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Opened 14 months ago
Closed 14 months ago
#15870 closed defect (can't reproduce)
glTexImage2D: out of memory
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Thu Jul 11 16:48:22 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\lucre\OneDrive - Nexus365\OXFORD\PAPER
> HHIP\Chimerasessions\figureONE_PTCH12to1SHH_pdb.cxs" format session
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 as #6.1, grid size
300,300,300, pixel 1.22, shown at level 0.122, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 2 as #6.3, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 3 as #6.4, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 4 as #6.5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 5 as #6.6, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 6 as #6.7, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 7 as #6.8, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 8 as #6.9, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian as #7, grid
size 300,300,300, pixel 1.22, shown at level 0.0796, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc as #8, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 as #9.1, grid size 300,300,300,
pixel 1.24, shown at level 0.108, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 1 as #9.2, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 2 as #9.3, grid size 300,300,300,
pixel 1.24, shown at level 0.242, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 3 as #9.4, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 4 as #9.5, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 5 as #9.6, grid size 300,300,300,
pixel 1.24, shown at level 0.0648, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 6 as #9.7, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 7 as #9.8, grid size 300,300,300,
pixel 1.24, shown at level 0.267, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 8 as #9.9, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian as #10, grid size
300,300,300, pixel 1.24, shown at level 0.0454, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc as #11, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 2, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian as #13,
grid size 300,300,300, pixel 1.24, shown at level 0.0777, step 1, values
float32
Opened cryosparc_P478_J315_map_sharp.mrc as #14, grid size 300,300,300, pixel
1.22, shown at level 0.0927, step 1, values float32
Restoring stepper: trimer_1_real_space_refined_020_real_space_refined_022.pdb
Log from Fri Jun 14 12:08:08 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/figureONE_PTCH12to1SHH_pdb.cxs"
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 as #6.1, grid size
300,300,300, pixel 1.22, shown at level 0.122, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 2 as #6.3, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 3 as #6.4, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 4 as #6.5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 5 as #6.6, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 6 as #6.7, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 7 as #6.8, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 8 as #6.9, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian as #7, grid
size 300,300,300, pixel 1.22, shown at level 0.0796, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc as #8, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 as #9.1, grid size 300,300,300,
pixel 1.24, shown at level 0.108, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 1 as #9.2, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 2 as #9.3, grid size 300,300,300,
pixel 1.24, shown at level 0.242, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 3 as #9.4, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 4 as #9.5, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 5 as #9.6, grid size 300,300,300,
pixel 1.24, shown at level 0.0648, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 6 as #9.7, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 7 as #9.8, grid size 300,300,300,
pixel 1.24, shown at level 0.267, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 8 as #9.9, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian as #10, grid size
300,300,300, pixel 1.24, shown at level 0.0454, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc as #11, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 2, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian as #13,
grid size 300,300,300, pixel 1.24, shown at level 0.0777, step 1, values
float32
Opened cryosparc_P478_J315_map_sharp.mrc as #14, grid size 300,300,300, pixel
1.22, shown at level 0.0927, step 1, values float32
Restoring stepper: trimer_1_real_space_refined_020_real_space_refined_022.pdb
Log from Thu Jun 13 15:38:57 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\lucre\OneDrive - Nexus365\OXFORD\PAPER
> HHIP\Chimerasessions\FIGURE one.2.cxs" format session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "NXmapHandler" returned None
Exception ignored in: <function Drawing.__del__ at 0x0000017188B29800>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1215, in __del__
if not self.was_deleted:
^^^^^^^^^^^^^^^^
AttributeError: 'MDFFMgr' object has no attribute 'was_deleted'
restore_snapshot for "MDFFMgr" returned None
restore_snapshot for "FastVolumeSurface" returned None
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 as #6.1, grid size
300,300,300, pixel 1.22, shown at level 0.122, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 2 as #6.3, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 3 as #6.4, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 4 as #6.5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 5 as #6.6, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 6 as #6.7, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 7 as #6.8, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 8 as #6.9, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian as #7, grid
size 300,300,300, pixel 1.22, shown at level 0.0796, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc as #8, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 as #9.1, grid size 300,300,300,
pixel 1.24, shown at level 0.108, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 1 as #9.2, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 2 as #9.3, grid size 300,300,300,
pixel 1.24, shown at level 0.242, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 3 as #9.4, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 4 as #9.5, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 5 as #9.6, grid size 300,300,300,
pixel 1.24, shown at level 0.0648, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 6 as #9.7, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 7 as #9.8, grid size 300,300,300,
pixel 1.24, shown at level 0.267, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 8 as #9.9, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian as #10, grid size
300,300,300, pixel 1.24, shown at level 0.0454, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc as #11, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 2, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian as #13,
grid size 300,300,300, pixel 1.24, shown at level 0.0777, step 1, values
float32
Opened cryosparc_P478_J315_map_sharp.mrc 0 as #16.1, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 1 as #16.2, grid size 300,300,300,
pixel 1.22, shown at level 0.169, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 2 as #16.3, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 3 as #16.4, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 4 as #16.5, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 5 as #16.6, grid size 300,300,300,
pixel 1.22, shown at level 0.0643, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 6 as #16.7, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 7 as #16.8, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 8 as #16.9, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
restore_snapshot for "ZoneColor" returned None
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
[Repeated 1 time(s)]
restore_snapshot for "Redust" returned None
Restoring stepper: trimer_1_real_space_refined_020_real_space_refined_022.pdb
Log from Fri May 3 17:35:07 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\lucre\OneDrive - Nexus365\OXFORD\PAPER
> HHIP\Chimerasessions\FIGURE one.cxs" format session
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 as #6.1, grid size
300,300,300, pixel 1.22, shown at level 0.122, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 2 as #6.3, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 3 as #6.4, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 4 as #6.5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 5 as #6.6, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 6 as #6.7, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 7 as #6.8, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 8 as #6.9, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian as #7, grid
size 300,300,300, pixel 1.22, shown at level 0.0796, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc as #8, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 as #9.1, grid size 300,300,300,
pixel 1.24, shown at level 0.108, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 1 as #9.2, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 2 as #9.3, grid size 300,300,300,
pixel 1.24, shown at level 0.242, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 3 as #9.4, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 4 as #9.5, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 5 as #9.6, grid size 300,300,300,
pixel 1.24, shown at level 0.0648, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 6 as #9.7, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 7 as #9.8, grid size 300,300,300,
pixel 1.24, shown at level 0.267, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 8 as #9.9, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian as #10, grid size
300,300,300, pixel 1.24, shown at level 0.0454, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc as #11, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 2, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian as #13,
grid size 300,300,300, pixel 1.24, shown at level 0.0777, step 1, values
float32
Opened cryosparc_P478_J315_map_sharp.mrc as #14, grid size 300,300,300, pixel
1.22, shown at level 0.113, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc as #15, grid size 300,300,300, pixel
1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 0 as #16.1, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 1 as #16.2, grid size 300,300,300,
pixel 1.22, shown at level 0.169, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 2 as #16.3, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 3 as #16.4, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 4 as #16.5, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 5 as #16.6, grid size 300,300,300,
pixel 1.22, shown at level 0.0643, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 6 as #16.7, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 7 as #16.8, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 8 as #16.9, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P930_J147_map_sharp (1).mrc as #17, grid size 300,300,300,
pixel 1.13, shown at level 0.134, step 1, values float32
Opened cryosparc_P818_J172_map_sharp.mrc as #18, grid size 300,300,300, pixel
1.24, shown at level 0.111, step 1, values float32
Opened cryosparc_P818_J172_map_sharp.mrc as #19, grid size 300,300,300, pixel
1.24, shown at level 0.208, step 1, values float32
Opened cryosparc_P930_J178_map_sharp.mrc as #3.1.1.1, grid size 300,300,300,
pixel 1.13, shown at level 0.318, step 1, values float32
Restoring stepper: trimer_1_real_space_refined_020_real_space_refined_022.pdb
Log from Fri Apr 26 17:30:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE one.cxs"
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 as #6.1, grid size
300,300,300, pixel 1.22, shown at level 0.122, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 2 as #6.3, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 3 as #6.4, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 4 as #6.5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 5 as #6.6, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 6 as #6.7, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 7 as #6.8, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 8 as #6.9, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian as #7, grid
size 300,300,300, pixel 1.22, shown at level 0.0796, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc as #8, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 as #9.1, grid size 300,300,300,
pixel 1.24, shown at level 0.108, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 1 as #9.2, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 2 as #9.3, grid size 300,300,300,
pixel 1.24, shown at level 0.242, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 3 as #9.4, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 4 as #9.5, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 5 as #9.6, grid size 300,300,300,
pixel 1.24, shown at level 0.0648, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 6 as #9.7, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 7 as #9.8, grid size 300,300,300,
pixel 1.24, shown at level 0.267, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 8 as #9.9, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian as #10, grid size
300,300,300, pixel 1.24, shown at level 0.0454, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc as #11, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 2, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian as #13,
grid size 300,300,300, pixel 1.24, shown at level 0.0777, step 1, values
float32
Opened cryosparc_P478_J315_map_sharp.mrc as #14, grid size 300,300,300, pixel
1.22, shown at level 0.113, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc as #15, grid size 300,300,300, pixel
1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 0 as #16.1, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 1 as #16.2, grid size 300,300,300,
pixel 1.22, shown at level 0.169, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 2 as #16.3, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 3 as #16.4, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 4 as #16.5, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 5 as #16.6, grid size 300,300,300,
