Crash opening PDB file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Current thread 0x00003974 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\pdb\pdb.py", line 74 in open_pdb
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\pdb\__init__.py", line 34 in open
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 421 in collated_open
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 179 in provider_open
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 118 in cmd_open
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\dialog.py", line 155 in _qt_safe
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "H:\\\Documents\\\Documents_local\\\Cryo-EM_everything\\\ChimeraX
> projects\\\P78-J513-early_model\\\P78-J513-J535-550merged-
> locres-350-early_5_more_models.cxs"

Opened cryosparc_P78_J535_004_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.82, shown at level 0.0842, step 1, values float32  
Opened cryosparc_P78_J513_003_volume_map_sharp(2).mrc as #2, grid size
256,256,256, pixel 0.82, shown at level 0.117, step 1, values float32  
Opened cryosparc_P78_J350_002_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.82, shown at level 0.106, step 1, values float32  
Opened cryosparc_P78_J543_010_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.82, shown at level 0.107, step 1, values float32  
Opened cryosparc_P78_J545_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 0.82, shown at level 0.0756, step 1, values float32  
Opened cryosparc_P78_J550_007_volume_map_sharp.mrc as #17, grid size
256,256,256, pixel 0.82, shown at level 0.0805, step 1, values float32  
Opened cryosparc_P78_J552_map_locres.mrc as #18, grid size 256,256,256, pixel
0.82, shown at level 4.03, step 1, values float32  
Opened merged_J350-J550.mrc as #7, grid size 256,256,256, pixel 0.82, shown at
level 0.145, step 1, values float32  
Log from Wed Jan 8 12:16:20 2025UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "H:\\\Documents\\\Documents_local\\\Cryo-EM_everything\\\ChimeraX
> projects\\\P78-J513-early_model\\\P78-J513-J535-550-locres-350-early_4.cxs"

Opened cryosparc_P78_J535_004_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.82, shown at level 0.0842, step 1, values float32  
Opened cryosparc_P78_J513_003_volume_map_sharp(2).mrc as #2, grid size
256,256,256, pixel 0.82, shown at level 0.117, step 1, values float32  
Opened cryosparc_P78_J350_002_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.82, shown at level 0.106, step 1, values float32  
Opened cryosparc_P78_J543_010_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.82, shown at level 0.107, step 1, values float32  
Opened cryosparc_P78_J545_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 0.82, shown at level 0.0756, step 1, values float32  
Opened cryosparc_P78_J550_007_volume_map_sharp.mrc as #17, grid size
256,256,256, pixel 0.82, shown at level 0.0805, step 1, values float32  
Opened cryosparc_P78_J552_map_locres.mrc as #18, grid size 256,256,256, pixel
0.82, shown at level 4.03, step 1, values float32  
Map values for surface "surface": minimum 0, mean 1.299, maximum 42.2  
Log from Tue Jan 7 17:39:44 2025UCSF 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 "H:\\\Documents\\\Documents_local\\\Cryo-EM_everything\\\ChimeraX
> projects\\\P78-J513-early_model\\\cryosparc_P78_J535_004_volume_map_sharp.mrc"

Opened cryosparc_P78_J535_004_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.82, shown at level 0.0409, step 1, values float32  

> open "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/cryosparc_P78_J513_003_volume_map_sharp(2).mrc"

Opened cryosparc_P78_J513_003_volume_map_sharp(2).mrc as #2, grid size
256,256,256, pixel 0.82, shown at level 0.0448, step 1, values float32  

> open "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/cryosparc_P78_J350_002_volume_map_sharp.mrc"

Opened cryosparc_P78_J350_002_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.82, shown at level 0.0655, step 1, values float32  

> surface dust #1 size 8.2

> surface dust #2 size 8.2

> surface dust #3 size 8.2

> open "H:/Documents/Documents_Hansmole/AlphaFold/SH-AMT1_homo_3er/ranked 4
> 130324 (probably mod 5).pdb"

Chain information for ranked 4 130324 (probably mod 5).pdb #4  
---  
Chain | Description  
B C D | No description available  
  

> select #4

12795 atoms, 13134 bonds, 1722 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,64.734,0,1,0,108.6,0,0,1,57.167

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.33094,0.72784,0.6006,71.458,-0.74086,0.59461,-0.31235,104.78,-0.58446,-0.3416,0.73601,53.947

> view matrix models
> #4,-0.033495,0.8741,0.48459,71.776,-0.78867,0.27471,-0.55003,101.88,-0.61391,-0.4006,0.68017,53.359

> view matrix models
> #4,0.056924,0.97628,0.20889,71.232,0.72666,-0.184,0.6619,104.51,0.68464,0.11412,-0.7199,50.703

> view matrix models
> #4,-0.069185,0.90946,0.40999,71.665,0.71184,-0.24293,0.659,104.15,0.69893,0.33744,-0.63058,52.4

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.069185,0.90946,0.40999,101.28,0.71184,-0.24293,0.659,131.84,0.69893,0.33744,-0.63058,55.812

> view matrix models
> #4,-0.069185,0.90946,0.40999,111.81,0.71184,-0.24293,0.659,108.94,0.69893,0.33744,-0.63058,100.81

> view matrix models
> #4,-0.069185,0.90946,0.40999,98.573,0.71184,-0.24293,0.659,108.89,0.69893,0.33744,-0.63058,100.62

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> fitmap #4 inMap #3

Fit molecule ranked 4 130324 (probably mod 5).pdb (#4) to map
cryosparc_P78_J350_002_volume_map_sharp.mrc (#3) using 12795 atoms  
average map value = 0.02722, steps = 96  
shifted from previous position = 4.54  
rotated from previous position = 2.07 degrees  
atoms outside contour = 10085, contour level = 0.065505  
  
Position of ranked 4 130324 (probably mod 5).pdb (#4) relative to
cryosparc_P78_J350_002_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.03576597 0.91333949 0.40562516 99.42705252  
0.72157039 -0.25721385 0.64278862 105.34427173  
0.69141664 0.31567706 -0.64983923 103.31315570  
Axis -0.68891682 -0.60189423 -0.40387739  
Axis point 0.00000000 12.13907854 22.43878453  
Rotation angle (degrees) 166.26627012  
Shift along axis -173.62892623  
  

