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#8860 feedback defect

Keyboard interrupt while saving .mrc file

Reported by:	cmajumdar@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.15.0-208-generic-x86_64-with-glibc2.27
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.
Fatal Python error: Aborted

Current thread 0x00007f4c323e3740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 819 in rapid_access_shown
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 839 in showEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 532 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 220 in build
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 688 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> camera ortho

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
> /media/HDD2-8TB/akent/230301/P20/J5/cryosparc_P20_J5_class_04_00142_volume_sharp.mrc
> /media/HDD2-8TB/akent/230301/P20/J5/cryosparc_P20_J5_class_03_00142_volume_sharp.mrc
> /media/HDD2-8TB/akent/230301/P20/J5/cryosparc_P20_J5_class_02_00142_volume_sharp.mrc
> /media/HDD2-8TB/akent/230301/P20/J5/cryosparc_P20_J5_class_01_00142_volume_sharp.mrc
> /media/HDD2-8TB/akent/230301/P20/J5/cryosparc_P20_J5_class_00_00142_volume_sharp.mrc

Opened cryosparc_P20_J5_class_04_00142_volume_sharp.mrc as #1.1, grid size
128,128,128, pixel 3.13, shown at level 1.91, step 1, values float32  
Opened cryosparc_P20_J5_class_03_00142_volume_sharp.mrc as #1.2, grid size
128,128,128, pixel 3.13, shown at level 2.33, step 1, values float32  
Opened cryosparc_P20_J5_class_02_00142_volume_sharp.mrc as #1.3, grid size
128,128,128, pixel 3.13, shown at level 1.71, step 1, values float32  
Opened cryosparc_P20_J5_class_01_00142_volume_sharp.mrc as #1.4, grid size
128,128,128, pixel 3.13, shown at level 2.39, step 1, values float32  
Opened cryosparc_P20_J5_class_00_00142_volume_sharp.mrc as #1.5, grid size
128,128,128, pixel 3.13, shown at level 1.99, step 1, values float32  

> hide #!1.5 models

> hide #!1.4 models

> hide #!1.3 models

> hide #!1.2 models

> volume #1.1 level 0.6726

> hide #!1.1 models

> show #!1.2 models

> volume #1.1 level 0.4962

> hide #!1.1 models

> volume #1.2 level 1.042

> hide #!1.2 models

> show #!1.3 models

> volume #1.3 level 1.319

> hide #!1.3 models

> show #!1.4 models

> volume #1.4 level 0.6768

> volume #1.5 level 1.112

> open /media/HDD4/akent/22Oct31/initial-model-1vy4-no-Esite.pdb

Summary of feedback from opening /media/HDD4/akent/22Oct31/initial-
model-1vy4-no-Esite.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
54299 messages similar to the above omitted  
  
Chain information for initial-model-1vy4-no-Esite.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
V | No description available  
W | No description available  
W | No description available  
X | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
  

> view

> select #2

144666 atoms, 157264 bonds, 18 pseudobonds, 10402 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #2

144666 atoms, 157264 bonds, 18 pseudobonds, 10402 residues, 2 models selected  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,81.311,0,1,0,194.44,0,0,1,72.181

> view matrix models #2,1,0,0,117.72,0,1,0,259.02,0,0,1,96.494

> view matrix models #2,1,0,0,83.622,0,1,0,237.28,0,0,1,180.6

> view matrix models #2,1,0,0,94.563,0,1,0,221.69,0,0,1,233.04

> view matrix models #2,1,0,0,113.94,0,1,0,215.35,0,0,1,218.3

> view matrix models #2,1,0,0,114.03,0,1,0,219.13,0,0,1,214.4

> view matrix models #2,1,0,0,110.32,0,1,0,220.78,0,0,1,211.96

> view matrix models #2,1,0,0,115.32,0,1,0,222.05,0,0,1,205.81

> fitmap #2 inMap #1.4

Fit molecule initial-model-1vy4-no-Esite.pdb (#2) to map
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) using 144666 atoms  
average map value = 1.708, steps = 48  
shifted from previous position = 3.24  
rotated from previous position = 2.3 degrees  
atoms outside contour = 21388, contour level = 0.67677  
  
