Crash while asking for registration

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x000033a8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000b78 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002140 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003ab0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002d60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000af8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000424c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003f50 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004f08 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003624 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000022f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003714 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003dbc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000043e8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003680 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001d94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003064 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004524 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000043dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001668 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1099 in read
  File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1241 in recv_into
  File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 704 in readinto
  File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 277 in _read_status
  File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 316 in begin
  File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1349 in getresponse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1350 in do_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1389 in https_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494 in _call_chain
  File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 534 in _open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 517 in open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 214 in urlopen
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 49 in load
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 456 in reload_available
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00004df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\ask.py", line 67 in _ask_gui
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\ask.py", line 30 in ask
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\registration\nag.py", line 220 in _ask_to_register
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\registration\nag.py", line 214 in _delayed_ask
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 134 in invoke
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 217 in _activate
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 186 in activate
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 54 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 139 in _redraw_timer_callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\gaya.yadav\\\OneDrive - Texas A&M
> AgriLife\\\Documents\\\Gaya\\\TAMU_cryo-EM\\\Data
> Processing\\\KayUTA\\\cryosparc_P27_J52_class_00_final_volume.mrc"

Opened cryosparc_P27_J52_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 1.66, shown at level 0.0746, step 1, values float32  

> open "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data
> Processing/KayUTA/cryosparc_P27_J52_class_01_final_volume.mrc"
> "C:/Users/gaya.yadav/OneDrive - Texas A&M AgriLife/Documents/Gaya/TAMU_cryo-
> EM/Data Processing/KayUTA/cryosparc_P27_J52_class_02_final_volume.mrc"
> "C:/Users/gaya.yadav/OneDrive - Texas A&M AgriLife/Documents/Gaya/TAMU_cryo-
> EM/Data Processing/KayUTA/cryosparc_P27_J52_class_03_final_volume.mrc"
> "C:/Users/gaya.yadav/OneDrive - Texas A&M AgriLife/Documents/Gaya/TAMU_cryo-
> EM/Data Processing/KayUTA/cryosparc_P27_J52_class_04_final_volume.mrc"
> "C:/Users/gaya.yadav/OneDrive - Texas A&M AgriLife/Documents/Gaya/TAMU_cryo-
> EM/Data Processing/KayUTA/cryosparc_P27_J53_009_volume_map_sharp.mrc"
> "C:/Users/gaya.yadav/OneDrive - Texas A&M AgriLife/Documents/Gaya/TAMU_cryo-
> EM/Data Processing/KayUTA/cryosparc_P27_J55_009_volume_map_sharp.mrc"

Opened cryosparc_P27_J52_class_01_final_volume.mrc as #2.1, grid size
128,128,128, pixel 1.66, shown at level 0.0695, step 1, values float32  
Opened cryosparc_P27_J52_class_02_final_volume.mrc as #2.2, grid size
128,128,128, pixel 1.66, shown at level 0.108, step 1, values float32  
Opened cryosparc_P27_J52_class_03_final_volume.mrc as #2.3, grid size
128,128,128, pixel 1.66, shown at level 0.0482, step 1, values float32  
Opened cryosparc_P27_J52_class_04_final_volume.mrc as #2.4, grid size
128,128,128, pixel 1.66, shown at level 0.0486, step 1, values float32  
Opened cryosparc_P27_J53_009_volume_map_sharp.mrc as #2.5, grid size
128,128,128, pixel 1.66, shown at level 0.224, step 1, values float32  
Opened cryosparc_P27_J55_009_volume_map_sharp.mrc as #2.6, grid size
128,128,128, pixel 1.66, shown at level 0.283, step 1, values float32  

> volume #1 level 0.08025

> show #!2.1 models

> show #!2.2 models

> show #!2.3 models

> show #!2.4 models

> view clip false

> select #2.1

2 models selected  

> ~select #2.1

Nothing selected  

> select #2.2

2 models selected  

> ~select #2.2

Nothing selected  

> ui tool show "Fit in Map"

Fit map cryosparc_P27_J52_class_01_final_volume.mrc in map
cryosparc_P27_J52_class_00_final_volume.mrc using 20971 points  
correlation = 0.792, correlation about mean = 0.3199, overlap = 774.5  
steps = 52, shift = 1.22, angle = 5.86 degrees  
  