pixel 1.22, shown at level 0.0643, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 6 as #16.7, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 7 as #16.8, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 8 as #16.9, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P930_J147_map_sharp (1).mrc as #17, grid size 300,300,300,
pixel 1.13, shown at level 0.134, step 1, values float32
Opened cryosparc_P818_J172_map_sharp.mrc as #18, grid size 300,300,300, pixel
1.24, shown at level 0.111, step 1, values float32
Opened cryosparc_P818_J172_map_sharp.mrc as #19, grid size 300,300,300, pixel
1.24, shown at level 0.208, step 1, values float32
Opened cryosparc_P930_J178_map_sharp.mrc as #3.1.1.1, grid size 300,300,300,
pixel 1.13, shown at level 0.318, step 1, values float32
Restoring stepper: trimer_1_real_space_refined_020_real_space_refined_022.pdb
Log from Fri Mar 8 17:22:54 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/478/hPtch_SHHFL_478_31_6.pdb"
Summary of feedback from opening C:/Users/lucre/OneDrive -
Nexus365/OXFORD/cryoEM_processing/478/hPtch_SHHFL_478_31_6.pdb
---
warnings | Cannot find LINK/SSBOND residue CS (1 )
Cannot find LINK/SSBOND residue CS (1 )
Chain information for hPtch_SHHFL_478_31_6.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> set bgColor white
> show atoms
> hide atoms
> lighting soft
> select /A
7959 atoms, 8165 bonds, 1 pseudobond, 998 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select /B
7925 atoms, 8139 bonds, 1 pseudobond, 984 residues, 2 models selected
> color sel deep pink
> select /C
1423 atoms, 1454 bonds, 17 pseudobonds, 179 residues, 2 models selected
> color sel light goldenrod yellow
> color sel light coral
> color sel khaki
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/P818/PTCH1_pSHH_HHIP-C_apo_f.pdb"
Chain information for PTCH1_pSHH_HHIP-C_apo_f.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!1 models
> hide #!2 atoms
> select #2/A
7957 atoms, 8163 bonds, 1 pseudobond, 999 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select #2/B
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> color sel medium purple
> color sel dark orchid
> select #2/C
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> color sel khaki
> select ::name="CLR"
139 atoms, 154 bonds, 5 residues, 2 models selected
> show sel & #!2 atoms
> color sel lawn green
> color sel byhetero
> color sel pale violet red
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.21
Changed 154 bond radii
> size =sel stickRadius 0.22
Changed 154 bond radii
> size =sel stickRadius 0.23
Changed 154 bond radii
> size =sel stickRadius 0.24
Changed 154 bond radii
> size =sel stickRadius 0.25
Changed 154 bond radii
> size =sel stickRadius 0.26
Changed 154 bond radii
> size =sel stickRadius 0.27
Changed 154 bond radii
> size =sel stickRadius 0.28
Changed 154 bond radii
> size =sel stickRadius 0.29
Changed 154 bond radii
> size =sel stickRadius 0.3
Changed 154 bond radii
> size =sel stickRadius 0.31
Changed 154 bond radii
> size =sel stickRadius 0.32
Changed 154 bond radii
> size =sel stickRadius 0.33
Changed 154 bond radii
> size =sel stickRadius 0.34
Changed 154 bond radii
> size =sel stickRadius 0.35
Changed 154 bond radii
> size =sel stickRadius 0.36
Changed 154 bond radii
> size =sel stickRadius 0.37
Changed 154 bond radii
> size =sel stickRadius 0.38
Changed 154 bond radii
> size =sel stickRadius 0.39
Changed 154 bond radii
> size =sel stickRadius 0.4
Changed 154 bond radii
> color sel & #!2 byhetero
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/P930/trimerok.pdb"
Summary of feedback from opening C:/Users/lucre/OneDrive -
Nexus365/OXFORD/cryoEM_processing/P930/trimerok.pdb
---
warning | Ignored bad PDB record found on line 66
Chain information for trimerok.pdb #3
---
Chain | Description
A | No description available
C | No description available
D | No description available
> hide #!2 models
> select add #2
13166 atoms, 13412 bonds, 41 pseudobonds, 1733 residues, 4 models selected
> select subtract #2
111 atoms, 123 bonds, 4 residues, 1 model selected
> select add #1
17391 atoms, 17758 bonds, 30 pseudobonds, 2245 residues, 3 models selected
> select add #2
30446 atoms, 31047 bonds, 71 pseudobonds, 3974 residues, 6 models selected
> select add #3
40510 atoms, 41431 bonds, 80 pseudobonds, 5225 residues, 9 models selected
> hide sel & #!3 atoms
> select #1/A#2/A#3/A
23818 atoms, 24500 bonds, 10 pseudobonds, 2979 residues, 6 models selected
> color sel royal blue
> select #1/C#2/C#3/C
4144 atoms, 4233 bonds, 18 pseudobonds, 518 residues, 5 models selected
> color sel khaki
> select #1/A
7959 atoms, 8165 bonds, 1 pseudobond, 998 residues, 2 models selected
> color sel deep pink
> select #2/B
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> select #2/B
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> color sel dark violet
> select #3/D
801 atoms, 823 bonds, 99 residues, 1 model selected
> color sel orange
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> show sel & #!3 atoms
> ui tool show "Selection Inspector"
Cannot increment value
> size =sel stickRadius 0.4
Changed 185 bond radii
> color sel pale violet red
> color sel & #!3 byhetero
> color sel plum
> color sel violet
> color sel turquoise
> color sel orchid
> color sel medium violet red
> color sel byhetero
> color sel dark violet
> color sel byhetero
> lighting soft
> graphics silhouettes true
> color sel salmon
> color sel byhetero
> select ::name="PLM"
51 atoms, 48 bonds, 3 residues, 3 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.4
Changed 48 bond radii
> show sel & #!3 atoms
> color sel & #!3 byhetero
> color sel magenta
> color sel byhetero
> ui mousemode right select
> select ::name="XXX"
232 atoms, 258 bonds, 3 residues, 3 models selected
> color sel salmon
> show sel & #!3 atoms
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.4
Changed 258 bond radii
> color sel byhetero
> select clear
> close #3
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/P930/RealSpaceRefine_23/hhip_ptch_shh_FINALFINAL3_real_space_refined_095_real_space_refined_023.pdb"
Chain information for
hhip_ptch_shh_FINALFINAL3_real_space_refined_095_real_space_refined_023.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close #3
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/P930/RealSpaceRefine_22/trimer_1_real_space_refined_020_real_space_refined_022.pdb"
Chain information for
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3
---
Chain | Description
A | No description available
B | No description available
D | No description available
> select add #3
10118 atoms, 10375 bonds, 24 pseudobonds, 1260 residues, 3 models selected
> hide sel atoms
> select #3/D
827 atoms, 849 bonds, 102 residues, 1 model selected
> color sel orange
> select #3/A
7956 atoms, 8166 bonds, 1 pseudobond, 988 residues, 2 models selected
> color sel royal blue
> select #3/B
1316 atoms, 1343 bonds, 17 pseudobonds, 167 residues, 2 models selected
> color sel khaki
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> show sel & #!3 atoms
> color sel light pink
> color sel salmon
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.4
Changed 185 bond radii
> color sel byhetero
> select ::name="PLM"
51 atoms, 48 bonds, 3 residues, 3 models selected
> show sel & #!3 atoms
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.4
Changed 48 bond radii
> color sel magenta
> color sel byhetero
> select ::name="XXX"
232 atoms, 258 bonds, 3 residues, 3 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.4
Changed 258 bond radii
> show sel & #!3 atoms
> color sel salmon
> color sel byhetero
> select ::name="PLM"
51 atoms, 48 bonds, 3 residues, 3 models selected
> color sel khaki
> color sel byhetero
> size =sel stickRadius 0.5
Changed 48 bond radii
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> color sel byhetero
> show sel & #!3 atoms
> size sel atomRadius 1.5
Changed 6 atom radii
> select ::name="ZN"
10 atoms, 10 residues, 3 models selected
> size sel atomRadius 1
Changed 10 atom radii
> show sel & #!3 atoms
> color sel byhetero
> select subtract #3/B:1@ZN
9 atoms, 9 residues, 3 models selected
> select clear
> select #3/E:2@ZN
1 atom, 1 residue, 1 model selected
> select add #3/E:1@ZN
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select #3/B:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #3/B:25
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #3/B:27
14 atoms, 11 bonds, 3 residues, 1 model selected
> select add #3/B:26
21 atoms, 18 bonds, 4 residues, 1 model selected
> select add #3/B:28
32 atoms, 28 bonds, 5 residues, 1 model selected
> select add #3/B:29
36 atoms, 31 bonds, 6 residues, 1 model selected
> select add #3/B:30
47 atoms, 42 bonds, 7 residues, 1 model selected
> select add #3/B:31
51 atoms, 45 bonds, 8 residues, 1 model selected
> select add #3/B:32
60 atoms, 53 bonds, 9 residues, 1 model selected
> size =sel stickRadius 0.4
Changed 53 bond radii
> size sel ballScale 0.26
Changed 1 ball scales
> size sel ballScale 0.27
Changed 1 ball scales
> size sel ballScale 0.28
Changed 1 ball scales
> size sel ballScale 0.29
Changed 1 ball scales
> size sel atomRadius 1.8
Changed 60 atom radii
> size =sel stickRadius 1
Changed 53 bond radii
> setattr sel r thin_rings true
Assigning thin_rings attribute to 9 items
> setattr sel r thin_rings false
Assigning thin_rings attribute to 9 items
> select clear
> show #!1 models
> hide #!3 models
> select add #1
17391 atoms, 17758 bonds, 30 pseudobonds, 2245 residues, 3 models selected
> select add #2
30446 atoms, 31047 bonds, 71 pseudobonds, 3974 residues, 6 models selected
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> show sel & #!1 atoms
> select clear
> select #1/A:138
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
108 atoms, 108 bonds, 12 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4366 atoms, 4468 bonds, 553 residues, 1 model selected
> select up
7931 atoms, 8134 bonds, 997 residues, 1 model selected
> color sel royal blue
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select #1/C:202@C10
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel khaki
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.5
Changed 30 bond radii
> select ::name="PLM"
51 atoms, 48 bonds, 3 residues, 3 models selected
> show sel & #!1 atoms
> select clear
[Repeated 2 time(s)]
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #1/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> select clear
> select #1/B:1501@C17
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
7925 atoms, 8139 bonds, 984 residues, 1 model selected
> select down
28 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/B:1502@C12
29 atoms, 31 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select up
58 atoms, 63 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel light pink
> color sel lawn green
> color sel byhetero
> show #!3 models
> hide #!3 models
> color sel spring green
> color sel byhetero
> color sel yellow
> color sel byhetero
> color sel yellow green
> color sel byhetero
> color sel hot pink
> color sel cornflower blue
> color sel cyan
> color sel byhetero
> select clear
> undo
> color sel gold
> color sel byhetero
> color sel medium orchid
> color sel pale violet red
> color sel aquamarine
> color sel light coral
> color sel byhetero
> select clear
> undo
> color sel medium aquamarine
> color sel byhetero
> select clear
> undo
> color sel magenta
> color sel byhetero
[Repeated 1 time(s)]
> select clear
> undo
> color sel cyan
> color sel byhetero
> color sel chocolate
> color sel coral
> color sel byhetero
> select clear
> undo
> color sel yellow
> color sel byhetero
> select clear
> undo
> color sel green yellow
> color sel byhetero
> select clear
> undo
> color sel dark orange
> color sel orange
> color sel light salmon
> color sel byhetero
> select clear
> undo
> color sel aquamarine
> color sel byhetero
> select clear
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> show sel & #!1 atoms
> select ::name="ZN"
10 atoms, 10 residues, 3 models selected
> show sel & #!1 atoms
> select clear
> select #1/E:2@ZN
1 atom, 1 residue, 1 model selected
> select add #1/E:1@ZN
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #1/E:3@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> toolshed show
ARB::createContext: wglCreateContextAttribsARB() failed (GL error code: 0x0)
for format: QSurfaceFormat(version 2.0, options
QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize 24, redBufferSize -1,
greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize
8, samples -1, swapBehavior QSurfaceFormat::DoubleBuffer, swapInterval 1,
colorSpace QColorSpace(), profile QSurfaceFormat::NoProfile), shared context:
0x30000 (The operation completed successfully.)
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:197@O
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> bond #1/C:197,#1/C:202
Missing or invalid "atoms" argument: only initial part "#1/C:197" of atom
specifier valid
> bond #1/C:197 #1/C:202
Created 0 bonds
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right "link markers"
> ui mousemode right select
> select clear
> ui mousemode right "mark maximum"
> ui mousemode right "mark point"
> marker #4 position 187.6,127.9,206.7 color yellow radius 1
> marker #4 position 187.5,126.2,205.6 color yellow radius 1
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> marker change #4:2 position 180.5,124.1,208.6
> marker change #4:2 position 178.9,125.4,207.7
> marker change #4:2 position 179,125.5,207.5
> marker change #4:1 position 187.6,127.9,206.7
> marker change #4:1 position 185.5,124.2,208.3
> marker change #4:1 position 180.2,126.6,209.1
> marker change #4:1 position 180,127.3,208.6
> ui mousemode right "resize markers"
> marker change #4:2 radius 0.316
> marker change #4:2 radius 0.2671
> marker change #4:1 radius 1
> ui mousemode right "move markers"
> marker change #4:2 position 179.3,125.7,207.9
> marker change #4:1 position 180.2,127.4,208.3
> ui mousemode right "resize markers"
> marker change #4:1 radius 1
> marker change #4:1 radius 1.866
> marker change #4:1 radius 0.2526
> ui mousemode right "move markers"
> marker change #4:1 position 180.3,127.2,208.5
> marker change #4:1 position 180.4,127.2,208.3
> ui mousemode right select
> select add #4/M:1@M
2 atoms, 2 residues, 1 model selected
> ui mousemode right "link markers"
> marker link #4:2,1 color #659cef radius 0.5
> ui mousemode right "resize markers"
> marker change #4:2,1 radius 0.2595 markers false
> color sel khaki
> marker change #4:2 radius 0.2671
> ui mousemode right select
> select clear
> undo
> select #1/B:1502@C10
1 atom, 1 residue, 1 model selected
> select #1/B:1502@C10
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/B:1502@C8
29 atoms, 31 bonds, 2 residues, 1 model selected
> select subtract #1/B:1502@C8
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select add #1/A:1501@C3