Position of initial-model-1vy4-no-Esite.pdb (#2) relative to
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) coordinates:  
Matrix rotation and translation  
0.99919594 0.03696137 -0.01553472 116.09241947  
-0.03692791 0.99931496 0.00243566 227.71503112  
0.01561410 -0.00186004 0.99987636 202.39374190  
Axis -0.05349473 -0.38789852 -0.92014839  
Axis point 3266.58673007 -2663.48398466 0.00000000  
Rotation angle (degrees) 2.30108651  
Shift along axis -280.77293067  
  

> show sel cartoons

> hide sel atoms

> view matrix models
> #2,0.9992,0.036961,-0.015535,114.08,-0.036928,0.99931,0.0024357,227.07,0.015614,-0.00186,0.99988,200.86

> fitmap #2 inMap #1.4

Fit molecule initial-model-1vy4-no-Esite.pdb (#2) to map
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) using 144666 atoms  
average map value = 1.708, steps = 52  
shifted from previous position = 2.61  
rotated from previous position = 0.00751 degrees  
atoms outside contour = 21398, contour level = 0.67677  
  
Position of initial-model-1vy4-no-Esite.pdb (#2) relative to
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) coordinates:  
Matrix rotation and translation  
0.99920076 0.03683795 -0.01551790 116.07339892  
-0.03680389 0.99931944 0.00247430 227.72141948  
0.01559849 -0.00190121 0.99987653 202.39669127  
Axis -0.05464909 -0.38863637 -0.91976913  
Axis point 3269.38460996 -2663.11965674 0.00000000  
Rotation angle (degrees) 2.29432272  
Shift along axis -281.00235934  
  

> view matrix models
> #2,0.9992,0.036838,-0.015518,114.9,-0.036804,0.99932,0.0024743,227.97,0.015598,-0.0019012,0.99988,200.68

> fitmap #2 inMap #1.4

Fit molecule initial-model-1vy4-no-Esite.pdb (#2) to map
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) using 144666 atoms  
average map value = 1.708, steps = 64  
shifted from previous position = 2.14  
rotated from previous position = 0.0263 degrees  
atoms outside contour = 21387, contour level = 0.67677  
  
Position of initial-model-1vy4-no-Esite.pdb (#2) relative to
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) coordinates:  
Matrix rotation and translation  
0.99920192 0.03670501 -0.01575659 116.08271098  
-0.03667636 0.99932498 0.00210365 227.72798261  
0.01582317 -0.00152408 0.99987364 202.43461124  
Axis -0.04536346 -0.39489301 -0.91760649  
Axis point 3234.67171756 -2745.02978305 0.00000000  
Rotation angle (degrees) 2.29159425  
Shift along axis -280.94941455  
  

> view matrix models
> #2,0.9992,0.036705,-0.015757,112.58,-0.036676,0.99932,0.0021037,228.01,0.015823,-0.0015241,0.99987,201.41

> fitmap #2 inMap #1.4

Fit molecule initial-model-1vy4-no-Esite.pdb (#2) to map
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) using 144666 atoms  
average map value = 1.708, steps = 52  
shifted from previous position = 3.62  
rotated from previous position = 0.00817 degrees  
atoms outside contour = 21382, contour level = 0.67677  
  
Position of initial-model-1vy4-no-Esite.pdb (#2) relative to
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) coordinates:  
Matrix rotation and translation  
0.99920708 0.03658370 -0.01571151 116.04595447  
-0.03655419 0.99932933 0.00216138 227.71632781  
0.01578004 -0.00158535 0.99987423 202.41872555  
Axis -0.04700000 -0.39503853 -0.91746148  
Axis point 3241.76938876 -2740.63958270 0.00000000  
Rotation angle (degrees) 2.28434809  
Shift along axis -281.12226505  
  

