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Opened 6 years ago
Closed 6 years ago
#2609 closed defect (duplicate)
Insufficient info when session save fails
| Reported by: | Owned by: | greg | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.4.0-169-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-06-29)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-06-29)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data/disk3/modeling/gp8/Figure3-20191123.cxs
opened ChimeraX session
> show #!2 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!17 models
> hide #!1.2 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!58 models
> hide #!58 models
> show #!17 models
> hide #!2 models
> show #!2 models
> hide #!17 models
> show #!17 models
> fitmap #2 inMap #17
Fit map gp8-subunit.mrc in map gp8-C12-clean.mrc using 25326 points
correlation = 0.9783, correlation about mean = 0.935, overlap = 7.831
steps = 44, shift = 0.00983, angle = 0.00962 degrees
Position of gp8-subunit.mrc (#2) relative to gp8-C12-clean.mrc (#17)
coordinates:
Matrix rotation and translation
0.99999997 -0.00018735 -0.00003999 210.01203510
0.00018733 0.99999986 -0.00047925 210.00943130
0.00004008 0.00047924 0.99999987 209.95762002
Axis 0.92856010 -0.07756707 0.36298689
Axis point 0.00000000 -244897.72185185 479531.91522894
Rotation angle (degrees) 0.02957142
Shift along axis 254.93084543
> view Figure2a
> view Figure2b
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!17 models
> hide #!8 models
> show #!8 models
> select clear
> select #1.1/E:367
9 atoms, 8 bonds, 1 model selected
> show selAtoms
> select clear
> show #!3 models
> hide #!8 models
> hide #!3 models
> select #1.1/E:367
9 atoms, 8 bonds, 1 model selected
> hide selAtoms
> select #1.1/E:368
11 atoms, 10 bonds, 1 model selected
> select #1.1/E:369
7 atoms, 6 bonds, 1 model selected
> select clear
> select #1.1/E:369
7 atoms, 6 bonds, 1 model selected
> show selAtoms
> select #1.1/E:370
7 atoms, 6 bonds, 1 model selected
> show selAtoms
> select clear
> select #1.1/E:371
5 atoms, 4 bonds, 1 model selected
> show selAtoms
> select #1.1/E:368
11 atoms, 10 bonds, 1 model selected
> show selAtoms
> select clear
> select #1.1/E:369
7 atoms, 6 bonds, 1 model selected
> hide selAtoms ribbons
> hide selAtoms
> show selAtoms ribbons
> select clear
> show #!3 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select clear
> surface dust #8 size 100
> surface dust #8 size 10
> open /data/disk3/modeling/gp8/dsDNA-1.pdb
/data/disk3/modeling/gp8/dsDNA-2.pdb
Chain information for dsDNA-1.pdb #10.1
---
Chain | Description
J L | No description available
Chain information for dsDNA-2.pdb #10.2
---
Chain | Description
I K | No description available
> view cofr false
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> hide #!1.1 models
> hide #!2 models
> show #!17 models
> show #!1.2 models
> show selAtoms surfaces
> select #10.1
650 atoms, 722 bonds, 1 model selected
> select #10.2
662 atoms, 746 bonds, 1 model selected
> select clear
Expected an objects specifier or a view name or a keyword
> view name Figure2
> show #!23 models
> show #!26 models
> show #!58 models
> view cofr false
> view cofr false
> hide #!23 models
> show #!23 models
> hide #!26 models
> show #!26 models
> select #58
2 models selected
> show selAtoms surfaces
> ~select #58
Nothing selected
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!58 models
> select #58
2 models selected
> show selAtoms surfaces
> show selAtoms ribbons
> show selAtoms
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> fitmap #10 inMap #8
Fit molecules dsDNA-1.pdb (#10.1), dsDNA-2.pdb (#10.2) to map gp8-genome-
