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Opened 15 months ago
Closed 15 months ago
#15617 closed defect (duplicate)
'pwd' failure when working directory removed
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_ChimeraXForFigures.cxs
Opened cNPC_CRmap_ring.em as #1.1, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_IRmap_ring.em as #1.2, grid size 150,150,150, pixel 9.66, shown at
level 0.28, step 1, values float32
Opened cNPC_NRmap_ring.em as #1.3, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_ring.em as #1.4, grid size 150,150,150, pixel 9.66, shown at level
0.0925, step 1, values float32
Opened cNPC_membranemap_ring.em as #1.5, grid size 150,150,150, pixel 9.66,
shown at level 0.15, step 1, values float32
Opened NE-NPC_ring.em as #2.1, grid size 150,150,150, pixel 9.66, shown at
level 0.145, step 1, values float32
Opened NE-NPC_CRmap_ring.em as #2.2, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRmap_ring.em as #2.3, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em as #2.4, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_IRmap_ring.em as #2.5, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_membranemap_ring.em as #2.6, grid size 150,150,150, pixel 9.66,
shown at level 0.11, step 1, values float32
Opened NE-NPC_CRmap_ring.em copy as #3.2, grid size 150,150,150, pixel 9.66,
shown at level 0.21, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em copy_rotated as #3.4, grid size 150,150,150,
pixel 9.66, shown at level 0.2, step 1, values float32
Opened NE-NPC_membranemap_ring.em copy as #3.3, grid size 150,150,150, pixel
9.66, shown at level 0.11, step 1, values float32
Opened NE-NPC_membranemap_ring_reoriented as #3.5, grid size 150,150,150,
pixel 9.66, shown at level 0.11, step 1, values float32
Frozen name "NR-innerY" not restored: nothing is selected by specifier
Frozen name "NR-outerY" not restored: nothing is selected by specifier
Log from Thu Jul 11 18:12:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_alignedCompositeMaps.cxs
Opened cNPC_CRmap_ring.em as #1.1, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_IRmap_ring.em as #1.2, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_NRmap_ring.em as #1.3, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_ring.em as #1.4, grid size 150,150,150, pixel 9.66, shown at level
0.0925, step 1, values float32
Opened NE_CR_box66_ref_16.em scaled as #7, grid size 66,66,66, pixel 9.66,
shown at level 0.192, step 1, values float32
Opened NE_NRrotatedshifted_ref_16.em scaled as #18, grid size 66,66,66, pixel
9.66, shown at level 0.161, step 1, values float32
Opened NE-NPC_ring.em as #2.1, grid size 150,150,150, pixel 9.66, shown at
step 1, values float32
Opened NE-NPC_CRmap_ring.em as #2.2, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRmap_ring.em as #2.3, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em as #2.4, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_IRmap_ring.em as #2.5, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_CRmap_ring.em copy as #10, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em copy_rotated as #12, grid size 150,150,150,
pixel 9.66, shown at level 0.2, step 1, values float32
Log from Wed Jul 10 10:30:24 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240709_alignedCompositeMaps_newColors.cxs
Opened cNPC_CRmap_ring.em as #1.1, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_IRmap_ring.em as #1.2, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_NRmap_ring.em as #1.3, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_ring.em as #1.4, grid size 150,150,150, pixel 9.66, shown at level
0.0925, step 1, values float32
Opened NE_CR_box66_ref_16.em scaled as #7, grid size 66,66,66, pixel 9.66,
shown at level 0.192, step 1, values float32
Opened NE_NRrotatedshifted_ref_16.em scaled as #18, grid size 66,66,66, pixel
9.66, shown at level 0.161, step 1, values float32
Opened NE-NPC_ring.em as #2.1, grid size 150,150,150, pixel 9.66, shown at
step 1, values float32
Opened NE-NPC_CRmap_ring.em as #2.2, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRmap_ring.em as #2.3, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em as #2.4, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_IRmap_ring.em as #2.5, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_CRmap_ring.em copy as #10, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em copy_rotated as #12, grid size 150,150,150,
pixel 9.66, shown at level 0.2, step 1, values float32