> ~select #2

Nothing selected  

> select #2

144666 atoms, 157264 bonds, 18 pseudobonds, 10402 residues, 2 models selected  

> ~select #2

Nothing selected  

> ui mousemode right select

Drag select of 6456 residues, 8 pseudobonds  

> select up

127241 atoms, 139500 bonds, 8 pseudobonds, 8231 residues, 2 models selected  

> select down

92485 atoms, 8 pseudobonds, 6456 residues, 2 models selected  

> select #2

144666 atoms, 157264 bonds, 18 pseudobonds, 10402 residues, 2 models selected  

> ~select #2

Nothing selected  

> select /:A /:B /:C /:D /:E /:F

Expected an objects specifier or a keyword  

> select /a

455 atoms, 469 bonds, 59 residues, 1 model selected  

> select /A /B /C /D /E /F

109189 atoms, 120883 bonds, 8 pseudobonds, 6192 residues, 2 models selected  

> select /A

92914 atoms, 104042 bonds, 8 pseudobonds, 4316 residues, 2 models selected  

> select /B

4419 atoms, 4759 bonds, 351 residues, 1 model selected  

> select /A

92914 atoms, 104042 bonds, 8 pseudobonds, 4316 residues, 2 models selected  

> open /media/HDD4/akent/22Oct31/7k00-aligned-toCS-maps.pdb

Summary of feedback from opening /media/HDD4/akent/22Oct31/7k00-aligned-toCS-
maps.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 AC5 2 VAL X
3 LYS X 5 0  
Start residue of secondary structure not found: SHEET 2 AC5 2 VAL X 17 VAL X
19 -1  
Start residue of secondary structure not found: SHEET 1 AC6 2 LEU X 34 LYS X
36 0  
Start residue of secondary structure not found: SHEET 2 AC6 2 ALA X 61 ARG X
63 -1  
Start residue of secondary structure not found: SHEET 1 AC7 4 ARG X 101 LEU X
105 0  
43 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 AD9 3 ARG B 95 LYS B 99
0  
Start residue of secondary structure not found: SHEET 2 AD9 3 VAL B 102 SER B
106 -1  
Start residue of secondary structure not found: SHEET 3 AD9 3 VAL B 113 GLN B
116 -1  
Start residue of secondary structure not found: SHEET 1 AE1 3 GLN C 18 ASN C
20 0  
Start residue of secondary structure not found: SHEET 2 AE1 3 GLN C 2 ILE C 4
-1  
Start residue of secondary structure not found: SHEET 3 AE1 3 VAL C 37 PRO C
38 -1  
24 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 AE8 3 VAL F 89 VAL F 90
0  
Start residue of secondary structure not found: SHEET 2 AE8 3 THR F 121 VAL F
122 1  
Start residue of secondary structure not found: SHEET 3 AE8 3 LYS F 141 ILE F
142 1  
Start residue of secondary structure not found: SHEET 1 AE9 4 LYS G 62 ILE G
65 0  
Start residue of secondary structure not found: SHEET 2 AE9 4 VAL G 101 ASP G
106 -1  
Start residue of secondary structure not found: SHEET 3 AE9 4 PHE G 31 ALA G
35 -1  
7 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 AF3 4 VAL I 47 SER I 52
0  
Start residue of secondary structure not found: SHEET 2 AF3 4 ILE I 35 ILE I
40 -1  
Start residue of secondary structure not found: SHEET 3 AF3 4 ARG I 25 ARG I
30 -1  
Start residue of secondary structure not found: SHEET 4 AF3 4 SER I 91 ASP I
93 1  
End residue of secondary structure not found: SHEET 1 AF4 4 LYS L 10 VAL L 14
0  
Start residue of secondary structure not found: SHEET 2 AF4 4 TYR L 2 SER L 7
-1  
Start residue of secondary structure not found: SHEET 3 AF4 4 VAL L 38 ALA L
42 -1  
Start residue of secondary structure not found: SHEET 4 AF4 4 VAL L 47 ILE L
49 -1  
Start residue of secondary structure not found: SHEET 1 AF5 4 THR L 19 LEU L
22 0  
Start residue of secondary structure not found: SHEET 2 AF5 4 TRP L 92 SER L
102 -1  
37 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 3 AG7 4 ARG Q 77 GLU Q 83
-1  
Start residue of secondary structure not found: SHEET 4 AG7 4 HIS Q 46 ALA Q
47 1  
Start residue of secondary structure not found: SHEET 1 AG8 2 VAL R 13 ARG R
18 0  
Start residue of secondary structure not found: SHEET 2 AG8 2 ALA R 24 PHE R
29 -1  
Start residue of secondary structure not found: SHEET 1 AG9 2 LEU R 33 VAL R
40 0  
Start residue of secondary structure not found: SHEET 2 AG9 2 ARG R 45 SER R
52 -1  
21 messages similar to the above omitted  
  