inside.mrc (#8) using 1312 atoms
average map value = 0.004113, steps = 268
shifted from previous position = 1.29
rotated from previous position = 17.1 degrees
atoms outside contour = 861, contour level = 0.0063631
Position of dsDNA-1.pdb (#10.1) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.57540529 0.65665986 -0.48755161 -118.84341650
-0.81657736 0.42777689 -0.38756722 399.94928195
-0.04593653 0.62113184 0.78235866 -320.36733752
Axis 0.54842266 -0.24010305 -0.80098883
Axis point 230.66376232 409.80790105 0.00000000
Rotation angle (degrees) 66.87300689
Shift along axis 95.40519250
Position of dsDNA-2.pdb (#10.2) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.57540529 0.65665986 -0.48755161 -118.84341650
-0.81657736 0.42777689 -0.38756722 399.94928195
-0.04593653 0.62113184 0.78235866 -320.36733752
Axis 0.54842266 -0.24010305 -0.80098883
Axis point 230.66376232 409.80790105 0.00000000
Rotation angle (degrees) 66.87300689
Shift along axis 95.40519250
> ~select #58
Nothing selected
> show #58 target m
> hide #!10 models
> hide #!17 models
> hide #!10.2 models
> show #!10.2 models
> show #!17 models
> hide #!23 models
> show #!23 models
> select #58
2 models selected
> ui mousemode rightMode "translate selected models"
> view Figure2
> surface dust #58 size 40
> hide #!58 models
> show #!58 models
> select clear
> select #1.2
8052 atoms, 8166 bonds, 2 pseudobonds, 2 models selected
> show selAtoms ribbons
> show selAtoms surfaces
> show selAtoms
> hide #!1.2 models
> show #!1.2 models
> hide selAtoms surfaces
> hide selAtoms
> select clear
> save session /data/disk3/modeling/gp8/Figure3-20191123.cxs
> save image /data/disk3/Paper-use/n1Figure2a.tif pixelSize 0.3 supersample 9
transparentBackground true
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #2 inMap #17
Fit map gp8-subunit.mrc in map gp8-C12-clean.mrc using 25326 points
correlation = 0.9535, correlation about mean = 0.8505, overlap = 7.034
steps = 76, shift = 2.8, angle = 4.07 degrees
Position of gp8-subunit.mrc (#2) relative to gp8-C12-clean.mrc (#17)
coordinates:
Matrix rotation and translation
0.86599186 -0.50005784 0.00047954 209.96759851
0.50005807 0.86599152 -0.00076990 210.02963839
-0.00003028 0.00090653 0.99999957 209.95590143
Axis 0.00167624 0.00050976 0.99999847
Axis point -286.86013263 496.05557460 0.00000000
Rotation angle (degrees) 30.00388577
Shift along axis 210.41459956
> open /data/disk3/modeling/gp8/gp8-subunit.mrc
Opened gp8-subunit.mrc, grid size 400,400,400, pixel 1.05, shown at level
-3.12e-06, step 2, values float32
> ~select #2
Nothing selected
> select #2
2 models selected
> hide #!11 models
> show #!11 models
> select #11
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode pivot
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> hide #!11 models
> show #!11 models
> fitmap #11 inMap #17
Fit map gp8-subunit.mrc in map gp8-C12-clean.mrc using 3776 points
correlation = 0.9454, correlation about mean = 0.8606, overlap = 0.8927
steps = 212, shift = 8.37, angle = 21.2 degrees
Position of gp8-subunit.mrc (#11) relative to gp8-C12-clean.mrc (#17)
coordinates:
Matrix rotation and translation
-0.86619752 0.49970171 -0.00029491 210.03682879
-0.49970180 -0.86619736 0.00051466 209.98245819
0.00000173 0.00059316 0.99999984 209.97462012
Axis 0.00007854 -0.00029682 -0.99999995
Axis point 133.13125839 76.83763536 0.00000000
Rotation angle (degrees) 150.01972832
Shift along axis -210.02043990
> select clear
> lighting soft
> select clear
> lighting simple
> lighting flat
> lighting full
> lighting shadows false
> lighting full
> lighting flat
> view name test
> view Figure2