57 atoms, 62 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel yellow
> color sel byhetero
> color sel cyan
> color sel magenta
> color sel cyan
> color sel yellow
> color sel magenta
> color sel hot pink
> color sel pale violet red
> color sel light steel blue
> color sel pale turquoise
> color sel orange
> color sel orange red
> color sel gold
> color sel byhetero
> select clear
> undo
> color sel yellow
> color sel byhetero
> select clear
> show #!2 models
> hide #!1 models
> hide #4 models
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> color sel yellow
> color sel byhetero
> select ::name="PLM"
51 atoms, 48 bonds, 3 residues, 3 models selected
> show sel & #!2 atoms
> select #2/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
[Repeated 1 time(s)]
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> select #2/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select #2/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #2/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> select #2/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> undo
[Repeated 5 time(s)]
> select clear
> select #2/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> select #2/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select ::name="XXX"
232 atoms, 258 bonds, 3 residues, 3 models selected
> show sel & #!2 atoms
> select clear
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> show sel & #!2 atoms
> select ::name="ZN"
10 atoms, 10 residues, 3 models selected
> show sel & #!2 atoms
> select subtract #2/L:2@ZN
9 atoms, 9 residues, 3 models selected
> hide sel & #!2 atoms
> select clear
> hide #!2 models
> show #!1 models
> select #1/B:190
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
37 atoms, 38 bonds, 4 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel royal blue
> select clear
> select #1/A:1501@C4
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
7925 atoms, 8139 bonds, 984 residues, 1 model selected
> select add #1/A:1501@C3
7926 atoms, 8139 bonds, 985 residues, 1 model selected
> select up
7953 atoms, 8170 bonds, 985 residues, 1 model selected
> select #1/B:1501@C13
1 atom, 1 residue, 1 model selected
> select #1/B:1501@C9
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/B:1502@C10
29 atoms, 31 bonds, 2 residues, 1 model selected
> select add #1/B:1502@C9
30 atoms, 31 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select up
58 atoms, 63 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel salmon
> color sel byhetero
> color sel dark salmon
> color sel byhetero
> color sel coral
> color sel byhetero
> select clear
> select #1/C:202@C3
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> show #4 models
> color sel khaki
> color sel byhetero
> select clear
> undo
[Repeated 2 time(s)]
> select clear
> select #1/B:1501@C17
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select add #1/A:1501@C3
57 atoms, 62 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel gold
> color sel byhetero
> color sel light salmon
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select #1/B:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel deep pink
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/B:1502@C10
29 atoms, 31 bonds, 2 residues, 1 model selected
> select add #1/B:1502@C5
30 atoms, 31 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select up
58 atoms, 63 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> hide #4 models
> show #!2 models
> hide #!1 models
> select #2/C:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> color sel dark salmon
> color sel byhetero
> show #!1 models
> hide #!2 models
> select clear
> select #1/B:398
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel teal
> color sel turquoise
> color sel dodger blue
> color sel dark olive green
> color sel royal blue
> select clear
> show #4 models
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> color sel deep pink
> color sel byhetero
> color sel hot pink
> color sel medium orchid
> color sel blue violet
> color sel hot pink
> color sel deep pink
> select clear
> undo
> color sel light coral
> color sel byhetero
> select clear
> undo
> color sel magenta
> color sel light salmon
> color sel salmon
> color sel byhetero
> select #1/A:1022
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:202@C5
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel khaki
> select clear
> select #1/B:364
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
60 atoms, 60 bonds, 7 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel light steel blue
> color sel salmon
> color sel deep sky blue
> color sel sea green
> color sel forest green
> color sel olive drab
> color sel green yellow
> select clear
> undo
> color sel fire brick
> color sel red
> color sel lime green
> color sel dark cyan
> select clear
> undo
> color sel deep pink
> select clear
> select #1/B:1501@C22
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select add #1/A:1501@C3
57 atoms, 62 bonds, 3 residues, 1 model selected
> select add #1/A:1501@O1
58 atoms, 62 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #1/C:166
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color sel dark sea green
> color sel green yellow
> color sel cyan
> color sel deep sky blue
> color sel red
> color sel orange red
> color sel crimson
> color sel fire brick
> color sel chocolate
> color sel coral
> color sel indian red
> color sel turquoise
> color sel medium spring green
> color sel pale violet red
> color sel lavender
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel sandy brown
> color sel cyan
> color sel deep sky blue
> color sel dark turquoise
> color sel turquoise
> color sel light blue
> color sel wheat
> color sel khaki
> color sel byhetero
> select clear
> view name 2to1
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/478/maps/cryosparc_P478_J216_010_volume_map_sharp.mrc"
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.22, shown at level 0.107, step 2, values float32
> volume #5 step 1
> ui tool show "Color Zone"
> undo
> color sel khaki
> select clear
> select #1/C:202@C3
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> view name 2to1
> view list
Named views: 2to1
> view 2to1
[Repeated 2 time(s)]
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> color sel light pink
> color sel aquamarine
> color sel byhetero
> select clear
> undo
> color sel light pink
> color sel byhetero
> select clear
> undo
> color sel medium spring green
> select clear
> undo
> color sel byhetero
> select clear
> select #1/C:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
132 atoms, 131 bonds, 17 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> undo
> color sel yellow
> select clear
> select #1/C:202@C3
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> view 2to1
> view name 2to1
> show #!5 models
> color zone #5 near #1 distance 5
> surface dust #5 size 12.2
> volume #5 level 0.3215
> color single #5
> select #1/A:564
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 138 bonds, 20 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4366 atoms, 4468 bonds, 553 residues, 1 model selected
> select up
7931 atoms, 8134 bonds, 997 residues, 1 model selected
> color sel royal blue
> color zone #5 near #1 distance 5
> select ::name="XXX"
232 atoms, 258 bonds, 3 residues, 3 models selected
> color sel medium spring green
> color sel byhetero
> color single #5
> color zone #5 near #1 distance 5
> color single #5
> select #1/A:561
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 138 bonds, 20 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4366 atoms, 4468 bonds, 553 residues, 1 model selected
> select up
7931 atoms, 8134 bonds, 997 residues, 1 model selected
> color sel royal blue
[Repeated 1 time(s)]
> select #1/B:451
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
117 atoms, 118 bonds, 16 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel deep pink
[Repeated 1 time(s)]
> select clear
> color zone #5 near #1 distance 5
> volume #5 level 0.4051
> select
40566 atoms, 41423 bonds, 95 pseudobonds, 5236 residues, 12 models selected
> hide sel & #4#!1 atoms
> undo
> show sel & #4#!1 atoms
> hide sel & #4#!1 atoms
> select ::name="HOH"
179 atoms, 179 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> color single #5
> color zone #5 near #1 distance 5
> view 2to1
> volume #5 level 0.3932
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #5 level 0.3693
> save C:\ProgramData\ChimeraX\image661.png supersample 3
> show #!1 models
> hide #!5 models
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> show sel & #!1 atoms
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> show sel & #!1 atoms
> select ::name="NA"
3 atoms, 3 residues, 1 model selected
> select ::name="PLM"
51 atoms, 48 bonds, 3 residues, 3 models selected
> show sel & #!1 atoms
> select ::name="ZN"
10 atoms, 10 residues, 3 models selected
> show sel & #!1 atoms
> select clear
> select #1/E:2@ZN
1 atom, 1 residue, 1 model selected
> select add #1/E:1@ZN
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #4 models
> show #4 models
> select add #4
6 atoms, 4 bonds, 3 residues, 2 models selected
> select add #1
17312 atoms, 17759 bonds, 27 pseudobonds, 2166 residues, 4 models selected
> select subtract #1
2 atoms, 1 bond, 2 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
2 atoms, 1 bond, 2 residues, 1 model selected
> color #4 yellow
> hide #4 models
> show #4 models
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right "mark point"
> marker #4 position 158.3,125.9,215.8 color yellow radius 0.2526
> ui mousemode right "move markers"
> marker change #4:3 position 164.8,138.2,212.6
> marker change #4:3 position 165.6,131.3,217.5
> marker change #4:3 position 173.7,138.3,213
> marker change #4:3 position 180.4,130.5,209.7
> marker change #4:3 position 179,127.3,208.7
> marker change #4:3 position 180.1,127.1,207.9
> marker change #4:3 position 180.2,126.8,208.3
> ui mousemode right "mark point"
> marker #4 position 145.9,150.2,216 color yellow radius 0.2526
> marker #4 position 145.8,150.1,216.1 color yellow radius 0.2526
> ui mousemode right "delete markers"
> marker delete #4:5
> ui mousemode right "move markers"
> marker change #4:4 position 186.4,142,216.2
> marker change #4:4 position 173.4,131.7,207.1
> marker change #4:4 position 179.3,131,209.5
> marker change #4:4 position 181.4,126.6,207.7
> marker change #4:4 position 179.4,125.7,208.1
> marker change #4:4 position 179.3,125.7,208
> marker change #4:3 position 180.3,126.8,208.2
> ui mousemode right "link markers"
> marker link #4:3,4 color #659cef radius 0.2595
> color sel yellow
> ui mousemode right "move markers"
> marker change #4:4 position 179.3,125.7,207.9
> ui mousemode right select
> select clear
> volume splitbyzone #5
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 as #6.1, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 2 as #6.3, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 3 as #6.4, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 4 as #6.5, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 5 as #6.6, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 6 as #6.7, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 7 as #6.8, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 8 as #6.9, grid size
300,300,300, pixel 1.22, shown at level 0.369, step 1, values float32
> surface dust #6.1 size 12.2
> surface dust #6.2 size 12.2
> surface dust #6.3 size 12.2
> surface dust #6.4 size 12.2
> surface dust #6.5 size 12.2
> surface dust #6.6 size 12.2
> surface dust #6.7 size 12.2
> surface dust #6.8 size 12.2
> surface dust #6.9 size 12.2
> volume #6.1 level 0.122
> ui tool show "Map Filter"
QWindowsWindow::setGeometry: Unable to set geometry 1920x1007+0+35 (frame:
1942x1063-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 619x671 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=951,
y=1063)))
> volume gaussian #6.1 sDev 4.18
Opened cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian as #7, grid
size 300,300,300, pixel 1.22, shown at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1457+0+35 (frame:
1942x1513-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 619x971 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=951,
y=1513)))
> hide #!6 models
> transparency #7.1 50
> color #7 white models
> show #!6 models
> hide #!1 models
> hide #4 models
> save C:\ProgramData\ChimeraX\image662.png supersample 3
> show #!1 models
> hide #!6 models
> hide #!7 models
> save C:\ProgramData\ChimeraX\image663.png supersample 3
> hide #!1 models
> show #!2 models
> select #2/C:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
103 atoms, 103 bonds, 13 residues, 1 model selected
> select up
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> color sel yellow
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/hhip/EMmaps/cryosparc_P818_cryosparc_P818_J83_012_volume_map_sharp.mrc"
Opened cryosparc_P818_cryosparc_P818_J83_012_volume_map_sharp.mrc as #8, grid
size 300,300,300, pixel 1.24, shown at level 0.143, step 2, values float32
> volume #8 step 1
> volume #8 level 0.5476
> close #8
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/hhip/EMmaps/cryosparc_P818_J131_map_sharp
> (1).mrc"
Opened cryosparc_P818_J131_map_sharp (1).mrc as #8, grid size 300,300,300,
pixel 1.24, shown at level 0.00979, step 2, values float32
> volume #8 step 1
> volume #8 level 0.3469
> surface dust #8 size 12.4
> ui tool show "Color Zone"
> color zone #8 near #2 distance 7.46
> color single #8
> select ::name="HOH"
98 atoms, 98 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color zone #8 near #2 distance 7.46
> volume #8 level 0.3116
> volume #8 level 0.2567
> volume #8 level 0.2881
> hide #!2 models
> save C:\ProgramData\ChimeraX\image664.png supersample 3
> show #!2 models
> volume splitbyzone #8
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 as #9.1, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 1 as #9.2, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 2 as #9.3, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 3 as #9.4, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 4 as #9.5, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 5 as #9.6, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 6 as #9.7, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 7 as #9.8, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
Opened cryosparc_P818_J131_map_sharp (1).mrc 8 as #9.9, grid size 300,300,300,
pixel 1.24, shown at level 0.288, step 1, values float32
> surface dust #9.1 size 12.4
> surface dust #9.2 size 12.4
> surface dust #9.3 size 12.4
> surface dust #9.4 size 12.4
> surface dust #9.5 size 12.4
> surface dust #9.6 size 12.4
> surface dust #9.7 size 12.4
> surface dust #9.8 size 12.4
> surface dust #9.9 size 12.4