Chain information for 7k00-aligned-toCS-maps.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!3 models

> hide #!1 models

> close #2

> show #!3 models

> show #!1.4 models

> fitmap #3 inMap #1.4

Fit molecule 7k00-aligned-toCS-maps.pdb (#3) to map
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) using 149338 atoms  
average map value = 1.761, steps = 60  
shifted from previous position = 9.67  
rotated from previous position = 1.38 degrees  
atoms outside contour = 17794, contour level = 0.67677  
  
Position of 7k00-aligned-toCS-maps.pdb (#3) relative to
cryosparc_P20_J5_class_01_00142_volume_sharp.mrc (#1.4) coordinates:  
Matrix rotation and translation  
0.99977555 0.02118043 -0.00049520 -9.95749081  
-0.02118470 0.99971078 -0.01138233 1.54787227  
0.00025397 0.01139027 0.99993510 -8.10399766  
Axis 0.47340738 -0.01557417 -0.88070591  
Axis point 67.66924929 524.46848865 0.00000000  
Rotation angle (degrees) 1.37819979  
Shift along axis 2.39918223  
  

> hide atoms

> show cartoons

> select /A /B/

Expected a keyword  

> hide #!1.4 models

> select /A /B

36584 atoms, 38362 bonds, 2 pseudobonds, 3903 residues, 2 models selected  

> select /A /B /C /D /E /F /G /H /I /J /K /L /M /N /O /P /Q /R /S /T /U /V /W

54114 atoms, 55856 bonds, 2 pseudobonds, 6372 residues, 2 models selected  

> select ~sel

95224 atoms, 98234 bonds, 5 pseudobonds, 11347 residues, 13 models selected  

> show #!1.4 models

> ~select #1

95224 atoms, 98234 bonds, 5 pseudobonds, 11347 residues, 2 models selected  

> select sel @ select sel @ ui tool show "Volume Viewer"

> ui tool show "Surface Zone"

> surface zone #1.4 nearAtoms sel distance 18.78

> surface zone #1.4 nearAtoms sel distance 5

> save /media/HDD2-8TB/akent/230301/7k00-aligned.pdb relModel #1.4.1

> hide #!1.4 models

> hide #!3 models

> show #!1.5 models

> show #!1.4 models

> show #!1.3 models

> show #!1.2 models

> show #!1.1 models

> surface unzone #1.4

> tile

2 models tiled  

> tile #1.1 #1.2 #1.3

3 models tiled  

> tile #1.1 #1.2 #1.3 #1.4 #1.5

5 models tiled  

> hide #!1.3 models

Drag select of 1.5 cryosparc_P20_J5_class_00_00142_volume_sharp.mrc  

> select clear

> hide #!1.5 models

> hide #!1.1 models

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right "rotate selected models"

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> hide #!1.2 models

> hide #!1.4 models

> open /media/HDD2-8TB/akent/230301/70S_4X_3P13875.mrc

Opened 70S_4X_3P13875.mrc as #2, grid size 128,128,128, pixel 3.14, shown at
level 15.5, step 1, values float32  

> view

> ui tool show "Map Coordinates"

> close

> open /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class005.mrc
> /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class004.mrc
> /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class003.mrc
> /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class002.mrc
> /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class001.mrc

Opened run_it070_class005.mrc as #1.1, grid size 128,128,128, pixel 3.14,
shown at level 0.106, step 1, values float32  
Opened run_it070_class004.mrc as #1.2, grid size 128,128,128, pixel 3.14,
shown at level 0.134, step 1, values float32  
Opened run_it070_class003.mrc as #1.3, grid size 128,128,128, pixel 3.14,
shown at level 0.0651, step 1, values float32  
Opened run_it070_class002.mrc as #1.4, grid size 128,128,128, pixel 3.14,
shown at level 0.117, step 1, values float32  
Opened run_it070_class001.mrc as #1.5, grid size 128,128,128, pixel 3.14,
shown at level 0.106, step 1, values float32  