> view test
> view name Figure2
> hide #!1.2 models
> select clear
> view name Figure2a
> surface dust #17 size 40
> surface dust #17 size 60
> surface dust #11 size 60
> surface dust #2 size 60
> save image /data/disk3/Paper-use/n1Figure2a.tif pixelSize 0.3 supersample 9
transparentBackground true
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> show #!58 models
> hide #!58 models
> hide #!23 models
> show #!23 models
> show #!58 models
> save image /data/disk3/Paper-use/n1Figure2a.tif pixelSize 0.3 supersample 9
transparentBackground true
> hide #!17 models
> hide #!23 models
> hide #!26 models
> hide #!58 models
> hide #!2 models
> hide #!11 models
> show #!1.2 models
> hide #!1.2 models
> show #!2 models
> show #!11 models
> show #!17 models
> show #!23 models
> show #!26 models
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting full
> lighting full
> lighting shadows false
> set silhouettes false
> set silhouettes true
> lighting soft
> lighting simple
> view Figure2
> view Figure2a
> show #!58 models
> view Figure2a
> view Figure2b
> hide #!11 models
> hide #!2 models
> show #!1.2 models
> show #!3 models
> open /data/disk3/modeling/gp8/dsDNA-s.pdb
Chain information for dsDNA-s.pdb #12
---
Chain | Description
K | No description available
L | No description available
> matchmaker #12 to #10.1
No chains in reference structure dsDNA-1.pdb #10.1 compatible with BLOSUM-62
similarity matrix
> matchmaker #12 to #10
Specify a single 'to' model only
> matchmaker #12 to #10.2
No chains in reference structure dsDNA-2.pdb #10.2 compatible with BLOSUM-62
similarity matrix
Expected a keyword
> hide #!12 models
> show #!12 models
> matchmaker #12 to #10.2
No chains in reference structure dsDNA-2.pdb #10.2 compatible with BLOSUM-62
similarity matrix
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> hide #!12 models
> show #!12 models
> fitmap #12 inMap #9
Fit molecule dsDNA-s.pdb (#12) to map gp8-with-genome.mrc (#9) using 656 atoms
average map value = 0.005706, steps = 112
shifted from previous position = 5.11
rotated from previous position = 11.2 degrees
atoms outside contour = 577, contour level = 0.0089726
Position of dsDNA-s.pdb (#12) relative to gp8-with-genome.mrc (#9)
coordinates:
Matrix rotation and translation
-0.97856810 -0.14318951 -0.14799054 453.24950265
-0.03169173 0.81482780 -0.57883613 124.58261908
0.20347008 -0.56174050 -0.80190243 400.99486569
Axis 0.04631470 -0.95216163 0.30206487
Axis point 210.40185031 0.00000000 242.35945485
Rotation angle (degrees) 169.36455870
Shift along axis 23.49578909
> fitmap #12 inMap #9
Fit molecule dsDNA-s.pdb (#12) to map gp8-with-genome.mrc (#9) using 656 atoms
average map value = 0.004752, steps = 80
shifted from previous position = 4.22
rotated from previous position = 15.8 degrees
atoms outside contour = 618, contour level = 0.0089726
Position of dsDNA-s.pdb (#12) relative to gp8-with-genome.mrc (#9)
coordinates:
Matrix rotation and translation
-0.97555865 0.11217868 -0.18894767 429.55425183
0.20638059 0.76299211 -0.61257657 60.30082257
0.07544756 -0.63659952 -0.76749507 474.52747264
Axis -0.08527792 -0.93856401 0.33440286
Axis point 194.97063072 0.00000000 264.41316450
Rotation angle (degrees) 171.90291082
Shift along axis 65.45566723
> fitmap #12 inMap #9
Fit molecule dsDNA-s.pdb (#12) to map gp8-with-genome.mrc (#9) using 656 atoms
average map value = 0.005206, steps = 112
shifted from previous position = 5.84
rotated from previous position = 12.9 degrees
atoms outside contour = 579, contour level = 0.0089726
Position of dsDNA-s.pdb (#12) relative to gp8-with-genome.mrc (#9)
coordinates:
Matrix rotation and translation