> volume #3 level 0.08647

> volume #3 level 0.09945

> fitmap #4 inMap #3

Fit molecule ranked 4 130324 (probably mod 5).pdb (#4) to map
cryosparc_P78_J350_002_volume_map_sharp.mrc (#3) using 12795 atoms  
average map value = 0.02722, steps = 48  
shifted from previous position = 0.00853  
rotated from previous position = 0.0155 degrees  
atoms outside contour = 11445, contour level = 0.099453  
  
Position of ranked 4 130324 (probably mod 5).pdb (#4) relative to
cryosparc_P78_J350_002_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.03598912 0.91328311 0.40573234 99.42423428  
0.72163307 -0.25711304 0.64275858 105.34710867  
0.69133963 0.31592220 -0.64980203 103.30725872  
Axis -0.68884290 -0.60194815 -0.40392312  
Axis point -0.00000000 12.13007150 22.43087499  
Rotation angle (degrees) 166.27654830  
Shift along axis -173.62936498  
  

> volume #3 level 0.1244

> surface dust #3 size 8.2

> volume #3 level 0.1494

> volume #3 level 0.1314

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.037709,0.9137,0.40464,99.422,0.71916,-0.25633,0.64583,105.36,0.69382,0.31536,-0.64743,103.31

> view matrix models
> #4,0.0007965,0.90131,0.43318,99.475,0.7751,-0.27426,0.56922,104.94,0.63184,0.3353,-0.69882,103.21

> view matrix models
> #4,-0.19153,0.84597,0.49764,99.39,0.80466,-0.15498,0.57315,105.67,0.56199,0.51021,-0.65104,104.43

> view matrix models
> #4,-0.18081,0.80779,0.56106,99.433,0.94495,-0.015509,0.32684,105.48,0.27272,0.58927,-0.76052,104.39

> fitmap #4 inMap #3

Fit molecule ranked 4 130324 (probably mod 5).pdb (#4) to map
cryosparc_P78_J350_002_volume_map_sharp.mrc (#3) using 12795 atoms  
average map value = 0.04903, steps = 120  
shifted from previous position = 3.71  
rotated from previous position = 16.4 degrees  
atoms outside contour = 11664, contour level = 0.1314  
  
Position of ranked 4 130324 (probably mod 5).pdb (#4) relative to
cryosparc_P78_J350_002_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.12381456 0.86789031 0.48107833 102.22810193  
0.99170505 0.09136400 0.09040855 105.40410893  
0.03451147 0.48828171 -0.87200340 106.06875296  
Axis 0.65141559 0.73113909 0.20271499  
Axis point 11.92402709 0.00000000 38.99560625  
Rotation angle (degrees) 162.21829990  
Shift along axis 165.15976934  
  

> volume #3 level 0.1064

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-early_1.cxs"

> show #!2 models

> volume #2 level 0.08113

> show #!1 models

> volume #1 level 0.0811

> volume #1 level 0.04521

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-early_1.cxs"

> ~select #4

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1 level 0.09089

> hide #!1 models

> volume #2 level 0.07204

> volume #2 level 0.1175

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> open H:/Download/cryosparc_P78_J543_010_volume_map_sharp.mrc

Opened cryosparc_P78_J543_010_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.82, shown at level 0.0488, step 1, values float32  

> surface dust #5 size 8.2

> volume #5 level 0.07768

> volume #5 level 0.1066

> show #!1 models

> volume #1 level 0.05723

> volume #1 level 0.03031

> volume #1 level 0.04041

> volume #1 level 0.04714

> volume #1 level 0.08416

> hide #!1 models

> surface dust #5 size 8.2

> volume #5 level 0.05841

> hide #!5 models

> show #!5 models

> open H:/Download/cryosparc_P78_J545_007_volume_map_sharp.mrc

Opened cryosparc_P78_J545_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 0.82, shown at level 0.062, step 1, values float32  

> surface dust #5 size 8.2

> surface dust #6 size 8.2

> hide #!5 models

> volume #6 level 0.09642

> volume #6 level 0.0584

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!6 models

> hide #4 models

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-350-early_2.cxs"

> ui tool show "Segment Map"

> open "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/cryosparc_P78_J535_004_volume_map.mrc"

Opened cryosparc_P78_J535_004_volume_map.mrc as #7, grid size 256,256,256,
pixel 0.82, shown at level 0.0317, step 1, values float32  

> hide #!5 models

> show #4 models

> volume #7 level 0.009683

> volume #7 level 0.004177

Segmenting cryosparc_P78_J535_004_volume_map.mrc, density threshold 0.004177  
Showing cryosparc_P78_J535_004_volume_map.seg - 0 regions, 0 surfaces  
Showing 39 region surfaces  
869 watershed regions, grouped to 39 regions  

> ui mousemode right select

> select #8

40 models selected  

> select clear

Grouped 12 regions  
Grouped 1 regions  
Grouped 2 regions  
Deleted 26 regions  

> hide #!7 models

> ui mousemode right "map eraser"

Can only have one displayed volume when erasing  

Segmenting cryosparc_P78_J535_004_volume_map.mrc, density threshold 0.004177  
Showing cryosparc_P78_J535_004_volume_map.seg - 0 regions, 0 surfaces  
Showing 39 region surfaces  
869 watershed regions, grouped to 39 regions  

> hide #!8 models

> show #!8 models

Segmenting cryosparc_P78_J535_004_volume_map.mrc, density threshold 0.004177  
Showing cryosparc_P78_J535_004_volume_map.seg - 0 regions, 0 surfaces  
Showing 39 region surfaces  
869 watershed regions, grouped to 39 regions  

> hide #9 models

> ui mousemode right select

Grouped 12 regions  
Showing 28 region surfaces  
Deleted 27 regions  

> show #9 models

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/cryosparc_P78_J535_004_volume_map.seg" models
> #8

No map chosen to save  
Please select one ore more regions to save to .mrc file  

> open "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/cryosparc_P78_J535_004_volume_map.seg"

Summary of feedback from opening H:/Documents/Documents_local/Cryo-
EM_everything/ChimeraX
projects/P78-J513-early_model/cryosparc_P78_J535_004_volume_map.seg  
---  
note | Showing 1 region surfaces  
  