Log from Wed Jul 10 08:49:01 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240709_alignedCompositeMaps_newColors.cxs
> format session
Opened cNPC_CRmap_ring.em as #1.1, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_IRmap_ring.em as #1.2, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_NRmap_ring.em as #1.3, grid size 150,150,150, pixel 9.66, shown at
level 0.2, step 1, values float32
Opened cNPC_ring.em as #1.4, grid size 150,150,150, pixel 9.66, shown at level
0.0925, step 1, values float32
Opened NE_CR_box66_ref_16.em scaled as #7, grid size 66,66,66, pixel 9.66,
shown at level 0.192, step 1, values float32
Opened NE_NRrotatedshifted_ref_16.em scaled as #18, grid size 66,66,66, pixel
9.66, shown at level 0.161, step 1, values float32
Opened NE-NPC_ring.em as #2.1, grid size 150,150,150, pixel 9.66, shown at
step 1, values float32
Opened NE-NPC_CRmap_ring.em as #2.2, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRmap_ring.em as #2.3, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em as #2.4, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_IRmap_ring.em as #2.5, grid size 150,150,150, pixel 9.66, shown
at level 0.2, step 1, values float32
Opened NE-NPC_CRmap_ring.em copy as #10, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em copy as #11, grid size 150,150,150, pixel 9.66,
shown at level 0.2, step 1, values float32
Opened NE-NPC_NRNBmap_ring.em copy_rotated as #12, grid size 150,150,150,
pixel 9.66, shown at level 0.2, step 1, values float32
Log from Tue Jul 9 15:24:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Tue May 7 09:28:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Mon May 6 17:54:25 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps.cxs
Opened cNPC_CRmap_ring.em as #1.1, grid size 150,150,150, pixel 1, shown at
level 0.339, step 1, values float32
Opened cNPC_IRmap_ring.em as #1.2, grid size 150,150,150, pixel 1, shown at
level 0.217, step 1, values float32
Opened cNPC_NRmap_ring.em as #1.3, grid size 150,150,150, pixel 1, shown at
level 0.346, step 1, values float32
Opened cNPC_ring.em as #1.4, grid size 150,150,150, pixel 1, shown at level
0.0925, step 1, values float32
Opened NE-NPC_ring.em as #2, grid size 150,150,150, pixel 1, shown at level
0.145, step 1, values float32
Log from Thu May 2 17:14:30 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open 240501_NE-NPC_fitting.cxs
Opened NE-NPC_IR as #2, grid size 56,56,56, pixel 1, shown at level -0.157,
step 1, values float32
Opened NE-NPC_CR as #3, grid size 66,66,66, pixel 1, shown at level -0.171,
step 1, values float32
Opened NE-NPC_NR as #4, grid size 66,66,66, pixel 1, shown at level -0.0979,
step 1, values float32
Opened NE-NPC_NB as #5, grid size 66,66,66, pixel 1, shown at level -0.148,
step 1, values float32
Opened NE-NPC_SUpadded.em as #1, grid size 100,100,150, pixel 1, shown at
level -0.152, step 1, values float32
Opened SUposition_NE-NPC_IR.mrc as #6, grid size 100,100,150, pixel 1, shown
at level -0.157, step 1, values float32
Opened SUposition_NE-NPC_CR.mrc as #7, grid size 100,100,150, pixel 1, shown
at level -0.171, step 1, values float32
Opened SUposition_NE-NPC_NR.mrc as #8, grid size 100,100,150, pixel 1, shown
at level -0.0979, step 1, values float32
Opened SUposition_NE-NPC_NB.mrc as #9, grid size 100,100,150, pixel 1, shown
at level -0.148, step 1, values float32
Log from Wed May 1 14:54:08 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240501_NE-
> NPC_fitting.cxs
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
Opened NE-NPC_SU as #1, grid size 100,100,100, pixel 1, shown at level -0.159,
step 1, values float32
Opened NE-NPC_IR as #2, grid size 56,56,56, pixel 1, shown at level -0.157,
step 1, values float32
Opened NE-NPC_CR as #3, grid size 66,66,66, pixel 1, shown at level -0.171,
step 1, values float32
Opened NE-NPC_NR as #4, grid size 66,66,66, pixel 1, shown at level -0.0979,
step 1, values float32
Opened NE-NPC_NB as #5, grid size 66,66,66, pixel 1, shown at level -0.148,
step 1, values float32
Log from Mon Apr 29 12:59:49 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
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #1 level -0.4445
> volume all capFaces false
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> volume #1 level -0.2279
> close #1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #1 level -0.1988
> volume all capFaces false
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_IRmap.em
Opened padded_IRmap.em as #2, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #2 level -0.09881