Position of cryosparc_P27_J52_class_01_final_volume.mrc (#2.1) relative to
cryosparc_P27_J52_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99479552 -0.04981346 0.08888476 -3.94061758  
0.04915358 0.99874511 0.00959882 -7.30134283  
-0.08925137 -0.00517986 0.99599566 10.44896372  
Axis -0.07233220 0.87186225 0.48438029  
Axis point 120.26394233 0.00000000 52.20545230  
Rotation angle (degrees) 5.86347519  
Shift along axis -1.01945954  
  
Fit map cryosparc_P27_J52_class_02_final_volume.mrc in map
cryosparc_P27_J52_class_00_final_volume.mrc using 20958 points  
correlation = 0.7541, correlation about mean = 0.1068, overlap = 720.6  
steps = 92, shift = 9.5, angle = 15.7 degrees  
  
Position of cryosparc_P27_J52_class_02_final_volume.mrc (#2.2) relative to
cryosparc_P27_J52_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96785072 -0.10957029 0.22640526 -11.95099802  
0.13225709 0.98734139 -0.08755022 -3.57325389  
-0.21394638 0.11467924 0.97009052 4.64974758  
Axis 0.37342050 0.81311759 0.44653881  
Axis point 26.10095539 0.00000000 47.76395040  
Rotation angle (degrees) 15.71067499  
Shift along axis -5.29193052  
  
Fit map cryosparc_P27_J52_class_02_final_volume.mrc in map
cryosparc_P27_J52_class_00_final_volume.mrc using 20958 points  
correlation = 0.7541, correlation about mean = 0.1069, overlap = 720.6  
steps = 48, shift = 0.00377, angle = 0.00949 degrees  
  
Position of cryosparc_P27_J52_class_02_final_volume.mrc (#2.2) relative to
cryosparc_P27_J52_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96783010 -0.10947608 0.22653893 -11.97460400  
0.13218445 0.98734816 -0.08758355 -3.56615320  
-0.21408449 0.11471092 0.97005631 4.66432091  
Axis 0.37342275 0.81336287 0.44609001  
Axis point 26.12101633 0.00000000 47.84591972  
Rotation angle (degrees) 15.71575862  
Shift along axis -5.29145915  
  
Fit map cryosparc_P27_J52_class_03_final_volume.mrc in map
cryosparc_P27_J52_class_00_final_volume.mrc using 20964 points  
correlation = 0.7952, correlation about mean = 0.4216, overlap = 732.2  
steps = 148, shift = 6.01, angle = 34 degrees  
  
Position of cryosparc_P27_J52_class_03_final_volume.mrc (#2.3) relative to
cryosparc_P27_J52_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.91932144 -0.27339985 0.28302051 5.55927460  
0.12757483 0.88745276 0.44289080 -48.20530389  
-0.37225362 -0.37105271 0.85073329 100.13161438  
Axis -0.72723725 0.58547030 0.35826039  
Axis point 0.00000000 200.20524827 164.48736298  
Rotation angle (degrees) 34.02907036  
Shift along axis 3.60750617  
  
Fit map cryosparc_P27_J52_class_04_final_volume.mrc in map
cryosparc_P27_J52_class_00_final_volume.mrc using 20966 points  
correlation = 0.8073, correlation about mean = 0.4798, overlap = 734.7  
steps = 204, shift = 4.37, angle = 29.8 degrees  
  
Position of cryosparc_P27_J52_class_04_final_volume.mrc (#2.4) relative to
cryosparc_P27_J52_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97324103 -0.12597997 0.19217424 -5.59000700  
0.02621421 0.89172698 0.45181391 -41.64206556  
-0.22828646 -0.43468615 0.87116775 86.96123985  
Axis -0.89284727 0.42347113 0.15328387  
Axis point 0.00000000 160.87970603 131.36323640  
Rotation angle (degrees) 29.76511484  
Shift along axis 0.68656486  
  

> ui tool show "Model Panel"

> close #2.5

> close #2.6

> ui tool show "Model Panel"

> volume #2.4 level 0.06807

> volume #2.2 level 0.05756

> volume #2.1 level 0.08156

> volume #2.2 level 0.07246

> volume #2.3 level 0.07168

> volume #2.4 level 0.1028

> volume #1 level 0.07264

> select #2.2

2 models selected  
Drag select of 2.1 cryosparc_P27_J52_class_01_final_volume.mrc , 2.2
cryosparc_P27_J52_class_02_final_volume.mrc , 2.3
cryosparc_P27_J52_class_03_final_volume.mrc , 2.4
cryosparc_P27_J52_class_04_final_volume.mrc , 1
cryosparc_P27_J52_class_00_final_volume.mrc  

