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Opened 3 years ago
Closed 3 years ago
#8087 closed defect (can't reproduce)
Crash using File→Open on Windows and/or in return statement
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
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 0x800706ba
Thread 0x000032fc (most recent call first):
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
Windows fatal exception: code 0x800706ba
Thread 0x00002af8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 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 0x000032fc (most recent call first):
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
Windows fatal exception: code 0x800706ba
Thread 0x00002af8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 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 0x000032fc (most recent call first):
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
Windows fatal exception: code 0x80010012
Thread 0x000032fc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
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
Windows fatal exception: code 0x80040155
Current thread 0x000032fc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
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
Windows fatal exception: code 0x80040155
Thread 0x000032fc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in
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
Windows fatal exception: code 0x800706ba
Thread 0x00003120 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 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 0x000032fc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 230 in done_current
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 493 in done_current
Windows fatal exception: access violation
===== 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
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
k.i.delaobecerra@uu.nl is subscribed to the ChimeraX announcements list
> open C:/Users/Delao002/Desktop/cryosparc_P12_J500.cif
> C:/Users/Delao002/Desktop/cryosparc_P12_J473.cif
Summary of feedback from opening
C:/Users/Delao002/Desktop/cryosparc_P12_J500.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Summary of feedback from opening
C:/Users/Delao002/Desktop/cryosparc_P12_J473.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for cryosparc_P12_J500.cif #1
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Ca | No description available
Chain information for cryosparc_P12_J473.cif #2
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
> hide #!1 models
> show #!1 models
> hide #2 models
> hide #!1 models
> open C:/Users/Delao002/Desktop/cryosparc_P12_J500_005_volume_map_sharp.mrc
Opened cryosparc_P12_J500_005_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.04, shown at level 0.0528, step 2, values float32
> volume #3 step 1
> volume #3 level 0.1445
> surface dust #3 size 5
QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"
> open C:/Users/Delao002/Downloads/C5B3G8_3_real_space_ref_in_localresmap-
> coot-0.pdb
Chain information for C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "C:/Users/Delao002/Downloads/cryosparc_P12_J473 (1).cif"
Summary of feedback from opening
C:/Users/Delao002/Downloads/cryosparc_P12_J473 (1).cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for cryosparc_P12_J473 (1).cif #5
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
> hide #!4 models
> color #3 #b2b2b296 models
> show #5 atoms
> style #5 sphere
Changed 501 atom styles
> hide #!3 models
> style #5 stick
Changed 501 atom styles
> hide #5 target m
> close #5
> show #!3 models
> show #!4 models
