237,0.9937,-0.1112,133.06,-0.78572,0.057663,0.61588,536.81
> view matrix models
> #31,0.56003,0.14772,0.8152,-175.14,0.10726,0.96277,-0.24815,149.31,-0.8215,0.2264,0.52333,526.81,#32,0.56003,0.14772,0.8152,-175.14,0.10726,0.96277,-0.24815,149.31,-0.8215,0.2264,0.52333,526.81
> view matrix models
> #31,0.55165,0.082767,0.82996,-158.03,0.15758,0.9668,-0.20116,118.11,-0.81905,0.24176,0.52029,522.49,#32,0.55165,0.082767,0.82996,-158.03,0.15758,0.9668,-0.20116,118.11,-0.81905,0.24176,0.52029,522.49
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.55165,0.082767,0.82996,-177.73,0.15758,0.9668,-0.20116,27.801,-0.81905,0.24176,0.52029,274.77,#32,0.55165,0.082767,0.82996,-177.73,0.15758,0.9668,-0.20116,27.801,-0.81905,0.24176,0.52029,274.77
> ui tool show "Fit in Map"
> hide #30 models
Fit map run_class001.mrc in map run_class001.mrc z flip using 138208 points
correlation = 0.8925, correlation about mean = 0.1243, overlap = 8.86e+04
steps = 168, shift = 40.9, angle = 19.2 degrees
Position of run_class001.mrc (#32) relative to run_class001.mrc z flip (#22)
coordinates:
Matrix rotation and translation
0.47600640 0.05174253 0.87791835 -141.80377599
0.10569021 0.98766677 -0.11551597 9.14665978
-0.87306786 0.14777372 0.46466702 344.11774280
Axis 0.14862594 0.98842447 0.03045324
Axis point 216.20040490 0.00000000 290.30060503
Rotation angle (degrees) 62.34347466
Shift along axis -1.55543515
Fit map run_class001.mrc in map run_class001.mrc z flip using 138149 points
correlation = 0.909, correlation about mean = 0.1323, overlap = 8.9e+04
steps = 268, shift = 52.6, angle = 33.1 degrees
Position of run_class001.mrc (#31) relative to run_class001.mrc z flip (#22)
coordinates:
Matrix rotation and translation
0.44994216 0.20496071 0.86921986 -171.11474991
0.44489563 0.79249128 -0.41716359 60.34601659
-0.77435130 0.57441160 0.26538911 268.20682239
Axis 0.51258632 0.84963007 0.12403230
Axis point 101.15935443 0.00000000 259.00446017
Rotation angle (degrees) 75.29091750
Shift along axis -3.17298007
> volume flip #31,32
Opened run_class001.mrc z flip as #33, grid size 240,240,240, pixel 2.5, shown
at step 1, values float32
Opened run_class001.mrc z flip as #34, grid size 240,240,240, pixel 2.5, shown
at step 1, values float32
Fit map run_class001.mrc z flip in map run_class001.mrc z flip using 138208
points
correlation = 0.9975, correlation about mean = 0.8805, overlap = 1.294e+05
steps = 360, shift = 39.3, angle = 62.6 degrees
Position of run_class001.mrc z flip (#34) relative to run_class001.mrc z flip
(#22) coordinates:
Matrix rotation and translation
0.99996857 -0.00567852 -0.00553268 2.79875576
0.00565736 0.99997666 -0.00383180 -0.55525559
0.00555431 0.00380038 0.99997736 -2.79125708
Axis 0.43370656 -0.63003073 0.64417380
Axis point 126.35469315 510.06967579 0.00000000
Rotation angle (degrees) 0.50413925
Shift along axis -0.23438785
Fit map run_class001.mrc z flip in map run_class001.mrc z flip using 138149
points
correlation = 0.9996, correlation about mean = 0.9733, overlap = 1.247e+05
steps = 336, shift = 25.4, angle = 64 degrees
Position of run_class001.mrc z flip (#33) relative to run_class001.mrc z flip
(#22) coordinates:
Matrix rotation and translation
0.92067633 -0.31308602 0.23309280 46.03767081
0.30969972 0.94941288 0.05197375 -92.55559939
-0.23757356 0.02433777 0.97106461 72.43747302
Axis -0.03537983 0.60255113 0.79729568
Axis point 310.71462385 68.36214620 0.00000000
Rotation angle (degrees) 22.98943203
Shift along axis 0.35579866
> transparency #22 60
> hide #!33 models
> volume #34 level 0.6024
> volume #34 level 0.5444
> hide #!22 models
> show #!33 models
> hide #!34 models
> volume #33 level 0.4499
> show #!22 models
> volume #33 level 0.5529
> hide #!22 models
> volume #33 level 0.6525
> show #!13 models
> volume #33 level 0.752
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> volume #33 level 0.7829