Opened cryosparc_P78_J535_004_volume_map.seg  

> hide #9 models

> select #10

2 models selected  
Saving 1 regions to mrc file...  
Opened cryosparc_P78_J535_004_volume_map_region_1201.mrc as #11, grid size
110,96,111, pixel 0.82, shown at step 1, values float32  
Wrote cryosparc_P78_J535_004_volume_map_region_1201.mrc  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+23 (frame:
1936x1094-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1017+0+23 (frame: 1936x1056-8-8) margins: 8, 31, 8, 8
minimum size: 493x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=509,1094
maxtrack=0,0)  

> hide #!10 models

> hide #10.1 models

> hide #!11 models

> show #!11 models

> hide #!8 models

> hide #!11 models

> show #!11 models

> volume #11 level 0.009776

> show #9 models

Drag select of eraser sphere, 12 of 1000 triangles, 11 residues, 11
cryosparc_P78_J535_004_volume_map_region_1201.mrc  

> ~select #11

81 atoms, 11 residues, 2 models selected  

> ~select #9

81 atoms, 11 residues, 1 model selected  

> select #9

1 model selected  
Drag select of eraser sphere, 38 of 1000 triangles, 25 residues, 11
cryosparc_P78_J535_004_volume_map_region_1201.mrc  

> ~select #11

181 atoms, 25 residues, 2 models selected  

> select #4

12795 atoms, 13134 bonds, 1722 residues, 1 model selected  

> ~select #4

Nothing selected  

> select #9

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,97.828,0,1,0,102.93,0,0,1,107.15

> view matrix models #9,1,0,0,104.04,0,1,0,105.65,0,0,1,104.5

> volume erase #11 center 104.04,105.65,104.5 radius 25.167

> view matrix models #9,1,0,0,102.79,0,1,0,112.67,0,0,1,113.54

> volume erase #11 center 102.79,112.67,113.54 radius 25.167

> view matrix models #9,1,0,0,101.01,0,1,0,121.66,0,0,1,96.447

> view matrix models #9,1,0,0,102.83,0,1,0,101.56,0,0,1,86.15

> volume erase #11 center 102.83,101.56,86.15 radius 25.167

> view matrix models #9,1,0,0,101.36,0,1,0,75.309,0,0,1,107.28

> view matrix models #9,1,0,0,98.062,0,1,0,76.04,0,0,1,107.37

> view matrix models #9,1,0,0,101.33,0,1,0,72.947,0,0,1,129.51

> view matrix models #9,1,0,0,107.39,0,1,0,78.577,0,0,1,136.48

> view matrix models #9,1,0,0,105.08,0,1,0,86.998,0,0,1,127.42

> volume erase #11 center 105.08,86.998,127.42 radius 25.167

> view matrix models #9,1,0,0,103.71,0,1,0,130.62,0,0,1,116.2

> view matrix models #9,1,0,0,97.436,0,1,0,138.83,0,0,1,112.58

> view matrix models #9,1,0,0,97.009,0,1,0,135.37,0,0,1,97.51

> view matrix models #9,1,0,0,93.824,0,1,0,139.85,0,0,1,97.325

> view matrix models #9,1,0,0,93.828,0,1,0,136.52,0,0,1,106.93

> volume erase #11 center 93.828,136.52,106.93 radius 25.167

> view matrix models #9,1,0,0,95.647,0,1,0,132.89,0,0,1,96.889

> view matrix models #9,1,0,0,102.33,0,1,0,102.64,0,0,1,119.59

> view matrix models #9,1,0,0,103.73,0,1,0,100.37,0,0,1,120.22

> view matrix models #9,1,0,0,103.41,0,1,0,97.301,0,0,1,116.68

> volume erase #11 center 103.41,97.301,116.68 radius 25.167

> view matrix models #9,1,0,0,101.4,0,1,0,104.15,0,0,1,104.37

> volume erase #11 center 101.4,104.15,104.37 radius 25.167

> view matrix models #9,1,0,0,96.123,0,1,0,109.69,0,0,1,93.968

> volume erase #11 center 96.123,109.69,93.968 radius 25.167

> view matrix models #9,1,0,0,96.115,0,1,0,113.12,0,0,1,89.256

> view matrix models #9,1,0,0,94.425,0,1,0,111.48,0,0,1,75.584

> view matrix models #9,1,0,0,95.222,0,1,0,108.61,0,0,1,84.523

> view matrix models #9,1,0,0,96.72,0,1,0,103.13,0,0,1,78.672

> volume erase #11 center 96.72,103.13,78.672 radius 25.167

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> volume resample #11 onGrid #1

Opened cryosparc_P78_J535_004_volume_map_region_1201.mrc resampled as #12,
grid size 256,256,256, pixel 0.82, shown at step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1055+0+23 (frame:
1936x1094-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1017+0+23 (frame: 1936x1056-8-8) margins: 8, 31, 8, 8
minimum size: 493x1055 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=509,1094
maxtrack=0,0)  

> view matrix models #9,1,0,0,92.421,0,1,0,115.42,0,0,1,98.926

> view matrix models #9,1,0,0,71.956,0,1,0,107.37,0,0,1,108.77

> view matrix models #9,1,0,0,73.732,0,1,0,105.68,0,0,1,107.96

> volume erase #12 center 73.732,105.68,107.96 radius 11.756

> view matrix models #9,1,0,0,92.587,0,1,0,70.296,0,0,1,99.183

> save from_J535.mrc models #12

> volume #12 level 0.002654

> open H:/Download/cryosparc_P78_J550_000_volume_map_half_A.mrc

Opened cryosparc_P78_J550_000_volume_map_half_A.mrc as #13, grid size
256,256,256, pixel 0.82, shown at level 0.115, step 1, values float32  

> surface dust #12 size 8.2

> surface dust #13 size 8.2

> hide #9 models

> hide #!12 models

> volume #13 level 0.05592

> view matrix models #9,1,0,0,93.988,0,1,0,67.476,0,0,1,92.447

> view matrix models #9,1,0,0,95.087,0,1,0,63.751,0,0,1,84.315

> volume #13 level 0.07152

> open H:/Download/cryosparc_P78_J551_map_half_A.mrc

Opened cryosparc_P78_J551_map_half_A.mrc as #14, grid size 256,256,256, pixel
0.82, shown at level 0.0382, step 1, values float32  