> ui mousemode right "translate selected models"
> select #4/B:394
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #4,0.39424,0.52571,0.75379,-118.79,0.90583,-0.083906,-0.41524,103.82,-0.15505,0.84651,-0.50929,146.24
> view matrix models
> #4,0.45766,-0.65705,-0.59902,306.54,-0.39268,-0.75382,0.52684,270.53,-0.79771,-0.0058886,-0.60301,414.49
> view matrix models
> #4,0.45766,-0.65705,-0.59902,301.51,-0.39268,-0.75382,0.52684,264.97,-0.79771,-0.0058886,-0.60301,413.73
> volume flip #3
Opened cryosparc_P12_J500_005_volume_map_sharp.mrc z flip as #5, grid size
320,320,320, pixel 1.04, shown at step 1, values float32
> surface dust #5 size 5
> view matrix models
> #4,0.45766,-0.65705,-0.59902,299.13,-0.39268,-0.75382,0.52684,267.06,-0.79771,-0.0058886,-0.60301,410.75
> view matrix models
> #4,-0.33107,-0.17837,0.92659,84.348,-0.53192,-0.7758,-0.3394,445.22,0.77939,-0.60524,0.16197,114.19
> view matrix models
> #4,-0.40603,-0.30323,0.86208,129.29,-0.67372,-0.53805,-0.50657,457.96,0.61745,-0.78648,0.014168,197.77
> view matrix models
> #4,-0.40603,-0.30323,0.86208,130.4,-0.67372,-0.53805,-0.50657,440.35,0.61745,-0.78648,0.014168,196.5
> view matrix models
> #4,0.46692,-0.73105,-0.49755,293.51,0.6134,0.67303,-0.41324,3.4392,0.63696,-0.11225,0.76268,-51.347
> view matrix models
> #4,0.88163,-0.036947,0.4705,-62.262,-0.04518,0.98574,0.16207,-39.346,-0.46978,-0.16414,0.86739,124.76
> view matrix models
> #4,0.88163,-0.036947,0.4705,-59.433,-0.04518,0.98574,0.16207,-17.98,-0.46978,-0.16414,0.86739,133.87
> view matrix models
> #4,0.88163,-0.036947,0.4705,-52.231,-0.04518,0.98574,0.16207,-24.042,-0.46978,-0.16414,0.86739,125.16
> ui tool show "Fit in Map"
Fit molecule C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb (#4) to map
cryosparc_P12_J500_005_volume_map_sharp.mrc (#3) using 13612 atoms
average map value = 0.09308, steps = 144
shifted from previous position = 12.7
rotated from previous position = 13.3 degrees
atoms outside contour = 9978, contour level = 0.14451
Position of C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb (#4) relative to
cryosparc_P12_J500_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.96575303 0.01093333 0.25923260 -42.15904384
-0.05262373 0.98660045 0.15443542 -14.94789719
-0.25407051 -0.16278827 0.95338773 64.40283449
Axis -0.52282090 0.84598220 -0.10474929
Axis point 220.37925498 0.00000000 186.40009582
Rotation angle (degrees) 17.66054785
Shift along axis 2.64982336
> view matrix models
> #4,0.95559,0.29294,0.032295,-48.555,-0.29467,0.95163,0.087003,43.317,-0.0052469,-0.092655,0.99568,3.4388
> view matrix models
> #4,0.95559,0.29294,0.032295,-48.414,-0.29467,0.95163,0.087003,41.844,-0.0052469,-0.092655,0.99568,15.9
Fit molecule C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb (#4) to map
cryosparc_P12_J500_005_volume_map_sharp.mrc z flip (#5) using 13612 atoms
average map value = 0.2747, steps = 136
shifted from previous position = 1.26
rotated from previous position = 14.2 degrees
atoms outside contour = 3389, contour level = 0.14451
Position of C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb (#4) relative to
cryosparc_P12_J500_005_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99846790 0.05390453 -0.01249609 -7.15314013
-0.05278486 0.99561921 0.07717607 -3.39421172
0.01660148 -0.07639823 0.99693917 10.03477436
Axis -0.81150265 -0.15375461 -0.56375790
Axis point 0.00000000 134.27457107 50.26822347
Rotation angle (degrees) 5.42964515
Shift along axis 0.66948458
> volume #5 level 0.1727
> style sel stick
Changed 7 atom styles
> select #4
13612 atoms, 13910 bonds, 5 pseudobonds, 1736 residues, 2 models selected
> show (#!4 & sel) target ab