> tile #1.1 #1.2 #1.3 #1.4 #1.5

5 models tiled  

> volume #1.1 level 0.08164

> volume #1.2 level 0.1082

> volume #1.2 level 0.07165

> volume #1.4 level 0.05591

> volume #1.5 level 0.06601

> volume #1.5 level 0.05489

> close

> open /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class004.mrc
> /media/HDD2-8TB/akent/230301/Class3D/job019/run_it070_class002.mrc

Opened run_it070_class004.mrc as #1.1, grid size 128,128,128, pixel 3.14,
shown at level 0.134, step 1, values float32  
Opened run_it070_class002.mrc as #1.2, grid size 128,128,128, pixel 3.14,
shown at level 0.117, step 1, values float32  

> volume #1.1 level 0.07235

> volume #1.2 level 0.07334

> fitmap #1.2 inMap #1.1

Fit map run_it070_class002.mrc in map run_it070_class004.mrc using 47809
points  
correlation = 0.9816, correlation about mean = 0.808, overlap = 724  
steps = 52, shift = 1.33, angle = 1.07 degrees  
  
Position of run_it070_class002.mrc (#1.2) relative to run_it070_class004.mrc
(#1.1) coordinates:  
Matrix rotation and translation  
0.99985513 0.01573482 0.00649082 -3.13377773  
-0.01578550 0.99984472 0.00783261 1.54510911  
-0.00636656 -0.00793394 0.99994826 2.34667296  
Axis -0.42026549 0.34272012 -0.84019036  
Axis point 98.59654883 203.41092135 0.00000000  
Rotation angle (degrees) 1.07480828  
Shift along axis -0.12509339  
  

> volume #1.2 level 0.08091

> volume #1.1 level 0.08712

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> close #1.1

> close #1.2

> open /media/HDD2-8TB/akent/230301/Class3D/Asiteclass4/run_it070_class003.mrc
> /media/HDD2-8TB/akent/230301/Class3D/Asiteclass4/run_it070_class002.mrc
> /media/HDD2-8TB/akent/230301/Class3D/Asiteclass4/run_it070_class001.mrc

Opened run_it070_class003.mrc as #2.1, grid size 128,128,128, pixel 3.14,
shown at level 1.76e-05, step 1, values float32  
Opened run_it070_class002.mrc as #2.2, grid size 128,128,128, pixel 3.14,
shown at level 2.64e-05, step 1, values float32  
Opened run_it070_class001.mrc as #2.3, grid size 128,128,128, pixel 3.14,
shown at level 1.73e-05, step 1, values float32  

> hide #!2.1 models

> hide #!2.2 models

> volume #2.3 level 0.07277

> hide #!2.3 models

> show #!2.2 models

> volume #2.2 level 0.03413

> hide #!2.2 models

> show #!2.1 models

> volume #2.1 level 0.009962

> show #!2.3 models

> volume #2.1 level 0.05637

> volume #2.3 level 0.06805

> volume #2.1 level 0.06093

> volume #2.3 level 0.08355

> volume #2.1 level 0.08413

> volume #2.3 level 0.08287

> volume #2.1 level 0.06797

> hide #!2.3 models

> volume #2.1 level 0.03938

> show #!2.3 models

> hide #!2.1 models

> volume #2.3 level 0.08624

> show #!2.1 models

> hide #!2.3 models

> volume #2.1 level 0.03316

> close #2.3

> close #2.2

> close #2.1

> open /media/HDD2-8TB/akent/230301/70S_0P81_496.mrc

Opened 70S_0P81_496.mrc as #3, grid size 496,496,496, pixel 0.81, shown at
level 19.6, step 2, values float32  

> view

> volume showOutlineBox true

> close

> open
> /media/HDD2-8TB/akent/230301/P20/J10/cryosparc_P20_J10_003_volume_map_sharp.mrc

Opened cryosparc_P20_J10_003_volume_map_sharp.mrc as #1, grid size
496,496,496, pixel 0.81, shown at level 0.743, step 2, values float32  

> volume #1 level 0.6294

> volume #1 step 1

> volume #1 level 0.9785

> open /media/HDD2-8TB/akent/230301/7k00-aligned.pdb

Chain information for 7k00-aligned.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> fitmap #2 inMap #1