> hide #!33 models
> show #!34 models
> volume #34 level 0.7726
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!33 models
> show #!34 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> volume #34 level 0.904
> volume #34 level 0.6682
> volume #34 level 0.6411
> close #33
> close #32
> close #31
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
> hide #!13 models
> show #!13 models
> volume #34 level 0.7184
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> hide #!13 models
> save "C:\Users\Leonie Anton\Desktop\image6.png" supersample 3
> hide #!34 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/037/run_it025_class001.mrc"
> "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/037/run_it025_class002.mrc"
> "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/037/run_it025_class003.mrc"
Opened run_it025_class001.mrc as #31.1, grid size 240,240,240, pixel 2.5,
shown at level 0.801, step 1, values float32
Opened run_it025_class002.mrc as #31.2, grid size 240,240,240, pixel 2.5,
shown at level 0.785, step 1, values float32
Opened run_it025_class003.mrc as #31.3, grid size 240,240,240, pixel 2.5,
shown at level 0.672, step 1, values float32
> hide #!31.3 models
> hide #!31.2 models
> volume #31.1 level 0.5918
> volume #31.2 level 0.6472
> save "C:\Users\Leonie Anton\Desktop\image5.png" supersample 3
> save "C:\Users\Leonie Anton\Desktop\image6.png" supersample 3
> volume #31.3 level 0.4971
> save "C:\Users\Leonie Anton\Desktop\image7.png" supersample 3
> show #!31.2 models
> hide #!31.2 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Refine3D/040/run_ct28_class001.mrc"
Opened run_ct28_class001.mrc as #32, grid size 240,240,240, pixel 2.5, shown
at level 0.788, step 1, values float32
> hide #!31.3 models
> hide #!32 models
> show #!32 models
> volume #32 level 0.6074
> show #!34 models
> volume flip #32
Opened run_ct28_class001.mrc z flip as #33, grid size 240,240,240, pixel 2.5,
shown at step 1, values float32
Fit map run_ct28_class001.mrc z flip in map run_class001.mrc z flip using
253910 points
correlation = 0.9982, correlation about mean = 0.9599, overlap = 1.865e+05
steps = 76, shift = 13.7, angle = 5.86 degrees
Position of run_ct28_class001.mrc z flip (#33) relative to run_class001.mrc z
flip (#34) coordinates:
Matrix rotation and translation
0.91195854 -0.32225969 0.25392974 46.73589174
0.32388136 0.94538939 0.03660273 -91.72254085
-0.25185807 0.04886294 0.96652984 70.87518517
Axis 0.01493959 0.61632426 0.78735076
Axis point 294.05074326 64.69213505 0.00000000
Rotation angle (degrees) 24.22531865
Shift along axis -0.02898163
> volume #32 level 0.6282
> volume #33 level 0.6629
> volume #34 level 0.6218
> volume #33 level 0.6144
> volume #33 level 0.6213
> show #!13 models
> volume #33 level 0.6802
> volume #33 level 0.597
> show #!34 models
> volume #33 level 0.6872
> volume #34 level 0.7687
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> volume #33 level 0.7218
> hide #!13 models
> hide #!33 models
> ui tool show "Side View"
> show #!13 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/041/run_it025_class001.mrc"
> "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/041/run_it025_class002.mrc"
> "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/Class3D/041/run_it025_class003.mrc"
Opened run_it025_class001.mrc as #35.1, grid size 240,240,240, pixel 2.5,
shown at level 0.798, step 1, values float32
Opened run_it025_class002.mrc as #35.2, grid size 240,240,240, pixel 2.5,
shown at level 0.795, step 1, values float32
Opened run_it025_class003.mrc as #35.3, grid size 240,240,240, pixel 2.5,
shown at level 0.781, step 1, values float32
> hide #!31 models
> hide #!34 models
> hide #!13 models
> hide #!35.1 models
> hide #!35.2 models
> volume #35.3 level 0.5997
> hide #!35.3 models