> volume all capFaces false
> close #2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_IRmap.em
Opened padded_IRmap.em as #2, grid size 250,250,250, pixel 1, shown at level
-9.67e-05, step 1, values float32
> volume #2 level -0.03341
> volume all capFaces false
> volume showOutlineBox true
> volume #2 level -0.2416
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #3, grid size 150,150,150, pixel 1, shown at
level 0.0885, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #4, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> close #1
> close #2
> close #3
> close #4
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
> format tom_em
Opened padded_shifted_IRmap.em as #1, grid size 150,150,150, pixel 1, shown at
level 0.0885, step 1, values float32
> volume #1 level -0.3488
> volume all capFaces false
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #2, grid size 150,150,150, pixel 1, shown at
level 0.0885, step 1, values float32
> volume #2 level -0.3113
> volume all capFaces false
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #3, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #3 level -0.37
> volume all capFaces false
> close #1
> close #2
> close #3
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #1, grid size 150,150,150, pixel 1, shown at
level 0.0885, step 1, values float32
> volume #1 level -0.6694
> volume all capFaces false
> volume #1 level -0.2988
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #2, grid size 150,150,150, pixel 1, shown at level
0.0885, step 1, values float32
> volume #2 level -0.1614
> volume all capFaces false
> volume #2 level -0.2155
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #3, grid size 150,150,150, pixel 1, shown at level
0.0885, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #4, grid size 150,150,150, pixel 1, shown at level
0.0885, step 1, values float32
> close #1
> close #2
> close #3
> volume #4 level -0.507
> volume showOutlineBox true
> volume all capFaces false
> volume #4 level -0.1614
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 150,150,150, pixel 1, shown at level
0.143, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #2, grid size 150,150,150, pixel 1, shown at level
0.143, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #3, grid size 150,150,150, pixel 1, shown at level
0.143, step 1, values float32
> volume #3 level -0.2812
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_IR/run2/NE_IR_ref_21.em
Opened NE_IR_ref_21.em as #5, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #5 level -0.2842
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #6, grid size 150,150,150, pixel 1, shown at level
0.143, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #7, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume #7 level -0.3808
> close #5
> close #3
> close #2
> close #1
> close #4
> close #6
> volume #7 level -0.2934
> volume all capFaces false
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #1 level -0.08632
> volume all capFaces false
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #2, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #2 level -0.005538
> volume all capFaces false
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #3, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #3 level -0.1899
> volume all capFaces false
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #4, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #4 level -0.3614
> volume all capFaces false
> close #2
> close #1
> close #7
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> volume #4 level -0.249
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #1 level 0.1531
> volume all capFaces false
> volume #1 level -0.2585
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #2, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #2 level -0.1728
> volume all capFaces false
> close #4
> close #3
> close #1
> close #2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume all capFaces false
> volume #1 level 0.0761
> volume all capFaces false
> volume #1 level -0.2238
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #2, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume showOutlineBox false
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #3, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume #3 level 0.01364
> volume all capFaces false
> volume #3 level -0.1279
> volume #2 level -0.09355
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #4, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> close #4