> ~select #4
Nothing selected
> volume #5 level 0.2318
> save C:/Users/Delao002/Desktop/cs_P12_J500_flipped.mrc models #5
> close #1
> close #2
> close #3
> show #!5 models
> save C:/Users/Delao002/Desktop/C5B3G8_3_real_space_ref_in_localresmap-
> coot-0_1.pdb relModel #5
> hide #!5 models
> hide #!4 models
> show #!5 models
> open "C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/NbC5 UMC/AF
> PREDICTION C5NbB3/AF_prediction_UC5Nb2.cif"
Summary of feedback from opening
C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/NbC5 UMC/AF
PREDICTION C5NbB3/AF_prediction_UC5Nb2.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for AF_prediction_UC5Nb2.cif #1
---
Chain | Description
A | No description available
> open C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/c5nbs2.pdb
> C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/c5nbs2_1.pdb
Summary of feedback from opening
C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/c5nbs2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU B 444
ASN B 446 1 3
Start residue of secondary structure not found: HELIX 2 2 GLN B 532 MET B 534
1 3
Start residue of secondary structure not found: HELIX 3 3 LEU B 620 GLU B 628
1 9
Start residue of secondary structure not found: HELIX 4 4 ALA B 643 LEU B 648
1 6
Start residue of secondary structure not found: HELIX 5 5 LYS B 681 GLU B 684
1 4
83 messages similar to the above omitted
Summary of feedback from opening
C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/c5nbs2_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU B 444
ASN B 446 1 3
Start residue of secondary structure not found: HELIX 2 2 GLN B 532 MET B 534
1 3
Start residue of secondary structure not found: HELIX 3 3 LEU B 620 GLU B 628
1 9
Start residue of secondary structure not found: HELIX 4 4 ALA B 643 LEU B 648
1 6
Start residue of secondary structure not found: HELIX 5 5 LYS B 681 GLU B 684
1 4
171 messages similar to the above omitted
Chain information for c5nbs2.pdb #2
---
Chain | Description
B | No description available
Chain information for c5nbs2_1.pdb
---
Chain | Description
3.1/B | No description available
3.2/B 3.3/B | No description available
> hide #!2 models
> close #2
> close #3.3
> close #3.2
> select #3.1/B:826
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models #3.1,1,0,0,106.91,0,1,0,48.171,0,0,1,99.446
> view matrix models
> #3.1,-0.4699,0.8281,0.30569,96.933,0.80833,0.26453,0.52596,20.428,0.35468,0.49424,-0.79368,184.12
> view matrix models
> #3.1,0.71618,-0.31305,0.62376,103.81,0.018818,-0.88477,-0.46565,288.47,0.69766,0.34523,-0.62777,160.26
> view matrix models
> #3.1,0.17648,-0.97914,-0.10074,278.63,-0.87954,-0.11092,-0.46271,270.72,0.44188,0.17027,-0.88077,220.04
> view matrix models
> #3.1,0.17648,-0.97914,-0.10074,289.08,-0.87954,-0.11092,-0.46271,282.29,0.44188,0.17027,-0.88077,203.91
> view matrix models
> #3.1,0.11039,-0.96575,-0.23481,304.55,-0.7953,0.055856,-0.60363,271.39,0.59608,0.25338,-0.7619,173.3
> view matrix models
> #3.1,0.11039,-0.96575,-0.23481,285.63,-0.7953,0.055856,-0.60363,274.61,0.59608,0.25338,-0.7619,172.91
Fit molecule c5nbs2_1.pdb (#3.1) to map cs_P12_J500_flipped.mrc (#5) using
11747 atoms
average map value = 0.2282, steps = 276
shifted from previous position = 7.84
rotated from previous position = 39 degrees
atoms outside contour = 6684, contour level = 0.23175
Position of c5nbs2_1.pdb (#3.1) relative to cs_P12_J500_flipped.mrc (#5)
coordinates:
Matrix rotation and translation
0.58413630 -0.71452305 -0.38502155 239.78688535
-0.80099472 -0.43084561 -0.41566757 313.84237877
0.13111921 0.55120674 -0.82400175 174.36749722
Axis 0.87944027 -0.46946637 -0.07865207