> surface dust #13 size 8.2

> surface dust #14 size 8.2

> hide #!13 models

> open H:/Download/cryosparc_P78_J551_map_locres.mrc

Opened cryosparc_P78_J551_map_locres.mrc as #15, grid size 256,256,256, pixel
0.82, shown at level 7.25, step 1, values float32  

> hide #!15 models

> show #!6 models

> hide #!14 models

> ui tool show "Surface Color"

> color radial #15.1 palette #ff0000:#ffffff:#0000ff

> show #!15 models

> hide #!15 models

> color radial #15.1 palette 109.5,#ff0000:158.8,#ffffff:208.1,#0000ff

> color radial #15.1 palette #ff0000:#ffffff:#0000ff

> color sample #6.1 map #15 palette 109.5,#ff0000:158.8,#ffffff:208.1,#0000ff

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> color single #6.1

> color sample #6.1 map #15 palette 4,#ff0000:3,#ffffff:2,#0000ff

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> color sample #6.1 map #15 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> color sample #6.1 map #15 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> key red-white-blue :0.0 :26.5 :52.9

> ui tool show "Color Key"

> ui mousemode left "color key"

> key red-white-blue :2 :26.5 :52.9

> key red-white-blue :2 :3 :52.9

> key red-white-blue :2 :3 :4

> key red-white-blue :2 :3 :4 white:

> key red:2 white:3 blue:4 white:5

> key red:2 white:3 blue:4 #ff2761:5

> key red:2 springgreen:3 blue:4 #ff2761:5

> ui mousemode left rotate

> key red-white-blue :0.0 :26.5 :52.9

> ui tool show "Color Key"

> ui mousemode left "color key"

> ui mousemode left rotate

> color sample #6.1 map #15 palette 2,#ff0000:3,#ffffff:4,#0000ff:5,#808080

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> color sample #6.1 map #15 palette
> 2,#ff0000:3,#ffffff:4,#0000ff:5,#808080:6,#3e8067:7,#801f66:8,#7e8006

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> key red:2 white:3 blue:4 #aaaaff:5 #3e8067:6 #801f66:7 #7e8006:8

> ui tool show "Color Key"

> ui mousemode left "color key"

> ui mousemode left rotate

> color gradient #6.1 map #15 palette
> 2,#ff0000:3,#ffffff:4,#0000ff:5,#aaaaff:6,#3e8067:7,#801f66:8,#7e8006

Map values for surface "surface": minimum 0, mean 0.1962, maximum 38.57  

> color single #6.1

> color gradient #6.1 map #15 palette
> 2,#ff0000:3,#ffffff:4,#0000ff:5,#aaaaff:6,#3e8067:7,#801f66:8,#7e8006

Map values for surface "surface": minimum 0, mean 0.1962, maximum 38.57  

> color single #6.1

> color sample #6.1 map #15 palette
> 2,#ff0000:3,#ffffff:4,#0000ff:5,#aaaaff:6,#3e8067:7,#801f66:8,#7e8006

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> color sample #6.1 map #15 palette
> 2,#0fc6ce:3,#5fd9de:4,#afecee:5,#ffffff:6,#deb4c9:7,#be6a93:8,#9e1f5e

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> color single #6.1

> color sample #6.1 map #15 palette
> 2,#ff0000:3,#ff4848:4,#ff9191:5,#ffdada:6,#dadaff:7,#9191ff:8,#4848ff

Map values for surface "surface": minimum 0, mean 1.598, maximum 52.93  

> volume #5 level 0.2511

> volume #5 level 0.1066

> hide #!5 models

> hide #!6 models

> show #!6 models

> volume #6 level 0.07559

> open H:/Download/cryosparc_P78_J550_005_volume_map_sharp.mrc

Opened cryosparc_P78_J550_005_volume_map_sharp.mrc as #17, grid size
256,256,256, pixel 0.82, shown at level 0.0503, step 1, values float32  

> hide #!6 models

QWindowsWindow::setGeometry: Unable to set geometry 1920x1047+0+23 (frame:
1936x1086-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1017+0+23 (frame: 1936x1056-8-8) margins: 8, 31, 8, 8
minimum size: 499x1047 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=515,1086
maxtrack=0,0)  

> surface dust #17 size 8.2

> volume #17 level 0.1031

> volume #17 level 0.0993

> volume #17 level 0.0767

> close #17

> hide #16 models

> show #!13 models

> hide #!13 models

> open H:/Download/cryosparc_P78_J550_007_volume_map_sharp.mrc

Opened cryosparc_P78_J550_007_volume_map_sharp.mrc as #17, grid size
256,256,256, pixel 0.82, shown at level 0.0603, step 1, values float32  

> surface dust #17 size 8.2

> open H:/Download/cryosparc_P78_J552_map_locres.mrc

Opened cryosparc_P78_J552_map_locres.mrc as #18, grid size 256,256,256, pixel
0.82, shown at level 4.03, step 1, values float32  

> hide #!18 models

> color sample #17.1 map #18 palette
> 2,#ff0000:3,#ff4848:4,#ff9191:5,#ffdada:6,#dadaff:7,#9191ff:8,#4848ff

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 3,#ff0000:4,#ff4848:5,#ff9191:6,#ffdada:7,#dadaff:8,#9191ff:9,#4848ff:10,#0000ff

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> view matrix models #9,1,0,0,93.327,0,1,0,72.455,0,0,1,77.433

> volume #17 level 0.07378

> volume #17 level 0.06028

> key red:3 #ff4848:4 #ff9191:5 #ffdada:6 #dadaff:7 #9191ff:8 #4848ff:9
> blue:10

> ui tool show "Color Key"

> ui mousemode left "color key"

> ui mousemode left rotate

> key red:3 #ff4848:4 #ff9191:5 #ffdada:6 #dadaff:7 #9191ff:8 #4848ff:9
> blue:10

> ui tool show "Color Key"

> ui mousemode left "color key"

