glDrawBuffer: invalid operation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.4.0-178-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.92 (2020-03-05)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.92 (2020-03-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /data/disk3/modeling/gp17-2020/Figure4-20200510-fiber-rotation.cxs

opened ChimeraX session  

> hide #!13 models

> show #!13 models

> hide #!46 models

> lighting flat

> hide #!98 models

> show #!68 models

> show #67 models

> show #!68.2 models

> hide #!68.2 models

> show #!66 models

> show #!62 models

> hide #!62 models

> close #62

> show #!9 models

> hide #!9 models

> close #9

> show #!7 models

> hide #!7 models

> hide #!66 models

> show #!66 models

> hide #67 models

> show #67 models

> show #!69 models

> hide #!69 models

> show #!69 models

> hide #!69 models

> show #!69 models

> show #!60 models

> show #60.1 models

> hide #60.1 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!71 models

> hide #!71 models

> show #!71 models

> show #!85 models

> hide #!85 models

> hide #!71 models

> hide #67 models

> hide #!68 models

> show #!68 models

> hide #!69 models

> show #!69 models

> hide #!69 models

> show #!69 models

> hide #!69 models

> show #!69 models

> show #60.1 models

> hide #!60 models

> show #!60 models

> show #!47 models

> hide #!47 models

> close #47

> show #!39 models

> close #39

> show #!27 models

> hide #!27 models

> show #!32 models

> hide #!32 models

> show #!32 models

> hide #!26 models

> show #!26 models

> show #!45 models

> hide #!32 models

> show #!36 models

> close #36

> show #!40 models

> hide #!40 models

> show #!40 models

> close #40

> show #!32 models

> hide #!32 models

> show #!33 models

> hide #!33 models

> show #!10 models

> hide #!45 models

> close #45

> show #!48 models

> hide #!48 models

> show #!48 models

> close #48

> show #!49 models

> close #49

> show #!33 models

> hide #!33 models

> close #50-51

> show #67 models

> hide #!68 models

> show #!68 models

> show #!65 models

> hide #!65 models

> close #65-66

> show #!53 models

> hide #!53 models

> show #!53 models

> fitmap #53 inMap #10

Fit map nochan-tail-new-gp12-re-sym.mrc in map fiber-c6-flip-trim.mrc using
5208 points  
correlation = 0.7841, correlation about mean = 0.3314, overlap = 26.96  
steps = 68, shift = 1.53, angle = 0.629 degrees  
  
Position of nochan-tail-new-gp12-re-sym.mrc (#53) relative to fiber-c6-flip-
trim.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.69898022 -0.71513998 -0.00123918 357.19635548  
0.71513185 -0.69897895 0.00386126 356.42508254  
-0.00362749 0.00181275 0.99999181 -53.42938190  
Axis -0.00143225 0.00166983 0.99999758  
Axis point 103.52761400 253.41694699 0.00000000  
Rotation angle (degrees) 134.34552025  
Shift along axis -53.34567998  
  

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!53 models

> hide #67 models

> hide #!68 models

> hide #!69 models

> show #!69 models

> show #!68 models

> show #67 models

> hide #!69 models

> show #!69 models

> fitmap #69 inMap #53

Multiple maps for #69  

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 12086
points  
correlation = 0.6431, correlation about mean = 0.3498, overlap = 2626  
steps = 64, shift = 8.38, angle = 6.13 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.63467186 -0.77093212 -0.05343414 30.33400579  
-0.77001407 -0.63673201 0.04062770 283.65953942  
-0.06534446 0.01535978 -0.99774451 505.76437641  
Axis -0.90406111 0.42613917 0.03284687  
Axis point 0.00000000 150.91951169 252.51827778  
Rotation angle (degrees) 179.19928395  
Shift along axis 110.06742130  
  

> show #!69.1 models

> hide #!69.2 models

> show #!69.2 models

> hide #!68 models

> show #!68.2 models

> hide #67 models

> show #67 models

> show #!64 models

> hide #!64 models

> show #!64 models

> hide #!64 models

> hide #67 models

> hide #!68 models

> hide #!68.2 models

> hide #!69 models

> show #!69 models

> hide #!69.3 models

> show #!69.3 models

> select #69.3

2 models selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> hide #!69.1 models