-0.99437530 0.10161551 0.02986654 339.70082323
0.06490070 0.80744020 -0.58636865 95.11235446
-0.08369959 -0.58113216 -0.80949352 531.10232633
Axis 0.04383166 0.95059670 -0.30731858
Axis point 175.72864330 0.00000000 275.54434731
Rotation angle (degrees) 176.57544799
Shift along axis -57.91447066
> fitmap #12 inMap #9
Fit molecule dsDNA-s.pdb (#12) to map gp8-with-genome.mrc (#9) using 656 atoms
average map value = 0.005206, steps = 76
shifted from previous position = 4.75
rotated from previous position = 0.0481 degrees
atoms outside contour = 579, contour level = 0.0089726
Position of dsDNA-s.pdb (#12) relative to gp8-with-genome.mrc (#9)
coordinates:
Matrix rotation and translation
-0.99431567 0.10206719 0.03030826 339.43172913
0.06505598 0.80774833 -0.58592689 94.82003576
-0.08428536 -0.58062457 -0.80979692 531.37309964
Axis 0.04398842 0.95067699 -0.30704769
Axis point 175.66870646 0.00000000 275.57382869
Rotation angle (degrees) 176.54471900
Shift along axis -58.08259300
> hide #!10 models
> hide #!10.1 models
> hide #!10.2 models
> hide #!12 models
> show #!12 models
> select #12
656 atoms, 734 bonds, 1 model selected
> color selAtoms bychain
> rainbow selAtoms
> color selAtoms bychain
> open /data/disk3/modeling/gp8/dsDNA-1.pdb
/data/disk3/modeling/gp8/dsDNA-2.pdb
Chain information for dsDNA-1.pdb #13.1
---
Chain | Description
J L | No description available
Chain information for dsDNA-2.pdb #13.2
---
Chain | Description
I K | No description available
> matchmaker #13.1 to #12
No chains in reference structure dsDNA-s.pdb #12 compatible with BLOSUM-62
similarity matrix
> matchmaker #13 to #12
No chains in reference structure dsDNA-s.pdb #12 compatible with BLOSUM-62
similarity matrix
> select #13
1312 atoms, 1468 bonds, 3 models selected
> close #13.1-2
> open /data/disk3/modeling/gp8/dsDNA-s-1.pdb
/data/disk3/modeling/gp8/dsDNA-s-2.pdb
Chain information for dsDNA-s-1.pdb #14.1
---
Chain | Description
K | No description available
Chain information for dsDNA-s-2.pdb #14.2
---
Chain | Description
L | No description available
> matchmaker #14.1 to #12
No chains in reference structure dsDNA-s.pdb #12 compatible with BLOSUM-62
similarity matrix
> select #14
656 atoms, 734 bonds, 3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> show #!8 models
> hide #!8 models
> fitmap #14 inMap #8
Fit molecules dsDNA-s-1.pdb (#14.1), dsDNA-s-2.pdb (#14.2) to map gp8-genome-
inside.mrc (#8) using 656 atoms
average map value = 0.003438, steps = 88
shifted from previous position = 5
rotated from previous position = 11 degrees
atoms outside contour = 495, contour level = 0.0063631
Position of dsDNA-s-1.pdb (#14.1) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.99522177 0.02385557 0.09468124 -229.67578666
-0.01301617 0.99345381 -0.11349057 -185.06754632
-0.09676882 0.11171590 0.98901737 -77.12487848
Axis 0.75603888 0.64271554 -0.12378184
Axis point 0.00000000 995.60396629 -85.19522930
Rotation angle (degrees) 8.56541115
Shift along axis -283.04295298
Position of dsDNA-s-2.pdb (#14.2) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.99522177 0.02385557 0.09468124 -229.67578666
-0.01301617 0.99345381 -0.11349057 -185.06754632
-0.09676882 0.11171590 0.98901737 -77.12487848
Axis 0.75603888 0.64271554 -0.12378184
Axis point 0.00000000 995.60396629 -85.19522930
Rotation angle (degrees) 8.56541115
Shift along axis -283.04295298
> fitmap #14 inMap #9
Fit molecules dsDNA-s-1.pdb (#14.1), dsDNA-s-2.pdb (#14.2) to map gp8-with-
genome.mrc (#9) using 656 atoms
average map value = 0.003808, steps = 216
shifted from previous position = 7.51
rotated from previous position = 14.4 degrees