> select clear

> ~select #2.2

Nothing selected  

> select #2.2

2 models selected  

> ~select #2.2

Nothing selected  

> select #2.2

2 models selected  
Drag select of 2.1 cryosparc_P27_J52_class_01_final_volume.mrc , 2.2
cryosparc_P27_J52_class_02_final_volume.mrc , 2.3
cryosparc_P27_J52_class_03_final_volume.mrc , 2.4
cryosparc_P27_J52_class_04_final_volume.mrc , 1
cryosparc_P27_J52_class_00_final_volume.mrc  

> select clear

> select #2.2

2 models selected  
Drag select of 2.1 cryosparc_P27_J52_class_01_final_volume.mrc , 2.2
cryosparc_P27_J52_class_02_final_volume.mrc , 2.3
cryosparc_P27_J52_class_03_final_volume.mrc , 1
cryosparc_P27_J52_class_00_final_volume.mrc  

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting simple

> select clear

> ui tool show "Side View"

> lighting soft

> lighting full

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #!2.3 models

> hide #!2.4 models

> show #!2.1 models

> hide #!2.1 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> vop gaussian #1 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #3, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> volume #!3 style surface

> volume #!3 style mesh

> volume #!3 style surface

> volume #!3 region all imageMode "full region"

> volume unzone #!3

> mousemode rightMode "crop volume"

> vop gaussian #3 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #4, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #4 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #5, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #5 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #6, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #6 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #7, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #7 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #8, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #8 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #9, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #9 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #10, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #10 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #11, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #11 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #12, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> vop gaussian #12 sdev 4.99

Opened cryosparc_P27_J52_class_00_final_volume.mrc gaussian as #13, grid size
128,128,128, pixel 1.66, shown at step 1, values float32  

> volume show

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> close #5

> close #13

> close #11

> close #3

> close #4

> close #6

> close #7

> close #8

> close #9

> close #12

> close #10

> show #!2 models

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #!2.3 models

> hide #!2.4 models

> show #!2.1 models

> show #!2.2 models

> show #!2.4 models

> show #!2.3 models

> volume #2.1 region 0,0,0,127,127,127

> volume #1 region 0,0,0,127,127,127

> view clip false

> move x 25 models #2.2

> move x 100 models #2.3

> move x -25 models #2.3

> move x 10 models #2.2

> move y 10 models #2.4

> move y -50 models #2.4

> move y -10 models #2.4

> move x 100 models #2.4

> move x 10 models #2.4

> move y -50 models #2.3

> move y 50 models #2.3

> move y -50 models #2.3

> move y 50 models #2.3

> move y -50 models #2.3

> move x -50 models #2.3

> move x 50 models #2.1

> move x -10 models #2.1

> move x -10 models #2.2

> move x 50 models #2.2

> move x 5 models #2.3

> move x 5 models #2.4

> move y 5 models #2.1

> move y -5 models #2.1

> move y -2.5 models #2.1

> move y 5 models #2.1

> move y 2 models #2

> volume #1 level 0.05107

> volume #2.1 level 0.05078

> volume #2.2 level 0.04495

> volume #2.3 level 0.04824

> volume #2.4 level 0.05974

> save C:\Windows\system32\image1.png supersample 3

Permission denied writing file C:\Windows\system32\image1.png  

> save "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data Processing/KayUTA/Ab-
> initio_J52.jpg" width 1278 height 834 supersample 3

> ui tool show "Color Actions"

> set bgColor white

> color #2.1 #daff52 models transparency 0

> color #2.1 #e2ff63 models transparency 0

> color #2.2 #60ffff models transparency 0

> color #2.3 #858dff models transparency 0

> color #2.4 #ff8af5 models transparency 0

> color #1 #9a9a9a models transparency 0

> save "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data Processing/KayUTA/Ab-
> initio_J52.jpg" width 1278 height 834 supersample 3

> volume #2.2 level 0.1355

> volume #2.3 level 0.1326

> volume #2.4 level 0.1583

> volume #2.2 level 0.1172

> volume #2.3 level 0.1197

> volume #2.4 level 0.1555

> volume #2.1 level 0.1324

> volume #1 level 0.1005

> save "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data Processing/KayUTA/Ab-
> initio_J52_low.jpg" width 1278 height 834 supersample 3