> show #!69.1 models

> hide #!69.2 models

> hide #!69.1 models

> hide #!69.3 models

> show #!69.3 models

> hide #!69.3 models

> show #!69.3 models

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 12086
points  
correlation = 0.6431, correlation about mean = 0.3498, overlap = 2626  
steps = 80, shift = 15.6, angle = 3.36 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.74424187 -0.66725443 -0.02958851 14.07150370  
-0.66530473 -0.73670179 -0.12099600 327.56252711  
0.05893718 0.10973566 -0.99221188 512.09520894  
Axis 0.93361078 -0.35820201 0.00788908  
Axis point 0.00000000 149.44447808 265.67693023  
Rotation angle (degrees) 172.90184542  
Shift along axis -100.15628445  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 12086
points  
correlation = 0.6427, correlation about mean = 0.3526, overlap = 2653  
steps = 76, shift = 4.49, angle = 9.94 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.99838108 0.03222871 -0.04686626 66.87882863  
0.02768284 -0.99513003 -0.09460357 315.59846015  
-0.04968698 0.09315300 -0.99441121 482.79776193  
Axis 0.99959430 0.01501722 -0.02420169  
Axis point 0.00000000 145.89735604 249.61671476  
Rotation angle (degrees) 174.61104551  
Shift along axis 59.90658445  
  

> ui mousemode rightMode "translate selected models"

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!53 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 "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 12086
points  
correlation = 0.6431, correlation about mean = 0.3499, overlap = 2626  
steps = 68, shift = 4.2, angle = 3.41 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.78205566 -0.62128407 -0.04893852 9.72940556  
-0.62231172 -0.78273001 -0.00786103 298.17607921  
-0.03342174 0.03660277 -0.99877082 508.91025723  
Axis 0.94393483 -0.32941021 -0.02181638  
Axis point 0.00000000 147.62440309 256.22198982  
Rotation angle (degrees) 178.65042404  
Shift along axis -100.14090359  
  

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 12086
points  
correlation = 0.6431, correlation about mean = 0.3498, overlap = 2626  
steps = 64, shift = 6.03, angle = 2.68 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.79160476 -0.60828850 -0.05785260 14.97403112  
-0.60737432 -0.79367564 0.03428332 289.09198928  
-0.06677037 0.00799933 -0.99773626 496.80395794  
Axis -0.94646554 0.32112198 0.03291897  
Axis point 0.00000000 148.89696425 247.71394829  
Rotation angle (degrees) 179.20440322  
Shift along axis 95.01566301  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> hide #!34 models

> hide #!38 models

> hide #!26 models

> hide #!22 models

> hide #!13 models

> hide #!11 models

> hide #!10 models

> show #!10 models

> hide #!4 models

> hide #!53 models

> show #!53 models

> hide #!60 models

> hide #60.1 models

> hide #!69 models

> hide #!69.3 models

> ~select #69.3

Nothing selected  

> show #!69.3 models

> hide #!69.3 models

> show #!69.3 models

> hide #!69.3 models

> hide #!95 models

> hide #!106 models

> hide #!53 models

> show #!53 models

> volume #53 level 1.027

> ui mousemode rightMode "translate selected models"

> show #!69.3 models

> hide #!69.3 models

> show #!69.3 models

> hide #!69.3 models

> show #!69.2 models

> hide #!69.2 models

> show #!69.1 models

> hide #!69.1 models

> show #!69.3 models

> select #69.3

2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> hide #!10 models

> show #!10 models

> hide #!10 models

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 12086
points  
correlation = 0.6426, correlation about mean = 0.3527, overlap = 2654  
steps = 56, shift = 1.78, angle = 2.26 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.95902707 0.27977135 -0.04466514 24.83151974  
0.27844499 -0.95986073 -0.03370027 304.77377510  
-0.05230069 0.01988266 -0.99843339 490.94471702  
Axis 0.98970185 0.14103219 -0.02449851  
Axis point 0.00000000 147.25065690 247.81054661  
Rotation angle (degrees) 178.44880006  
Shift along axis 55.53130263  
  

> volume #69.3 level 0.1235

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 10533
points  
correlation = 0.6459, correlation about mean = 0.3267, overlap = 2551  
steps = 72, shift = 2.01, angle = 9.5 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.46402664 0.88455760 -0.04729763 68.23029410  
0.88358322 -0.46598712 -0.04622374 304.10564341  
-0.06292763 -0.02034237 -0.99781072 488.85128887  
Axis 0.85556884 0.51668604 -0.03221022  
Axis point 0.00000000 129.26125413 246.59793302  
Rotation angle (degrees) 179.13335460  
Shift along axis 199.75684701  
  

> volume #69.3 level 0.0818

> 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"

