Opened 18 months ago

Closed 18 months ago

#15512 closed defect (can't reproduce)

Crash showing save dialog

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.4.0-210-generic-x86_64-with-glibc2.23
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: Segmentation fault

Current thread 0x00007f885a40b700 (most recent call first):
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 39 in display
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 27 in _file_save
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 45 in run_provider
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1284 in run_provider
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 381 in run_provider
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 165 in callback
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 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 =====
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
> /home/aiguser/Documents/Cryo/C16LKA90/job106/postprocess_lowpass15_inverted.mrc
> format mrc

Opened postprocess_lowpass15_inverted.mrc as #1, grid size 512,512,512, pixel
1.65, shown at level 0.0158, step 2, values float32  

> transparency 50

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #2  
---  
Chain | Description  
A | No description available  


> ui mousemode right "translate selected models"

> select #2

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models #2,1,0,0,481.57,0,1,0,345.6,0,0,1,307.28

> view matrix models #2,1,0,0,434.05,0,1,0,303.55,0,0,1,318.45

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.20213,-0.33159,-0.92151,423.64,0.97212,-0.046291,0.22989,342.95,-0.11889,-0.94229,0.31299,333.34

> view matrix models
> #2,0.84867,0.075941,0.52345,421.59,-0.52775,0.055366,0.8476,285.39,0.035386,-0.99557,0.087065,341.81

> view matrix models
> #2,0.78149,0.077396,0.6191,418.16,-0.62279,0.15646,0.76658,282.3,-0.037538,-0.98465,0.17048,338.26

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78149,0.077396,0.6191,426.21,-0.62279,0.15646,0.76658,286.75,-0.037538,-0.98465,0.17048,362.22

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78149,0.077396,0.6191,412.28,-0.62279,0.15646,0.76658,235.04,-0.037538,-0.98465,0.17048,401.66

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78149,0.077396,0.6191,395.32,-0.62279,0.15646,0.76658,228.39,-0.037538,-0.98465,0.17048,399.64

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.08289,0.21729,0.97258,361.32,-0.99645,-0.0034887,-0.084144,228.99,-0.01489,-0.9761,0.2168,399.69

> view matrix models
> #2,-0.28401,0.21656,0.93405,355.33,-0.95848,-0.038096,-0.2826,233.15,-0.025616,-0.97553,0.21838,399.31

> view matrix models
> #2,-0.19643,0.21835,0.9559,357.86,-0.98042,-0.030173,-0.19457,231.22,-0.013643,-0.9754,0.22,399.68

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.19643,0.21835,0.9559,370.44,-0.98042,-0.030173,-0.19457,227.52,-0.013643,-0.9754,0.22,387.67

> fitmap #2 inMap #1

Fit molecule C8_P32.pdb (#2) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01638, steps = 156  
shifted from previous position = 18.4  
rotated from previous position = 41.8 degrees  
atoms outside contour = 979, contour level = 0.015832  

Position of C8_P32.pdb (#2) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.13689565 -0.24533771 0.95972339 384.15378379  
-0.89231542 0.39017219 0.22702172 208.99268679  
-0.43015436 -0.88745427 -0.16550574 393.75179996  
Axis -0.58800166 0.73330465 -0.34134783  
Axis point 434.11702783 0.00000000 116.98254922  
Rotation angle (degrees) 108.61569694  
Shift along axis -207.03407626  


> ~select #2

Nothing selected  

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #3  
---  
Chain | Description  
A | No description available  


WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xc678fe0
invalid) "/org/a11y/atspi/accessible/2147484288"  

> select #3

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models #3,1,0,0,335.97,0,1,0,-109.42,0,0,1,458.75

> view matrix models #3,1,0,0,564.21,0,1,0,8.385,0,0,1,465.52

> view matrix models #3,1,0,0,573.01,0,1,0,247.23,0,0,1,459.34

> view matrix models #3,1,0,0,572.57,0,1,0,248.17,0,0,1,471.7

> view matrix models #3,1,0,0,426.95,0,1,0,237.03,0,0,1,457.67

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.54341,-0.13915,-0.82786,424.36,0.83238,-0.038588,0.55286,267.65,-0.10887,-0.98952,0.094855,476.2

> view matrix models
> #3,0.76159,0.29067,0.57922,408.71,-0.58125,-0.088889,0.80886,219.14,0.2866,-0.95268,0.10126,488.53