> close #2.4

> close #2.3

> volume #2.2 region 10,0,0,127,127,127

> close #1

> volume #2.1 region 0,0,0,127,127,127

> view clip false

> volume #2.1 region 0,0,0,127,127,127

> save "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data Processing/KayUTA/Ab-
> initio_J52_cls02_03.jpg" width 1278 height 834 supersample 3

> close #2.1

> open "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data
> Processing/KayUTA/g6p_6Aresampled.mrc"

Opened g6p_6Aresampled.mrc as #1, grid size 128,128,128, pixel 1.66, shown at
level 0.157, step 1, values float32  

> volume #1 region 0,0,0,127,127,127

> move y 2 models #1

> move x 2 models #1

> move x -20 models #1

> move x 20 models #1

> move x -2 models #1

> move x 2 models #1

> move x -2 models #1

> ui tool show "Fit in Map"

Fit map g6p_6Aresampled.mrc in map cryosparc_P27_J52_class_02_final_volume.mrc
using 20969 points  
correlation = 0.8451, correlation about mean = 0.08487, overlap = 1397  
steps = 92, shift = 1.75, angle = 16 degrees  
  
Position of g6p_6Aresampled.mrc (#1) relative to
cryosparc_P27_J52_class_02_final_volume.mrc (#2.2) coordinates:  
Matrix rotation and translation  
0.99997880 -0.00454019 0.00466759 -0.03822732  
0.00453325 0.99998861 0.00149639 -0.57835021  
-0.00467433 -0.00147520 0.99998799 0.82742657  
Axis -0.22246182 0.69936411 0.67926473  
Axis point 152.87969388 0.00000000 0.96934276  
Rotation angle (degrees) 0.38267391  
Shift along axis 0.16606843  
  

> move x 100 models #1

> save "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data
> Processing/KayUTA/J52_cls03_frompdb.jpg" width 1251 height 834 supersample 3

> close #2.2

> open "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data
> Processing/KayUTA/cryosparc_P27_J52_class_03_final_volume.mrc"

Opened cryosparc_P27_J52_class_03_final_volume.mrc as #3, grid size
128,128,128, pixel 1.66, shown at level 0.0482, step 1, values float32  

> volume #1 region 0,0,0,118,127,127

> view clip false

> close #3

> open "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data
> Processing/KayUTA/cryosparc_P27_J52_class_01_final_volume.mrc"

Opened cryosparc_P27_J52_class_01_final_volume.mrc as #3, grid size
128,128,128, pixel 1.66, shown at level 0.0695, step 1, values float32  

> ui mousemode right distance

> ui mousemode right translate

> select #3

4 models selected  

> ui mousemode right rotate

> ui mousemode right select

> select #3

4 models selected  
Drag select of 3 cryosparc_P27_J52_class_01_final_volume.mrc  

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right "contour level"

> volume #3 level 0.1365

> volume #3 level 0.07274

> ui mousemode right "move planes"

> volume #3 region 0,0,0,127,127,127

> ui mousemode right "crop volume"

> volume #3 region 0,0,0,127,127,127

> volume #3 region 0,0,0,121,127,127

> ui mousemode right translate

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,51.979,0,1,0,-89.991,0,0,1,2.9297

> view matrix models #3,1,0,0,53.392,0,1,0,-93.483,0,0,1,-1.9832

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.98136,0.080454,0.1745,28.298,0.0042546,0.89881,-0.43832,-36.661,-0.19211,0.43089,0.88172,-14.847

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.98136,0.080454,0.1745,25.343,0.0042546,0.89881,-0.43832,-38.151,-0.19211,0.43089,0.88172,-14.124

> view matrix models
> #3,0.98136,0.080454,0.1745,26.914,0.0042546,0.89881,-0.43832,-37.228,-0.19211,0.43089,0.88172,-15.7

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.82311,-0.4859,0.29392,91.094,0.5618,0.77228,-0.29659,-97.814,-0.082876,0.40925,0.90865,-27.815

> view matrix models
> #3,0.14963,-0.89173,0.42711,191.27,0.9882,0.12052,-0.094578,-95.174,0.032864,0.43622,0.89924,-41.921