> key blue:10 #4848ff:9 #9191ff:8 #dadaff:7 #ffdada:6 #ff9191:5 #ff4848:4
> red:3

> key red:3 #ff4848:4 #ff9191:5 #ffdada:6 #dadaff:7 #9191ff:8 #4848ff:9
> blue:10

> key delete

> ui mousemode left rotate

> key red:3 #ff4848:4 #ff9191:5 #ffdada:6 #dadaff:7 #9191ff:8 #4848ff:9
> blue:10

> ui tool show "Color Key"

> ui mousemode left "color key"

> ui mousemode left rotate

> color sample #17.1 map #18 palette
> 2,#ff0000:3,#ff4848:4,#ff9191:5,#ffdada:6,#dadaff:7,#9191ff:8,#4848ff:15,#fff23e

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 2,#ff0000:3,#ff4848:4,#ff9191:5,#ffdada:6,#dadaff:7,#9191ff:8,#4848ff:13,#fff23e

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 2,#ff0000:3,#ff4848:4,#ff9191:5,#ffdada:6,#dadaff:7,#9191ff:8,#4848ff:13,#0000ff

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 2,#0fc6ce:3,#53d6dc:4,#98e6ea:5,#dcf6f8:6,#f1dfe8:7,#d59fba:8,#b95f8c:9,#9e1f5e

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 2,#9e1f5e:3,#b95f8c:4,#d59fba:5,#f1dfe8:6,#dcf6f8:7,#98e6ea:8,#53d6dc:9,#0fc6ce

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> key #9e1f5e:2 #b95f8c:3 #d59fba:4 #f1dfe8:5 #dcf6f8:6 #98e6ea:7 #53d6dc:8
> #0fc6ce:9

> ui tool show "Color Key"

> ui mousemode left "color key"

> ui mousemode left rotate

> color sample #17.1 map #18 palette
> #9e1f5e:#b95f8c:#d59fba:#f1dfe8:#dcf6f8:#98e6ea:#53d6dc:#0fc6ce

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 1,#9e1f5e:2,#b95f8c:3,#d59fba:4,#f1dfe8:5,#dcf6f8:6,#98e6ea:7,#53d6dc:8,#0fc6ce

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> color sample #17.1 map #18 palette
> 3,#9e1f5e:4,#b95f8c:5,#d59fba:6,#f1dfe8:7,#dcf6f8:8,#98e6ea:9,#53d6dc:10,#0fc6ce

Map values for surface "surface": minimum 0, mean 0.6727, maximum 43.09  

> volume #17 level 0.04677

> volume #17 level 0.05353

> surface dust #17 size 8.2

> surface dust #17 size 8.2

> surface dust #17 size 8.2

> volume #17 level 0.08053

> hide #4 models

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-550-locres-350-early_3.cxs"

> close #9-15

Showing cryosparc_P78_J535_004_volume_map.seg - 1 regions, 1 surfaces  
Showing cryosparc_P78_J535_004_volume_map.seg - 1 regions, 1 surfaces  

> hide #!17 models

> show #!17 models

> show #4 models

> show #!18 models

> hide #!17 models

> hide #!8 models

> hide #19 models

> show #19 models

> show #!17 models

> hide #!18 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> close #7,8

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-550-locres-350-early_4.cxs"

——— End of log from Tue Jan 7 17:39:44 2025 ———

opened ChimeraX session  

> hide #!17 models

> show #!17 models

> open "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/merged_J350-J550.mrc"

Opened merged_J350-J550.mrc as #7, grid size 256,256,256, pixel 0.82, shown at
level 0.0991, step 1, values float32  

> hide #4 models

> show #4 models

> hide #!17 models

> hide #19 models

> volume #7 level 0.1188

> surface dust #7 size 8.2

> volume #7 level 0.1384

> ui mousemode right select

> select clear

> select /C:128

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right pivot

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.16827,0.89383,0.41564,102.1,0.97498,0.21304,-0.063434,105.47,-0.14525,0.39457,-0.90731,105.34

> undo

> ui mousemode right pivot

> ui mousemode right tug

> ui mousemode right select

> open "H:/Documents/Documents_Hansmole/AlphaFold/AF 3 google 140524/Sh-
> Amt1-TEV-10xHis/fold_sh_amt1_tev_10xhis_model_0.cif"
> "H:/Documents/Documents_Hansmole/AlphaFold/AF 3 google 140524/Sh-
> Amt1-TEV-10xHis/fold_sh_amt1_tev_10xhis_model_1.cif"
> "H:/Documents/Documents_Hansmole/AlphaFold/AF 3 google 140524/Sh-
> Amt1-TEV-10xHis/fold_sh_amt1_tev_10xhis_model_2.cif"
> "H:/Documents/Documents_Hansmole/AlphaFold/AF 3 google 140524/Sh-
> Amt1-TEV-10xHis/fold_sh_amt1_tev_10xhis_model_3.cif"
> "H:/Documents/Documents_Hansmole/AlphaFold/AF 3 google 140524/Sh-
> Amt1-TEV-10xHis/fold_sh_amt1_tev_10xhis_model_4.cif"

Chain information for fold_sh_amt1_tev_10xhis_model_0.cif #8  
---  
Chain | Description  
A B C | .  
  
Chain information for fold_sh_amt1_tev_10xhis_model_1.cif #9  
---  
Chain | Description  
A B C | .  
  
Chain information for fold_sh_amt1_tev_10xhis_model_2.cif #10  
---  
Chain | Description  
A B C | .  
  
Chain information for fold_sh_amt1_tev_10xhis_model_3.cif #11  
---  
Chain | Description  
A B C | .  
  
Chain information for fold_sh_amt1_tev_10xhis_model_4.cif #12  
---  
Chain | Description  
A B C | .  
  