> view matrix models
> #3,0.74896,0.36,0.55629,407.87,-0.58917,-0.022377,0.8077,218.21,0.30322,-0.93268,0.19534,487.64

> view matrix models
> #3,0.47143,0.42149,0.77466,395.43,-0.73908,-0.29044,0.60779,218.75,0.48117,-0.85906,0.1746,492.89

> view matrix models
> #3,-0.055327,0.39947,0.91508,376.8,-0.90097,-0.41498,0.12668,221.04,0.43034,-0.81745,0.38287,488.12

> view matrix models
> #3,-0.23268,0.43203,0.87133,371.29,-0.94439,0.11368,-0.30855,219.75,-0.23236,-0.89467,0.38155,467.51

> view matrix models
> #3,0.030622,0.30731,0.95112,380.08,-0.90736,0.40767,-0.10251,215.21,-0.41924,-0.85987,0.29132,462.27

> view matrix models
> #3,0.31055,0.20949,0.92718,390.47,-0.8068,0.57387,0.14057,213.57,-0.50263,-0.7917,0.34723,458.14

> view matrix models
> #3,0.095857,0.41591,0.90434,381.66,-0.99107,-0.044745,0.12563,214.27,0.092715,-0.90831,0.4079,477.82

> view matrix models
> #3,-0.45981,0.60806,0.64718,365.01,-0.80703,0.017944,-0.59024,228.84,-0.37051,-0.79369,0.48247,460.68

> view matrix models
> #3,-0.39954,0.69347,0.59955,366.68,-0.55142,0.34066,-0.7615,235.95,-0.73233,-0.63486,0.24629,450.38

> view matrix models
> #3,-0.77135,0.17368,0.61225,359.93,-0.47494,0.48328,-0.73544,236.59,-0.42362,-0.85806,-0.29029,469.64

> view matrix models
> #3,-0.78641,0.13904,0.60185,359.94,-0.47256,0.49205,-0.73115,236.52,-0.3978,-0.85939,-0.32124,470.89

> fitmap #3 inMap #1

Fit molecule C8_P32.pdb (#3) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.0163, steps = 368  
shifted from previous position = 15  
rotated from previous position = 68.2 degrees  
atoms outside contour = 1044, contour level = 0.015832  

Position of C8_P32.pdb (#3) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.20251033 -0.26165250 0.94367766 401.56488343  
-0.87616424 0.38201310 0.29394253 207.04040107  
-0.43740803 -0.88634303 -0.15188897 470.19007199  
Axis -0.61542558 0.72012697 -0.32041927  
Axis point 491.79082211 0.00000000 152.26282015  
Rotation angle (degrees) 106.48012710  
Shift along axis -248.69588493  


> ~select #3

Nothing selected  

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #4  
---  
Chain | Description  
A | No description available  


> select #4

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models
> #4,0.97337,-0.22894,0.011503,1.3823,0.20816,0.90381,0.37389,2.8975,-0.095994,-0.36154,0.9274,1.6132

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.97337,-0.22894,0.011503,399.35,0.20816,0.90381,0.37389,-82.529,-0.095994,-0.36154,0.9274,511.56

> view matrix models
> #4,0.97337,-0.22894,0.011503,527.9,0.20816,0.90381,0.37389,-66.273,-0.095994,-0.36154,0.9274,517.47

> view matrix models
> #4,0.97337,-0.22894,0.011503,619.57,0.20816,0.90381,0.37389,-17.314,-0.095994,-0.36154,0.9274,525.7

> view matrix models
> #4,0.97337,-0.22894,0.011503,635.98,0.20816,0.90381,0.37389,225.24,-0.095994,-0.36154,0.9274,533.68

> view matrix models
> #4,0.97337,-0.22894,0.011503,450.5,0.20816,0.90381,0.37389,253.3,-0.095994,-0.36154,0.9274,538.2

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.8507,0.23582,0.46978,435.74,-0.50311,0.10639,0.85765,232.37,0.15227,-0.96595,0.20915,561.85

> view matrix models
> #4,0.63444,0.35331,0.6875,424.7,-0.77294,0.28239,0.56817,225.55,0.0065949,-0.89187,0.45225,553.21

> view matrix models
> #4,0.60931,0.40604,0.68108,423.42,-0.76605,0.52318,0.37342,225.78,-0.2047,-0.74927,0.62983,542.59