Axis point 0.00000000 190.56364681 155.33227260
Rotation angle (degrees) 146.65287657
Shift along axis 49.82543663
> select #1/A:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #1,1,0,0,156.68,0,1,0,294.66,0,0,1,161.29
> view matrix models #1,1,0,0,141.31,0,1,0,254.88,0,0,1,122.86
> view matrix models #1,1,0,0,143.47,0,1,0,255.08,0,0,1,117.04
> view matrix models
> #1,-0.99386,0.10798,0.024274,142.7,0.010337,-0.1278,0.99175,261.06,0.11019,0.9859,0.12589,111.82
> view matrix models
> #1,-0.87223,0.4673,0.14435,142.15,0.30843,0.29647,0.90387,259.76,0.37958,0.83291,-0.40272,110.7
> view matrix models
> #1,-0.77243,-0.44817,-0.45,142.8,-0.28244,-0.39222,0.87543,261.33,-0.56884,0.80331,0.17638,112.27
> view matrix models
> #1,-0.77243,-0.44817,-0.45,145.12,-0.28244,-0.39222,0.87543,268.08,-0.56884,0.80331,0.17638,119.64
> view matrix models
> #1,-0.75739,-0.46073,-0.46269,145.11,-0.27325,-0.41993,0.86545,268.13,-0.59303,0.78191,0.19215,119.74
> view matrix models
> #1,-0.53091,-0.55213,-0.64288,144.87,-0.07998,-0.72259,0.68664,268.44,-0.84365,0.41596,0.33947,121.08
> view matrix models
> #1,-0.69564,-0.50223,-0.51367,145.09,-0.22982,-0.52187,0.82148,268.28,-0.68064,0.68951,0.24761,120.13
> view matrix models
> #1,-0.69564,-0.50223,-0.51367,138.99,-0.22982,-0.52187,0.82148,263.32,-0.68064,0.68951,0.24761,127.37
> view matrix models
> #1,-0.69564,-0.50223,-0.51367,144.52,-0.22982,-0.52187,0.82148,268.63,-0.68064,0.68951,0.24761,122.48
> view matrix models
> #1,-0.69564,-0.50223,-0.51367,141.75,-0.22982,-0.52187,0.82148,264.5,-0.68064,0.68951,0.24761,121.87
> view matrix models
> #1,-0.79451,-0.5392,-0.27931,142.53,-0.33729,0.0093673,0.94135,263.43,-0.50496,0.84212,-0.18931,120.19
> view matrix models
> #1,-0.25561,0.96583,0.042756,139.68,-0.62781,-0.19946,0.75237,263.32,0.73519,0.16547,0.65735,124.89
> view matrix models
> #1,0.15351,0.74515,0.64899,142.21,-0.77663,-0.3151,0.54549,262.96,0.61097,-0.58776,0.53034,126.46
> view matrix models
> #1,0.15351,0.74515,0.64899,130.92,-0.77663,-0.3151,0.54549,221.67,0.61097,-0.58776,0.53034,142.11
> view matrix models
> #1,0.15351,0.74515,0.64899,161.39,-0.77663,-0.3151,0.54549,215.14,0.61097,-0.58776,0.53034,160.65
> view matrix models
> #1,0.38021,0.4807,0.79017,162.58,-0.78861,-0.27788,0.54852,215.05,0.48325,-0.83169,0.27343,160.49
> view matrix models
> #1,0.38021,0.4807,0.79017,164.25,-0.78861,-0.27788,0.54852,216.44,0.48325,-0.83169,0.27343,156.42
Fit molecule AF_prediction_UC5Nb2.cif (#1) to map cs_P12_J500_flipped.mrc (#5)
using 909 atoms
average map value = 0.2243, steps = 72
shifted from previous position = 2.34
rotated from previous position = 20.4 degrees
atoms outside contour = 518, contour level = 0.23175
Position of AF_prediction_UC5Nb2.cif (#1) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.47706984 0.29680162 0.82723224 162.93877242
-0.86540626 -0.00545213 0.50104120 218.13014292
0.15322001 -0.95492360 0.25425293 158.11275556
Axis -0.73491848 0.34021705 -0.58664059
Axis point 0.00000000 192.40860664 -143.14447766
Rotation angle (degrees) 97.87802704
Shift along axis -138.29048347
> open "C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/NbC5 UMC/AF
> prediction c5Nbg8/AF_prediction_UC5Nb1.cif"
Summary of feedback from opening
C:/Users/Delao002/surfdrive3/20210922CopyPhD/Complement/C5/NbC5 UMC/AF
prediction c5Nbg8/AF_prediction_UC5Nb1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for AF_prediction_UC5Nb1.cif #2
---
Chain | Description
A | No description available
> select clear
> select #2/A:123
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,29.767,0,1,0,117.97,0,0,1,165.01
> view matrix models #2,1,0,0,109.98,0,1,0,84.757,0,0,1,186.53