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 13146
points  
correlation = 0.6407, correlation about mean = 0.3734, overlap = 2680  
steps = 60, shift = 2.51, angle = 4.83 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.89737969 0.44078863 -0.02037138 -8.03530024  
0.43482234 -0.89120322 -0.12917552 327.83619054  
-0.07509414 0.10706153 -0.99141244 481.35243074  
Axis 0.97390953 0.22559974 -0.02459659  
Axis point 0.00000000 149.76556966 250.43632414  
Rotation angle (degrees) 173.03385474  
Shift along axis 54.29447465  
  

> volume #69.3 level 0.1504

> volume #69.3 level 0.157

> fitmap #69.3 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 8444
points  
correlation = 0.6524, correlation about mean = 0.2934, overlap = 2430  
steps = 76, shift = 10.6, angle = 7.16 degrees  
  
Position of nochan-new-trim.mrc (#69.3) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
0.85387765 0.52036727 0.01052572 -34.38657386  
0.51080195 -0.83395847 -0.20879317 341.84847140  
-0.09987112 0.18366037 -0.97790314 443.79571257  
Axis 0.96237376 0.27071491 -0.02345606  
Axis point 0.00000000 151.94276274 239.06725620  
Rotation angle (degrees) 168.23496160  
Shift along axis 49.04104426  
  

> hide #!69.3 models

> show #!69.2 models

> show #!69.3 models

> hide #!69.3 models

> show #!69.3 models

> hide #!69.2 models

> show #!69.2 models

> show #!69.1 models

> close #69#69.1-3

> show #!10 models

> open /data/disk3/modeling/nochan-new.mrc

Opened nochan-new.mrc, grid size 160,160,160, pixel 5.4, shown at level 0.13,
step 1, values float32  

> select clear

> hide #!9 models

> close #9

> open /data/disk3/modeling/nochan-new-trim.mrc

Opened nochan-new-trim.mrc, grid size 87,89,43, pixel 5.4,5.4,5.4, shown at
level 0.24, step 1, values float32  

> hide #!9 models

> show #!9 models

> select #9

2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #9 inMap #53

Fit map nochan-new-trim.mrc in map nochan-tail-new-gp12-re-sym.mrc using 3327
points  
correlation = 0.6955, correlation about mean = 0.1329, overlap = 1623  
steps = 76, shift = 35, angle = 8.97 degrees  
  
Position of nochan-new-trim.mrc (#9) relative to nochan-tail-new-gp12-re-
sym.mrc (#53) coordinates:  
Matrix rotation and translation  
-0.48882935 0.87237933 0.00026846 -0.04011887  
-0.87237937 -0.48882938 -0.00001773 0.00571885  
0.00011575 -0.00024289 0.99999992 5.72297384  
Axis -0.00012905 0.00008752 -0.99999999  
Axis point -0.01860648 0.01508006 0.00000000  
Rotation angle (degrees) 119.26367195  
Shift along axis -5.72296809  
  

> save session /data/disk3/modeling/gp17-2020/Figure4-20200510-fiber-ET.cxs

> select #10

3 models selected  

> vop gaussian #10 sdev 3.15

> hide #!9 models

> show #!9 models

> hide #!36 models

> show #!36 models

> surface dust #36 size 30

> surface dust #36 size 100

> volume #36 level 0.002037

> volume #36 level 0.001282

> hide #!53 models

> volume #9 level 0.06763

> lighting soft

> select #36

2 models selected  

> ~select #36

Nothing selected  

> select #36

2 models selected  

> ~select #36

Nothing selected  

> select #36

2 models selected  

> ~select #36

Nothing selected  

> select #36

2 models selected  

> ~select #36

Nothing selected  

> select #36

2 models selected  

> save /data/disk3/modeling/gp17-2020/Free-lp20.mrc models #36

> hide #!36 models

> show #!36 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!36 models

> select clear

> select clear

> save image /data/disk3/Paper-use/Figure4-20200507-A6.tif pixelSize 0.1
> supersample 1 transparentBackground true

> save image /data/disk3/Paper-use/Figure4-20200507-A5.tif pixelSize 0.1
> supersample 1 transparentBackground true

> save image /data/disk3/Paper-use/Figure4-20200507-A4.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!36 models

> lighting soft

> save image /data/disk3/Paper-use/Figure4-20200507-A3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!36 models

> hide #!9 models

> save image /data/disk3/Paper-use/Figure4-20200507-A2.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!53 models