Fit molecule 7k00-aligned.pdb (#2) to map
cryosparc_P20_J10_003_volume_map_sharp.mrc (#1) using 149338 atoms  
average map value = 0.8719, steps = 96  
shifted from previous position = 1.31  
rotated from previous position = 2.09 degrees  
atoms outside contour = 93606, contour level = 0.97851  
  
Position of 7k00-aligned.pdb (#2) relative to
cryosparc_P20_J10_003_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99934097 -0.03576462 0.00620569 6.94739911  
0.03574335 0.99935485 0.00350553 -7.09044814  
-0.00632706 -0.00328141 0.99997460 2.61901143  
Axis -0.09308080 0.17188281 0.98071008  
Axis point 205.22309265 192.30166605 0.00000000  
Rotation angle (degrees) 2.08930916  
Shift along axis 0.70309529  
  

> select /Y /Z

3234 atoms, 3577 bonds, 1 pseudobond, 182 residues, 2 models selected  

> surface zone nearatoms sel distance 3

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface zone #1 nearAtoms sel distance 3

> hide ~sel

> style sel stick

Changed 3234 atom styles  

> select clear

> volume #1 level 0.1366

> volume #1 level 0.383

> volume #1 level 0.4651

> volume #1 level 0.7321

> transparency 50

> select /a:2447-2453 /a:2602-2611 /a:2499-2507 /a:2057-2064 /a:2582-2588

876 atoms, 975 bonds, 41 residues, 1 model selected  

> show sel

> surface zone #1 nearAtoms sel distance 3

> style sel stick

Changed 876 atom styles  

> hide ~sel

> select clear

> select /Z:74-76 /Y:74-76

124 atoms, 136 bonds, 6 residues, 1 model selected  

> show sel

> select clear

> open /media/HDD4/akent/22Oct31/P19/J35/CS-P19-J35-lp4.mrc

Opened CS-P19-J35-lp4.mrc as #3, grid size 496,496,496, pixel 0.83, shown at
level 0.484, step 2, values float32  

> ui tool show "Surface Zone"

> surface unzone #1

> volume #3 step 1

> ui tool show "Map Coordinates"

> fitmap #3 inMap #1

Fit map CS-P19-J35-lp4.mrc in map cryosparc_P20_J10_003_volume_map_sharp.mrc
using 1220406 points  
correlation = 0.8256, correlation about mean = 0.559, overlap = 1.241e+06  
steps = 60, shift = 0.412, angle = 0.247 degrees  
  
Position of CS-P19-J35-lp4.mrc (#3) relative to
cryosparc_P20_J10_003_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999251 -0.00348783 -0.00167704 1.02408217  
0.00349100 0.99999212 0.00188903 -1.01900952  
0.00167044 -0.00189487 0.99999681 -0.37054590  
Axis -0.43919401 -0.38854060 0.81002767  
Axis point 331.85595447 248.32744967 0.00000000  
Rotation angle (degrees) 0.24681780  
Shift along axis -0.35399661  
  

> vop #3 onGrid #1

> volume #3 onGrid #1

Expected a keyword  

> vop #3 ongrid #1

> volume #3 ongrid #1

Expected a keyword  

> vop resample #3 ongrid #1

Opened CS-P19-J35-lp4.mrc resampled as #4, grid size 496,496,496, pixel 0.81,
shown at step 1, values float32  

> save /media/HDD2-8TB/akent/230301/CSP19J35_resampP20.mrc models #4

> save /media/HDD2-8TB/akent/230301/7k00_aligned_P20.pdb relModel #1

> close #3

> close #4

> close #1

> open
> /media/HDD2-8TB/akent/230301/P20/J10/cryosparc_P20_J10_003_volume_map_sharp.mrc

Opened cryosparc_P20_J10_003_volume_map_sharp.mrc as #1, grid size
496,496,496, pixel 0.81, shown at level 0.743, step 2, values float32  

> close #1

> open /media/HDD2-8TB/akent/230301/Refine3D/Init_refinement/run_class001.mrc

Opened run_class001.mrc as #1, grid size 496,496,496, pixel 0.81, shown at
level 0.0131, step 2, values float32  
Must specify one map, got 0  
Must specify one map, got 0  