> view matrix models
> #3,-0.28386,-0.84217,0.45845,228.53,0.94574,-0.32474,-0.010971,-52.295,0.15811,0.43046,0.88865,-53.434

> view matrix models
> #3,-0.15612,-0.88638,0.43585,222.11,0.9875,-0.1304,0.088519,-87.903,-0.021626,0.44422,0.89565,-36.627

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.9706,-0.11727,0.2102,250.57,0.19682,-0.88937,0.41265,41.883,0.13855,0.44189,0.88631,-52.328

> view matrix models
> #3,-0.96323,0.10026,0.24926,222.55,0.033645,-0.87545,0.48214,50.287,0.26656,0.4728,0.83989,-64.221

> view matrix models
> #3,-0.82298,-0.51951,0.22982,275.57,0.5632,-0.69332,0.44957,-21.6,-0.074218,0.49942,0.86317,-33.475

> view matrix models
> #3,-0.95914,-0.28185,-0.024829,291.78,0.23606,-0.8455,0.47897,26.035,-0.15599,0.45353,0.87748,-21.474

> view matrix models
> #3,-0.93012,-0.26332,0.25602,256.93,0.35214,-0.83742,0.41801,19.371,0.10432,0.47895,0.87162,-51.083

> view matrix models
> #3,-0.63107,-0.70955,0.31352,266.56,0.77304,-0.54161,0.33025,-47.231,-0.064519,0.45078,0.8903,-32.217

> view matrix models
> #3,-0.94243,-0.29164,0.16365,271.04,0.33384,-0.7918,0.51147,6.5418,-0.019582,0.53666,0.84357,-41.126

> ui mousemode right "move picked models"

> view matrix models
> #1,0.96625,-0.1142,0.23089,41.532,0.13707,0.98687,-0.085488,-100.05,-0.21809,0.11425,0.96922,9.8295

> ui mousemode right "translate selected atoms"

> ui mousemode right pivot

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.94243,-0.29164,0.16365,274.86,0.33384,-0.7918,0.51147,3.9039,-0.019582,0.53666,0.84357,-37.451

> view matrix models
> #3,-0.94243,-0.29164,0.16365,271.93,0.33384,-0.7918,0.51147,6.0269,-0.019582,0.53666,0.84357,-38.993

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.99183,-0.11147,-0.06204,281.99,0.091835,-0.96141,0.25933,76.396,-0.088554,0.25151,0.96379,-14.192

> view matrix models
> #3,-0.97765,0.20383,-0.051543,245.91,-0.2099,-0.93222,0.2948,101.45,0.012038,0.29902,0.95417,-28.854

> view matrix models
> #3,-0.87651,0.48101,0.019189,198.28,-0.40467,-0.75783,0.5118,80.499,0.26072,0.44083,0.85889,-60.094

> view matrix models
> #3,-0.64188,-0.61254,0.46128,242.61,0.76675,-0.51936,0.37729,-54.436,0.0084718,0.59587,0.80304,-43.942

> view matrix models
> #3,-0.5092,-0.70661,0.49134,235.38,0.86042,-0.40477,0.30959,-69.319,-0.019872,0.5804,0.81409,-40.476

> view matrix models
> #3,0.017258,-0.94248,0.33381,221.45,0.99313,-0.022501,-0.11487,-78.874,0.11578,0.3335,0.93561,-41.516

> view matrix models
> #3,-0.45994,-0.79346,0.3986,249.23,0.85287,-0.51969,-0.050378,-18.11,0.24712,0.31678,0.91574,-51.523

> ui mousemode right translate

> view clip false

> ui tool show "Fit in Map"

Fit map cryosparc_P27_J52_class_01_final_volume.mrc in map g6p_6Aresampled.mrc
using 20557 points  
correlation = 0.8195, correlation about mean = 0.2128, overlap = 1256  
steps = 76, shift = 4.19, angle = 8.06 degrees  
  
Position of cryosparc_P27_J52_class_01_final_volume.mrc (#3) relative to
g6p_6Aresampled.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.35505629 -0.91469944 0.19302845 220.53395358  
0.93275571 -0.33283185 0.13852710 27.42154142  
-0.06246464 0.22923330 0.97136516 -13.87486607  
Axis 0.04857762 0.13682908 0.98940286  
Axis point 101.11738824 91.26318926 0.00000000  
Rotation angle (degrees) 110.99346644  
Shift along axis 0.73724717  
  