> hide #!53 models

> show #!46 models

> hide #!46 models

> show #!7 models

> hide #!7 models

> save image /data/disk3/Paper-use/Figure4-20200507-A1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!17 models

> hide #!17 models

> close #17

> show #!28 models

> hide #!28 models

> show #!59 models

> hide #!59 models

> show #!63 models

> hide #!63 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!11 models

> hide #!11 models

> hide #!9 models

> hide #!10 models

> show #!9 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!23 models

> select #23

37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected  

> show #!43 models

> show #!44 models

> hide #!44 models

> hide #!43 models

> close #42-44

> show #!13 models

> hide #!13 models

> show #!12 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!13 models

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!2 models

> hide #!2 models

> show #!57 models

> hide #!57 models

> show #!57 models

> close #57

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!13 models

> show #!13 models

> hide #!26 models

> show #!26 models

> hide #!12 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!23 models

> show #!23 models

> hide #!21 models

> show #!68 models

> show #!68.2 models

> hide #!68.2 models

> hide #!68 models

> hide #!13 models

> open /data/disk3/modeling/nochan-new-fiber.mrc

Opened nochan-new-fiber.mrc, grid size 109,119,39, pixel 5.4,5.4,5.4, shown at
level 0.0674, step 1, values float32  

> select clear

> select #17

2 models selected  

> ui mousemode rightMode "rotate selected models"

> lighting flat

> 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 "rotate selected models"

> hide #!17 models

> show #!17 models

> fitmap #17 inMap #9

Fit map nochan-new-fiber.mrc in map nochan-new-trim.mrc using 5055 points  
correlation = 0.9968, correlation about mean = 0.9806, overlap = 211.2  
steps = 72, shift = 5.08, angle = 3.6 degrees  
  
Position of nochan-new-fiber.mrc (#17) relative to nochan-new-trim.mrc (#9)
coordinates:  
Matrix rotation and translation  
0.49990218 -0.86608188 -0.00000835 0.00243498  
0.86608188 0.49990218 0.00000538 -0.00068897  
-0.00000049 -0.00000992 1.00000001 0.00824612  
Axis -0.00000883 -0.00000454 1.00000000  
Axis point 0.00181409 0.00176408 0.00000000  
Rotation angle (degrees) 60.00647141  
Shift along axis 0.00824610  
  

> show #!94 models

> hide #!94 models

> select clear

> show #!98 models

> select clear

> save session /data/disk3/modeling/gp17-2020/Figure4-20200510-fiber-ET.cxs

> lighting soft

> hide #!98 models

> show #!98 models

> hide #!26 models

> show #!26 models

> hide #!17 models

> show #!17 models

> hide #!9 models

> show #!9 models

> transparency #9 70

> transparency #9 90

> transparency #9 70

> transparency #9 80

> hide #!17 models

> show #!17 models

> hide #!98 models

> select #26

2 models selected  

> hide #!26 models

> show #!26 models

> hide #!23 models

> show #!23 models

> hide #!26 models

> show #!26 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> select clear

> transparency #9 10

> transparency #9 30

> transparency #9 10

> transparency #9 10

> transparency #9 30

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!9 models

> show #!9 models

> hide #!17 models

> show #!17 models

> hide #!13 models

> show #!13 models

> show #!10 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> show #!27 models

> hide #!27 models

> show #!55 models

> hide #!55 models

> show #!60 models

> hide #!60 models

> show #!70 models

> hide #!70 models

> show #!89 models

> hide #!89 models

> show #!92 models

> hide #!10 models

> hide #!13 models

> show #!13 models

> hide #!17 models

> show #!22 models

> hide #!22 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!8 models

> hide #!13 models

> show #!13 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!92 models

> show #!92 models

> volume #92 level 0.00156

> volume #92 level 0.0003444

> show #!56 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!36 models

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!41 models

> hide #!41 models

> show #!37 models

> hide #!37 models

> show #!54 models

> hide #!26 models

> show #!14 models

> hide #!14 models

> hide #!13 models

> hide #!9 models

> hide #!56 models

> show #!56 models

> hide #!54 models

> show #!54 models

> hide #!54 models

> show #!54 models

> hide #!54 models

> volume #94 level 0.01004

> volume #92 level 0.002996

> hide #!92 models

> hide #!56 models

> show #!100 models

> show #!101 models

> show #!102 models

> show #!103 models

> show #!104 models

> hide #!104 models

> hide #!103 models

> hide #!102 models

> hide #!101 models

> hide #!100 models

> show #!91 models

> show #!56 models

> hide #!56 models

> show #!26 models

> show #!33 models

> surface dust #33 size 30

> show #!97 models

> hide #!97 models

> surface dust #91 size 30

> show #!35 models

> hide #!35 models

> show #!11 models

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!97 models

> hide #!97 models

> show #!97 models

> view name p1

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!97 models

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!91 models

> show #!91 models

> show #!97 models

> hide #!97 models

> show #!97 models

> hide #!97 models

> view name p2

> save image /data/disk3/Paper-use/Figure4-20200512-2.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!106.2 models