> show #!35.2 models
> hide #!35.2 models
> show #!35.1 models
> show #!35.2 models
> show #!35.3 models
> volume #35.3 level 0.7108
> show #!33 models
> hide #!33 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/M/RefineJ40_2.5Apix_240box/RefineJ040_2.5Apix_240box_filtsharp.mrc"
Opened RefineJ040_2.5Apix_240box_filtsharp.mrc as #36, grid size 240,240,240,
pixel 2.5, shown at level 0.00591, step 1, values float32
> hide #!35 models
> hide #!35.1 models
> hide #!35.2 models
> hide #!35.3 models
> show #!13 models
> select #36
2 models selected
> view matrix models #36,1,0,0,72.396,0,1,0,-81.928,0,0,1,-23.475
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.64273,-0.73193,0.22623,329.39,0.59478,0.66287,0.45479,-283.29,-0.48284,-0.15775,0.86138,202.8
> view matrix models
> #36,0.42601,-0.53865,0.72689,180.45,0.83083,0.55094,-0.078668,-154.87,-0.3581,0.63744,0.68223,-22.191
> view matrix models
> #36,0.31879,-0.1679,0.93284,35.007,0.44283,0.89655,0.010036,-178.12,-0.83802,0.40989,0.36016,279.91
> view matrix models
> #36,0.15115,-0.030864,0.98803,23.649,0.62256,0.77935,-0.070895,-168.5,-0.76784,0.62582,0.13701,261.13
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.15115,-0.030864,0.98803,-49.941,0.62256,0.77935,-0.070895,-90.733,-0.76784,0.62582,0.13701,281.53
> view matrix models
> #36,0.15115,-0.030864,0.98803,-42.733,0.62256,0.77935,-0.070895,-93.92,-0.76784,0.62582,0.13701,283.1
> ~select #36
Nothing selected
Fit map RefineJ040_2.5Apix_240box_filtsharp.mrc in map EMD-2660.map gaussian
using 138137 points
correlation = 0.5335, correlation about mean = 0.07965, overlap = 38.14
steps = 116, shift = 13.1, angle = 3.76 degrees
Position of RefineJ040_2.5Apix_240box_filtsharp.mrc (#36) relative to
EMD-2660.map gaussian (#13) coordinates:
Matrix rotation and translation
-0.19607524 0.97368379 0.11616528 -25.53022262
0.96567884 0.21231405 -0.14962328 -66.69627949
-0.17034928 0.08284093 -0.98189536 563.72877383
Axis 0.62990733 0.77636735 -0.02169098
Axis point 47.97389452 0.00000000 279.43918137
Rotation angle (degrees) 169.36670300
Shift along axis -80.09031981
> volume flip #36
Opened RefineJ040_2.5Apix_240box_filtsharp.mrc z flip as #37, grid size
240,240,240, pixel 2.5, shown at step 1, values float32
> select #37
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #37,0.63982,0.4417,-0.62891,165.76,0.74045,-0.57347,0.35052,165.78,-0.20584,-0.68995,-0.69398,774.82
> view matrix models
> #37,0.63618,0.060484,-0.76916,325.21,0.40282,-0.8763,0.26427,379.39,-0.65803,-0.47796,-0.58185,804.13
> view matrix models
> #37,0.61174,0.079116,-0.78709,331.7,0.42564,-0.8716,0.2432,377.75,-0.66679,-0.48379,-0.56687,803.95
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.61174,0.079116,-0.78709,336.3,0.42564,-0.8716,0.2432,249.44,-0.66679,-0.48379,-0.56687,647.62
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.48726,-0.32739,-0.80957,777.5,-0.63967,0.76492,0.075671,97.817,0.59448,0.55472,-0.58213,-21.906
> view matrix models
> #37,0.053335,0.11388,-0.99206,543.85,0.99765,0.03664,0.057842,-135.37,0.042936,-0.99282,-0.11166,468.64
> view matrix models
> #37,0.94903,-0.097089,0.29987,-26.875,0.098882,0.99506,0.0092288,-161.32,-0.29929,0.020894,0.95393,-61.358
> view matrix models
> #37,0.95782,0.10432,0.26778,-81.588,-0.067724,0.98748,-0.14245,-67.072,-0.27929,0.1183,0.95289,-96.549
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.95782,0.10432,0.26778,-75.16,-0.067724,0.98748,-0.14245,53.107,-0.27929,0.1183,0.95289,59.231
Fit map RefineJ040_2.5Apix_240box_filtsharp.mrc z flip in map EMD-2660.map
gaussian using 138137 points
correlation = 0.8286, correlation about mean = 0.2944, overlap = 83.37
steps = 228, shift = 14, angle = 12.7 degrees
Position of RefineJ040_2.5Apix_240box_filtsharp.mrc z flip (#37) relative to
EMD-2660.map gaussian (#13) coordinates:
Matrix rotation and translation