> volume #9.1 level 0.1084
> volume gaussian #9.1 sDev 4.18
Opened cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian as #10, grid size
300,300,300, pixel 1.24, shown at step 1, values float32
> volume #10 color white
> hide #!9 models
> transparency #10.1 50
> volume #10 level 0.04497
> volume #10 level 0.04543
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/hhip/EMmaps/cryosparc_P818_J127_005_volume_map_sharp
> (1).mrc"
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc as #11, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 2, values float32
> color zone #8 near #2 distance 7.46
> undo
> color zone #11 near #2 distance 5
> volume splitbyzone #11
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 as #12.1, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 1 as #12.2, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 2 as #12.3, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 3 as #12.4, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 4 as #12.5, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 5 as #12.6, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 6 as #12.7, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 7 as #12.8, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 8 as #12.9, grid size
300,300,300, pixel 1.24, shown at level 0.252, step 1, values float32
> surface dust #10 size 12.4
> surface dust #12.1 size 12.4
> surface dust #12.2 size 12.4
> surface dust #12.3 size 12.4
> surface dust #12.4 size 12.4
> surface dust #12.5 size 12.4
> surface dust #12.6 size 12.4
> surface dust #12.7 size 12.4
> surface dust #12.8 size 12.4
> surface dust #12.9 size 12.4
> volume #12.1 level 0.1152
> volume #12.1 level 0.2322
> volume gaussian #12.1 sDev 4.18
Opened cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian as #13,
grid size 300,300,300, pixel 1.24, shown at step 1, values float32
> volume #13 level 0.07768
> close #12.2
> close #12.3
> close #12.4
> close #12.5
> close #12.6
> close #12.7
> close #12.8
> close #12.9
> close #12.1
> volume #13 color white
> transparency #13.1 50
> hide #!2 models
> volume #9.3 level 0.1527
> volume #9.3 level 0.04025
> volume #9.3 level 0.242
> volume #9.6 level 0.06482
> volume #9.8 level 0.2666
> volume #8 level 0.2519
> volume #8 level 0.2809
> volume #8 level 0.2881
> save C:\ProgramData\ChimeraX\image665.png supersample 3
> hide #!13 models
> hide #12 models
> hide #!8 models
> show #!2 models
> save C:\ProgramData\ChimeraX\image666.png supersample 3
QWindowsWindow::setGeometry: Unable to set geometry 999x155+998+260 (frame:
1021x211+987+215) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 995x146+1000+267 (frame:
1017x202+989+222) margins: 11, 45, 11, 11 minimum size: 142x72 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=235, y=164)))
QWindowsWindow::setGeometry: Unable to set geometry 995x146+1526+276 (frame:
1013x193+1517+238) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 999x155+1524+269 (frame:
1017x202+1515+231) margins: 9, 38, 9, 9 minimum size: 142x72 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=196, y=137)))
QWindowsWindow::setGeometry: Unable to set geometry 999x155+1275+441 (frame:
1021x211+1264+396) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 995x146+1277+448 (frame:
1017x202+1266+403) margins: 11, 45, 11, 11 minimum size: 142x72 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=235, y=164)))
> show #!8 models
> hide #!2 models
> save C:\ProgramData\ChimeraX\image667.png supersample 3
> save C:\ProgramData\ChimeraX\image668.png supersample 3
> hide #!8 models
> hide #!13 models
> show #!7 models
> show #!1 models
> hide #!1 models
> open C:/Users/lucre/Downloads/cryosparc_P478_J314__localfilter.mrc
Opened cryosparc_P478_J314__localfilter.mrc as #14, grid size 300,300,300,
pixel 1.22, shown at level 0.0957, step 2, values float32
> volume #14 step 1
> volume #14 level 0.1864
> close #14
> show #!5 models
> view 2to1
> volume #7 level 0.08161
> volume #7 level 0.07957
> save C:\ProgramData\ChimeraX\image669.png supersample 3
> open C:/Users/lucre/Downloads/cryosparc_P478_J315_map_sharp.mrc
Opened cryosparc_P478_J315_map_sharp.mrc as #14, grid size 300,300,300, pixel
1.22, shown at level 0.00212, step 2, values float32
> hide #!5 models
> hide #!7 models
> volume #14 level 0.06715
> volume #14 step 1
> volume #14 level 0.1826
> show #!5 models
> color zone #14 near #1 distance 7.35
> hide #!5 models
> surface dust #14 size 12.2
> volume #14 level 0.1074
> open C:/Users/lucre/Downloads/cryosparc_P478_J315_map_sharp.mrc
Opened cryosparc_P478_J315_map_sharp.mrc as #15, grid size 300,300,300, pixel
1.22, shown at level 0.00212, step 2, values float32
> volume #15 step 1
> volume #15 level 0.1686
> color zone #15 near #1 distance 7.35
> volume #15 level 0.2115
> volume #14 level 0.1343
> show #!7 models
> volume #15 level 0.1928
> volume #14 level 0.1128
> color zone #15 near #1 distance 7.35
> color zone #15 near #1 distance 12.24
[Repeated 1 time(s)]
> hide #!7 models
> hide #!14 models
> show #!1 models
> select #1/B:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> select clear
> select #1/B:1501@C17
1 atom, 1 residue, 1 model selected
> select #1/B:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
117 atoms, 118 bonds, 16 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel hot pink
> color sel pale violet red
> color sel light pink
> select clear
> select #1/B:1502@C9
1 atom, 1 residue, 1 model selected
> select #1/B:1502@C8
1 atom, 1 residue, 1 model selected
> select ::name="CLR"
167 atoms, 185 bonds, 6 residues, 3 models selected
> select clear
> select #1/B:1501@C17
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/B:1502@C8
29 atoms, 31 bonds, 2 residues, 1 model selected
> select up
30 atoms, 32 bonds, 2 residues, 1 model selected
> select up
56 atoms, 62 bonds, 2 residues, 1 model selected
> select add #1/A:1501@C3
57 atoms, 62 bonds, 3 residues, 1 model selected
> select up
58 atoms, 63 bonds, 3 residues, 1 model selected
> select up
84 atoms, 93 bonds, 3 residues, 1 model selected
> color sel dark violet
> color sel byhetero
> select clear
> select #1/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
80 atoms, 80 bonds, 10 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4366 atoms, 4468 bonds, 553 residues, 1 model selected
> select up
7931 atoms, 8134 bonds, 997 residues, 1 model selected
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light blue
> select clear
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> color sel black
> select clear
> select add #1/C:204@CA
1 atom, 1 residue, 1 model selected
> select add #1/C:205@CA
2 atoms, 2 residues, 1 model selected
> color sel forest green
> select clear
> show #4 models
> select #1/C:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color sel dark goldenrod
> color sel dark orange
> color sel maroon
> color sel goldenrod
> color sel yellow
> undo
[Repeated 4 time(s)]
> select clear
> select #1/C:202@C8
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel blue violet
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #1/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Side View"
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right "link markers"
> ui mousemode right "mark point"
> marker #4 position 179.2,170,217.9 color yellow radius 0.2526
> marker #4 position 179,169.7,219.4 color yellow radius 0.2526
> ui mousemode right "move markers"
> marker change #4:6 position 179,169.8,217.6
> marker change #4:7 position 178.8,169.5,219
> marker change #4:7 position 178.9,169.5,218.9
> marker change #4:6 position 178.7,170,217.6
> marker change #4:6 position 178.7,170.1,217.7
> ui mousemode right "link markers"
> marker link #4:7,6 color #659cef radius 0.2595
> color sel yellow
> ui mousemode right select
> select #1/C:24@SG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:24@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> view 2to1
> view name 2to1
> select clear
[Repeated 1 time(s)]
> select #1/E:3@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save C:\ProgramData\ChimeraX\image670.png supersample 3
> save C:\ProgramData\ChimeraX\image671.png supersample 3
> hide #!1 models
> hide #4 models
> show #!7 models
> show #!5 models
> hide #!5 models
> show #!15 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!14 models
> save C:\ProgramData\ChimeraX\image672.png supersample 3
> hide #!14 models
> show #!15 models
> volume #15 level 0.09609
> volume #15 level 0.1283
> volume splitbyzone #15
Opened cryosparc_P478_J315_map_sharp.mrc 0 as #16.1, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 1 as #16.2, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 2 as #16.3, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 3 as #16.4, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 4 as #16.5, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 5 as #16.6, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 6 as #16.7, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 7 as #16.8, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
Opened cryosparc_P478_J315_map_sharp.mrc 8 as #16.9, grid size 300,300,300,
pixel 1.22, shown at level 0.128, step 1, values float32
> volume #16.2 level 0.1694
> volume #16.6 level 0.06433
> save C:\ProgramData\ChimeraX\image673.png supersample 3
> save C:\ProgramData\ChimeraX\image674.png supersample 3
> hide #!7 models
> hide #!16 models
> show #!2 models
> select ::name="ZN"
10 atoms, 10 residues, 3 models selected
> color sel black
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> color sel dark green
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
81 atoms, 90 bonds, 1 residue, 1 model selected
> select add #2/I:1@C3
82 atoms, 90 bonds, 2 residues, 1 model selected
> select up
109 atoms, 121 bonds, 2 residues, 1 model selected
> color sel dark violet
> color sel byhetero
> select clear
> select #2/A:564
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
137 atoms, 138 bonds, 20 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4316 atoms, 4418 bonds, 546 residues, 1 model selected
> select up
7957 atoms, 8163 bonds, 999 residues, 1 model selected
> color sel pale turquoise
> show #!1 models
> color sel sky blue
> color sel light sky blue
> color sel light steel blue
> color sel powder blue
> color sel light blue
> select clear
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #2/B:394
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> select up
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> color sel orchid
> select clear
> select #2/M:1@CA
1 atom, 1 residue, 1 model selected
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> color sel dark olive green
> color sel green
> select clear
> select ::name="CA"
6 atoms, 6 residues, 3 models selected
> color sel & #!2 byhetero
> select clear
> save C:\ProgramData\ChimeraX\image675.png supersample 3
> save C:\ProgramData\ChimeraX\image676.png supersample 3
> open "C:/Users/lucre/Downloads/cryosparc_P930_J147_map_sharp (1).mrc"
Opened cryosparc_P930_J147_map_sharp (1).mrc as #17, grid size 300,300,300,
pixel 1.13, shown at level 0.00143, step 2, values float32
> volume #17 step 1
> volume #17 level 0.2052
> hide #!2 models
> show #!3 models
> volume #17 level 0.1651
> surface dust #17 size 11.3
> volume #17 level 0.1342
> select #3/A:1511@C25
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
81 atoms, 90 bonds, 1 residue, 1 model selected
> select add #3/A:1503@C3
82 atoms, 90 bonds, 2 residues, 1 model selected
> select up
109 atoms, 121 bonds, 2 residues, 1 model selected
> color sel dark violet
> color sel byhetero
> select #3/A:144
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
108 atoms, 108 bonds, 12 residues, 1 model selected
> select up
4259 atoms, 4359 bonds, 539 residues, 1 model selected
> select up
4267 atoms, 4366 bonds, 540 residues, 1 model selected
> select up
7847 atoms, 8045 bonds, 986 residues, 1 model selected
> color sel light steel blue
> select clear
> select #3/B:159
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
108 atoms, 108 bonds, 14 residues, 1 model selected
> select up
1313 atoms, 1343 bonds, 164 residues, 1 model selected
> select up
1316 atoms, 1343 bonds, 167 residues, 1 model selected
> select up
10118 atoms, 10375 bonds, 1260 residues, 1 model selected
> select down
1316 atoms, 1343 bonds, 167 residues, 1 model selected
> color sel yellow
> undo
> select down
1313 atoms, 1343 bonds, 164 residues, 1 model selected
> color sel yellow
> select clear
> select #3/C:201@C3
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
10118 atoms, 10375 bonds, 1260 residues, 1 model selected
> select down
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> open C:/Users/lucre/Downloads/cryosparc_P818_J172_map_sharp.mrc
Opened cryosparc_P818_J172_map_sharp.mrc as #18, grid size 300,300,300, pixel
1.24, shown at level 0.00134, step 2, values float32
> volume #18 step 1
> volume #18 level 0.1334
> hide #!3 models
> color zone #18 near #2 distance 7.46
> surface dust #18 size 12.4
> volume #18 level 0.1169
> undo
> show #!2 models
> select #2/A:145
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
108 atoms, 108 bonds, 12 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4316 atoms, 4418 bonds, 546 residues, 1 model selected
> select up
7957 atoms, 8163 bonds, 999 residues, 1 model selected
> color sel royal blue
> select #2/B:295
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
38 atoms, 38 bonds, 4 residues, 1 model selected
> select up
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> select up
12957 atoms, 13289 bonds, 1631 residues, 1 model selected
> select down
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> color sel medium orchid
> color zone #18 near #2 distance 7.46
> hide #!2 models
> show #!13 models
> volume #18 level 0.1114
> save C:\ProgramData\ChimeraX\image677.png supersample 3
> open C:/Users/lucre/Downloads/cryosparc_P818_J172_map_sharp.mrc
Opened cryosparc_P818_J172_map_sharp.mrc as #19, grid size 300,300,300, pixel
1.24, shown at level 0.00134, step 2, values float32
> color zone #19 near #2 distance 7.46
> volume #19 step 1
> volume #19 level 0.1004
> volume #19 level 0.1334
> volume #19 level 0.1307
> volume #19 level 0.2298
> volume #19 level 0.2243
> volume #19 level 0.227
> volume #19 level 0.2077
> save C:\ProgramData\ChimeraX\image678.png supersample 3
> hide #!13 models
> open C:/Users/lucre/Downloads/cryosparc_P930_J178_map_sharp.mrc
Opened cryosparc_P930_J178_map_sharp.mrc as #20, grid size 300,300,300, pixel
1.13, shown at level 0.00143, step 2, values float32
> show #!3 models
> volume #20 step 1
> color zone #19 near #2 distance 5.77
> volume #20 level 0.1917
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 58 residues in model #3 to IUPAC-IUB
standards.