Fit map cryosparc_P27_J52_class_01_final_volume.mrc in map g6p_6Aresampled.mrc
using 20557 points  
correlation = 0.8194, correlation about mean = 0.2128, overlap = 1256  
steps = 44, shift = 0.0232, angle = 0.0376 degrees  
  
Position of cryosparc_P27_J52_class_01_final_volume.mrc (#3) relative to
g6p_6Aresampled.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.35513779 -0.91461757 0.19326628 220.48815871  
0.93269314 -0.33275842 0.13912352 27.34747727  
-0.06293384 0.22966615 0.97123262 -13.85173967  
Axis 0.04849142 0.13721170 0.98935410  
Axis point 101.11958505 91.20895094 0.00000000  
Rotation angle (degrees) 110.99778105  
Shift along axis 0.73990229  
  
Fit map cryosparc_P27_J52_class_01_final_volume.mrc in map g6p_6Aresampled.mrc
using 20557 points  
correlation = 0.8195, correlation about mean = 0.2128, overlap = 1256  
steps = 28, shift = 0.0322, angle = 0.0564 degrees  
  
Position of cryosparc_P27_J52_class_01_final_volume.mrc (#3) relative to
g6p_6Aresampled.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.35484887 -0.91480456 0.19291164 220.54379525  
0.93284675 -0.33269531 0.13824171 27.43040025  
-0.06228335 0.22901191 0.97142902 -13.87896779  
Axis 0.04860782 0.13665798 0.98942502  
Axis point 101.11745110 91.28630654 0.00000000  
Rotation angle (degrees) 110.98095321  
Shift along axis 0.73653898  
  
Fit map cryosparc_P27_J52_class_01_final_volume.mrc in map g6p_6Aresampled.mrc
using 20557 points  
correlation = 0.8194, correlation about mean = 0.2128, overlap = 1256  
steps = 40, shift = 0.0414, angle = 0.0667 degrees  
  
Position of cryosparc_P27_J52_class_01_final_volume.mrc (#3) relative to
g6p_6Aresampled.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.35534350 -0.91457790 0.19307581 220.51768703  
0.93260054 -0.33293261 0.13932733 27.35576426  
-0.06314446 0.22957167 0.97124129 -13.81277290  
Axis 0.04833536 0.13723297 0.98935879  
Axis point 101.13183531 91.20403965 0.00000000  
Rotation angle (degrees) 111.00917325  
Shift along axis 0.74712529  
  

> open "C:/Users/gaya.yadav/OneDrive - Texas A&M
> AgriLife/Documents/Gaya/TAMU_cryo-EM/Data
> Processing/KayUTA/cryosparc_P27_J52_class_02_final_volume.mrc"

Opened cryosparc_P27_J52_class_02_final_volume.mrc as #4, grid size
128,128,128, pixel 1.66, shown at level 0.108, step 1, values float32  

> ui mousemode right "translate selected models"

> select #4

2 models selected  

> ~select #3

2 models selected  

> view matrix models #4,1,0,0,4.3557,0,1,0,-2.7419,0,0,1,1.0951

> color #4 #fffa70 models transparency 0

> view matrix models #4,1,0,0,72.888,0,1,0,-41.376,0,0,1,3.3918

> view matrix models #4,1,0,0,42.87,0,1,0,-89.07,0,0,1,-1.9735

> view matrix models #4,1,0,0,53.162,0,1,0,-90.701,0,0,1,-2.7595

> view matrix models #4,1,0,0,46.915,0,1,0,-97.353,0,0,1,-4.4565

> view matrix models #4,1,0,0,47.694,0,1,0,-96.73,0,0,1,-3.6418

> view matrix models #4,1,0,0,51.888,0,1,0,-95.863,0,0,1,-4.7514

> view matrix models #4,1,0,0,51.741,0,1,0,-95.53,0,0,1,-6.2545

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.82228,-0.55658,0.11866,116.63,0.56355,0.8254,-0.033702,-133.83,-0.079186,0.094585,0.99236,-6.9206

> ui mousemode right "translate selected models"

> ui tool show "Fit in Map"

Fit map cryosparc_P27_J52_class_02_final_volume.mrc in map g6p_6Aresampled.mrc
using 20958 points  
correlation = 0.8437, correlation about mean = 0.1649, overlap = 1346  
steps = 116, shift = 1.55, angle = 25.6 degrees  
  