> select #8

13314 atoms, 13659 bonds, 1788 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,121.57,0,1,0,6.7988,0,0,1,76.677

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.64527,-0.14947,-0.74919,134.07,-0.71264,0.47112,0.51979,12.172,0.27527,0.86931,-0.41052,74.662

> view matrix models
> #8,-0.42935,-0.17039,-0.88692,133.21,-0.80778,0.51167,0.29274,13.137,0.40393,0.84212,-0.35732,73.873

> view matrix models
> #8,0.22495,0.13624,-0.9648,128.07,-0.96296,0.18218,-0.1988,16.796,0.14869,0.97378,0.17218,73.488

> view matrix models
> #8,0.3828,0.19578,-0.90285,126.7,-0.80639,0.54767,-0.22314,14.268,0.45078,0.81347,0.36752,71.891

> view matrix models
> #8,0.038902,0.16048,-0.98627,129.14,-0.87749,0.47765,0.043109,14.341,0.47801,0.86377,0.1594,72.025

> view matrix models
> #8,0.018071,0.1454,-0.98921,129.35,-0.62816,0.77138,0.10191,11.365,0.77787,0.61954,0.10528,71.448

> view matrix models
> #8,-0.19784,0.09643,-0.97548,130.84,-0.62648,0.75295,0.20149,11.187,0.75391,0.65098,-0.088548,71.94

> view matrix models
> #8,-0.33762,0.056888,-0.93956,131.77,-0.62044,0.73719,0.26758,11.055,0.70786,0.67328,-0.21359,72.433

> view matrix models
> #8,-0.43695,0.087425,-0.89523,132.12,-0.075351,0.98821,0.13328,6.971,0.89632,0.12569,-0.42521,74.29

> view matrix models
> #8,-0.45868,0.17887,-0.87041,131.78,0.50755,0.85676,-0.091389,4.6067,0.72939,-0.48369,-0.48376,78.187

> view matrix models
> #8,-0.34302,-0.010404,-0.93927,132.1,-0.7993,0.52848,0.28605,13.027,0.49341,0.84888,-0.1896,72.879

> view matrix models
> #8,-0.47899,0.44085,-0.75909,130.44,-0.2976,0.73198,0.61289,8.2567,0.82583,0.51948,-0.21941,72.426

> view matrix models
> #8,-0.80786,-0.36942,-0.45924,135.31,-0.47311,0.87114,0.1315,9.9053,0.35148,0.3235,-0.87853,77.836

> view matrix models
> #8,-0.53576,-0.18922,-0.8229,133.78,-0.40351,0.91346,0.052667,9.4932,0.74172,0.36026,-0.56574,74.524

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.53576,-0.18922,-0.8229,108.34,-0.40351,0.91346,0.052667,104.93,0.74172,0.36026,-0.56574,106.8

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.63052,-0.047027,-0.77474,108.16,0.27263,0.92114,-0.27779,101.64,0.72671,-0.38637,-0.56798,110.26

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.63052,-0.047027,-0.77474,87.062,0.27263,0.92114,-0.27779,98.585,0.72671,-0.38637,-0.56798,104.78

> fitmap #8 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_0.cif (#8) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.04542, steps = 156  
shifted from previous position = 3.96  
rotated from previous position = 4.03 degrees  
atoms outside contour = 11947, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_0.cif (#8) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.66372039 -0.08314607 -0.74334513 90.62351920  
0.21134416 0.93246005 -0.29300497 99.73827839  
0.71750184 -0.35157502 -0.60132031 103.66846470  
Axis -0.03927226 -0.97952380 0.19746092  
Axis point 15.98680278 0.00000000 81.86420514  
Rotation angle (degrees) 131.78139193  
Shift along axis -80.78453767  
  

> view matrix models
> #8,-0.66372,-0.083146,-0.74335,91.767,0.21134,0.93246,-0.293,104.4,0.7175,-0.35158,-0.60132,106.84

> hide #4 models

> view matrix models
> #8,-0.66372,-0.083146,-0.74335,91.872,0.21134,0.93246,-0.293,104.33,0.7175,-0.35158,-0.60132,106.47

> fitmap #8 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_0.cif (#8) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.0653, steps = 156  
shifted from previous position = 3.88  
rotated from previous position = 14.5 degrees  
atoms outside contour = 11177, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_0.cif (#8) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.52385782 -0.10050401 -0.84585574 95.61257883  
0.08392602 0.98209328 -0.16866897 105.45267889  
0.84766114 -0.15934787 -0.50604234 107.22703711  
Axis 0.00547156 -0.99410736 0.10826184  
Axis point 15.13051459 0.00000000 86.37765714  
Rotation angle (degrees) 121.59445293  
Shift along axis -92.69953748  
  

> select #9

13314 atoms, 13659 bonds, 1788 residues, 1 model selected  

> view matrix models #9,1,0,0,73.854,0,1,0,18.556,0,0,1,65.114

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.45012,0.82408,-0.34392,72.798,-0.79567,0.54496,0.26444,13.085,0.40535,0.15462,0.90099,67.716

> view matrix models
> #9,0.4857,0.63147,-0.60443,73.709,-0.7225,0.67922,0.12903,14.041,0.49202,0.37403,0.78614,68.744

> view matrix models
> #9,0.35947,0.73255,-0.57806,73.037,-0.78485,0.57243,0.23735,13.257,0.50477,0.36837,0.78071,68.825

> view matrix models
> #9,0.31731,0.72367,-0.61287,72.925,-0.9065,0.42126,0.02809,13.198,0.27851,0.54666,0.78968,67.748

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.31731,0.72367,-0.61287,64.516,-0.9065,0.42126,0.02809,101.78,0.27851,0.54666,0.78968,101.22

> view matrix models
> #9,0.31731,0.72367,-0.61287,77.024,-0.9065,0.42126,0.02809,105.92,0.27851,0.54666,0.78968,100.56

> fitmap #9 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_1.cif (#9) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.04267, steps = 100  
shifted from previous position = 3.61  
rotated from previous position = 5.33 degrees  
atoms outside contour = 11897, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_1.cif (#9) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
0.32381873 0.65998485 -0.67790960 79.82246357  
-0.88977438 0.45600792 0.01892983 107.20664786  
0.32162554 0.59705676 0.73490152 102.38075475  
Axis 0.29914015 -0.51718935 -0.80189173  
Axis point 98.29168987 -71.76167998 0.00000000  
Rotation angle (degrees) 75.08628660  
Shift along axis -113.66631339  
  

> view matrix models
> #9,0.32382,0.65998,-0.67791,87.049,-0.88977,0.45601,0.01893,112.97,0.32163,0.59706,0.7349,109.17