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #4, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> close #1
> close #2
> close #3
> close #4
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #1, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap.em
Opened shifted_IRmap.em as #2, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #2 level 0.2302
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/shifted_IRmap_2.em
Opened shifted_IRmap_2.em as #3, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> volume #3 level -0.2071
> volume all capFaces false
> volume #3 level -0.1042
> volume #2 level -0.1343
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_2.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_2.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #4, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #5, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume #5 level 0.1165
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #5, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #6, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume #6 level 0.07367
> close #6
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap.em
Opened padded_shifted_IRmap.em as #6, grid size 100,100,100, pixel 1, shown at
level 0.189, step 1, values float32
> volume #6 level 0.1337
> volume #5 level 0.09511
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap2.em
Opened padded_shifted_IRmap2.em as #7, grid size 100,100,100, pixel 1, shown
at level 0.189, step 1, values float32
> volume #6 level 0.02222
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap3.em
Opened padded_shifted_IRmap3.em as #8, grid size 90,90,90, pixel 1, shown at
level 0.221, step 1, values float32
> volume #8 level -0.03222
> volume all capFaces false
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap3.em
Opened padded_shifted_IRmap3.em as #1, grid size 90,90,90, pixel 1, shown at
level 0.221, step 1, values float32
> volume #1 level -0.1994
> volume all capFaces false
> volume #1 level -0.02793
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap4.em
Opened padded_shifted_IRmap4.em as #2, grid size 90,90,90, pixel 1, shown at
level 0.221, step 1, values float32
> volume #2 level 0.2208
> volume #2 level 0.2165
> volume #2 level 0.1993
> volume #2 level 0.1479
> volume #2 level 0.07926
> volume #2 level 0.01923
> volume #2 level -0.02793
> volume #2 level -0.07938
> volume #2 level -0.1566
> volume #2 level -0.1909
> volume #2 level -0.208
> volume #2 level -0.2209
> volume #2 level -0.2252
> volume #2 level -0.2295
> volume #2 level -0.2252
> volume #2 level -0.2209
> volume #2 level -0.2166
> volume #2 level -0.2123
> volume #2 level -0.208
> volume #2 level -0.2037
> volume all capFaces false
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap5.em
Opened padded_shifted_IRmap5.em as #3, grid size 150,150,150, pixel 1, shown
at level 0.0885, step 1, values float32
> volume #!1,3,8 showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated.em
Opened padded_shifted_IRmap_rotated.em as #4, grid size 150,150,150, pixel 1,
shown at level 0.0885, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated.em
Opened padded_shifted_IRmap_rotated.em as #5, grid size 150,150,150, pixel 1,
shown at level 0.0885, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated45.em
Opened padded_shifted_IRmap_rotated45.em as #6, grid size 150,150,150, pixel
1, shown at level 0.0885, step 1, values float32
> volume #6 level 0.007056
> volume all capFaces false
> volume #6 level -0.06155
> volume #6 level -0.1773
> volume #4 level -0.1602
> close #4
> volume #5 level -0.2631
> close #7
> close #8
> close #1
> close #2
> close #3
> close #5
> close #6
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated45.em
Opened padded_shifted_IRmap_rotated45.em as #1, grid size 150,150,150, pixel
1, shown at level 0.0882, step 1, values float32
> volume showOutlineBox true
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
> close #1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated45.em
Opened padded_shifted_IRmap_rotated45.em as #1, grid size 150,150,150, pixel
1, shown at level 0.0882, step 1, values float32
> close #1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_0.em
Opened padded_shifted_IRmap_rotated_0.em as #1, grid size 150,150,150, pixel
1, shown at level 0.0885, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/padded_shifted_IRmap_rotated_45.em
Opened padded_shifted_IRmap_rotated_45.em as #2, grid size 150,150,150, pixel