> view matrix models #2,1,0,0,96.013,0,1,0,91.931,0,0,1,189.92
> view matrix models #2,1,0,0,95.748,0,1,0,91.551,0,0,1,190.36
> view matrix models
> #2,0.99725,0.044338,0.059457,95.767,-0.053328,0.98578,0.15934,92.057,-0.051547,-0.16207,0.98543,190.88
> view matrix models
> #2,0.26622,0.3358,0.90353,98.025,-0.38908,0.89504,-0.218,91.89,-0.8819,-0.2935,0.36893,190.96
> view matrix models
> #2,0.44907,0.19041,0.87297,98.111,0.13984,0.95001,-0.27915,90.816,-0.88248,0.24743,0.4,189.45
> view matrix models
> #2,0.44907,0.19041,0.87297,117.7,0.13984,0.95001,-0.27915,121.18,-0.88248,0.24743,0.4,159.5
> view matrix models
> #2,-0.014824,0.61978,-0.78464,113.08,0.22721,-0.76211,-0.60627,125.26,-0.97373,-0.18726,-0.12952,159.62
> view matrix models
> #2,0.45575,0.25436,-0.85299,113.3,0.23978,-0.95796,-0.15755,126.91,-0.8572,-0.13272,-0.49758,158.4
> view matrix models
> #2,0.30908,0.90168,-0.30239,112.96,0.9035,-0.37766,-0.20265,124.14,-0.29693,-0.21057,-0.93139,156.76
> view matrix models
> #2,0.45885,0.85934,0.22581,114.15,0.54729,-0.07315,-0.83374,122.23,-0.69994,0.50615,-0.50387,156.28
> view matrix models
> #2,0.45885,0.85934,0.22581,141.63,0.54729,-0.07315,-0.83374,114.41,-0.69994,0.50615,-0.50387,169.76
> view matrix models
> #2,0.27375,0.4233,-0.86364,140.52,0.52429,-0.81848,-0.23498,118.08,-0.80634,-0.38847,-0.44598,172.67
> view matrix models
> #2,0.2404,0.52149,-0.81869,140.39,0.53655,-0.77425,-0.33563,117.69,-0.8089,-0.35858,-0.46594,172.54
> view matrix models
> #2,0.2404,0.52149,-0.81869,139.48,0.53655,-0.77425,-0.33563,116.36,-0.8089,-0.35858,-0.46594,170.74
Fit molecule AF_prediction_UC5Nb1.cif (#2) to map cs_P12_J500_flipped.mrc (#5)
using 956 atoms
average map value = 0.1488, steps = 92
shifted from previous position = 5.23
rotated from previous position = 6.98 degrees
atoms outside contour = 749, contour level = 0.23175
Position of AF_prediction_UC5Nb1.cif (#2) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.27517216 0.53586583 -0.79820304 142.49531530
0.62370255 -0.73132982 -0.27595620 118.10048933
-0.73162518 -0.42190581 -0.53546249 167.14788873
Axis -0.79801331 -0.36402987 0.48026764
Axis point 0.00000000 32.40145074 123.86115947
Rotation angle (degrees) 174.75322315
Shift along axis -76.42954143
> view matrix models
> #2,0.27517,0.53587,-0.7982,140.6,0.6237,-0.73133,-0.27596,115.68,-0.73163,-0.42191,-0.53546,169.35
> view matrix models
> #2,0.9206,-0.023967,0.38976,144.19,0.3219,-0.51847,-0.79219,114.24,0.22107,0.85476,-0.46959,164.4
> view matrix models
> #2,0.5761,0.79991,-0.16809,140.92,-0.088968,-0.14306,-0.98571,113.27,-0.81252,0.58282,-0.011251,167.81
Fit molecule AF_prediction_UC5Nb1.cif (#2) to map cs_P12_J500_flipped.mrc (#5)
using 956 atoms
average map value = 0.1509, steps = 124
shifted from previous position = 4.09
rotated from previous position = 13.5 degrees
atoms outside contour = 766, contour level = 0.23175
Position of AF_prediction_UC5Nb1.cif (#2) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.64183443 0.68488943 -0.34492757 141.22255282
-0.14077505 -0.33692369 -0.93094834 117.00788526
-0.75381095 0.64607189 -0.11983388 164.75488224
Axis 0.86343716 0.22386847 -0.45206103
Axis point 0.00000000 -34.21778333 157.11517341
Rotation angle (degrees) 114.04547417
Shift along axis 73.65191330
> view matrix models
> #2,0.64183,0.68489,-0.34493,141.41,-0.14078,-0.33692,-0.93095,116.93,-0.75381,0.64607,-0.11983,165.51
Fit molecule AF_prediction_UC5Nb1.cif (#2) to map cs_P12_J500_flipped.mrc (#5)
using 956 atoms
average map value = 0.1509, steps = 68
shifted from previous position = 0.776
rotated from previous position = 0.169 degrees