> view matrix models
> #4,0.3336,-0.11372,0.93583,416.64,-0.73417,0.59138,0.33357,226.61,-0.59137,-0.79833,0.11379,537.28

> fitmap #4 inMap #1

Fit molecule C8_P32.pdb (#4) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01612, steps = 100  
shifted from previous position = 18.7  
rotated from previous position = 17.4 degrees  
atoms outside contour = 1100, contour level = 0.015832  

Position of C8_P32.pdb (#4) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.28967471 -0.31011574 0.90549257 419.40257951  
-0.83145227 0.38708821 0.39855970 206.24272175  
-0.47410514 -0.86832652 -0.14571677 547.30385646  
Axis -0.65160886 0.70958077 -0.26814366  
Axis point 567.36715872 0.00000000 178.85934915  
Rotation angle (degrees) 103.56079134  
Shift along axis -273.69662724  


> ~select #4

Nothing selected  

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #5  
---  
Chain | Description  
A | No description available  


WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xfe2c580
invalid) "/org/a11y/atspi/accessible/2147484372"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xf96a7c0
invalid) "/org/a11y/atspi/accessible/2147484374"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xfe2c580
invalid) "/org/a11y/atspi/accessible/2147484372"  

> select #5

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,375.28,0,1,0,-62.096,0,0,1,614.98

> view matrix models #5,1,0,0,550.93,0,1,0,173.97,0,0,1,610.34

> view matrix models #5,1,0,0,453.97,0,1,0,220.65,0,0,1,608.37

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.79727,-0.43772,-0.41564,457.36,0.6034,0.55919,0.56852,237.41,-0.016432,-0.70406,0.70995,618.95

> view matrix models
> #5,0.65835,0.59895,0.45589,430.76,-0.75086,0.48014,0.45351,195.93,0.05274,-0.64088,0.76583,619.8

> view matrix models
> #5,0.6635,0.56717,0.48794,430.84,-0.74011,0.59307,0.31702,196.86,-0.10958,-0.57147,0.81327,613.21

> view matrix models
> #5,0.078249,0.86466,0.49622,408.7,-0.96955,-0.04986,0.23977,197.16,0.23206,-0.49987,0.83443,623.24

> view matrix models
> #5,0.50658,0.6964,0.50833,424.15,-0.8232,0.56596,0.045016,197.98,-0.25635,-0.44126,0.85998,606.5

> view matrix models
> #5,0.1321,0.82295,0.55255,410.15,-0.97766,0.016225,0.20957,196.6,0.1635,-0.56789,0.80671,622.09

> view matrix models
> #5,-0.079127,0.75508,0.65085,402.75,-0.74158,0.39173,-0.54462,210.07,-0.66618,-0.52575,0.52895,598.41

> view matrix models
> #5,-0.37027,0.39223,0.84205,394.65,-0.81526,0.29728,-0.49697,208.06,-0.44525,-0.8705,0.2097,613.29

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.37027,0.39223,0.84205,409.93,-0.81526,0.29728,-0.49697,213.62,-0.44525,-0.8705,0.2097,620.2

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.10127,0.29258,0.95086,424.81,-0.90954,0.41448,-0.030666,203.31,-0.40309,-0.86174,0.30809,620.2

> view matrix models
> #5,0.021374,0.045048,0.99876,424.19,-0.94659,0.32239,0.0057166,202.61,-0.32173,-0.94553,0.049533,627.05

> fitmap #5 inMap #1

Fit molecule C8_P32.pdb (#5) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01508, steps = 140  
shifted from previous position = 10.7  
rotated from previous position = 20.2 degrees  
atoms outside contour = 1234, contour level = 0.015832  

Position of C8_P32.pdb (#5) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.31564750 -0.02969592 0.94841173 411.56984452  
-0.88888278 0.35901765 -0.28459398 213.24591043  
-0.33204527 -0.93285823 -0.13971922 620.94570653  
Axis -0.38754913 0.76549030 -0.51364411  
Axis point 421.74341470 0.00000000 279.89485167  
Rotation angle (degrees) 123.24186822  
Shift along axis -315.21096603  


> ~select #5

Nothing selected  

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #6  
---  
Chain | Description  
A | No description available  


> select #6

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,482.18,0,1,0,-109.7,0,0,1,583.5