> fitmap #9 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_1.cif (#9) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.0657, steps = 244  
shifted from previous position = 10.8  
rotated from previous position = 20.2 degrees  
atoms outside contour = 11114, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_1.cif (#9) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
0.46205371 0.71008819 -0.53130137 93.87444337  
-0.88685191 0.36977317 -0.27705867 104.75764221  
-0.00027510 0.59920161 0.80059812 106.38172402  
Axis 0.46182724 -0.27987392 -0.84165681  
Axis point 145.04947872 -71.42003279 0.00000000  
Rotation angle (degrees) 71.56597329  
Shift along axis -75.50205910  
  

> view matrix models
> #9,0.46205,0.71009,-0.5313,96.198,-0.88685,0.36977,-0.27706,102.43,-0.0002751,0.5992,0.8006,106.58

> undo

> select #10

13314 atoms, 13659 bonds, 1788 residues, 1 model selected  

> view matrix models #10,1,0,0,-14.493,0,1,0,35.868,0,0,1,59.849

> view matrix models #10,1,0,0,20.122,0,1,0,52.116,0,0,1,75.202

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.8415,-0.53977,0.023054,23.61,-0.056336,-0.045229,0.99739,54.525,-0.53732,-0.8406,-0.068468,85.671

> view matrix models
> #10,-0.77312,-0.60898,-0.17729,26.457,0.21958,-0.51921,0.82596,58.017,-0.59504,0.59963,0.53513,73.957

> view matrix models
> #10,-0.92763,-0.2164,-0.30443,24.654,-0.14983,-0.531,0.83402,58.41,-0.34213,0.81927,0.46015,72.641

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.92763,-0.2164,-0.30443,92.646,-0.14983,-0.531,0.83402,104.38,-0.34213,0.81927,0.46015,104.74

> fitmap #10 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_2.cif (#10) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.06648, steps = 240  
shifted from previous position = 2.15  
rotated from previous position = 26.9 degrees  
atoms outside contour = 11082, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_2.cif (#10) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.95907379 -0.27712967 -0.05810858 94.22397087  
-0.02794497 -0.11157812 0.99336267 105.37221402  
-0.28177392 0.95433195 0.09926727 105.61341782  
Axis -0.11578066 0.66348042 0.73918101  
Axis point 54.55483476 11.60878778 0.00000000  
Rotation angle (degrees) 170.29620980  
Shift along axis 137.07052022  
  

> select #11

13314 atoms, 13659 bonds, 1788 residues, 1 model selected  

> view matrix models #11,1,0,0,83.621,0,1,0,79.455,0,0,1,49.591

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.43853,0.89864,-0.01174,86.7,0.61959,0.31176,0.72036,82.247,0.651,0.30862,-0.6935,38.42

> view matrix models
> #11,-0.43115,0.8946,0.11746,87.324,0.64989,0.21759,0.72822,82.36,0.62591,0.39031,-0.67521,38.442

> view matrix models
> #11,-0.32395,0.92852,0.18138,87.219,0.89142,0.23535,0.38728,79.825,0.31691,0.28715,-0.90394,38.534

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.32395,0.92852,0.18138,106.38,0.89142,0.23535,0.38728,103.04,0.31691,0.28715,-0.90394,97.393

> view matrix models
> #11,-0.32395,0.92852,0.18138,89.531,0.89142,0.23535,0.38728,103.94,0.31691,0.28715,-0.90394,101.51

> fitmap #11 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_3.cif (#11) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.06538, steps = 116  
shifted from previous position = 7.37  
rotated from previous position = 7.98 degrees  
atoms outside contour = 11141, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_3.cif (#11) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.30846534 0.90229414 0.30118832 93.78024606  
0.88868752 0.16043582 0.42952860 105.31771860  
0.33923975 0.40015699 -0.85134644 107.22394624  
Axis -0.58793303 -0.76167737 -0.27236435  
Axis point 5.73144152 0.00000000 34.75761193  
Rotation angle (degrees) 178.56867690  
Shift along axis -164.55860700  
  

> select #12

13314 atoms, 13659 bonds, 1788 residues, 1 model selected  

> view matrix models #12,1,0,0,59.609,0,1,0,40.252,0,0,1,64.536

> view matrix models #12,1,0,0,89.626,0,1,0,97.201,0,0,1,72.625

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.64458,0.7645,0.0079751,91.016,-0.72746,0.61649,-0.30124,92.188,-0.23521,0.18837,0.95352,72.264

> view matrix models
> #12,0.58746,0.76695,0.25822,92.193,-0.74443,0.63728,-0.19923,92.749,-0.31736,-0.075189,0.94532,71.14

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.58746,0.76695,0.25822,89.09,-0.74443,0.63728,-0.19923,103.95,-0.31736,-0.075189,0.94532,104.54

> fitmap #12 inMap #7

Fit molecule fold_sh_amt1_tev_10xhis_model_4.cif (#12) to map
merged_J350-J550.mrc (#7) using 13314 atoms  
average map value = 0.06353, steps = 88  
shifted from previous position = 6.63  
rotated from previous position = 6.52 degrees  
atoms outside contour = 11224, contour level = 0.13838  
  
Position of fold_sh_amt1_tev_10xhis_model_4.cif (#12) relative to
merged_J350-J550.mrc (#7) coordinates:  
Matrix rotation and translation  
0.60171390 0.77048064 0.21047557 95.11067087  
-0.71187105 0.63683293 -0.29611388 105.70364340  
-0.36218779 0.02834438 0.93167409 106.59603796  
Axis 0.20004736 0.35308022 -0.91395591  
Axis point 187.76075970 -37.04860226 0.00000000  
Rotation angle (degrees) 54.18920623  
Shift along axis -41.07557471  
  

> ~select #12

Nothing selected  

> volume #7 level 0.05991

> show #4 models

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-550merged-
> locres-350-early_5_more_models.cxs"

> open "H:/Documents/Documents_Hansmole/AlphaFold/SH-AMT1_homo_3er/ranked 3
> 150224.pdb"

Chain information for ranked 3 150224.pdb #13  
---  
Chain | Description  
B C D | No description available  
  