1, shown at level 0.0882, step 1, values float32
> vop max #1-2
Opened volume maximum as #3, grid size 150,150,150, pixel 1, shown at step 1,
values float32
> volume #3 level 0.0854
> volume #3 level 0.1822
> volume #3 level 0.1791
> volume #3 level 0.1166
> volume #3 level 0.06041
> volume #3 level 0.001049
> volume #3 level -0.03644
> volume #3 level -0.05519
[Repeated 1 time(s)]
> volume #3 level -0.05831
> volume #3 level -0.05519
> volume all capFaces false
> volume #3 level -0.05831
> vop min #1-2
Opened volume minimum as #4, grid size 150,150,150, pixel 1, shown at step 1,
values float32
> volume #4 level -0.07065
> volume all capFaces false
> volume #!3-4 showOutlineBox true
> volume #4 level 0.008937
> volume #4 level -0.1559
> volume #4 level -0.1218
> volume #4 level -0.2497
> view all
> volume #4 level -0.281
> volume #3 level -0.02707
> volume #3 level 0
> volume #3 level 1e-05
> volume #3 level -1e-05
> volume #3 level 0.1312
> volume #3 level 0.2093
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/wholering.em
Opened wholering.em as #5, grid size 150,150,150, pixel 1, shown at level
-0.000121, step 1, values float32
> volume #5 level -0.4215
> volume all capFaces false
> volume #5 level -0.225
> volume #5 level -0.1333
> volume #5 level -0.1093
> volume #5 level -0.2753
> close #1
> close #2
> close #3
> close #4
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/wholering.em
Opened wholering.em as #1, grid size 150,150,150, pixel 1, shown at level
-0.000121, step 1, values float32
> volume #1 level -0.1147
> volume all capFaces false
> close #1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/wholering.em
Opened wholering.em as #1, grid size 150,150,150, pixel 1, shown at level
0.346, step 1, values float32
> volume #1 level 0.07652
> close #5
> volume #1 level 0.04683
> volume #1 level 0.2652
> volume #1 level 0.008662
> volume all capFaces false
> volume #1 level -0.1
> volume #1 level 0
> volume #1 level 0.1
> volume #1 level 0.2548
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/IRmap_315deg.em_wholering.em
Opened IRmap_315deg.em_wholering.em as #2, grid size 150,150,150, pixel 1,
shown at level 0.346, step 1, values float32
> volume #2 level 0.1717
> volume #2 level 0.2311
> close #1
> close #2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/motl_SU_16_cleaned_updated.em
Opened motl_SU_16_cleaned_updated.em as #1, grid size 20,1629,1, pixel 1,
shown at step 1, values float32
> close #1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/IRmap__wholering.em
Opened IRmap__wholering.em as #1, grid size 150,150,150, pixel 1, shown at
level 0.346, step 1, values float32
> volume #1 level 0.1993
> close #1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/ref_16.em
Opened ref_16.em as #1, grid size 100,100,100, pixel 1, shown at level 0.157,
step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/ref_16.em
Opened ref_16.em as #2, grid size 100,100,100, pixel 1, shown at level 0.157,
step 1, values float32
> close #1
> close #2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_*/ref_1.em
> format tom_em
Opened ref_1.em as #1, grid size 66,66,66, pixel 1, shown at level 0.326, step
1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/ref_16.em
Opened ref_16.em as #2, grid size 100,100,100, pixel 1, shown at level 0.157,
step 1, values float32
> close #1
> close #2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/ref_16.em
Opened ref_16.em as #1, grid size 100,100,100, pixel 1, shown at level 0.157,
step 1, values float32
> volume #1 level -0.04744
> volume all capFaces false
[Repeated 1 time(s)]
> rename #1 NE-NPC_SU
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_IR/run2/NE_IR_ref_21.em
Opened NE_IR_ref_21.em as #2, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> rename #2 NE-NPC_IR
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NE_CR_box66_ref_16.em
Opened NE_CR_box66_ref_16.em as #3, grid size 66,66,66, pixel 1, shown at
level 0.285, step 1, values float32
> rename #3 NE-NPC_CR
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NE_NRrotatedshifted_ref_16.em
Opened NE_NRrotatedshifted_ref_16.em as #4, grid size 66,66,66, pixel 1, shown
at level 0.244, step 1, values float32
> rename #4 NE-NPC_NR
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240104_NRbasket_centered/run2_correctedShift/NE_NRbasket_ref_16.em
Opened NE_NRbasket_ref_16.em as #5, grid size 66,66,66, pixel 1, shown at
level 0.145, step 1, values float32