> show #!106 models

> hide #!106 models

> show #!106 models

> save image /data/disk3/Paper-use/Figure4-20200512-3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> lighting soft

> lighting full

> save image /data/disk3/Paper-use/Figure4-20200512-3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!98 models

> show #!97 models

> hide #!98 models

> show #!98 models

> hide #!23 models

> show #!34 models

> view p1

> hide #!106.2 models

> hide #!98 models

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> view p2

> save image /data/disk3/Paper-use/Figure4-20200512-2.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!106.2 models

> save image /data/disk3/Paper-use/Figure4-20200512-3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!97 models

> save image /data/disk3/Paper-use/Figure4-20200512-3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!106.2 models

> save image /data/disk3/Paper-use/Figure4-20200512-2.tif pixelSize 0.1
> supersample 1 transparentBackground true

> view p1

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!106.2 models

> show #!98 models

> show #!97 models

> view p3

> view p2

> view p1

> view p2

> hide #!97 models

> view name p3

> hide #!91 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> show #!56 models

> hide #!56 models

> show #!38 models

> hide #!38 models

> show #!38 models

> show #!56 models

> hide #!56 models

> show #!106.3 models

> hide #!106.3 models

> hide #!38 models

> show #!35 models

> surface dust #35 size 30

> hide #!106.2 models

> hide #!106 models

> show #!106 models

> hide #!98 models

> view p1

> save image /data/disk3/Paper-use/Figure4-20200512-1.tif pixelSize 0.1
> supersample 1 transparentBackground true

> view p2

> save image /data/disk3/Paper-use/Figure4-20200512-2.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!97 models

> hide #!97 models

> show #!106.2 models

> save image /data/disk3/Paper-use/Figure4-20200512-3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> show #!98 models

> save image /data/disk3/Paper-use/Figure4-20200512-3.tif pixelSize 0.1
> supersample 1 transparentBackground true

> view p3

> save image /data/disk3/Paper-use/Figure4-20200512-4.tif pixelSize 0.1
> supersample 1 transparentBackground true

> hide #!106.2 models

> hide #!98 models

> hide #!35 models

> show #!35 models

> hide #!26 models

> show #!26 models

> show #!38 models

> surface dust #38 size 30

> view p1

> save image /data/disk3/Paper-use/Figure4-20200512-5.tif pixelSize 0.1
> supersample 1 transparentBackground true

> open /data/disk3/modeling/gp17-2020/fiber-commposed-c5.pdb

Chain information for fiber-commposed-c5.pdb #39  
---  
Chain | Description  
0 1 2 3 K | No description available  
4 5 6 7 I L s t u v | No description available  
A M N O P | No description available  
B C Q R S T U V W X | No description available  
D H J Y Z a b o p q r w x y z | No description available  
E c d e f | No description available  
F g h i j | No description available  
G k l m n | No description available  
  

> select #39

69885 atoms, 63470 bonds, 1 model selected  

> lighting flat

> hide sel atoms

> show sel cartoons

> hide sel surfaces

> show sel surfaces

> 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"

> fitmap #39 inMap #35

Fit molecule fiber-commposed-c5.pdb (#39) to map shaft-C-4.6-c6-cut.mrc (#35)
using 69885 atoms  
average map value = 0.006762, steps = 268  
shifted from previous position = 20.2  
rotated from previous position = 9.6 degrees  
atoms outside contour = 44055, contour level = 0.0096381  
  
Position of fiber-commposed-c5.pdb (#39) relative to shaft-C-4.6-c6-cut.mrc
(#35) coordinates:  
Matrix rotation and translation  
-0.23506271 -0.10839032 -0.96591767 463.01585913  
-0.06444897 0.99331381 -0.09578047 170.55446705  
0.96984109 0.03973799 -0.24047669 126.25089808  
Axis 0.06981910 -0.99730276 0.02263858  
Axis point 186.78577684 0.00000000 250.27279341  
Rotation angle (degrees) 103.95222830  
Shift along axis -134.90894937  
  