-0.07252885 0.67514054 0.73411503 -147.24833631
0.07376506 0.73766884 -0.67112104 180.70066312
-0.99463478 0.00547640 -0.10330406 557.90598344
Axis 0.34672182 0.88589646 -0.30817438
Axis point 134.27722759 0.00000000 367.04627923
Rotation angle (degrees) 102.65512167
Shift along axis -62.90446416
> ~select #37
Nothing selected
> volume #37 level 0.00447
> show #30 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/M/RefineJ40_2.5Apix_240box/RefineJ040_2.5Apix_240box_filt.mrc"
Opened RefineJ040_2.5Apix_240box_filt.mrc as #38, grid size 240,240,240, pixel
2.5, shown at level 0.00568, step 1, values float32
> volume flip #38
Opened RefineJ040_2.5Apix_240box_filt.mrc z flip as #39, grid size
240,240,240, pixel 2.5, shown at step 1, values float32
Fit map RefineJ040_2.5Apix_240box_filt.mrc z flip in map
RefineJ040_2.5Apix_240box_filtsharp.mrc z flip using 138130 points
correlation = 0.9995, correlation about mean = 0.9944, overlap = 11.1
steps = 96, shift = 13.7, angle = 5.9 degrees
Position of RefineJ040_2.5Apix_240box_filt.mrc z flip (#39) relative to
RefineJ040_2.5Apix_240box_filtsharp.mrc z flip (#37) coordinates:
Matrix rotation and translation
0.99999996 -0.00001310 -0.00010493 0.02839863
0.00001309 0.99999997 -0.00003114 0.01087506
0.00010492 0.00003114 0.99999996 -0.07041513
Axis 0.28246714 -0.95188937 0.11882316
Axis point 658.99641613 0.00000000 299.41727156
Rotation angle (degrees) 0.00631566
Shift along axis -0.01069712
> hide #!37 models
> volume #39 level 0.003625
> hide #!39 models
> show #!37 models
> hide #!37 models
> show #!37 models
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/M/RefineJ38_2.5Apix_240box/RefineJ038_2.5Apx_240box_filtsharp.mrc"
Opened RefineJ038_2.5Apx_240box_filtsharp.mrc as #40, grid size 240,240,240,
pixel 2.5, shown at level 0.00357, step 1, values float32
> volume flip #40
Opened RefineJ038_2.5Apx_240box_filtsharp.mrc z flip as #41, grid size
240,240,240, pixel 2.5, shown at step 1, values float32
> hide #!37 models
Fit map RefineJ038_2.5Apx_240box_filtsharp.mrc z flip in map EMD-2660.map
gaussian using 138209 points
correlation = 0.8251, correlation about mean = 0.3062, overlap = 50.62
steps = 372, shift = 18.7, angle = 22.3 degrees
Position of RefineJ038_2.5Apx_240box_filtsharp.mrc z flip (#41) relative to
EMD-2660.map gaussian (#13) coordinates:
Matrix rotation and translation
-0.09678132 0.64142310 0.76105833 -138.06808701
-0.34041879 0.69720051 -0.63089341 304.90022804
-0.93527986 -0.32013725 0.15087649 561.55594884
Axis 0.15659354 0.85480396 -0.49476121
Axis point 182.99664063 0.00000000 437.14831188
Rotation angle (degrees) 97.14334521
Shift along axis -38.82674704
> show #!37 models
> close #38
> close #40
> close #36
> volume #37 level 0.005101
> hide #!13 models
> volume #41 level 0.002935
> volume #37 level 0.004412
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/M/RefineJ38_2.5Apix_240box/RefineJ038_2.5Apx_240box_mask.mrc"
Opened RefineJ038_2.5Apx_240box_mask.mrc as #36, grid size 240,240,240, pixel
2.5, shown at level 5e-05, step 1, values float32
> volume flip #36
Opened RefineJ038_2.5Apx_240box_mask.mrc z flip as #38, grid size 240,240,240,
pixel 2.5, shown at step 1, values float32
> select #38
2 models selected
> ~select #38
Nothing selected
Fit map RefineJ038_2.5Apx_240box_mask.mrc z flip in map
RefineJ038_2.5Apx_240box_filtsharp.mrc z flip using 30636 points
correlation = 0.9336, correlation about mean = 0, overlap = 178.9
steps = 248, shift = 17.9, angle = 22.3 degrees
Position of RefineJ038_2.5Apx_240box_mask.mrc z flip (#38) relative to
RefineJ038_2.5Apx_240box_filtsharp.mrc z flip (#41) coordinates:
Matrix rotation and translation
0.99999978 -0.00043120 -0.00050684 0.19971590
0.00043121 0.99999991 0.00001993 0.05486399
0.00050683 -0.00002015 0.99999987 -0.17539290