Position of cryosparc_P27_J52_class_02_final_volume.mrc (#4) relative to
g6p_6Aresampled.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99876854 -0.04542610 0.01994649 2.95819150  
0.04553689 0.99894946 -0.00513547 -4.03286863  
-0.01969225 0.00603745 0.99978786 1.26517225  
Axis 0.11189532 0.39697671 0.91098240  
Axis point 88.99259572 62.99764107 0.00000000  
Rotation angle (degrees) 2.86172562  
Shift along axis -0.11739746  
  

> hide #!3 models

> select #4

3 models selected  

> ~select #4

Nothing selected  

> show #!3 models

> close session

> open "C:\Users\gaya.yadav\OneDrive - Texas A&M
> AgriLife\Documents\Gaya\TAMU_cryo-
> EM\ApoF\WFV\alinged_wfv_real_space_refined_003-coot-0.pdb" format pdb

Chain information for alinged_wfv_real_space_refined_003-coot-0.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | No description available  
  

> ui mousemode right "rotate selected models"

> volume style surface

No volumes specified  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> rainbow

> color bychain

> color bfactor

34176 atoms, 4176 residues, atom bfactor range 0 to 43.7  

> mlp

Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_A SES
surface": minimum -25.15, mean -4.541, maximum 21.88  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_B SES
surface": minimum -24.91, mean -4.442, maximum 21.94  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_C SES
surface": minimum -24.94, mean -4.481, maximum 22.07  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_D SES
surface": minimum -24.81, mean -4.434, maximum 21.97  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_E SES
surface": minimum -24.95, mean -4.436, maximum 22.23  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_F SES
surface": minimum -28.47, mean -4.587, maximum 21.78  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_G SES
surface": minimum -24.79, mean -4.443, maximum 21.98  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_H SES
surface": minimum -25.57, mean -4.507, maximum 21.9  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_I SES
surface": minimum -24.81, mean -4.407, maximum 21.97  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_J SES
surface": minimum -25.17, mean -4.559, maximum 21.89  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_K SES
surface": minimum -24.93, mean -4.474, maximum 21.92  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_L SES
surface": minimum -24.94, mean -4.473, maximum 22.05  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_M SES
surface": minimum -25.55, mean -4.548, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_N SES
surface": minimum -28.41, mean -4.598, maximum 21.79  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_O SES
surface": minimum -24.94, mean -4.461, maximum 22.21  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_P SES
surface": minimum -24.97, mean -4.408, maximum 22.07  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_Q SES
surface": minimum -25.22, mean -4.576, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_R SES
surface": minimum -24.92, mean -4.47, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_S SES
surface": minimum -24.98, mean -4.458, maximum 21.75  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_T SES
surface": minimum -25.04, mean -4.51, maximum 21.9  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_U SES
surface": minimum -24.71, mean -4.45, maximum 21.72  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_V SES
surface": minimum -28.59, mean -4.6, maximum 21.89  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_W SES
surface": minimum -24.94, mean -4.461, maximum 22.21  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_X SES
surface": minimum -25.52, mean -4.562, maximum 21.9  
To also show corresponding color key, enter the above mlp command and add key
true  

> interfaces ~solvent

60 buried areas: C U 1525, D M 1514, H I 1514, E J 1502, F R 1491, A W 1464, O
Q 1462, B V 1462, G X 1462, L T 1461, K N 1451, P S 1450, H S 663, L V 663, G
P 662, T W 662, A Q 662, F I 662, M U 662, E S 662, N P 662, D V 662, G N 660,
D L 660, T X 660, A J 660, E H 660, B R 657, O U 657, B K 657, W X 657, M O
657, C I 657, C F 657, J Q 657, K R 657, M V 513, F K 513, A T 513, D T 512, H
P 512, J W 512, R V 512, I U 511, L X 511, C M 511, B L 511, C R 511, K P 511,
Q U 511, G W 511, A O 511, D O 511, N X 511, G S 511, E Q 511, B N 511, F H
511, J S 511, E I 511  