atoms outside contour = 572, contour level = 0.0089726
Position of dsDNA-s-1.pdb (#14.1) relative to gp8-with-genome.mrc (#9)
coordinates:
Matrix rotation and translation
-0.69477806 0.70527359 -0.14097013 30.97768158
0.71611871 0.69655443 -0.04456348 -284.61794284
0.06676393 -0.13191308 -0.98901036 215.74077303
Axis -0.38716648 -0.92075590 0.04806965
Axis point 69.08366450 0.00000000 104.49104668
Rotation angle (degrees) 173.52289030
Shift along axis 260.44071294
Position of dsDNA-s-2.pdb (#14.2) relative to gp8-with-genome.mrc (#9)
coordinates:
Matrix rotation and translation
-0.69477806 0.70527359 -0.14097013 30.97768158
0.71611871 0.69655443 -0.04456348 -284.61794284
0.06676393 -0.13191308 -0.98901036 215.74077303
Axis -0.38716648 -0.92075590 0.04806965
Axis point 69.08366450 0.00000000 104.49104668
Rotation angle (degrees) 173.52289030
Shift along axis 260.44071294
> show #!10 models
> show #!10.1 models
> show #!10.2 models
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> fitmap #14 inMap #8
Fit molecules dsDNA-s-1.pdb (#14.1), dsDNA-s-2.pdb (#14.2) to map gp8-genome-
inside.mrc (#8) using 656 atoms
average map value = 0.003411, steps = 92
shifted from previous position = 4.18
rotated from previous position = 11.6 degrees
atoms outside contour = 494, contour level = 0.0063631
Position of dsDNA-s-1.pdb (#14.1) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.90899697 0.41123487 0.06789983 -285.08986847
-0.37991118 0.88448020 -0.27085470 -48.75892827
-0.17144095 0.22041019 0.96022255 -79.78000478
Axis 0.51092072 0.24891697 -0.82280032
Axis point -228.56961513 528.18200076 0.00000000
Rotation angle (degrees) 28.73533210
Shift along axis -92.15223207
Position of dsDNA-s-2.pdb (#14.2) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.90899697 0.41123487 0.06789983 -285.08986847
-0.37991118 0.88448020 -0.27085470 -48.75892827
-0.17144095 0.22041019 0.96022255 -79.78000478
Axis 0.51092072 0.24891697 -0.82280032
Axis point -228.56961513 528.18200076 0.00000000
Rotation angle (degrees) 28.73533210
Shift along axis -92.15223207
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14 inMap #8
Fit molecules dsDNA-s-1.pdb (#14.1), dsDNA-s-2.pdb (#14.2) to map gp8-genome-
inside.mrc (#8) using 656 atoms
average map value = 0.003411, steps = 144
shifted from previous position = 3.54
rotated from previous position = 6.3 degrees
atoms outside contour = 491, contour level = 0.0063631
Position of dsDNA-s-1.pdb (#14.1) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.87499589 0.48156704 0.04975309 -288.52324812
-0.43697503 0.82982794 -0.34704237 -10.82943318
-0.20841067 0.28191980 0.93652881 -80.15811105
Axis 0.55037581 0.22590721 -0.80377385
Axis point -149.81962857 449.59736934 0.00000000
Rotation angle (degrees) 34.84744620
Shift along axis -96.81367143
Position of dsDNA-s-2.pdb (#14.2) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.87499589 0.48156704 0.04975309 -288.52324812
-0.43697503 0.82982794 -0.34704237 -10.82943318
-0.20841067 0.28191980 0.93652881 -80.15811105
Axis 0.55037581 0.22590721 -0.80377385
Axis point -149.81962857 449.59736934 0.00000000
Rotation angle (degrees) 34.84744620
Shift along axis -96.81367143
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14 inMap #8
Fit molecules dsDNA-s-1.pdb (#14.1), dsDNA-s-2.pdb (#14.2) to map gp8-genome-
inside.mrc (#8) using 656 atoms
average map value = 0.002687, steps = 84
shifted from previous position = 2.87
rotated from previous position = 5.13 degrees
atoms outside contour = 548, contour level = 0.0063631
Position of dsDNA-s-1.pdb (#14.1) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.83770464 0.53652982 0.10191508 -300.05157939