Axis -0.03010488 -0.76130627 0.64769318
Axis point 139.92060571 0.00000000 384.39186645
Rotation angle (degrees) 0.03814464
Shift along axis -0.16138151
> hide #!37 models
> volume #38 level 0.08997
> volume #38 level 0.00519
> volume #41 level 0.005948
> volume #41 level 0.004756
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/M/RefineJ38_2.5Apix_240box/RefineJ038_2.5Apx_240box_denoised.mrc"
Opened RefineJ038_2.5Apx_240box_denoised.mrc as #40, grid size 240,240,240,
pixel 2.5, shown at level 0.00318, step 1, values float32
> volume flip #40
Opened RefineJ038_2.5Apx_240box_denoised.mrc z flip as #42, grid size
240,240,240, pixel 2.5, shown at step 1, values float32
Fit map RefineJ038_2.5Apx_240box_denoised.mrc z flip in map
RefineJ038_2.5Apx_240box_filtsharp.mrc z flip using 138179 points
correlation = 0.9899, correlation about mean = 0.883, overlap = 3.859
steps = 160, shift = 18.7, angle = 22.3 degrees
Position of RefineJ038_2.5Apx_240box_denoised.mrc z flip (#42) relative to
RefineJ038_2.5Apx_240box_filtsharp.mrc z flip (#41) coordinates:
Matrix rotation and translation
0.99999999 -0.00011839 -0.00007390 0.10989080
0.00011839 0.99999999 0.00007221 -0.09689214
0.00007389 -0.00007222 0.99999999 -0.00955072
Axis -0.45959124 -0.47024859 0.75342030
Axis point 866.67275857 881.03872145 0.00000000
Rotation angle (degrees) 0.00900331
Shift along axis -0.01213717
> volume #42 level 0.001429
> hide #!42 models
> volume #41 level 0.003311
> open "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/M/RefineJ38_2.5Apix_240box/mask.mrc"
Opened mask.mrc as #43, grid size 240,240,240, pixel 2.5, shown at level 1,
step 1, values float32
> volume #43 level 0.995
> volume flip #43
Opened mask.mrc z flip as #44, grid size 240,240,240, pixel 2.5, shown at step
1, values float32
Fit map mask.mrc z flip in map RefineJ038_2.5Apx_240box_filtsharp.mrc z flip
using 467653 points
correlation = 0.7155, correlation about mean = 0, overlap = 1126
steps = 176, shift = 19.1, angle = 22.2 degrees
Position of mask.mrc z flip (#44) relative to
RefineJ038_2.5Apx_240box_filtsharp.mrc z flip (#41) coordinates:
Matrix rotation and translation
0.99999822 -0.00183044 0.00045101 0.18664226
0.00182973 0.99999710 0.00156786 -1.04193200
-0.00045388 -0.00156703 0.99999867 0.38437973
Axis -0.63933230 0.18454255 0.74645714
Axis point 567.10355220 92.79367157 0.00000000
Rotation angle (degrees) 0.14047183
Shift along axis -0.02468422
> hide #!44 models
> show #!13 models
> volume #41 level 0.00303
> transparency #41 50
> close #1
> close #2
> close #4
> close #5
> close #6
> close #7
> close #9
> close #11
> close #12
> show #!15.1 models
> hide #!15.1 models
> close #15
> close #16
> close #17
> close #18
> close #19
> show #!31.1 models
> show #!10 models
> close #31
> show #!35.1 models
> show #!20 models
> close #35
> close #20
> volume #41 level 0.003558
> transparency #41 30
> transparency #41 20
> hide #!10 models
> show #!41 models
> hide #!41 models
> show #!41 models
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/ribosome_M_relion.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 621, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\lz4\frame\\__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\lz4\frame\\__init__.py", line 695, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save 'C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/ribosome_M_relion.cxs':
[Errno 28] No space left on device
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/ribosomes.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 621, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\lz4\frame\\__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\lz4\frame\\__init__.py", line 695, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save 'C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/ribosomes.cxs':