Chain information for
trimer_1_real_space_refined_020_real_space_refined_022.pdb
---
Chain | Description
3.2/A | No description available
3.2/B | No description available
3.2/D | No description available
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
> volume #!20 style mesh
Drag select of 20 cryosparc_P930_J178_map_sharp.mrc , 1 residues, 1 bonds
> select #20
2 models selected
> select clear
[Repeated 1 time(s)]
> isolde tutorial
> isolde sim start #3.2/A:1174,1178
> clipper associate #20 toModel #3
Opened cryosparc_P930_J178_map_sharp.mrc as #3.1.1.1, grid size 300,300,300,
pixel 1.13, shown at step 1, values float32
> isolde sim start #3.2/A:1174,1178
Sim termination reason: None
ISOLDE: stopped sim
> addh #3.2
Summary of feedback from adding hydrogens to
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2
---
notes | No usable SEQRES records for
trimer_1_real_space_refined_020_real_space_refined_022.pdb (#3.2) chain A;
guessing termini instead
No usable SEQRES records for
trimer_1_real_space_refined_020_real_space_refined_022.pdb (#3.2) chain B;
guessing termini instead
No usable SEQRES records for
trimer_1_real_space_refined_020_real_space_refined_022.pdb (#3.2) chain D;
guessing termini instead
Chain-initial residues that are actual N termini:
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/A LEU 79,
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/D PRO 826
Chain-initial residues that are not actual N termini:
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/A LEU 734,
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/B CYS 24
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/A ALA 1178,
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/A PHE 613,
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/B ALA 187,
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/D ARG 927
922 hydrogen bonds
Adding 'H' to trimer_1_real_space_refined_020_real_space_refined_022.pdb
#3.2/A LEU 734
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/A ALA 1178 is
not terminus, removing H atom from 'C'
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/B ALA 187 is
not terminus, removing H atom from 'C'
trimer_1_real_space_refined_020_real_space_refined_022.pdb #3.2/D ARG 927 is
not terminus, removing H atom from 'C'
10161 hydrogens added
Loading residue template for CLR from internal database
Loading residue template for PLM from internal database
Loading residue template for XXX from internal database
> isolde sim start #3.2/A:1178
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #3.2/A:1178
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui mousemode right select
> select clear
Drag select of 476 atoms, 1246 residues, 471 bonds, 24 pseudobonds
> isolde sim start #3.2/A:79-1178/B:24-187/C-D
Sim termination reason: None
ISOLDE: stopped sim
> isolde restrain ligands #3
> isolde sim start #3.2/A:79-1178,1504-1510,1512/B:24-187/C-D
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #3.2/A:79-1178,1504-1510,1512/B:24-187/C-D
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #3.2/A:79-1178,1504-1510,1512/B:24-187/C-D
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #3.2/A:79-1178,1504-1510,1512/B:24-187/C-D
Sim termination reason: None
ISOLDE: stopped sim
Fetching CCD XXX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/XXX/XXX.cif
Fetching CCD PLM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif
Deleted the following atoms from residue XXX A1511: H382, O12, C16, C29, C51,
C39, O5, C40, O21, H112, H511, H121, H3, H392, H35, H532, H14, H21, H8, O22,
C38, O10, O11, C14, C15, C28, C27, C53, H4, C26, C52, O9, HO12, H36, H391,
H152, H321, H522, C, C19, C25, C31, C54, C43, O15, H201, H211, H222, H2, H151,
H542, HO7, H262, H452, H48, H523, HO19, HO22, H28, O3, C42, O23, C41, O14,
C30, O13, C17, C18, H47, H221, H541, H22, C55, H231, H29, H44, O6, H16, HO8,
HO20, C21, C10, C7, C46, O18, C34, H191, H192, H242, H261, H543, H241, HO11,
H31, H49, H27, H42, H18, H311, H46, H7, H82, HO9, HO23, H50, C45, C44, O17,
C33, O16, C32, C20, O, H43, C8, H533, H37, H33, O8, H34, C48, H202, O7, H25,
H41, H81, H451, H6, H512, O1, C13, C24, C49, O20, C37, H122, H111, H13, H32,
H521, H9, H232, HO15, H531, H30, HO21, C47, O2, O4, C36, O19, C35, C9, C11,
C12, C23, H552, H40, H10, H381, O24, C22, C50, H551, H322
> isolde sim start #3.2/C
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui mousemode right select
> isolde sim start #3.2/A:79-1178/B:24-187/D
ISOLDE: started sim
> ui mousemode right "isolde tug residue"
> ui mousemode right "isolde tug atom"
> ui tool show "Ramachandran Plot"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 40 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui mousemode right select
> select clear
> hide #!3 models
> show #!3 models
> save "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/P930/ISOLDE_PTCH1_SHH_CDON.pdb" models #3
> open "C:/Users/lucre/OneDrive -
> Nexus365/OXFORD/cryoEM_processing/P930/ISOLDE_PTCH1_SHH_CDON.pdb"
Chain information for ISOLDE_PTCH1_SHH_CDON.pdb #20
---
Chain | Description
A | No description available
B | No description available
D | No description available
> hide #!3 models
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE one.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
——— End of log from Fri Mar 8 17:22:54 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!20 models
> ui mousemode right select
> select #1/B:425
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> ui tool show "Color Actions"
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> color sel #ffdbf9ff
> color sel #ffdbf8ff
> color sel #ffdbf7ff
> select clear
> select #1/A:575
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
166 atoms, 169 bonds, 22 residues, 1 model selected
> select up
4295 atoms, 4396 bonds, 544 residues, 1 model selected
> select up
4366 atoms, 4468 bonds, 553 residues, 1 model selected
> select up
7931 atoms, 8134 bonds, 997 residues, 1 model selected
> color sel #ffdcf9ff
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> color sel #e9d9ffff
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> color sel #d7ffffff
> color sel #d4ffffff
> color sel #d3feffff
> select clear
> select #1/C:166
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> select up
1423 atoms, 1454 bonds, 179 residues, 1 model selected
> select down
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color sel #cffbffff
> color sel #cffff9ff
> color sel #cffff7ff
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> color sel #eeffb8ff
> color sel #f6ffb8ff
> color sel #f9ffb8ff
> color sel #fbffb8ff
> color sel #feffb8ff
> color sel #feffb7ff
> color sel #fffdb5ff
> color sel #fffab5ff
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel purple
> color sel dark violet
> color sel byhetero
> select clear
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/C:201@C2
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #1/B:448
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
117 atoms, 118 bonds, 16 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel #fff2aeff
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> color sel #ffd7f0ff
> color sel #ffd5efff
> color sel #ffd5eeff
> select clear
> select #1/C:32
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
478 atoms, 490 bonds, 60 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> select down
478 atoms, 490 bonds, 60 residues, 1 model selected
> select clear
> select #1/C:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color sel #ffff7fff
> select clear
> select ::name="CLR"
287 atoms, 308 bonds, 7 residues, 4 models selected
> color (#!1 & sel) #ffff80ff
> color (#!1 & sel) #90c9ffff
> color (#!1 & sel) #9096ffff
> color (#!1 & sel) #b28effff
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> color (#!1 & sel) #6923ffff
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> color (#!1 & sel) #7d20ffff
> color (#!1 & sel) #7d21ffff
> color (#!1 & sel) #8921ffff
> color sel & #!1 byhetero
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> list view
Unknown command: list view
> view list
Named views: 2to1
> view 2to1
> select clear
> select #1/C:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
478 atoms, 490 bonds, 60 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> ui tool show "Selection Inspector"
Cannot increment value
[Repeated 1 time(s)]
> select clear
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/2to1coplex.png" width 1469 height 884 supersample 3
> transparentBackground true
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> ui tool show "Side View"
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/2to1coplex2.png" width 1469 height 884 supersample 3
> transparentBackground true
> select ::name="CLR"
287 atoms, 308 bonds, 7 residues, 4 models selected
> color (#!1 & sel) #9021ffff
> color (#!1 & sel) #2f1cffff
> color (#!1 & sel) #b7ff42ff
> color (#!1 & sel) #ffcc4bff
> color (#!1 & sel) #ffa850ff
> color (#!1 & sel) #ff9f50ff
> color (#!1 & sel) #ff9050ff
> color (#!1 & sel) #ff8a50ff
> color (#!1 & sel) #ff8250ff
> color (#!1 & sel) #ff814fff
> color (#!1 & sel) #ff7f4cff
> color (#!1 & sel) #ff7146ff
> color (#!1 & sel) #ff6640ff
> color (#!1 & sel) #ff643dff
> color (#!1 & sel) #ff5938ff
> color (#!1 & sel) #ff6435ff
> color (#!1 & sel) #ff6e34ff
> color (#!1 & sel) #ff8533ff
> color (#!1 & sel) #ff8c2eff
> color (#!1 & sel) #ff8b2cff
> color (#!1 & sel) #ff9326ff
> color (#!1 & sel) #ff9d25ff
> color (#!1 & sel) #ff9c23ff
> color (#!1 & sel) #ff9b20ff
> color (#!1 & sel) #ff9717ff
> color (#!1 & sel) #ff930eff
> color (#!1 & sel) #ff920cff
> color (#!1 & sel) #ffa60cff
> color (#!1 & sel) #ffae0cff
> color (#!1 & sel) #ffa60cff
> color (#!1 & sel) #ffa811ff
> color (#!1 & sel) #3ec5ffff
> color (#!1 & sel) #3597ffff
> color (#!1 & sel) #2e93ffff
> color (#!1 & sel) #2c8bffff
> color (#!1 & sel) #2684ffff
> color (#!1 & sel) #2583ffff
> color (#!1 & sel) #238dffff
> color (#!1 & sel) #2298ffff
> color (#!1 & sel) #229fffff
> color (#!1 & sel) #22a7ffff
> color (#!1 & sel) #18a3ffff
> color (#!1 & sel) #17a2ffff
> color (#!1 & sel) #14a1ffff
> color (#!1 & sel) #0ca2ffff
> color (#!1 & sel) #0ba1ffff
> color (#!1 & sel) #08a0ffff
> color (#!1 & sel) #00a6ffff
> color (#!1 & sel) #00b3ffff
> color (#!1 & sel) #00aeffff
> color (#!1 & sel) #00a6ffff
> color (#!1 & sel) #0099ffff
> color (#!1 & sel) #007bffff
> color (#!1 & sel) #0066ffff
> color (#!1 & sel) #0062ffff
> color (#!1 & sel) #0066ffff
> color (#!1 & sel) #0073ffff
> color (#!1 & sel) #007bffff
> color (#!1 & sel) #0073ffff
> color sel & #!1 byhetero
> select clear
> select #1/C:204@CA
1 atom, 1 residue, 1 model selected
> select #1/C:205@CA
1 atom, 1 residue, 1 model selected
> select #1/C:204@CA
1 atom, 1 residue, 1 model selected
> select #1/C:205@CA
1 atom, 1 residue, 1 model selected
> select #1/C:204@CA
1 atom, 1 residue, 1 model selected
> select ::name="CA"
8 atoms, 8 residues, 4 models selected
> color (#!1 & sel) #0289ffff
> color (#!1 & sel) #02a6ffff
> color (#!1 & sel) #19ff98ff
> color (#!1 & sel) #23ff74ff
> color (#!1 & sel) #29ff54ff
> color (#!1 & sel) #3eff30ff
> color (#!1 & sel) #66ff37ff
> color (#!1 & sel) #8bff3dff
> color (#!1 & sel) #a6ff41ff
> color (#!1 & sel) #c7ff45ff
> color (#!1 & sel) #f6ff45ff
> color (#!1 & sel) #d4ff3aff
> color (#!1 & sel) #b1ff34ff
> color (#!1 & sel) #b1ff33ff
> color (#!1 & sel) #67ff26ff
> color (#!1 & sel) #5eff19ff
> color (#!1 & sel) #35ff11ff
> color (#!1 & sel) #34ff10ff
> color (#!1 & sel) #33ff0fff
> color (#!1 & sel) #2eff0eff
> color (#!1 & sel) #2bff0aff
> color (#!1 & sel) #00ff15ff
> color (#!1 & sel) #00ff11ff
> color (#!1 & sel) #04ff00ff
> color (#!1 & sel) #04fe00ff
> color (#!1 & sel) #04fa00ff
> color (#!1 & sel) #04e300ff
> color (#!1 & sel) #04d300ff
> color (#!1 & sel) #03ca00ff
> color (#!1 & sel) #03cb00ff
> color (#!1 & sel) #03d000ff
> color (#!1 & sel) #04d300ff
> select clear
> view list
Named views: 2to1
> view 2to1
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 1 item
> select clear
> setattr =sel p display false
Assigning display attribute to 1 item
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/2to1coplex3.png" width 1469 height 884 supersample 3
> transparentBackground true
No visible atoms or bonds selected
> hide #!1 models
> show #!2 models
> show #!20 models
> ui tool show Matchmaker
> show #!1 models
> matchmaker #!2,20 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hPtch_SHHFL_478_31_6.pdb, chain A (#1) with PTCH1_pSHH_HHIP-
C_apo_f.pdb, chain A (#2), sequence alignment score = 4860.7
RMSD between 960 pruned atom pairs is 0.464 angstroms; (across all 991 pairs:
0.742)
Matchmaker hPtch_SHHFL_478_31_6.pdb, chain B (#1) with
ISOLDE_PTCH1_SHH_CDON.pdb, chain A (#20), sequence alignment score = 4766.2
RMSD between 750 pruned atom pairs is 1.202 angstroms; (across all 971 pairs:
1.777)
> matchmaker #!2,20 to #1/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hPtch_SHHFL_478_31_6.pdb, chain A (#1) with PTCH1_pSHH_HHIP-
C_apo_f.pdb, chain A (#2), sequence alignment score = 4860.7
RMSD between 960 pruned atom pairs is 0.464 angstroms; (across all 991 pairs:
0.742)
Matchmaker hPtch_SHHFL_478_31_6.pdb, chain A (#1) with
ISOLDE_PTCH1_SHH_CDON.pdb, chain A (#20), sequence alignment score = 4728.4
RMSD between 879 pruned atom pairs is 1.099 angstroms; (across all 980 pairs:
1.560)
> select #1/A#2/A#3.2/A#20/A
47720 atoms, 48536 bonds, 4 pseudobonds, 3973 residues, 8 models selected
> color (#!1-2,20 & sel) #0059ffff
> color (#!1-2,20 & sel) #089cffff
> color (#!1-2,20 & sel) #0cd6ffff
> color (#!1-2,20 & sel) #08deffff
> color (#!1-2,20 & sel) #05f3ffff
> color (#!1-2,20 & sel) #46f0ffff
> color (#!1-2,20 & sel) #47f0ffff
> color (#!1-2,20 & sel) #49f0ffff
> color (#!1-2,20 & sel) #92f4ffff
> color (#!1-2,20 & sel) #a6ffffff
> color (#!1-2,20 & sel) #b3feffff
> color (#!1-2,20 & sel) #bdfeffff
> color (#!1-2,20 & sel) #cdf8ffff
> color (#!1-2,20 & sel) #d9f6ffff
> color (#!1-2,20 & sel) #dbf7ffff
> color (#!1-2,20 & sel) #d7f6ffff
> color (#!1-2,20 & sel) #d3f5ffff
> color (#!1-2,20 & sel) #d2f5ffff
> color (#!1-2,20 & sel) #cdf7ffff
> color (#!1-2,20 & sel) #cbf6ffff
> color (#!1-2,20 & sel) #c5f4ffff
> hide sel & #!1-2,20 atoms
> select clear
> select #2/C
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> color sel #ffff7fff
> hide sel atoms
> select #20/B:101
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
274 atoms, 273 bonds, 17 residues, 1 model selected
> select up
2597 atoms, 2627 bonds, 164 residues, 1 model selected
> select down
274 atoms, 273 bonds, 17 residues, 1 model selected
> select up
2597 atoms, 2627 bonds, 164 residues, 1 model selected
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE one.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 147, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 741, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save 'C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
HHIP/Chimerasessions/FIGURE one.cxs': [Errno 28] No space left on device
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE one.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
Ran out of memory trying to save a session including 30 maps (3.0 Gbytes).