atoms outside contour = 766, contour level = 0.23175
Position of AF_prediction_UC5Nb1.cif (#2) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.63979315 0.68585285 -0.34680051 141.22586179
-0.14161415 -0.33831019 -0.93031804 117.03195408
-0.75538742 0.64432296 -0.11932207 164.77120287
Axis 0.86275039 0.22386596 -0.45337158
Axis point 0.00000000 -34.13880715 157.26023908
Rotation angle (degrees) 114.13698114
Shift along axis 73.33955794
> view matrix models
> #2,0.21088,-0.45491,-0.86521,143.92,0.92788,-0.18529,0.32358,118.09,-0.30751,-0.87105,0.38303,169.78
Fit molecule AF_prediction_UC5Nb1.cif (#2) to map cs_P12_J500_flipped.mrc (#5)
using 956 atoms
average map value = 0.1588, steps = 84
shifted from previous position = 6.37
rotated from previous position = 21.4 degrees
atoms outside contour = 737, contour level = 0.23175
Position of AF_prediction_UC5Nb1.cif (#2) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.16731723 -0.11305261 -0.97939984 144.87395441
0.97220431 -0.14610595 0.18295305 113.11851342
-0.16377946 -0.98278795 0.08546420 165.92430395
Axis -0.65146840 -0.45580528 0.60649029
Axis point -0.00000000 97.68043632 106.50739142
Rotation angle (degrees) 116.52973898
Shift along axis -45.30934020
> volume #5 level 0.1577
> view matrix models
> #2,0.16732,-0.11305,-0.9794,144.17,0.9722,-0.14611,0.18295,111.08,-0.16378,-0.98279,0.085464,169.78
> view matrix models
> #2,0.16732,-0.11305,-0.9794,144.19,0.9722,-0.14611,0.18295,111.14,-0.16378,-0.98279,0.085464,169.58
> view matrix models
> #2,0.19395,0.13696,-0.9714,143.44,0.95227,0.21166,0.21997,110.21,0.23574,-0.9677,-0.089374,168.53
Fit molecule AF_prediction_UC5Nb1.cif (#2) to map cs_P12_J500_flipped.mrc (#5)
using 956 atoms
average map value = 0.1997, steps = 64
shifted from previous position = 1.75
rotated from previous position = 9.65 degrees
atoms outside contour = 336, contour level = 0.15765
Position of AF_prediction_UC5Nb1.cif (#2) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.31767232 0.12436140 -0.94000986 142.70566537
0.94002964 0.08856048 0.32939538 110.54031475
0.12421179 -0.98827693 -0.08877019 167.23260710
Axis -0.70091504 -0.56609595 0.43388188
Axis point 0.00000000 100.77548139 98.00600615
Rotation angle (degrees) 109.95418868
Shift along axis -90.04177389
> view matrix models
> #2,0.31767,0.12436,-0.94001,142.77,0.94003,0.08856,0.3294,110.22,0.12421,-0.98828,-0.08877,167.16
Fit molecule AF_prediction_UC5Nb1.cif (#2) to map cs_P12_J500_flipped.mrc (#5)
using 956 atoms
average map value = 0.1997, steps = 48
shifted from previous position = 0.341
rotated from previous position = 0.0612 degrees
atoms outside contour = 337, contour level = 0.15765
Position of AF_prediction_UC5Nb1.cif (#2) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.31745820 0.12523446 -0.93996629 142.72095547
0.93999281 0.08914157 0.32934374 110.55253397
0.12503526 -0.98811442 -0.08942077 167.21007378
Axis -0.70083953 -0.56654184 0.43342162
Axis point 0.00000000 100.71734064 98.01336804
Rotation angle (degrees) 109.96283295
Shift along axis -90.18466234
> select #2
956 atoms, 975 bonds, 128 residues, 1 model selected
> ~select #2
Nothing selected
> open C:/Users/Delao002/Desktop/5I5K_noEcunoCtc.pdb
Chain information for 5I5K_noEcunoCtc.pdb #6
---
Chain | Description
A | No description available
> color #6 #3658d3 transparency 0
> color #6 springgreen transparency 0
> select #6/A:67
6 atoms, 5 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.42357,-0.58416,0.69235,13.402,-0.76275,-0.6423,-0.075287,129.43,0.48867,-0.4962,-0.71762,116.02
> view matrix models
> #6,0.5239,-0.83458,0.1703,56.307,-0.2779,-0.35646,-0.89202,144.56,0.80517,0.42,-0.41868,32.155