[Errno 28] No space left on device
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 621, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\lz4\frame\\__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\lz4\frame\\__init__.py", line 695, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save 'C:/Users/Leonie Anton/Documents/Uni/Columbia
university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs':
[Errno 28] No space left on device
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
——— End of log from Thu Sep 23 17:22:34 2021 ———
opened ChimeraX session
> hide #!13 models
> ui tool show "Side View"
> ui tool show "Hide Dust"
> surface dust #41 size 15
> transparency #41 0
> color #41 lightgrey
> color #41 #6ed3cbcc models
> hide #30 models
> view name side
> volume #37 level 0.003953
> volume #41 level 0.0031
> view name rack_side
> view name rack_front
> show #30 models
> hide #30 models
> show #30 models
> select #30
2510 atoms, 2566 bonds, 323 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.48097,0.77691,-0.4063,244.31,-0.69409,0.054291,-0.71784,232.35,-0.53564,0.62727,0.56536,168.63
> view matrix models
> #30,0.48097,0.77691,-0.4063,244.37,-0.69409,0.054291,-0.71784,232.1,-0.53564,0.62727,0.56536,168.77
> ~select #30
Nothing selected
> view name rack_front_model
> view side
> hide #30 models
> view rack_front
> view side
> view list
Named views: rack_front, rack_front_model, rack_side, side
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 350
> wait 350
> view rack_side
> wait
wait requires a frame count argument unless motion is in progress
> view rack_front 300
> wait 300
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 350
> wait 350
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 350
> wait 350
> view rack_side
> wait
wait requires a frame count argument unless motion is in progress
> view rack_front 300
> wait 300
> movie encode "C:\Users\Leonie Anton/Desktop/movie1.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie1.mp4
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 350
> wait 350
> view rack_side 300
> wait 300
> view rack_front 300
> wait 300
> rock y 300
> wait 300
> movie encode "C:\Users\Leonie Anton/Desktop/movie1.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie1.mp4
> stop
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 350
> wait 350
> view rack_side 200
> wait 200
> view rack_front 100
> wait 100
> stop
> movie encode "C:\Users\Leonie Anton/Desktop/movie1.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie1.mp4
> view rack_side 200
> wait 200
> view rack_front 100
> wait 100
[Repeated 1 time(s)]
> view rack_front
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> rock y 100
> wait 100
> stop
> movie encode "C:\Users\Leonie Anton/Desktop/movie2.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie2.mp4
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 100
> movie encode "C:\Users\Leonie Anton/Desktop/movie3.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie3.mp4
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 50
> stop
> movie encode "C:\Users\Leonie Anton/Desktop/movie4.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie4.mp4
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 100
> wait 200
> stop
> movie encode "C:\Users\Leonie Anton/Desktop/movie5.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie5.mp4
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 200
> stop
> movie encode "C:\Users\Leonie Anton/Desktop/movie6.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie6.mp4
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 100
> stop
> movie encode "C:\Users\Leonie Anton/Desktop/movie7.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie7.mp4
> view rack_front
> show #30 models
> select #30
2510 atoms, 2566 bonds, 323 residues, 1 model selected