> select #13

12795 atoms, 13134 bonds, 1722 residues, 1 model selected  

> view matrix models #13,1,0,0,101.77,0,1,0,59.181,0,0,1,57.915

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.29975,-0.88648,-0.35256,108.7,-0.92754,-0.35726,0.10968,66.263,-0.22319,0.29414,-0.92934,66.739

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.29975,-0.88648,-0.35256,89.983,-0.92754,-0.35726,0.10968,111.75,-0.22319,0.29414,-0.92934,109.92

> volume #7 level 0.1449

> view matrix models
> #13,0.29975,-0.88648,-0.35256,91.703,-0.92754,-0.35726,0.10968,107.61,-0.22319,0.29414,-0.92934,111.03

> view matrix models
> #13,0.29975,-0.88648,-0.35256,97.861,-0.92754,-0.35726,0.10968,119.45,-0.22319,0.29414,-0.92934,179.88

> view matrix models
> #13,0.29975,-0.88648,-0.35256,114.96,-0.92754,-0.35726,0.10968,110.21,-0.22319,0.29414,-0.92934,106.66

> fitmap #13 inMap #7

Fit molecule ranked 3 150224.pdb (#13) to map merged_J350-J550.mrc (#7) using
12795 atoms  
average map value = 0.04357, steps = 284  
shifted from previous position = 5.23  
rotated from previous position = 10.8 degrees  
atoms outside contour = 11961, contour level = 0.14492  
  
Position of ranked 3 150224.pdb (#13) relative to merged_J350-J550.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.39866966 -0.85978405 -0.31911421 113.14638625  
-0.85089848 -0.47657832 0.22100875 110.24755539  
-0.34210271 0.18342431 -0.92158626 112.23045908  
Axis -0.83623971 0.51148567 0.19770065  
Axis point 0.00000000 90.50214187 68.69416362  
Rotation angle (degrees) 178.71232448  
Shift along axis -16.03942191  
  

> view matrix models
> #13,0.39867,-0.85978,-0.31911,95.454,-0.8509,-0.47658,0.22101,98.955,-0.3421,0.18342,-0.92159,104.65

> fitmap #13 inMap #7

Fit molecule ranked 3 150224.pdb (#13) to map merged_J350-J550.mrc (#7) using
12795 atoms  
average map value = 0.04724, steps = 116  
shifted from previous position = 4.77  
rotated from previous position = 4.51 degrees  
atoms outside contour = 11667, contour level = 0.14492  
  
Position of ranked 3 150224.pdb (#13) relative to merged_J350-J550.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.46039279 -0.82416486 -0.32983442 99.50192957  
-0.83027690 -0.53125751 0.16853994 100.58839403  
-0.31413171 0.19625933 -0.92887218 102.77960925  
Axis 0.85450492 -0.48406704 -0.18841563  
Axis point 0.00000000 77.97461156 62.87606822  
Rotation angle (degrees) 179.07064680  
Shift along axis 16.96807727  
  

> view matrix models
> #13,0.46039,-0.82416,-0.32983,43.009,-0.83028,-0.53126,0.16854,100.1,-0.31413,0.19626,-0.92887,94.447

> view matrix models
> #13,0.46039,-0.82416,-0.32983,36.575,-0.83028,-0.53126,0.16854,155.57,-0.31413,0.19626,-0.92887,28.781

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.29222,-0.82664,-0.48091,37.736,-0.92204,-0.37702,0.087784,155.59,-0.25388,0.41776,-0.87237,27.485

> view matrix models
> #13,-0.02005,-0.9127,-0.40814,38.487,-0.92,0.17666,-0.34986,155.54,0.39142,0.36847,-0.84322,25.95

> view matrix models
> #13,-0.068141,-0.85954,-0.50651,38.877,-0.91227,0.25921,-0.31714,155.04,0.40389,0.44046,-0.80179,25.434

> view matrix models
> #13,-0.10415,-0.8897,-0.44451,38.781,-0.9827,0.16089,-0.091781,154.5,0.15317,0.42726,-0.89106,26.539

> view matrix models
> #13,0.040413,-0.83106,-0.55472,38.734,-0.98399,0.06333,-0.16657,155.25,0.17356,0.55257,-0.8152,25.625

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.040413,-0.83106,-0.55472,79.405,-0.98399,0.06333,-0.16657,122.88,0.17356,0.55257,-0.8152,100.47

> view matrix models
> #13,0.040413,-0.83106,-0.55472,87.856,-0.98399,0.06333,-0.16657,97.146,0.17356,0.55257,-0.8152,97.563

> view matrix models
> #13,0.040413,-0.83106,-0.55472,103.41,-0.98399,0.06333,-0.16657,104.4,0.17356,0.55257,-0.8152,104.11

> fitmap #13 inMap #7

Fit molecule ranked 3 150224.pdb (#13) to map merged_J350-J550.mrc (#7) using
12795 atoms  
average map value = 0.06928, steps = 104  
shifted from previous position = 2.91  
rotated from previous position = 9.06 degrees  
atoms outside contour = 10832, contour level = 0.14492  
  
Position of ranked 3 150224.pdb (#13) relative to merged_J350-J550.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.04911924 -0.89518816 -0.44297341 102.03099339  
-0.98676584 0.11211357 -0.11714823 106.00893053  
0.15453304 0.43135680 -0.88884803 106.46632622  
Axis 0.67198462 -0.73201725 -0.11219367  
Axis point 84.50104656 0.00000000 62.03277603  
Rotation angle (degrees) 155.91300781  
Shift along axis -20.98195586  
  

> save "H:/Documents/Documents_local/Cryo-EM_everything/ChimeraX
> projects/P78-J513-early_model/P78-J513-J535-550merged-
> locres-350-early_5_more_models.cxs"

——— End of log from Wed Jan 8 12:16:20 2025 ———

opened ChimeraX session  




OpenGL version: 3.3.0 - Build 31.0.101.2115
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteDesk 800 G5 Desktop Mini
OS: Microsoft Windows 10 Enterprise LTSC (Build 17763)
Memory: 8,353,259,520
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500T CPU @ 2.20GHz
OSLanguage: en-US
Locale: ('en_GB', '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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-maskChains: 1.4
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1