To save the session you will either have to save the maps to separate files
(then only the path to the file is included in the session) or close some of
the maps.
#6.1 "cryosparc_P478_J216_010_volume_map_sharp.mrc 0" (102 MB)
#6.2 "cryosparc_P478_J216_010_volume_map_sharp.mrc 1" (102 MB)
#6.3 "cryosparc_P478_J216_010_volume_map_sharp.mrc 2" (102 MB)
#6.4 "cryosparc_P478_J216_010_volume_map_sharp.mrc 3" (102 MB)
#6.5 "cryosparc_P478_J216_010_volume_map_sharp.mrc 4" (102 MB)
#6.6 "cryosparc_P478_J216_010_volume_map_sharp.mrc 5" (102 MB)
#6.7 "cryosparc_P478_J216_010_volume_map_sharp.mrc 6" (102 MB)
#6.8 "cryosparc_P478_J216_010_volume_map_sharp.mrc 7" (102 MB)
#6.9 "cryosparc_P478_J216_010_volume_map_sharp.mrc 8" (102 MB)
#7 "cryosparc_P478_J216_010_volume_map_sharp.mrc 0 gaussian" (102 MB)
#9.1 "cryosparc_P818_J131_map_sharp (1).mrc 0" (102 MB)
#9.2 "cryosparc_P818_J131_map_sharp (1).mrc 1" (102 MB)
#9.3 "cryosparc_P818_J131_map_sharp (1).mrc 2" (102 MB)
#9.4 "cryosparc_P818_J131_map_sharp (1).mrc 3" (102 MB)
#9.5 "cryosparc_P818_J131_map_sharp (1).mrc 4" (102 MB)
#9.6 "cryosparc_P818_J131_map_sharp (1).mrc 5" (102 MB)
#9.7 "cryosparc_P818_J131_map_sharp (1).mrc 6" (102 MB)
#9.8 "cryosparc_P818_J131_map_sharp (1).mrc 7" (102 MB)
#9.9 "cryosparc_P818_J131_map_sharp (1).mrc 8" (102 MB)
#10 "cryosparc_P818_J131_map_sharp (1).mrc 0 gaussian" (102 MB)
#13 "cryosparc_P818_J127_005_volume_map_sharp (1).mrc 0 gaussian" (102 MB)
#16.1 "cryosparc_P478_J315_map_sharp.mrc 0" (102 MB)
#16.2 "cryosparc_P478_J315_map_sharp.mrc 1" (102 MB)
#16.3 "cryosparc_P478_J315_map_sharp.mrc 2" (102 MB)
#16.4 "cryosparc_P478_J315_map_sharp.mrc 3" (102 MB)
#16.5 "cryosparc_P478_J315_map_sharp.mrc 4" (102 MB)
#16.6 "cryosparc_P478_J315_map_sharp.mrc 5" (102 MB)
#16.7 "cryosparc_P478_J315_map_sharp.mrc 6" (102 MB)
#16.8 "cryosparc_P478_J315_map_sharp.mrc 7" (102 MB)
#16.9 "cryosparc_P478_J315_map_sharp.mrc 8" (102 MB)
[Repeated 1 time(s)]
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE one.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
——— End of log from Fri Apr 26 17:30:01 2024 ———
opened ChimeraX session
> hide sel cartoons
> ui mousemode right select
> select clear
> undo
> hide sel atoms
> select #20/E:2@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:582
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A#2/A#3.2/A#20/A
47720 atoms, 48536 bonds, 4 pseudobonds, 3973 residues, 8 models selected
> ui tool show "Color Actions"
> color sel yellow
> color (#!1-2,20 & sel) #ffff7fff
> select #1/B#2/B#3.2/B#20/B
16648 atoms, 17008 bonds, 35 pseudobonds, 1771 residues, 7 models selected
> select #1/C#2/C
2783 atoms, 2844 bonds, 17 pseudobonds, 348 residues, 3 models selected
> color (#!1-2 & sel) #0000ffff
> color sel dark slate blue
> color sel medium blue
> color (#!1-2 & sel) #011affff
> color (#!1-2 & sel) #1924ffff
> color (#!1-2 & sel) #1414ffff
> color (#!1-2 & sel) #1e40ffff
> color (#!1-2 & sel) #1e47ffff
> color (#!1-2 & sel) #1e4fffff
> select #1/B
7925 atoms, 8139 bonds, 1 pseudobond, 984 residues, 2 models selected
> color sel violet
> color sel hot pink
> color sel deep pink
> color sel hot pink
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!20 models
> select #1/C:202@C10
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> select ::name="CLR"
287 atoms, 308 bonds, 7 residues, 4 models selected
> color (#!1 & sel) #005500ff
> color (#!1 & sel) #00557fff
> color sel & #!1 byhetero
> select clear
> undo
> color (#!1 & sel) #000000ff
> color (#!1 & sel) #00007fff
> color sel slate blue
> color sel dark slate blue
> color sel & #!1 byhetero
> select clear
> select #1/B:402
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel plum
> color sel violet
> select clear
> graphics silhouettes false
> lighting simple
> lighting full
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> ui tool show "Side View"
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select ::name="CLR"
287 atoms, 308 bonds, 7 residues, 4 models selected
> ui tool show "Selection Inspector"
> select clear
[Repeated 2 time(s)]
> select #1/C:202@C9
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> select ::name="CLR"
287 atoms, 308 bonds, 7 residues, 4 models selected
> select #1/C:202@C11
1 atom, 1 residue, 1 model selected
> select #1/B:851
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
139 atoms, 145 bonds, 15 residues, 1 model selected
> select clear
[Repeated 3 time(s)]
> select #1/B:1502@C13
1 atom, 1 residue, 1 model selected
> select #1/B:1502@C13
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> size sel ballScale 0.26
Changed 1 ball scales
> size sel ballScale 0.27
Changed 1 ball scales
> size sel ballScale 0.28
Changed 1 ball scales
> size sel ballScale 0.29
Changed 1 ball scales
> size sel ballScale 0.3
Changed 1 ball scales
> size sel ballScale 0.31
Changed 1 ball scales
> size sel ballScale 0.32
Changed 1 ball scales
> size sel ballScale 0.33
Changed 1 ball scales
> size sel ballScale 0.34
Changed 1 ball scales
> size sel ballScale 0.35
Changed 1 ball scales
> size sel ballScale 0.36
Changed 1 ball scales
> size =sel stickRadius 0.41
Changed 31 bond radii
> size =sel stickRadius 0.42
Changed 31 bond radii
> size =sel stickRadius 0.43
Changed 31 bond radii
> size =sel stickRadius 0.44
Changed 31 bond radii
> size =sel stickRadius 0.45
Changed 31 bond radii
> size =sel stickRadius 0.46
Changed 31 bond radii
> size =sel stickRadius 0.47
Changed 31 bond radii
> size =sel stickRadius 0.48
Changed 31 bond radii
> size =sel stickRadius 0.49
Changed 31 bond radii
> size =sel stickRadius 0.5
Changed 31 bond radii
> size =sel stickRadius 0.51
Changed 31 bond radii
> size =sel stickRadius 0.52
Changed 31 bond radii
> size =sel stickRadius 0.53
Changed 31 bond radii
> size =sel stickRadius 0.54
Changed 31 bond radii
> size =sel stickRadius 0.55
Changed 31 bond radii
> size =sel stickRadius 0.56
Changed 31 bond radii
> size =sel stickRadius 0.57
Changed 31 bond radii
> size =sel stickRadius 0.58
Changed 31 bond radii
> size =sel stickRadius 0.59
Changed 31 bond radii
> size =sel stickRadius 0.6
Changed 31 bond radii
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> size =sel stickRadius 0.6
Changed 30 bond radii
> select #1/C:201@CA
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> size =sel stickRadius 0.6
Changed 16 bond radii
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> size =sel stickRadius 0.6
Changed 31 bond radii
> select clear
> select #1/C:42
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:41
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
478 atoms, 490 bonds, 60 residues, 1 model selected
> select down
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> size =sel stickRadius 0.4
Changed 5 bond radii
> size =sel stickRadius 0.6
Changed 5 bond radii
> undo
[Repeated 2 time(s)]
> redo
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #1/C:26
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:25
4 atoms, 3 bonds, 1 residue, 1 model selected
> size =sel stickRadius 0.4
Changed 3 bond radii
> select clear
> select #1/C GLY25
Expected a keyword
> select #1/C residues 25
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select #1/C:25
4 atoms, 3 bonds, 1 residue, 1 model selected
> size #1/C:24-34 stickRadius 0.5
Changed 83 bond radii
> size #1/C:24-34 stickRadius 1
Changed 83 bond radii
> undo
[Repeated 1 time(s)]
> cartoon #1/C:24-34 width 1 [ thickness t ]
Expected a keyword
> cartoon #1/C:24-34 width 1 thickness 1
Expected a keyword
> cartoon style #1/C:24-34 width 1 thickness 1
> select clear
> cartoon style #1/C:24-34 width 0.5 thickness 1
> cartoon style #1/C:24-34 width 1 thickness 1
> cartoon style #1/C:24-34 width 1 thickness 0.5
> cartoon style #1/C:24-34 width 1 thickness 0.8
> cartoon style #1/C:24-34 width 2 thickness 0.8
> cartoon style #1/C:24-34 width 5 thickness 0.8
> cartoon style #1/C:24-34 width 0.1 thickness 0.8
> size =sel stickRadius 0.4
Changed 1 bond radii
> select clear
> show #!2 models
> hide #!1 models
> show #!20 models
> show #!1 models
> cartoon style #1/C:24-34 width 0.1 thickness 0.8
> cartoon style width 0.1 thickness 0.8
> cartoon style width 1 thickness 0.8
> undo
[Repeated 1 time(s)]
> cartoon style width 2 thickness 0.8
> cartoon style width 2 thickness 0.4
> cartoon style width 2 thickness 0.8
> cartoon style width 3 thickness 0.8
> select ::name="CA"
8 atoms, 8 residues, 4 models selected
> color (#!1-2,20 & sel) byhetero
> select clear
> select #20/B:2@CA
1 atom, 1 residue, 1 model selected
> select #20/B:189@CA
1 atom, 1 residue, 1 model selected
> select #20/B:2@CA
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1.01
Changed 1 atom radii
> size sel atomRadius 1.02
Changed 1 atom radii
> size sel atomRadius 1.03
Changed 1 atom radii
> size sel atomRadius 1.04
Changed 1 atom radii
> size sel atomRadius 1.05
Changed 1 atom radii
> size sel atomRadius 1.06
Changed 1 atom radii
> size sel atomRadius 1.07
Changed 1 atom radii
> size sel atomRadius 1.08
Changed 1 atom radii
> size sel atomRadius 1.09
Changed 1 atom radii
> size sel atomRadius 1.1
Changed 1 atom radii
> size sel atomRadius 1.11
Changed 1 atom radii
> size sel atomRadius 1.12
Changed 1 atom radii
> size sel atomRadius 1.13
Changed 1 atom radii
> size sel atomRadius 1.14
Changed 1 atom radii
> size sel atomRadius 1.15
Changed 1 atom radii
> size sel atomRadius 1.16
Changed 1 atom radii
> size sel atomRadius 1.17
Changed 1 atom radii
> size sel atomRadius 1.18
Changed 1 atom radii
> size sel atomRadius 1.19
Changed 1 atom radii
> size sel atomRadius 1.4
Changed 1 atom radii
> select #20/B:189@CA
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1.4
Changed 1 atom radii
> select #2/C:125
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:125
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #1/C:204@CA
1 atom, 1 residue, 1 model selected
> select #20/B:2@CA
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1.5
Changed 1 atom radii
> select #20/B:189@CA
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1.5
Changed 1 atom radii
> select #2/M:1@CA
1 atom, 1 residue, 1 model selected
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> select #20/B:1@ZN
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1
Changed 1 atom radii
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> select ::name="ZN"
13 atoms, 13 residues, 4 models selected
> color sel & #!1-2,20 byhetero
> color sel #8083b4 atoms
> color sel #8084b5 atoms
> color sel #8386b8 atoms
> color sel #868abd atoms
> color sel #888bbf atoms
> color sel #8a8dc2 atoms
> color sel #8d91c7 atoms
> color sel #8f93ca atoms
> color sel #9498d0 atoms
> color sel #9498d1 atoms
> color sel #969ad3 atoms
> color sel #969bd4 atoms
> color sel #989cd6 atoms
> color sel #9b9fda atoms
> color sel #9ca0dc atoms
> color sel #9da1dd atoms
> color sel #9ea2de atoms
> select clear
> select #20/E:1@ZN
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
[Repeated 3 time(s)]
> select #2/I:1@C3
1 atom, 1 residue, 1 model selected
> select #2/I:1@C4
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select up
12957 atoms, 13289 bonds, 1631 residues, 1 model selected
> select down
28 atoms, 31 bonds, 1 residue, 1 model selected
> select ::name="CLR"
287 atoms, 308 bonds, 7 residues, 4 models selected
> show sel & #!1-2,20 atoms
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
74 atoms, 77 bonds, 1 residue, 1 model selected
> hide #* target a
> show sel target ab
> undo
[Repeated 1 time(s)]
> delete hydrogens
Missing or invalid "atoms" argument: invalid atoms specifier
> delete :H
> delete ::H
> delete ::hydrogens
> select clear
> select #20/A:1503@C8
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
74 atoms, 77 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> style sel stick
Changed 74 atom styles
> hide sel target a
> undo
> ui tool show "Selection Inspector"
> hide sel atoms
> show sel atoms
> select #1/A:111
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #20/A:483
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:110
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #20/A:1503@H273
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #20/A:1503@H272
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #20/A:1503@H271
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 75 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H261
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 75 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H261
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H262
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!2 models
> hide #!1 models
> show #!1 models
> select #20/A:1503@H25
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 75 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H231
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H232
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H221
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H222
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H20
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H212
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select down
1 bond, 1 model selected
> show sel atoms
> undo
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> undo
[Repeated 2 time(s)]
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select clear
> select #20/A:1503@H212
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H213
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H211
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H17
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H162
1 atom, 1 residue, 1 model selected
> select #20/A:1503@C3
1 atom, 1 residue, 1 model selected
> select #20/A:1503@O1
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 75 bonds, 1 residue, 1 model selected
> select up
15901 atoms, 16102 bonds, 988 residues, 1 model selected
> select down
73 atoms, 75 bonds, 1 residue, 1 model selected
> delete @H
> select clear
> select #20/A:1503@H22
1 atom, 1 residue, 1 model selected
> delete #20/A:1503@H22
> select #20/A:1503@C14
1 atom, 1 residue, 1 model selected
> select #20/A:1503@H14
1 atom, 1 residue, 1 model selected