> view matrix models #6,1,0,0,632.71,0,1,0,159.38,0,0,1,661.74

> view matrix models #6,1,0,0,463.31,0,1,0,184.21,0,0,1,684.71

> view matrix models #6,1,0,0,463.64,0,1,0,231.81,0,0,1,687.62

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.7312,-0.406,-0.54818,466.29,0.68187,0.45824,0.57014,252.15,0.019725,-0.79068,0.61191,701.55

> view matrix models
> #6,0.54414,0.49864,0.67473,434.96,-0.83838,0.35388,0.41459,206.09,-0.032046,-0.79128,0.61061,699.9

> view matrix models
> #6,0.32669,0.53633,0.77822,426.19,-0.85712,0.5151,0.0048141,209.1,-0.39828,-0.6686,0.62798,686.54

> view matrix models
> #6,-0.033432,0.65828,0.75203,413.61,-0.95183,0.2085,-0.22482,212.21,-0.3048,-0.72332,0.6196,690.25

> view matrix models
> #6,-0.032776,0.5596,0.82811,413.68,-0.66222,0.60843,-0.43736,220.15,-0.7486,-0.56272,0.35064,677.7

> view matrix models
> #6,-0.28978,0.28106,0.91489,407.15,-0.72879,0.55483,-0.40128,218.09,-0.62039,-0.78305,0.044058,688.12

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.28978,0.28106,0.91489,415.62,-0.72879,0.55483,-0.40128,222.15,-0.62039,-0.78305,0.044058,691.21

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.27249,0.13357,0.95284,434.85,-0.9178,0.3333,0.21575,210.36,-0.28877,-0.93331,0.21341,701.31

> view matrix models
> #6,0.47548,0.062104,0.87753,443.14,-0.85218,0.2802,0.44191,210.11,-0.21844,-0.95793,0.18615,704.2

> fitmap #6 inMap #1

Fit molecule C8_P32.pdb (#6) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01547, steps = 108  
shifted from previous position = 8.96  
rotated from previous position = 25.1 degrees  
atoms outside contour = 1117, contour level = 0.015832  

Position of C8_P32.pdb (#6) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.42329826 -0.36347785 0.82988097 453.48259088  
-0.78483583 0.31048737 0.53631176 207.72624560  
-0.45260501 -0.87834017 -0.15384168 704.85544408  
Axis -0.72346253 0.65587198 -0.21548531  
Axis point 0.00000000 661.66657059 43.00426498  
Rotation angle (degrees) 102.12399440  
Shift along axis -343.72183457  


> volume #1 level 0.01713

> ~select #6

Nothing selected  

> volume #1 level 0.01763

> volume #1 level 0.01503

> transparency 0

> transparency 50

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #7  
---  
Chain | Description  
A | No description available  


> ui mousemode right "translate selected models"

> select #7

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models #7,1,0,0,377.23,0,1,0,-70.123,0,0,1,257.15

> view matrix models #7,1,0,0,500.56,0,1,0,194.88,0,0,1,317.6

> view matrix models #7,1,0,0,401.76,0,1,0,214.66,0,0,1,314.71

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.98479,-0.13356,0.11112,401.22,-0.002207,0.62993,0.77665,208.4,-0.17373,-0.76509,0.62005,322

> view matrix models
> #7,0.54417,0.42183,0.72522,373.22,-0.83675,0.33585,0.4325,188.94,-0.061125,-0.84218,0.53572,327.54

> view matrix models
> #7,0.33138,-0.17311,0.92748,369.94,-0.82521,0.42338,0.37386,189.15,-0.4574,-0.88926,-0.0025547,322.18

> view matrix models
> #7,0.27846,-0.25955,0.92471,369.17,-0.81948,0.43794,0.36969,189.24,-0.50092,-0.86072,-0.090745,321.62

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.27846,-0.25955,0.92471,381.72,-0.81948,0.43794,0.36969,197.57,-0.50092,-0.86072,-0.090745,312.13

> view matrix models
> #7,0.27846,-0.25955,0.92471,373.54,-0.81948,0.43794,0.36969,199.92,-0.50092,-0.86072,-0.090745,313.8

> fitmap #7 inMap #1

Fit molecule C8_P32.pdb (#7) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01555, steps = 80  
shifted from previous position = 12.3  
rotated from previous position = 9.66 degrees  
atoms outside contour = 1048, contour level = 0.015032  