> view matrix models
> #30,0.48097,0.77691,-0.4063,245.17,-0.69409,0.054291,-0.71784,231.48,-0.53564,0.62727,0.56536,168.64
> ~select #30
Nothing selected
> view rack_front
> select #30
2510 atoms, 2566 bonds, 323 residues, 1 model selected
> view matrix models
> #30,0.48097,0.77691,-0.4063,243.92,-0.69409,0.054291,-0.71784,232.48,-0.53564,0.62727,0.56536,168.82
> ~select #30
Nothing selected
> view name rack_front
> view rack_front
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/rack_front_model.png"
> width 3000 height 1895 supersample 3 transparentBackground true
> hide #30 models
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 100
> stop
> wait 50
> movie encode "C:\Users\Leonie Anton/Desktop/movie8.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie8.mp4
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 100
> stop
> view rack_front 50
> wait 50
> movie encode "C:\Users\Leonie Anton/Desktop/movie9.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie9.mp4
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 100
> stop
> view rack_front 50
> wait 100
[Repeated 1 time(s)]
> movie encode "C:\Users\Leonie Anton/Desktop/movie10.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie10.mp4
> view side
[Repeated 1 time(s)]
> movie record
> view side
> wait
wait requires a frame count argument unless motion is in progress
> turn y 1 300
> wait 300
> view rack_side 100
> wait 100
> view rack_front 100
> wait 100
> stop
> wait 5
> rock y 50
> wait 100
> stop
> view rack_front 50
> wait 100
[Repeated 1 time(s)]
> movie encode "C:\Users\Leonie Anton/Desktop/movie11.mp4"
Movie saved to C:\Users\Leonie Anton/Desktop/movie11.mp4
> view side
[Repeated 1 time(s)]
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1283, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1283, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
> hide #!41 models
> show #!41 models
> close #37
> close #39
> close #36,38
> close #40
> close #44
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1283, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes_2.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1283, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
> save "C:/Users/Leonie Anton/Documents/Uni/Columbia
> university/research/Projects/Pf_api_mito_tomo/Ribosome_test/relion/ribosomes.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1283, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 616, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File "C:\Program Files\ChimeraX 1.3.dev202109170828\bin\lib\site-
packages\chimerax\core\session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9749
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20QES1H500
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 16,941,092,864
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
OSLanguage: de-DE
Locale: ('de_CH', 'cp1252')
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: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.29.1
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202109170828
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.1
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.1
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2
ChimeraX-ModelPanel: 1.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13
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
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
distlib: 0.3.2
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.8.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.20
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.1
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.0
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session code trying to take len() of 'SurfaceUpdaters' |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Leonie,
--Eric