> select up
72 atoms, 74 bonds, 1 residue, 1 model selected
> select clear
> delete #20/A:1503@H
> select #20/A:1503@HO1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> delete #20/A:1503@H1
> delete #20/A:1503@H
> delete #20/A:1503@H2
> delete #20/A:1503@H3
> delete #20/A:1503@H4
> select #20/A:1503@H21
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #20/A:1503@H12
1 atom, 1 residue, 1 model selected
> delete #20/A:1503@H12
> delete #20/A:1503@H11
> delete #20/A:1503@H10
> delete #20/A:1503@H9
> delete #20/A:1503@H8
> delete #20/A:1503@H7
> delete #20/A:1503@H6
> delete #20/A:1503@H5
> delete #20/A:1503@H4
> delete #20/A:1503@H13
> delete #20/A:1503@H41
> select #20/A:1503@H42
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H71
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H72
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H121
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H112
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H122
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> select #20/A:1503@H152
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H151
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H14
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H161
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H162
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #20/A:1503@H193
1 atom, 1 residue, 1 model selected
> hide #!20 models
> select #1/A:1501@C3
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.5
Changed 31 bond radii
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> size =sel stickRadius 0.6
Changed 31 bond radii
> select clear
> select #1/C:166
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel navy
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel indigo
> color sel magenta
> color sel byhetero
> select #1/C:197
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select #1/C:201@C2
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:24@N
1 atom, 1 residue, 1 model selected
> select clear
> select #1/C:24@N
1 atom, 1 residue, 1 model selected
> select #1/A:371
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/B:398
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> color sel deep pink
> color sel hot pink
> select clear
> select #1/A:1501@C4
1 atom, 1 residue, 1 model selected
> select clear
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel dark olive green
> color sel byhetero
> select #1/C:202@C8
1 atom, 1 residue, 1 model selected
> select #1/C:202@C8
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel dark olive green
> select clear
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> ui tool show "Color Zone"
> color zone #5 near #1 distance 1.22
> hide #!5 models
> show #!5 models
> color #5 lightgrey models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!14 models
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!15 models
> color #15 white models
> color zone #15 near #1 distance 7.35
> hide #!1 models
> show #!7 models
> show #!1 models
> hide #!7 models
> hide #!15 models
> select #1/C:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 3 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel royal blue
> select clear
> select #1/C:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
132 atoms, 131 bonds, 17 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color sel byhetero
> select clear
> select ::name="CLR"
278 atoms, 298 bonds, 7 residues, 4 models selected
> color sel slate blue
> color sel dark red
> color sel sienna
> color sel saddle brown
> color sel dark green
> color sel byhetero
> select clear
> select #1/C:202@C3
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 1 model selected
> color sel royal blue
> select clear
> name list ok
Expected a keyword
> name viwe ok
"ok": invalid atom specifier
> name view ok
"ok": invalid atom specifier
> view name ok
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE one.2.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
——— End of log from Fri May 3 17:35:07 2024 ———
opened ChimeraX session
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!16 models
> hide #!16 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui mousemode right select
> select #1/B:401
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
173 atoms, 176 bonds, 21 residues, 1 model selected
> select up
4202 atoms, 4301 bonds, 533 residues, 1 model selected
> select up
4246 atoms, 4346 bonds, 538 residues, 1 model selected
> select up
7799 atoms, 7999 bonds, 981 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> select clear
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> size sel atomRadius 1.4
Changed 1 atom radii
> select clear
> select #1/C:205@CA
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1.6
Changed 1 atom radii
> select #1/C:204@CA
1 atom, 1 residue, 1 model selected
> size sel atomRadius 1.7
Changed 1 atom radii
> select clear
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> color sel black
> select clear
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> color sel purple
> select clear
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> save C:\ProgramData\ChimeraX\image682.png supersample 3
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!16 models
> color #16 white models
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> select add #1
17310 atoms, 17758 bonds, 27 pseudobonds, 2164 residues, 3 models selected
> select subtract #1
Nothing selected
> show #!1 models
> hide #!1 models
> color zone #16.1 near #1 distance 5
> hide #!16.1 models
> hide #!16.2 models
> hide #!16.3 models
> hide #!16.4 models
> hide #!16.6 models
> hide #!16.5 models
> hide #!16.7 models
> hide #!16.8 models
> hide #!16.9 models
> close #16.9
> close #16.8
> close #16.7
> hide #!16 models
> show #!16 models
> open C:/Users/lucre/Downloads/cryosparc_P478_J315_map_sharp.mrc
Opened cryosparc_P478_J315_map_sharp.mrc as #14, grid size 300,300,300, pixel
1.22, shown at level 0.00212, step 2, values float32
> volume #14 step 1
> volume #14 level 0.1145
> close #16
> color zone #14 near #1 distance 7.35
> color single #14
> show #!1 models
> hide #!14 models
> select #1/C:166
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select #1/C:197@O
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/C:201@CB
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> color zone #14 near #1 distance 5
> hide #!1 models
> show #!1 models
> hide #!14 models
> hide #!1 models
> show #!14 models
> color zone #14 near #1 distance 6
[Repeated 2 time(s)]
> color zone #14 near #1 distance 7
[Repeated 1 time(s)]
> color zone #14 near #1 distance 8
[Repeated 1 time(s)]
> color zone #14 near #1 distance 21.2
[Repeated 1 time(s)]
> show #!1 models
> show #!20 models
> hide #!20 models
> show #!14 models
> select #14
2 models selected
> select clear
> color zone #14 near #1 distance 21.2
[Repeated 1 time(s)]
> color #14 #ffaaffff models
> color zone #14 near #1 distance 21.2
> hide #!1 models
> volume #14 level 0.07082
> surface dust #14 size 12.2
> volume #14 level 0.07706
> volume #14 level 0.04896
> volume #14 level 0.07706
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #12 models
> hide #12 models
> show #!10 models
> hide #!10 models
> show #!7 models
> lighting flat
> graphics silhouettes false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> volume #14 level 0.09267
> graphics silhouettes true
> ui tool show "Side View"
> lighting simple
> lighting soft
> save C:\ProgramData\ChimeraX\image683.png supersample 3
> hide #!14 models
> ui tool show "Side View"
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> show #!14 models
> hide #!14 models
> select add #7
2 models selected
> hide #!7 models
> select subtract #7
Nothing selected
> show #!14 models
> lighting soft
> show #!7 models
> hide #!14 models
> hide #!7 models
> show #!7 models
> select add #7
3 models selected
> lighting flat
> lighting full
> transparency sel 0
> transparency sel 50
> show #!14 models
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> lighting simple
> lighting soft
> set bgColor white
> view
[Repeated 1 time(s)]
> view orient
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> save C:\ProgramData\ChimeraX\image684.png supersample 3
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/figureONE_PTCH12to1SHH_pdb.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
——— End of log from Thu Jun 13 15:38:57 2024 ———
opened ChimeraX session
> hide #!7 models
> hide #!14 models
> show #!1 models
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting shadows true
> lighting shadows false
> select ::name="CLR"
278 atoms, 298 bonds, 7 residues, 4 models selected
> show sel & #!1 surfaces
> transparency (#!1 & sel) 70
> ui mousemode right select
> select clear
> select #1/C:201@C5
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!1 & sel) 70
> select clear
> select #1/C:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #* target a
> show sel target ab
> undo
[Repeated 1 time(s)]
> hide sel target a
> show (sel-residues & sidechain) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select clear
> save C:\ProgramData\ChimeraX\image692.png supersample 3
> save C:\ProgramData\ChimeraX\image693.png supersample 3
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/figureONE_PTCH12to1SHH_pdb.cxs"
Taking snapshot of stepper:
trimer_1_real_space_refined_020_real_space_refined_022.pdb
——— End of log from Fri Jun 14 12:08:08 2024 ———
opened ChimeraX session
> close #5
> close #4
> close #3
> close #6
> close #7
> close #8
> close #9
> close #10
> close #11
> close #12
> close #13
> close #20
> close #14
> ui mousemode right select
> select #1/B:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/B:378
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> show (sel-residues & sidechain) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show sel target ab
> show (sel-residues & sidechain) target ab
[Repeated 1 time(s)]
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #1/B:377
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> cartoon sel
> select #1/B:379
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:378@C
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
118 atoms, 123 bonds, 13 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> show sel target ab
> save "C:/Users/lucre/OneDrive - Nexus365/OXFORD/PAPER
> HHIP/Chimerasessions/FIGURE1.2_zoomoninterfaces.cxs"
——— End of log from Thu Jul 11 16:48:22 2024 ———
opened ChimeraX session
> hide #!2 target m
[Repeated 1 time(s)]
> hide #!1 target m
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> ui mousemode right select
> select #2/C:182
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
30 atoms, 30 bonds, 4 residues, 1 model selected
> select up
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> select up
12957 atoms, 13289 bonds, 1631 residues, 1 model selected
> select down
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> select down
30 atoms, 30 bonds, 4 residues, 1 model selected
> select up
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel #649ce5ff
> color sel #116cffff
> color sel #55aaffff
> color sel #5555ffff
> color sel #5053ffff
> color sel #5255ffff
> color sel #535cffff
> color sel #535effff
> color sel #5465ffff
> color sel #556cffff
> color sel #5770ffff
> color sel #5877ffff
> color sel #5871ffff
> color sel #5770ffff
> color sel #5776ffff
> color sel #5877ffff
> color sel #587cffff
> color sel #587fffff
> color sel #5980ffff
> color sel #5985ffff
> color sel #5a86ffff
> color sel #5c90ffff
> color sel #5c8dffff
> color sel #588affff
> color sel #5487ffff
> color sel #5387ffff
> color sel #5381ffff
> color sel #537bffff
> color sel #527affff
> color sel #5079ffff
> color sel #4f78ffff
> color sel #4f7effff
> color sel #4f87ffff
> color sel #4e86ffff
> color sel #5289ffff
> color sel #5588ffff
> color sel #5789ffff
> color sel #588affff
> color sel #598bffff
> color sel #5a8cffff
> color sel #5c8dffff
> color sel #5d8effff
> color sel #5e8effff
> color sel #6090ffff
> color sel #6190ffff
> color sel #6291ffff
> color sel #6392ffff
> color sel #6593ffff
> color sel #6694ffff
> color sel #6795ffff
> color sel #6996ffff
> color sel #6a97ffff
> color sel #6b97ffff
> color sel #6c98ffff
> color sel #6b97ffff
> color sel #6b92ffff
> select #1/C:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 52 bonds, 6 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> select up
1423 atoms, 1454 bonds, 179 residues, 3 models selected
> select up
17310 atoms, 17758 bonds, 2164 residues, 3 models selected
> select up
17310 atoms, 17758 bonds, 27 pseudobonds, 2164 residues, 7 models selected
> select down
17310 atoms, 17758 bonds, 2164 residues, 5 models selected
> select down
1423 atoms, 1454 bonds, 179 residues, 5 models selected
> select down
1420 atoms, 1454 bonds, 176 residues, 3 models selected
> select down
51 atoms, 52 bonds, 6 residues, 3 models selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #6bb7ffff
> color (#!1 & sel) #6bb3ffff
> color (#!1 & sel) #6baeffff
> color (#!1 & sel) #67a1ffff
> color (#!1 & sel) #6394ffff
> color (#!1 & sel) #6287ffff
> color (#!1 & sel) #6082ffff
> color (#!1 & sel) #5e7cffff
> color (#!1 & sel) #5d73ffff
> color (#!1 & sel) #5c6cffff
> color (#!1 & sel) #5a65ffff
> color (#!1 & sel) #585bffff
> color (#!1 & sel) #5858ffff
> color (#!1 & sel) #5e58ffff
> color (#!1 & sel) #6358ffff
> color (#!1 & sel) #6257ffff
> color (#!1 & sel) #5e4fffff
> color (#!1 & sel) #5b4fffff
> color (#!1 & sel) #4c4fffff
> color (#!1 & sel) #4b5dffff
> color (#!1 & sel) #495bffff
> color (#!1 & sel) #3e58ffff
> color (#!1 & sel) #3a54ffff
> color (#!1 & sel) #3c59ffff
> color (#!1 & sel) #3c60ffff
> color (#!1 & sel) #3d67ffff
> color (#!1 & sel) #3e6bffff
> color (#!1 & sel) #406dffff
> color (#!1 & sel) #417affff
> color (#!1 & sel) #427effff
> color (#!1 & sel) #4284ffff
> color (#!1 & sel) #4183ffff
> color (#!1 & sel) #3e82ffff
> color (#!1 & sel) #3a7fffff
> color (#!1 & sel) #377dffff
> color (#!1 & sel) #347bffff
> color (#!1 & sel) #357cffff
> color (#!1 & sel) #3e82ffff
> color (#!1 & sel) #4787ffff