> lighting soft

> hide #!39 models

> show #!39 models

> close #39

> view p2

> open /data/disk3/modeling/gp17-2020/fiber-commposed.pdb

Chain information for fiber-commposed.pdb #39  
---  
Chain | Description  
A | No description available  
B C | No description available  
D H J | No description available  
E | No description available  
F | No description available  
G | No description available  
I L | No description available  
K | No description available  
  

> select #39

13977 atoms, 12694 bonds, 1 model selected  

> hide sel atoms

> show sel cartoons

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> show #!95 models

> select #95

2 models selected  

> hide #!34 models

> hide #!26 models

> hide #!33 models

> hide #!11 models

> show #!94 models

> hide #!94 models

> show #!94 models

> hide #!95 models

> select #94

2 models selected  

> show #39 surfaces

> select #39

13977 atoms, 12694 bonds, 1 model selected  

> lighting flat

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> hide #!94 models

> hide #94.1 models

> show #!95 models

> hide #!95 models

> show #!95 models

> show #!92 models

> hide #!92 models

> show #!92 models

> hide #!92 models

> show #!96 models

> hide #!95 models

> hide #!96 models

> show #!95 models

> fitmap #39 inMap #95

Fit molecule fiber-commposed.pdb (#39) to map shaft-C-4.6.mrc (#95) using
13977 atoms  
average map value = 0.009329, steps = 236  
shifted from previous position = 13.7  
rotated from previous position = 11.7 degrees  
atoms outside contour = 8359, contour level = 0.012415  
  
Position of fiber-commposed.pdb (#39) relative to shaft-C-4.6.mrc (#95)
coordinates:  
Matrix rotation and translation  
0.99996451 0.00655470 -0.00529765 1.81567659  
-0.00656873 0.99997498 -0.00263252 1.91763072  
0.00528027 0.00266723 0.99998253 -1.40026659  
Axis 0.29994145 -0.59866068 -0.74272506  
Axis point 332.69727000 -255.22210628 0.00000000  
Rotation angle (degrees) 0.50619474  
Shift along axis 0.43659964  
  

> hide sel surfaces

> show sel atoms

> hide sel atoms

> select clear

> show #!97 models

> select #97

2 models selected  

> 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"

> lighting soft

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> surface dust #97 size 30

> select #97

2 models selected  

> select #97

2 models selected  

> ui mousemode rightMode "rotate selected models"

> select clear

> show #!89 models

> select #89

16722 atoms, 16974 bonds, 1 model selected  

> show sel cartoons

> hide #!39 models

> show #!41 models

> hide #!41 models

> show #!41 models

> show #!37 models

> lighting flat

> show #!11 models

> hide #!95 models

> lighting soft

> lighting soft

> lighting full

> select #97

2 models selected  

> ui mousemode rightMode "rotate selected models"

> fitmap #97 inMap #11

Fit map fiber-6-fromtail-clean-link-C1.mrc in map fiber-6-fromtail-clean-
link.mrc using 5406 points  
correlation = 0.9889, correlation about mean = 0.8337, overlap = 0.5285  
steps = 108, shift = 5.52, angle = 26.3 degrees  
  
Position of fiber-6-fromtail-clean-link-C1.mrc (#97) relative to
fiber-6-fromtail-clean-link.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.49911947 0.86653319 -0.00011107 132.89663012  
-0.86653319 -0.49911947 0.00000874 496.67734866  
-0.00004787 0.00010064 1.00000001 -0.00956458  
Axis 0.00005303 -0.00003647 -1.00000000  
Axis point 209.99504876 209.92968068 0.00000000  
Rotation angle (degrees) 119.94176128  
Shift along axis -0.00150225  
  

> select clear

> view name test

Unknown command: vim p1  

> view p1

> view test

> view p1

> fitmap #97 inMap #11

Fit map fiber-6-fromtail-clean-link-C1.mrc in map fiber-6-fromtail-clean-
link.mrc using 5406 points  
correlation = 0.8986, correlation about mean = 0.4457, overlap = 0.4208  
steps = 176, shift = 18.1, angle = 17.6 degrees  
  
Position of fiber-6-fromtail-clean-link-C1.mrc (#97) relative to
fiber-6-fromtail-clean-link.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.68873134 -0.48293808 0.54075873 420.54741263  
0.70993249 -0.29787187 0.63817572 86.73506812  
-0.14712257 0.82343379 0.54800712 -113.29972912  
Axis 0.13333643 0.49509118 0.85854884  
Axis point 198.86452953 174.94228296 0.00000000  
Rotation angle (degrees) 135.99655505  
Shift along axis 1.74270530  
  