> color bfactor

34176 atoms, 4176 residues, 24 surfaces, atom bfactor range 0 to 43.7  

> color bfactor

34176 atoms, 4176 residues, 24 surfaces, atom bfactor range 0 to 43.7  

> color bfactor

34176 atoms, 4176 residues, 24 surfaces, atom bfactor range 0 to 43.7  

> mlp

Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_A SES
surface": minimum -25.15, mean -4.541, maximum 21.88  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_B SES
surface": minimum -24.91, mean -4.442, maximum 21.94  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_C SES
surface": minimum -24.94, mean -4.481, maximum 22.07  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_D SES
surface": minimum -24.81, mean -4.434, maximum 21.97  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_E SES
surface": minimum -24.95, mean -4.436, maximum 22.23  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_F SES
surface": minimum -28.47, mean -4.587, maximum 21.78  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_G SES
surface": minimum -24.79, mean -4.443, maximum 21.98  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_H SES
surface": minimum -25.57, mean -4.507, maximum 21.9  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_I SES
surface": minimum -24.81, mean -4.407, maximum 21.97  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_J SES
surface": minimum -25.17, mean -4.559, maximum 21.89  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_K SES
surface": minimum -24.93, mean -4.474, maximum 21.92  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_L SES
surface": minimum -24.94, mean -4.473, maximum 22.05  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_M SES
surface": minimum -25.55, mean -4.548, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_N SES
surface": minimum -28.41, mean -4.598, maximum 21.79  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_O SES
surface": minimum -24.94, mean -4.461, maximum 22.21  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_P SES
surface": minimum -24.97, mean -4.408, maximum 22.07  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_Q SES
surface": minimum -25.22, mean -4.576, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_R SES
surface": minimum -24.92, mean -4.47, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_S SES
surface": minimum -24.98, mean -4.458, maximum 21.75  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_T SES
surface": minimum -25.04, mean -4.51, maximum 21.9  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_U SES
surface": minimum -24.71, mean -4.45, maximum 21.72  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_V SES
surface": minimum -28.59, mean -4.6, maximum 21.89  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_W SES
surface": minimum -24.94, mean -4.461, maximum 22.21  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_X SES
surface": minimum -25.52, mean -4.562, maximum 21.9  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_A SES
surface": minimum -25.15, mean -4.541, maximum 21.88  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_B SES
surface": minimum -24.91, mean -4.442, maximum 21.94  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_C SES
surface": minimum -24.94, mean -4.481, maximum 22.07  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_D SES
surface": minimum -24.81, mean -4.434, maximum 21.97  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_E SES
surface": minimum -24.95, mean -4.436, maximum 22.23  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_F SES
surface": minimum -28.47, mean -4.587, maximum 21.78  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_G SES
surface": minimum -24.79, mean -4.443, maximum 21.98  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_H SES
surface": minimum -25.57, mean -4.507, maximum 21.9  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_I SES
surface": minimum -24.81, mean -4.407, maximum 21.97  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_J SES
surface": minimum -25.17, mean -4.559, maximum 21.89  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_K SES
surface": minimum -24.93, mean -4.474, maximum 21.92  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_L SES
surface": minimum -24.94, mean -4.473, maximum 22.05  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_M SES
surface": minimum -25.55, mean -4.548, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_N SES
surface": minimum -28.41, mean -4.598, maximum 21.79  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_O SES
surface": minimum -24.94, mean -4.461, maximum 22.21  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_P SES
surface": minimum -24.97, mean -4.408, maximum 22.07  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_Q SES
surface": minimum -25.22, mean -4.576, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_R SES
surface": minimum -24.92, mean -4.47, maximum 21.91  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_S SES
surface": minimum -24.98, mean -4.458, maximum 21.75  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_T SES
surface": minimum -25.04, mean -4.51, maximum 21.9  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_U SES
surface": minimum -24.71, mean -4.45, maximum 21.72  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_V SES
surface": minimum -28.59, mean -4.6, maximum 21.89  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_W SES
surface": minimum -24.94, mean -4.461, maximum 22.21  
Map values for surface "alinged_wfv_real_space_refined_003-coot-0.pdb_X SES
surface": minimum -25.52, mean -4.562, maximum 21.9  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 472.91
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP EliteDesk 805 G8 Desktop Mini PC
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 33,618,325,504
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 PRO 5750GE with Radeon Graphics    
OSLanguage: en-US
Locale: ('en_US', '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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    pandas: 1.4.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    Send2Trash: 1.8.0
    SEQCROW: 1.6.6
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    starfile: 0.4.11
    suds-jurko: 0.6
    superqt: 0.3.3
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.3.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1