> color (#!1 & sel) #4c8bffff
> color (#!1 & sel) #508dffff
> color (#!1 & sel) #528fffff
> color (#!1 & sel) #538fffff
> color (#!1 & sel) #5490ffff
> color (#!1 & sel) #5590ffff
> color (#!1 & sel) #5792ffff
> color (#!1 & sel) #5892ffff
> color (#!1 & sel) #5993ffff
> color (#!1 & sel) #5a94ffff
> color (#!1 & sel) #5d96ffff
> color (#!1 & sel) #6198ffff
> color (#!1 & sel) #6299ffff
> color (#!1 & sel) #6287ffff
> color (#!1 & sel) #6284ffff
> color (#!1 & sel) #627fffff
> color (#!1 & sel) #627affff
> color (#!1 & sel) #627fffff
> select #2/C:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 52 bonds, 6 residues, 1 model selected
> select up
1360 atoms, 1390 bonds, 169 residues, 1 model selected
> color sel #649ce5ff
> color sel #627fffff
> select clear
> select #2/L:2@ZN
1 atom, 1 residue, 1 model selected
> color sel purple
> select #1/C:203@ZN
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> size sel atomRadius 1
Changed 1 atom radii
> select clear
> select #1/C:205@CA
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 1 item
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 1 item
> select #2/B:309
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
84 atoms, 85 bonds, 11 residues, 1 model selected
> select up
3523 atoms, 3615 bonds, 453 residues, 1 model selected
> color sel medium purple
> select #1/C:202@C3
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 30 bonds, 1 residue, 2 models selected
> transparency sel 50
> select clear
> select #1/C:201@C3
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 2 models selected
> transparency sel 50
> select clear
> view list
Named views: 2to1, ok
> view 2to1
> view ok
Drag select of 4 atoms, 123 residues, 1 bonds, 1 pseudobonds
> select clear
> hide #!2 models
Drag select of 12 residues
> view sel
> select #1/A:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Side View"
> graphics silhouettes true
> graphics silhouettes width 1.5 depthJump 0.04
> graphics silhouettes width 1 depthJump 0.04
> graphics silhouettes width 0.6 depthJump 0.04
> lighting flat
> graphics silhouettes width 1 depthJump 0.04
> select #1/C:44
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.21
Changed 12 bond radii
> size =sel stickRadius 0.22
Changed 12 bond radii
> size =sel stickRadius 0.23
Changed 12 bond radii
> size =sel stickRadius 0.24
Changed 12 bond radii
> size =sel stickRadius 0.25
Changed 12 bond radii
> size =sel stickRadius 0.26
Changed 12 bond radii
> size =sel stickRadius 0.27
Changed 12 bond radii
> size =sel stickRadius 0.28
Changed 12 bond radii
> size =sel stickRadius 0.29
Changed 12 bond radii
> size =sel stickRadius 0.3
Changed 12 bond radii
> size =sel stickRadius 0.31
Changed 12 bond radii
> select clear
> select #1/C:44
12 atoms, 12 bonds, 1 residue, 1 model selected
> cartoon #1/C:44 suppressBackboneDisplay false
> select clear
> select #1/B:380
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> size =sel stickRadius 0.31
Changed 8 bond radii
> select #1/B:379
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> cartoon #1/B:380 suppressBackboneDisplay false
> cartoon #1/B:379 suppressBackboneDisplay false
> color sel byhetero
> size =sel stickRadius 0.31
Changed 12 bond radii
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> select #1/B:379@OH
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:379@CZ
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/B:379@CG
1 atom, 1 residue, 1 model selected
> select #1/B:379@CE2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:379@CE1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:379@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:379@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:379@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:379@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@OH
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@CZ
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@CE2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@CE1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:44@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/C:44@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide sel atoms
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> select #1/B:380@OE2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:380@OE1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:380@CD
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:380@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:380@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B:379
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:378
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> cartoon #1/B:378 suppressBackboneDisplay false
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 3 bond radii
> select #1/C:44
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:222
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> cartoon #1/B:222 suppressBackboneDisplay false
> color sel byhetero
> hide sel atoms
> select #1/B:221
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 8 bond radii
> select clear
> select #1/B:221@CG
1 atom, 1 residue, 1 model selected
> select #1/B:378
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/C:44
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/B:221
25 atoms, 23 bonds, 3 residues, 1 model selected
> select add #1/B:379
37 atoms, 35 bonds, 4 residues, 1 model selected
> select add #1/B:380
46 atoms, 43 bonds, 5 residues, 1 model selected
> view sel
> select #1/B:221
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:221
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:44
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/B:379
24 atoms, 24 bonds, 2 residues, 1 model selected
> select add #1/B:380
33 atoms, 32 bonds, 3 residues, 1 model selected
> select add #1/B:378
37 atoms, 35 bonds, 4 residues, 1 model selected
> view sel
> select clear
> select #1/C:43
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
478 atoms, 490 bonds, 60 residues, 1 model selected
> select up
1420 atoms, 1454 bonds, 176 residues, 1 model selected
> color (#!1 & sel) cornflower blue
> color sel byhetero
> select clear
> save C:\ProgramData\ChimeraX\image752.png supersample 3
> view list
Named views: 2to1, ok
> view name 2
> save C:\ProgramData\ChimeraX\image753.png supersample 3
> save C:\ProgramData\ChimeraX\image754.png supersample 3
> select #1/C:155
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 10 bond radii
> select #1/B:947
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 8 bond radii
> select clear
> select #1/C:123
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 10 bond radii
> select #1/B:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 8 bond radii
> select #1/B:954
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.31
Changed 7 bond radii
> select clear
> select #1/B:951
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> size =sel stickRadius 0.31
Changed 7 bond radii
> select clear
> select #1/B:217
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> show sel atoms
> size =sel stickRadius 0.31
Changed 7 bond radii
> select #1/C:177
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> size =sel stickRadius 0.31
Changed 5 bond radii
> select clear
> select #1/B:958
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> size =sel stickRadius 0.31
Changed 8 bond radii
> select #1/C:151
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> cartoon #1/C:151 suppressBackboneDisplay false
> cartoon #1/C:151 suppressBackboneDisplay true
> size =sel stickRadius 0.31
Changed 5 bond radii
> select clear
> select #1/B:273
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/C:132
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> cartoon #1/C:132 suppressBackboneDisplay true
> cartoon #1/C:132 suppressBackboneDisplay false
> hide sel atoms
> select #1/B:273
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B:221
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #1/B:217
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add #1/B:951
36 atoms, 32 bonds, 4 residues, 1 model selected
> select add #1/B:214
40 atoms, 35 bonds, 5 residues, 1 model selected
> select up
398 atoms, 408 bonds, 47 residues, 1 model selected
> select down
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #1/B:212@CD
41 atoms, 35 bonds, 6 residues, 1 model selected
> select add #1/C:123@CZ
42 atoms, 35 bonds, 7 residues, 1 model selected
> select subtract #1/C:123
41 atoms, 35 bonds, 6 residues, 1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\sideview\tool.py", line 117, in exposeEvent
self.render()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\sideview\tool.py", line 288, in render
self.view.draw()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\view.py", line 260, in _draw_scene
r.outline.set_outline_mask() # copy depth to outline framebuffer
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1900, in set_outline_mask
mfb = self._mask_framebuffer()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1961, in _mask_framebuffer
t.initialize_8_bit(size)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 2970, in initialize_8_bit
self.initialize_texture(size, format, iformat, tdtype, ncomp)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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.
GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
1292,
882,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
1292,
882,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
1292,
882,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
)
)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\view.py", line 237, in _draw_scene
silhouette.start_silhouette_drawing(r)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1820, in start_silhouette_drawing
fb = self._silhouette_framebuffer(r)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1856, in _silhouette_framebuffer
dt.initialize_depth(size, depth_compare_mode=False)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 2982, in initialize_depth
self.initialize_texture(size, format, iformat, tdtype, ncomp,
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
1292,
882,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
1292,
882,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
1292,
882,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
)
)
Exception ignored in: <function Texture.__del__ at 0x0000023E6573DC60>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\sideview\tool.py", line 113, in _redraw
self.render()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\sideview\tool.py", line 288, in render
self.view.draw()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\view.py", line 260, in _draw_scene
r.outline.set_outline_mask() # copy depth to outline framebuffer
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1900, in set_outline_mask
mfb = self._mask_framebuffer()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1961, in _mask_framebuffer
t.initialize_8_bit(size)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 2970, in initialize_8_bit
self.initialize_texture(size, format, iformat, tdtype, ncomp)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
)
)
Error processing trigger "frame drawn":
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
33321,
497,
146,
0,
GL_RED,
GL_UNSIGNED_BYTE,
c_void_p(None),
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Exception ignored in: <function Texture.__del__ at 0x0000023E6573DC60>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
QOpenGLFramebufferObject: An undefined error has occurred: 1285
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
[Repeated 2 time(s)]QOpenGLFramebufferObject: Framebuffer incomplete, missing
attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
QOpenGLFramebufferObject: An undefined error has occurred: 1285
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
[Repeated 2 time(s)]QOpenGLFramebufferObject: Framebuffer incomplete, missing
attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
Exception ignored in: <function Texture.__del__ at 0x0000023E6573DC60>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3076, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
390,
27,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
320,
22,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
[Repeated 1 time(s)]QOpenGLFramebufferObject: An undefined error has occurred:
1285
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
[Repeated 2 time(s)]QOpenGLFramebufferObject: Framebuffer incomplete, missing
attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
QOpenGLFramebufferObject: An undefined error has occurred: 1285
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
[Repeated 2 time(s)]QOpenGLFramebufferObject: Framebuffer incomplete, missing
attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
[Repeated 7 time(s)]Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 151, in status
self._draw_text(msg, color, secondary)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 161, in _draw_text
draw_overlays(dlist, self._renderer)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3088, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3125, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_RGBA8,
480,
33,
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
array([[[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
...,
[0, 0, 0, 0],
[0, 0, 0...,
)
)
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
[Repeated 37 time(s)]
OpenGL version: 3.3.0 - Build 31.0.101.5186
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 13 9305
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 16,889,540,608
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 14 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glTexImage2D: out of memory |
comment:2 by , 14 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
The first glTexImage2D() call that failed with "out of memory" was only trying to allocate less than 100 Kbytes. Not sure why OpenGL was out of memory. Appears the user was working with lots of maps.
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