> view name test

> view p1

> view test

> view name p1

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!13 models

> hide #!13 models

> show #!13 models

> select #13

2 models selected  

> hide #!89 surfaces

> show #!89 surfaces

> save session /data/disk3/modeling/gp17-2020/Figure4-20200510-fiber-ET.cxs

> show #!27 models

> hide #!27 models

> hide #!41 models

> show #!39 models

> hide #!39 models

> show #!39 models

> hide #!38 models

> hide #!39 models

> show #!39 models

> hide #!97 models

> show #!97 models

> hide #!97 models

> show #!11 models

> hide #!13 models

> hide #13.1 models

> hide #!11 models

> show #!11 models

> hide #!39 models

> show #!39 models

> hide #!37 models

> hide #!35 models

> show #!35 models

> hide #!89 models

> show #!90 models

> hide #!90 models

> close #90

> show #!33 models

> select clear

> lighting soft

> lighting full

> save image /data/disk3/Paper-use/Figure4-20200512-6.tif pixelSize 0.1
> supersample 1 transparentBackground true

> view p2

> show #13.1 models

> hide #13.1 models

> save image /data/disk3/Paper-use/Figure4-20200512-7.tif pixelSize 0.1
> supersample 1 transparentBackground true

> view p3

> hide #!35 models

> show #!35 models

> hide #!35 models

> show #!35 models

> hide #!13 models

> hide #!11 models

> show #!11 models

> hide #!39 models

> show #!21 models

> hide #!21 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> show #!39 models

> hide #!39 models

> show #!54 models

> hide #!54 models

> show #!23 models

> hide #!23 models

> show #!26 models

> show #!34 models

> show #!46 models

> select #46

2 models selected  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #!46 models

> show #!46 models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #!52 models

> hide #!52 models

> show #!56 models

> hide #!56 models

> show #!68 models

> show #!68.2 models

> hide #!68.2 models

> lighting flat

> show #!63 models

> hide #!63 models

> show #!89 models

> hide #!89 models

> show #!89 models

> hide #!89 models

> show #!89 models

> hide #!89 models

> show #!91 models

> hide #!91 models

> show #!91 models

> show #!94 models

> show #94.1 models

> hide #94.1 models

> hide #!94 models

> hide #!91 models

> show #!98 models

> hide #!98 models

> show #!98 models

> show #!36 models

> lighting soft

> hide #46.1 models

> hide #!46 models

> show #!46 models

> view orient

> view

> show #46.1 models

> graphics silhouettes false

> lighting flat

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #!46 models

> show #!46 models

> hide #46.1 models

> show #46.1 models

> hide #!46 models

> show #!46 models

> hide #46.1 models

> hide #!46 models

> show #46.1 models

> hide #!46 models

> hide #46.1 models

> show #46.1 models

> hide #!46 models

> hide #46.1 models

> show #!46 models

> show #46.1 models

> hide #46.1 models

> hide #!46 models

> show #!100 models

> show #!101 models

> show #!102 models

> show #!103 models

> show #!104 models

> show #!105 models

> show #!106.2 models

> hide #!35 models

> hide #!36 models

> show #!36 models

> show #!53 models

> hide #!53 models

> show #!46 models

> show #46.1 models

> lighting soft

> open /data/disk3/modeling/tail-adsorbed-new-lp-OM.mrc

Opened tail-adsorbed-new-lp-OM.mrc, grid size 160,160,160, pixel 5.4, shown at
level 0.0803, step 1, values float32  

> hide #!46 models

> show #!46 models

> hide #!40 models

> show #!40 models

> matchmaker #40 to #46

No 'to' model specified  

> select #40

2 models selected  

> lighting flat

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> volume #40 level 0.03056

> ui mousemode rightMode "rotate selected models"

> view p3

> view p3

> hide #!46 models

> show #!46 models

> hide #!46 models

> show #!46 models

> fitmap #40 inMap #46

Fit map tail-adsorbed-new-lp-OM.mrc in map tail-adsorbed-new-lp-OM.mrc using
99204 points  
correlation = 0.9817, correlation about mean = 0.8795, overlap = 597.7  
steps = 128, shift = 20.1, angle = 1.31 degrees  
  