> rename #5 NE-NPC_NB
> ui tool show "Volume Viewer"
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/240429_NE-
> NPC_fitting.cxs
> volume #5 level -0.239
> volume #4 level -0.2063
> volume #3 level -0.03485
> volume #2 level -0.1571
> volume #1 level -0.2361
> volume all capFaces false
> volume #3 level -0.1714
Drag select of 1 NE-NPC_SU , 2 NE-NPC_IR , 3 NE-NPC_CR , 4 NE-NPC_NR , 5 NE-
NPC_NB
Drag select of 1 NE-NPC_SU
Drag select of 1 NE-NPC_SU , 2 NE-NPC_IR , 3 NE-NPC_CR , 4 NE-NPC_NR , 5 NE-
NPC_NB
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-0.059563,0,1,0,-0.056785,0,0,1,-0.099994,#2,1,0,0,-0.059563,0,1,0,-0.056785,0,0,1,-0.099994,#3,1,0,0,-0.059563,0,1,0,-0.056785,0,0,1,-0.099994,#4,1,0,0,-0.059563,0,1,0,-0.056785,0,0,1,-0.099994,#5,1,0,0,-0.059563,0,1,0,-0.056785,0,0,1,-0.099994
> ui mousemode right select
> select #1
2 models selected
> select #1
2 models selected
> view initial
[Repeated 1 time(s)]
> view initial all
> select clear
Drag select of 2 NE-NPC_IR , 3 NE-NPC_CR
> select clear
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-8.0395,0,1,0,9.1075,0,0,1,32.976
> view matrix models #2,1,0,0,18.623,0,1,0,14.956,0,0,1,26.386
> ui mousemode right select
> select #5
2 models selected
Drag select of 1 NE-NPC_SU , 2 NE-NPC_IR , 3 NE-NPC_CR , 4 NE-NPC_NR , 5 NE-
NPC_NB
> select #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,5.0432,0,1,0,29.936,0,0,1,-18.893
> ui mousemode right select
> select #3
2 models selected
> select clear
> select #3
2 models selected
Drag select of 1 NE-NPC_SU , 2 NE-NPC_IR , 3 NE-NPC_CR , 4 NE-NPC_NR , 5 NE-
NPC_NB
> select clear
[Repeated 1 time(s)]Drag select of 1 NE-NPC_SU , 2 NE-NPC_IR , 3 NE-NPC_CR , 4
NE-NPC_NR , 5 NE-NPC_NB
> select #3
2 models selected
Drag select of 1 NE-NPC_SU , 3 NE-NPC_CR , 4 NE-NPC_NR
Drag select of 3 NE-NPC_CR , 4 NE-NPC_NR
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-4.3177,0,1,0,18.476,0,0,1,73.491,#4,1,0,0,-4.3177,0,1,0,18.476,0,0,1,73.491
> ui mousemode right select
> select clear
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,61.111,0,1,0,4.1066,0,0,1,-9.5113
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.74326,-0.64045,0.19338,86.288,-0.66841,-0.72304,0.17444,79.845,0.0281,-0.25891,-0.96549,47.953
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.74326,-0.64045,0.19338,39.854,-0.66841,-0.72304,0.17444,83.649,0.0281,-0.25891,-0.96549,59.688
> view matrix models
> #4,0.74326,-0.64045,0.19338,36.622,-0.66841,-0.72304,0.17444,93.904,0.0281,-0.25891,-0.96549,56.392
> view matrix models
> #4,0.74326,-0.64045,0.19338,39.489,-0.66841,-0.72304,0.17444,86.393,0.0281,-0.25891,-0.96549,62.482
> ui mousemode right select
> ui mousemode right "translate selected models"
> select #5
2 models selected
> select clear
> select #5
2 models selected
Drag select of 5 NE-NPC_NB
> view matrix models #5,1,0,0,-18.785,0,1,0,94.957,0,0,1,-76.873
> ui tool show "Fit in Map"
> fitmap #2 inMap #1 metric correlation rotate false
Fit map NE-NPC_IR in map NE-NPC_SU using 155717 points
correlation = 0.6961, correlation about mean = 0.7124, overlap = 1147
steps = 76, shift = 6.11, angle = 0 degrees
Position of NE-NPC_IR (#2) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 16.13577062
0.00000000 1.00000000 0.00000000 20.01597232
0.00000000 0.00000000 1.00000000 24.04345045
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 24.04345045
> fitmap #2 inMap #1 metric correlation
Fit map NE-NPC_IR in map NE-NPC_SU using 155717 points
correlation = 0.7006, correlation about mean = 0.7171, overlap = 1144
steps = 40, shift = 0.0721, angle = 0.505 degrees
Position of NE-NPC_IR (#2) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.99997271 0.00524716 -0.00520096 16.12345949
-0.00527205 0.99997466 -0.00478328 20.24038252
0.00517573 0.00481057 0.99997503 23.72195442
Axis 0.54456768 -0.58900395 -0.59709329
Axis point 1929.12540421 -4858.79308083 0.00000000
Rotation angle (degrees) 0.50470677
Shift along axis -17.30557013
> fitmap #4 inMap #1 metric correlation
Fit map NE-NPC_NR in map NE-NPC_SU using 274093 points
correlation = 0.5721, correlation about mean = 0.5788, overlap = 1014
steps = 180, shift = 4.69, angle = 28.6 degrees
Position of NE-NPC_NR (#4) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.95222925 -0.30472325 -0.02007977 27.82834647
-0.30470601 -0.95243811 0.00398677 91.53140637
-0.02033960 0.00232211 -0.99979043 59.27939689
Axis -0.98798513 0.15421017 0.01022766
Axis point 0.00000000 47.95016885 29.76380642
Rotation angle (degrees) 179.95173095