Position of C8_P32.pdb (#7) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.12934670 -0.21411149 0.96820747 369.35371602  
-0.87484761 0.43501795 0.21307519 212.56530999  
-0.46680947 -0.87459456 -0.13104680 314.48990437  
Axis -0.56707402 0.74816903 -0.34448534  
Axis point 394.98075562 0.00000000 66.68244759  
Rotation angle (degrees) 106.45971221  
Shift along axis -158.75327819  


> ~select #7

Nothing selected  

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #8  
---  
Chain | Description  
A | No description available  


WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xc005c00
invalid) "/org/a11y/atspi/accessible/2147484544"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xb595710
invalid) "/org/a11y/atspi/accessible/2147484546"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0xc005c00
invalid) "/org/a11y/atspi/accessible/2147484544"  

> select #8

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models #8,1,0,0,409.13,0,1,0,184.2,0,0,1,241.81

> view matrix models #8,1,0,0,425.83,0,1,0,226.25,0,0,1,242.66

> view matrix models #8,1,0,0,387.13,0,1,0,223.71,0,0,1,241.06

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.58249,-0.51861,-0.6259,387.15,0.79494,0.20278,0.5718,250.35,-0.16962,-0.83062,0.53038,250.33

> view matrix models
> #8,0.4009,0.68761,0.60536,352.73,-0.8072,-0.047372,0.58838,200.94,0.43325,-0.72453,0.53605,268.65

> view matrix models
> #8,0.56323,0.56146,0.60625,359.29,-0.82577,0.35603,0.43744,198.07,0.029759,-0.747,0.66416,254.18

> view matrix models
> #8,0.44658,-0.20297,0.87142,360.07,-0.87901,0.082331,0.46965,198.8,-0.16707,-0.97572,-0.14165,260.63

> view matrix models
> #8,0.47462,-0.2316,0.84917,361.57,-0.85048,0.12785,0.51023,198.72,-0.22674,-0.96437,-0.13629,258.51

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.47462,-0.2316,0.84917,372.86,-0.85048,0.12785,0.51023,199.34,-0.22674,-0.96437,-0.13629,247.21

> fitmap #8 inMap #1

Fit molecule C8_P32.pdb (#8) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01566, steps = 128  
shifted from previous position = 18.3  
rotated from previous position = 32.7 degrees  
atoms outside contour = 1002, contour level = 0.015032  

Position of C8_P32.pdb (#8) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.02092069 -0.16432581 0.98618424 350.14515805  
-0.89448450 0.44370825 0.05495878 218.26454235  
-0.44660923 -0.88097674 -0.15626957 237.11480038  
Axis -0.50301639 0.77005155 -0.39242211  
Axis point 333.62389634 0.00000000 41.89358530  
Rotation angle (degrees) 111.51476653  
Shift along axis -101.10289483  


> ~select #8

Nothing selected  

> open /home/aiguser/Documents/ML_Xray/C8_P32.pdb

Summary of feedback from opening /home/aiguser/Documents/ML_Xray/C8_P32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE SeMet_B4_P31_CTPR8nowater  

Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 10210.321  

Ignored bad PDB record found on line 3  
REMARK RFZ=7.8 TFZ=10.5 PAK=0 LLG=259 TFZ==12.3 LLG=10210 TFZ==92.7  

Ignored bad PDB record found on line 4  
REMARK ENSEMBLE ensemble1 EULER 139.91 179.80 140.08 FRAC 0.329 0.661 0.331  

Chain information for C8_P32.pdb #9  
---  
Chain | Description  
A | No description available  


WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x16fee760
invalid) "/org/a11y/atspi/accessible/2147484602"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x17431810
invalid) "/org/a11y/atspi/accessible/2147484604"  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x16fee760
invalid) "/org/a11y/atspi/accessible/2147484602"  

> select #9

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models #9,1,0,0,381.28,0,1,0,-2.742,0,0,1,156.42

> view matrix models #9,1,0,0,473.27,0,1,0,200.12,0,0,1,161.86

> view matrix models #9,1,0,0,372.03,0,1,0,252.58,0,0,1,154.21

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.85012,-0.32522,0.41417,365.22,-0.15908,0.59115,0.79072,241.47,-0.50199,-0.73809,0.45081,152.8