> view matrix models
> #6,0.48015,-0.83283,0.27541,51.403,-0.38188,-0.48111,-0.78912,149.45,0.7897,0.27372,-0.54904,49.295
> view matrix models
> #6,0.48015,-0.83283,0.27541,50.531,-0.38188,-0.48111,-0.78912,170.14,0.7897,0.27372,-0.54904,74.937
> view matrix models
> #6,0.43969,-0.80007,0.40813,41.994,-0.50918,-0.59638,-0.62054,171.33,0.73987,0.065037,-0.6696,96.42
> view matrix models
> #6,0.43969,-0.80007,0.40813,30.728,-0.50918,-0.59638,-0.62054,140.52,0.73987,0.065037,-0.6696,87.831
> view matrix models
> #6,0.50928,-0.83639,0.20269,42.838,-0.31025,-0.39812,-0.86327,136.32,0.80273,0.37676,-0.46225,54.504
> view matrix models
> #6,0.43706,-0.51965,0.73413,-5.5822,-0.79574,-0.60387,0.046297,110.83,0.41926,-0.60441,-0.67743,139.55
> view matrix models
> #6,0.44486,-0.80739,0.38758,32.222,-0.48977,-0.58164,-0.64948,140.7,0.74982,0.099107,-0.65418,84.518
> view matrix models
> #6,0.44486,-0.80739,0.38758,87.144,-0.48977,-0.58164,-0.64948,303.35,0.74982,0.099107,-0.65418,140.57
> view matrix models
> #6,0.074871,0.43841,0.89565,-27.381,0.87749,-0.45564,0.14967,248.46,0.47371,0.77472,-0.41881,80.784
> view matrix models
> #6,-0.54143,0.80239,0.25105,-20.259,0.58214,0.14235,0.80053,174.72,0.6066,0.57957,-0.54417,100.5
> view matrix models
> #6,-0.54143,0.80239,0.25105,95.727,0.58214,0.14235,0.80053,179.53,0.6066,0.57957,-0.54417,132.45
> view matrix models
> #6,-0.20783,0.93864,0.27523,82.664,0.57457,-0.11057,0.81095,197.81,0.79163,0.32668,-0.51634,148.85
> view matrix models
> #6,-0.20783,0.93864,0.27523,69.189,0.57457,-0.11057,0.81095,149.08,0.79163,0.32668,-0.51634,155.08
Fit molecule 5I5K_noEcunoCtc.pdb (#6) to map cs_P12_J500_flipped.mrc (#5)
using 11805 atoms
average map value = 0.2788, steps = 144
shifted from previous position = 18.8
rotated from previous position = 8.51 degrees
atoms outside contour = 3466, contour level = 0.15765
Position of 5I5K_noEcunoCtc.pdb (#6) relative to cs_P12_J500_flipped.mrc (#5)
coordinates:
Matrix rotation and translation
-0.31118239 0.92921996 0.19928828 89.19728120
0.59964864 0.02929758 0.79972694 134.88227661
0.73728356 0.36836388 -0.56632237 162.20287877
Axis -0.56440142 -0.70392050 -0.43121568
Axis point -19.26459015 -0.00000000 35.23360348
Rotation angle (degrees) 157.53356916
Shift along axis -215.23389725
> select #6
11805 atoms, 12064 bonds, 3 pseudobonds, 1492 residues, 2 models selected
> ~select #6
Nothing selected
> hide #!3.1 models
> volume #5 level 0.2071
> show #!3.1 models
> hide #!3.1 models
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C #1/A
Alignment identifier is 1
> select #4/C:120 #1/A:120
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #4/C:41-120 #1/A:41-120
1238 atoms, 1260 bonds, 160 residues, 2 models selected
Seqview [ID: 1] region chains A,C [41-120] RMSD: 1.331
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> view matrix models
> #4,0.99847,0.053905,-0.012496,-4.3904,-0.052785,0.99562,0.077176,0.45916,0.016601,-0.076398,0.99694,12.126,#1,0.47707,0.2968,0.82723,165.7,-0.86541,-0.0054521,0.50104,221.98,0.15322,-0.95492,0.25425,160.2
> view matrix models
> #4,0.99847,0.053905,-0.012496,-5.0519,-0.052785,0.99562,0.077176,-4.4056,0.016601,-0.076398,0.99694,10.104,#1,0.47707,0.2968,0.82723,165.04,-0.86541,-0.0054521,0.50104,217.12,0.15322,-0.95492,0.25425,158.18
> ui tool show "Fit in Map"
Fit molecule C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb (#4) to map
cs_P12_J500_flipped.mrc (#5) using 13612 atoms
average map value = 0.2747, steps = 68
shifted from previous position = 2.34
rotated from previous position = 0.0116 degrees
atoms outside contour = 5463, contour level = 0.20705