> fitmap #2 inMap #1

Fit molecule 7k00-aligned.pdb (#2) to map run_class001.mrc (#1) using 149338
atoms  
average map value = 0.01445, steps = 72  
shifted from previous position = 0.944  
rotated from previous position = 1.98 degrees  
atoms outside contour = 78475, contour level = 0.013129  
  
Position of 7k00-aligned.pdb (#2) relative to run_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99801518 -0.05701158 0.02674653 6.84890402  
0.05739778 0.99825462 -0.01390012 -8.43625621  
-0.02590738 0.01540772 0.99954560 2.54614907  
Axis 0.22664922 0.40719365 0.88477311  
Axis point 153.04905075 113.33307526 0.00000000  
Rotation angle (degrees) 3.70702339  
Shift along axis 0.36987304  
  

> select /a:2447-2453 /a:2602-2611 /a:2499-2507 /a:2057-2064 /a:2582-2588
> /Y:74-76 /Z:74-76

1000 atoms, 1111 bonds, 47 residues, 1 model selected  

> surface zone #1 nearAtoms sel distance 3

> select clear

> transparency 50

> volume #1 level 0.7321

> volume #1 level 00.3

> volume #1 step 1

> volume #1 level 0.003335

> volume #1 level 0.00733

> volume #1 level 0.00857

> ui tool show "Surface Zone"

> surface unzone #1

> transparency 0

> volume #1 level 0.00485

> volume #1 level 0.00361

> volume #1 level 0.002783

> volume #1 level 0.003059

> open /media/HDD2-8TB/akent/230301/MaskCreate/70S-mask/mask.mrc

Opened mask.mrc as #3, grid size 496,496,496, pixel 0.81, shown at level 1,
step 2, values float32  

> volume #3 step 1

> volume #3 level 0.8869

> volume #3 level 0.8528

> open /media/HDD2-8TB/akent/230301/PostProcess/init-
> refinement/postprocess_masked.mrc

Opened postprocess_masked.mrc as #4, grid size 496,496,496, pixel 0.81, shown
at level 0.0266, step 2, values float32  

> volume #4 step 1

> close

> open /media/HDD4/cmajumdar/22Jul28/Refine3D/Asite-shiny-
> ctfr/run_half1_class001_unfil_0p8232.mrc

Opened run_half1_class001_unfil_0p8232.mrc as #1, grid size 464,464,464, pixel
0.823, shown at level 0.0114, step 2, values float32  

> close

> open /media/HDD4/cmajumdar/22Jul28/Refine3D/Asite-shiny-
> ctfr/run_half1_class001_unfil.mrc

Opened run_half1_class001_unfil.mrc as #1, grid size 464,464,464, pixel 0.81,
shown at level 0.0114, step 2, values float32  

> save /media/HDD4/cmajumdar/22Jul28/Refine3D/Asite-shiny-
> ctfr/run_it017_half1_class001-try2-0p8232.mrc models #1

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 129, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 129, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  


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

Log:
> camera ortho

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 470.182.03
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: Z10PE-D8 WS
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 40 Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
Cache Size: 25600 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        1.6G        123G         17M        805M        123G
	Swap:            0B          0B          0B

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:24b0] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:14ad]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    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-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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (5)

comment:1 by pett, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Input/Output
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Keyboard interrupt while saving .mrc file

comment:2 by pett, 3 years ago

Hi Chandrima,

It looks like you hit the interrupt key a couple of times while saving a .mrc file. Was the save hung? Did ChimeraX crash after that?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by pett, 3 years ago

Status:	accepted → feedback

in reply to: 4 ; follow-up: 4 comment:4 by cmajumdar@…, 3 years ago

Hi Eric

It looks like it saved, but chimerax froze simultaneously, and I also
couldn't launch chimerax after it froze.
what is an interrupt key?

Chandrima

On Mon, Apr 17, 2023 at 1:47 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:5 by pett, 3 years ago

The "interrupt key" is whatever key on the keyboard you use to interrupt programs (defaults to control-C).

So you can't run ChimeraX now? Try upgrading to the ChimeraX 1.6 release candidate and see if that works...

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