Shift along axis -12.77262918
> fitmap #4 inMap #1 metric correlation envelope false
Fit map NE-NPC_NR in map NE-NPC_SU using 287496 points
correlation = 0.592, correlation about mean = 0.5926, overlap = 1674
steps = 44, shift = 0.158, angle = 0.207 degrees
Position of NE-NPC_NR (#4) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.95172729 -0.30647385 -0.01699820 27.92776385
-0.30644153 -0.95187866 0.00453903 91.50895933
-0.01757132 0.00088903 -0.99984522 59.15315526
Axis -0.98785810 0.15511234 0.00874858
Axis point 0.00000000 47.97478114 29.65652584
Rotation angle (degrees) 179.89415005
Shift along axis -12.87699277
> fitmap #2 inMap #1 metric correlation envelope false
Fit map NE-NPC_IR in map NE-NPC_SU using 175616 points
correlation = 0.8052, correlation about mean = 0.8131, overlap = 2493
steps = 60, shift = 0.0092, angle = 0.0525 degrees
Position of NE-NPC_IR (#2) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.99997665 0.00452404 -0.00512162 16.13907932
-0.00454572 0.99998072 -0.00422991 20.20495210
0.00510238 0.00425310 0.99997794 23.73023305
Axis 0.52736099 -0.63559237 -0.56383750
Axis point -2672.10345149 0.00000000 4987.01031584
Rotation angle (degrees) 0.46082859
Shift along axis -17.71098779
> fitmap #3 inMap #1 metric correlation envelope false
Fit map NE-NPC_CR in map NE-NPC_SU using 287496 points
correlation = 0.03554, correlation about mean = 0.03593, overlap = 59.44
steps = 224, shift = 18.8, angle = 37.3 degrees
Position of NE-NPC_CR (#3) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.80775006 0.24156100 -0.53776214 17.59966193
-0.14998904 0.96638684 0.20880554 34.00035403
0.57012553 -0.08800426 0.81683054 56.82482452
Axis -0.24490270 -0.91413652 -0.32307444
Axis point -59.70435799 0.00000000 29.59365133
Rotation angle (degrees) 37.29903150
Shift along axis -53.74981842
> view matrix models #5,1,0,0,-18.672,0,1,0,94.915,0,0,1,-76.921
> select #3
2 models selected
> view matrix models
> #3,0.80775,0.24156,-0.53776,17.445,-0.14999,0.96639,0.20881,17.65,0.57013,-0.088004,0.81683,34.742
> fitmap #3 inMap #1 metric correlation envelope false
Fit map NE-NPC_CR in map NE-NPC_SU using 287496 points
correlation = 0.1156, correlation about mean = 0.1156, overlap = 329.8
steps = 272, shift = 1.47, angle = 18.7 degrees
Position of NE-NPC_CR (#3) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.91190417 0.24574224 -0.32869672 7.05173838
-0.08944605 0.90066427 0.42520968 10.97718429
0.40053737 -0.35834986 0.84330018 49.63943481
Axis -0.69857747 -0.65014397 -0.29883497
Axis point 0.00000000 99.25807500 38.49763879
Rotation angle (degrees) 34.11287707
Shift along axis -26.89693474
> volume #1 level -0.1594
> fitmap #3 inMap #1 metric correlation
Fit map NE-NPC_CR in map NE-NPC_SU using 267871 points
correlation = 0.1616, correlation about mean = 0.1765, overlap = 284.7
steps = 72, shift = 1.27, angle = 3.57 degrees
Position of NE-NPC_CR (#3) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.91504064 0.20189280 -0.34919897 7.84010164
-0.06074100 0.92481876 0.37552734 10.55322729
0.39876203 -0.32241208 0.85850993 47.87787899
Axis -0.66080732 -0.70816762 -0.24866103
Axis point -104.27381398 0.00000000 1.34583980
Rotation angle (degrees) 31.87690030
Shift along axis -24.55961304
> view matrix models
> #3,0.91504,0.20189,-0.3492,32.724,-0.060741,0.92482,0.37553,3.6675,0.39876,-0.32241,0.85851,38.892
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8599,-0.47786,-0.17951,52.779,0.41893,0.86156,-0.28672,4.9162,0.29167,0.17135,0.94105,24.511
> view matrix models
> #3,0.90831,-0.33377,-0.25213,48.147,0.32046,0.94264,-0.093423,1.1418,0.26885,0.0040609,0.96317,30.2
> fitmap #3 inMap #1 metric correlation
Fit map NE-NPC_CR in map NE-NPC_SU using 267871 points
correlation = 0.6116, correlation about mean = 0.6164, overlap = 1065
steps = 176, shift = 13.5, angle = 25.2 degrees
Position of NE-NPC_CR (#3) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.99995916 -0.00080687 0.00900111 13.77205779
0.00085428 0.99998578 -0.00526453 3.17916892
-0.00899673 0.00527200 0.99994563 43.10109914
Axis 0.50362733 0.86026455 0.07940038
Axis point 4679.88698514 0.00000000 -776.22400587
Rotation angle (degrees) 0.59936176
Shift along axis 13.09315448
> fitmap #4 inMap #1 metric correlation envelope false
Fit map NE-NPC_NR in map NE-NPC_SU using 287496 points
correlation = 0.592, correlation about mean = 0.5926, overlap = 1674
steps = 36, shift = 0.00394, angle = 0.00818 degrees