Position of C5B3G8_3_real_space_ref_in_localresmap-coot-0.pdb (#4) relative to
cs_P12_J500_flipped.mrc (#5) coordinates:
Matrix rotation and translation
0.99846740 0.05392780 -0.01243556 -7.16979562
-0.05280953 0.99560311 0.07736671 -3.41640989
0.01655310 -0.07659142 0.99692515 10.08253497
Axis -0.81214939 -0.15291897 -0.56305343
Axis point 0.00000000 134.52729179 50.48301792
Rotation angle (degrees) 5.43890915
Shift along axis 0.66837312
Fit molecule AF_prediction_UC5Nb2.cif (#1) to map cs_P12_J500_flipped.mrc (#5)
using 909 atoms
average map value = 0.2243, steps = 60
shifted from previous position = 2.34
rotated from previous position = 0.0226 degrees
atoms outside contour = 435, contour level = 0.20705
Position of AF_prediction_UC5Nb2.cif (#1) relative to cs_P12_J500_flipped.mrc
(#5) coordinates:
Matrix rotation and translation
0.47705440 0.29677523 0.82725061 162.93357100
-0.86547715 -0.00508413 0.50092261 218.13833407
0.15286727 -0.95493383 0.25442677 158.13001640
Axis -0.73483680 0.34039187 -0.58664151
Axis point 0.00000000 192.47916539 -143.21028577
Rotation angle (degrees) 97.86280368
Shift along axis -138.24270007
> select #1
909 atoms, 925 bonds, 120 residues, 1 model selected
> ~select #1
Nothing selected
> select #6/A:888
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:888-895
56 atoms, 56 bonds, 8 residues, 1 model selected
> select #6/A:887
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:882-887
51 atoms, 50 bonds, 6 residues, 1 model selected
> show sel atoms
> select #6
11805 atoms, 12064 bonds, 3 pseudobonds, 1492 residues, 2 models selected
> ~select #6
Nothing selected
> save C:/Users/Delao002/Desktop/AF_Nb2.pdb models #1 relModel #5
> save C:/Users/Delao002/Desktop/AF_Nb1.pdb models #2 relModel #5
> save C:/Users/Delao002/Desktop/5I5K_noEcunoCtc_1.pdb models #6 relModel #5
> open C:/Users/Delao002/Downloads/cryosparc_P25_J586_005_volume_map_sharp.mrc
Opened cryosparc_P25_J586_005_volume_map_sharp.mrc as #7, grid size
420,420,420, pixel 1.04, shown at level 0.0438, step 2, values float32
> volume #7 step 1
> hide #1 models
> hide #2 models
> hide #!3 models
> hide #!6 models
> volume #7 level 0.122
> surface dust #7 size 5
> volume flip #7
Opened cryosparc_P25_J586_005_volume_map_sharp.mrc z flip as #8, grid size
420,420,420, pixel 1.04, shown at step 1, values float32
> surface dust #8 size 5
> volume #8 level 0.1147
> lighting full
> volume #8 level 0.122
> open
> C:/Users/Delao002/Downloads/cryosparc_P12_J290_005_volume_segmap_achain(1).mrc
Opened cryosparc_P12_J290_005_volume_segmap_achain(1).mrc as #9, grid size
320,320,320, pixel 1.04, shown at level 6.49e-05, step 2, values float32
> volume #9 step 1
===== 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 - Build 25.20.100.6472
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 850 G5
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 8,425,529,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US
Locale: ('nl_NL', '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-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-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
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
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
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
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
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
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using File→Open on Windows and/or in return statement |
comment:2 by , 3 years ago
| Cc: | added |
|---|---|
| Resolution: | → can't reproduce |
| Status: | accepted → closed |
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