-0.48238250 0.81442550 -0.32251858 -4.61185608
-0.25604308 0.22101326 0.94106062 -57.30052616
Axis 0.44956184 0.29607158 -0.84275487
Axis point -127.51801473 446.96387026 0.00000000
Rotation angle (degrees) 37.19379592
Shift along axis -87.96688304
Position of dsDNA-s-2.pdb (#14.2) relative to gp8-genome-inside.mrc (#8)
coordinates:
Matrix rotation and translation
0.83770464 0.53652982 0.10191508 -300.05157939
-0.48238250 0.81442550 -0.32251858 -4.61185608
-0.25604308 0.22101326 0.94106062 -57.30052616
Axis 0.44956184 0.29607158 -0.84275487
Axis point -127.51801473 446.96387026 0.00000000
Rotation angle (degrees) 37.19379592
Shift along axis -87.96688304
> hide #!14 models
> show #!14 models
> hide #!10 models
> hide #!12 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> close #12
> show selAtoms ribbons
> show selAtoms surfaces
> select clear
> select clear
> view Figure2b
> select #14
656 atoms, 734 bonds, 3 models selected
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> view Figure2b
> hide #!23 models
> hide #!26 models
> hide #!58 models
> hide #!14.1 models
> show #!14.1 models
> hide selAtoms surfaces
> select clear
> select #14
656 atoms, 734 bonds, 3 models selected
> ui mousemode rightMode "rotate selected models"
> select clear
> view name Figure2b
> save image /data/disk3/Paper-use/n1Figure2b.tif pixelSize 0.3 supersample 9
transparentBackground true
> hide #!17 models
> hide #!3 models
> show #!3 models
> hide #!1.2 models
> save image /data/disk3/Paper-use/n1Figure2c.tif pixelSize 0.3 supersample 9
transparentBackground true
> view Figure2b
> view Figure2s
> view Figure2a
> show #!17 models
> lighting flat
> show #!1.2 models
> select #14.1
331 atoms, 373 bonds, 1 model selected
> select #14
656 atoms, 734 bonds, 3 models selected
> show selAtoms surfaces
> select clear
> select #14
656 atoms, 734 bonds, 3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> select clear
> select clear
> save image /data/disk3/Paper-use/n1Figure2d.tif pixelSize 0.3 supersample 9
transparentBackground true
> save session /data/disk3/modeling/gp8/Figure3-20191123.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1355, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 763, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery
self.processed[key] = self.process(obj)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.molobject.Residue'>": Residue already deleted
RuntimeError: Error while saving session data for "": Residue already deleted
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1355, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 855, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 595, in file_save_cb
self.save_dialog.display(self, session)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 138, in display
fmt.save(session, filename)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 1056, in save
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 950, in save_session
save(session, filename, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export
result = self.export_func(session, path, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 763, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery
self.processed[key] = self.process(obj)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.molobject.Residue'>": Residue already deleted
RuntimeError: Error while saving session data for "": Residue already deleted
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Insufficient info when session save fails |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hopefully fixed by changes made in September. The reporting ChimeraX is from June.