> view matrix models
> #9,-0.20418,0.25931,0.94396,318.16,-0.93746,0.22592,-0.26484,233.77,-0.28193,-0.939,0.19697,165.3

> view matrix models
> #9,-0.70607,0.46551,0.53363,305.08,-0.58862,0.033121,-0.80773,254.1,-0.39368,-0.88442,0.25062,160.42

> view matrix models
> #9,-0.57148,0.36962,0.73266,307.86,-0.79771,-0.040726,-0.60167,245.44,-0.19255,-0.92829,0.31812,166.51

> view matrix models
> #9,-0.69817,0.48347,0.52803,305.23,-0.57151,0.06785,-0.81778,254.42,-0.4312,-0.87273,0.22894,159.37

> view matrix models
> #9,-0.8302,0.12927,0.54227,304.47,-0.53668,-0.44848,-0.71473,259.61,0.1508,-0.8844,0.4417,175.56

> view matrix models
> #9,-0.61458,0.49447,0.61465,306.69,-0.65745,0.10955,-0.7455,250.27,-0.43596,-0.86226,0.25776,158.73

> view matrix models
> #9,-0.78649,0.040718,0.61626,305.85,-0.56788,0.34458,-0.74751,250.73,-0.24279,-0.93787,-0.24789,172.32

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.78649,0.040718,0.61626,315.3,-0.56788,0.34458,-0.74751,247.67,-0.24279,-0.93787,-0.24789,163.42

> fitmap #9 inMap #1

Fit molecule C8_P32.pdb (#9) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01543, steps = 200  
shifted from previous position = 5.63  
rotated from previous position = 50.4 degrees  
atoms outside contour = 1056, contour level = 0.015032  

Position of C8_P32.pdb (#9) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.05656479 -0.13376401 0.98939760 334.91528596  
-0.89031778 0.45521529 0.01064363 223.76782870  
-0.45181266 -0.88027622 -0.14484164 159.37226999  
Axis -0.48012861 0.77668746 -0.40771694  
Axis point 296.72665009 0.00000000 3.59250904  
Rotation angle (degrees) 111.90665606  
Shift along axis -51.98351725  


> ~select #9

Nothing selected  

> select #5

2297 atoms, 2368 bonds, 272 residues, 1 model selected  

> view matrix models
> #5,-0.31565,-0.029696,0.94841,413.6,-0.88888,0.35902,-0.28459,213.12,-0.33205,-0.93286,-0.13972,630.54

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.46634,-0.36499,0.8058,444.24,-0.73869,0.34048,0.58173,206.95,-0.48668,-0.86652,-0.11084,624.47

> fitmap #5 inMap #1

Fit molecule C8_P32.pdb (#5) to map postprocess_lowpass15_inverted.mrc (#1)
using 2297 atoms  
average map value = 0.01519, steps = 60  
shifted from previous position = 3.42  
rotated from previous position = 10.5 degrees  
atoms outside contour = 1064, contour level = 0.015032  

Position of C8_P32.pdb (#5) relative to postprocess_lowpass15_inverted.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.31971478 -0.32957320 0.88834901 435.18505653  
-0.83467153 0.34577393 0.42867684 206.36538263  
-0.44844833 -0.87853395 -0.16453633 626.29351541  
Axis -0.67495513 0.69023162 -0.26079857  
Axis point 624.02671430 0.00000000 227.03931249  
Rotation angle (degrees) 104.44933535  
Shift along axis -314.62692634  


> ~select #5

Nothing selected  

QAccessibleTree::indexFromLogical: invalid index: -1 0 for
QTreeView(0x19cbadf0, name="treeView")  

Requested invalid tree cell: -1 0  


===== 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: 4.5 (Core Profile) Mesa 18.0.5
OpenGL renderer: Mesa DRI Intel(R) HD Graphics 530 (Skylake GT2) 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: HP
Model: HP ProDesk 490 G3 MT Business PC
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.5G         31G        518M         23G         54G
	Swap:          8.2G        251M        8.0G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:1912] (rev 06)	
	DeviceName: Onboard IGD	
	Subsystem: Hewlett-Packard Company Skylake Integrated Graphics [103c:805f]
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-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 (2)

comment:1 by Eric Pettersen, 18 months ago

Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash showing save dialog

comment:2 by Eric Pettersen, 18 months ago

Resolution: → can't reproduce
Status: accepted → closed
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