Position of tail-adsorbed-new-lp-OM.mrc (#40) relative to tail-adsorbed-new-
lp-OM.mrc (#46) coordinates:  
Matrix rotation and translation  
-0.73646054 -0.67648043 -0.00030455 -0.74033266  
0.67648045 -0.73646059 0.00005674 0.04523188  
-0.00026267 -0.00016424 0.99999995 0.00552790  
Axis -0.00016333 -0.00003095 0.99999999  
Axis point -0.37897650 -0.12159109 0.00000000  
Rotation angle (degrees) 137.43077860  
Shift along axis 0.00564742  
  

> show #!38 models

> lighting soft

> lighting full

> lighting simple

> lighting soft

> fitmap #40 inMap #46

Fit map tail-adsorbed-new-lp-OM.mrc in map tail-adsorbed-new-lp-OM.mrc using
99204 points  
correlation = 0.9818, correlation about mean = 0.8796, overlap = 597.6  
steps = 64, shift = 0.988, angle = 0.49 degrees  
  
Position of tail-adsorbed-new-lp-OM.mrc (#40) relative to tail-adsorbed-new-
lp-OM.mrc (#46) coordinates:  
Matrix rotation and translation  
-0.73646274 -0.67647811 -0.00003342 0.18899435  
0.67647810 -0.73646275 0.00003155 -0.27295731  
-0.00004596 0.00000062 1.00000000 -0.06448400  
Axis -0.00002286 0.00000927 1.00000000  
Axis point 0.14766465 -0.09966514 0.00000000  
Rotation angle (degrees) 137.43096092  
Shift along axis -0.06449085  
  

> lighting full

> select clear

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!36 models

> hide #!36 models

> show #!36 models

> hide #!105 models

> show #!105 models

> hide #!104 models

> show #!104 models

> hide #!103 models

> hide #!102 models

> hide #!101 models

> hide #!100 models

> show #!100 models

> hide #!104 models

> hide #!105 models

> show #!96 models

> show #!101 models

> show #!102 models

> show #!103 models

> show #!104 models

> show #!105 models

> hide #!96 models

> hide #!102 models

> show #!102 models

> hide #!100 models

> select clear

> hide #!36 models

> show #!36 models

> show #!100 models

> hide #!100 models

> show #!100 models

> view p3

> save image /data/disk3/Paper-use/Figure4-20200512-8.tif pixelSize 0.1
> supersample 1 transparentBackground true

Image size 17726 x 10720 too large, exceeds maximum OpenGL render buffer size
16384  

> save image /data/disk3/Paper-use/Figure4-20200512-9.tif pixelSize 0.1
> supersample 1 transparentBackground true

Image size 17726 x 10720 too large, exceeds maximum OpenGL render buffer size
16384  

> save image /data/disk3/Paper-use/Figure4-20200512-9.tif pixelSize 0.1
> supersample 2 transparentBackground true

Image size 17726 x 10720 too large, exceeds maximum OpenGL render buffer size
16384  

> save image /data/disk3/Paper-use/Figure4-20200512-9.tif pixelSize 0.1
> supersample 5 transparentBackground true

Image size 17726 x 10720 too large, exceeds maximum OpenGL render buffer size
16384  

> hide #!106.2 models

> hide #!36 models

> show #!52 models

> hide #!52 models

> show #!53 models

> hide #!53 models

> show #!54 models

> hide #!54 models

> show #!55 models

> hide #!55 models

> show #!63 models

> hide #!63 models

> hide #63.1 models

> show #63.1 models

> show #!64 models

> hide #!64 models

> show #67 models

> hide #67 models

> hide #!68 models

> show #!68.2 models

> hide #!68.2 models

> show #!70 models

> hide #!70 models

> save session /data/disk3/modeling/gp17-2020/Figure4-20200512-fiber-ET.cxs

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 201, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings +
transparent_drawings, camera)  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 559, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, drawings,
self._shadow_bounds)  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1330, in use_shadow_map  
shadow_map = self._finish_rendering_shadowmap() # Depth texture  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1360, in
_finish_rendering_shadowmap  
fb = r.pop_framebuffer()  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 644, in pop_framebuffer  
fb.activate()  
File "/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2137, in activate  
GL.glDrawBuffer(self._draw_buffer)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  




OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

This is the third report by the same user of this error in 5 months on the same Linux system Quadro K2200 graphics. No user email. Another report #2729 on modern graphics (RTX 2080) gave the same error when the person switched users and came back. Possibly the opengl context was invalidated.