Position of NE-NPC_NR (#4) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.95172420 -0.30649112 -0.01685958 27.92772098
-0.30645919 -0.95187312 0.00451008 91.50956209
-0.01743048 0.00087442 -0.99984770 59.14988189
Axis -0.98785732 0.15512130 0.00867786
Axis point 0.00000000 47.97509681 29.65406058
Rotation angle (degrees) 179.89456576
Shift along axis -12.88022642
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99996,-0.00080687,0.0090011,30.347,0.00085428,0.99999,-0.0052645,-31.59,-0.0089967,0.005272,0.99995,66.476
> view matrix models
> #3,0.99996,-0.00080687,0.0090011,34.887,0.00085428,0.99999,-0.0052645,-39.689,-0.0089967,0.005272,0.99995,71.101
> select #5
2 models selected
> view matrix models #5,1,0,0,20.82,0,1,0,9.588,0,0,1,-18.126
> volume #5 level -0.1482
> fitmap #5 inMap #1 metric correlation envelope false
Fit map NE-NPC_NB in map NE-NPC_SU using 287496 points
correlation = 0.5525, correlation about mean = 0.5532, overlap = 672
steps = 108, shift = 12.1, angle = 0.862 degrees
Position of NE-NPC_NB (#5) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.99989272 -0.01460344 0.00113799 24.35700693
0.01459941 0.99988740 0.00347110 -2.14494081
-0.00118855 -0.00345412 0.99999333 -21.37826951
Axis -0.23005252 0.07728662 0.97010444
Axis point 16.23184642 1250.18236646 0.00000000
Rotation angle (degrees) 0.86241386
Shift along axis -26.50832007
> volume #4 level -0.09794
> view matrix models
> #5,0.99989,-0.014603,0.001138,24.184,0.014599,0.99989,0.0034711,-2.039,-0.0011886,-0.0034541,0.99999,-21.347
> select #3
2 models selected
> view matrix models
> #3,0.99996,-0.00080687,0.0090011,0.25277,0.00085428,0.99999,-0.0052645,-26.722,-0.0089967,0.005272,0.99995,64.947
> view matrix models
> #3,0.99996,-0.00080687,0.0090011,-4.4549,0.00085428,0.99999,-0.0052645,1.1062,-0.0089967,0.005272,0.99995,42.922
> view matrix models
> #3,0.99996,-0.00080687,0.0090011,12.021,0.00085428,0.99999,-0.0052645,3.6625,-0.0089967,0.005272,0.99995,45.854
> view matrix models
> #3,0.99996,-0.00080687,0.0090011,13.043,0.00085428,0.99999,-0.0052645,2.49,-0.0089967,0.005272,0.99995,45.806
> fitmap #3 inMap #1 metric correlation envelope false
Fit map NE-NPC_CR in map NE-NPC_SU using 287496 points
correlation = 0.7028, correlation about mean = 0.7044, overlap = 2191
steps = 56, shift = 2.81, angle = 0.0822 degrees
Position of NE-NPC_CR (#3) relative to NE-NPC_SU (#1) coordinates:
Matrix rotation and translation
0.99996409 0.00051733 0.00845873 13.73797267
-0.00047177 0.99998537 -0.00538781 3.20126318
-0.00846140 0.00538363 0.99994971 43.15390915
Axis 0.53636859 0.84254549 -0.04925275
Axis point 5152.84327817 0.00000000 -1098.74219589
Rotation angle (degrees) 0.57532105
Shift along axis 7.94037809
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_CompositeMaps
> volume resample #2 onGrid #1
Opened NE-NPC_IR resampled as #6, grid size 100,100,100, pixel 1, shown at
step 1, values float32
> volume resample #3 onGrid #1
Opened NE-NPC_CR resampled as #7, grid size 100,100,100, pixel 1, shown at
step 1, values float32
> volume resample #4-5 onGrid #1
Opened NE-NPC_NR resampled as #8, grid size 100,100,100, pixel 1, shown at
step 1, values float32
Opened NE-NPC_NB resampled as #9, grid size 100,100,100, pixel 1, shown at
step 1, values float32
> save 240429_NE-NPC_fitting.cxs
> save #6 SUposition_NE-NPC_IR.mrc
Cannot determine format for '#6'
> save SUposition_NE-NPC_IR.mrc #6
> save SUposition_NE-NPC_CR.mrc #7
> save SUposition_NE-NPC_NR.mrc #8
> save SUposition_NE-NPC_NB.mrc #9
> save 240429_NE-NPC_fitting.cxs
——— End of log from Mon Apr 29 12:59:49 2024 ———
opened ChimeraX session
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps
> close #1
> open NE-NPC_SUpadded.em
Opened NE-NPC_SUpadded.em as #1, grid size 100,100,150, pixel 1, shown at
level 0.138, step 1, values float32
> volume #1 level -0.07083
> volume all capFaces false
> show all
> view all
Drag select of 2 NE-NPC_IR , 3 NE-NPC_CR , 4 NE-NPC_NR , 5 NE-NPC_NB
Drag select of 2 NE-NPC_IR , 3 NE-NPC_CR , 4 NE-NPC_NR , 1 NE-NPC_SUpadded.em
> select #4
2 models selected
Drag select of 4 NE-NPC_NR , 5 NE-NPC_NB
> select #2-5
8 models selected
> view orient
> turn x -90
> view all
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99998,0.004524,-0.0051216,12.271,-0.0045457,0.99998,-0.0042299,20.205,0.0051024,0.0042531,0.99998,49.353,#3,0.99996,0.00051733,0.0084587,9.8698,-0.00047177,0.99999,-0.0053878,3.2013,-0.0084614,0.0053836,0.99995,68.777,#4,0.95172,-0.30649,-0.01686,24.06,-0.30646,-0.95187,0.0045101,91.51,-0.01743,0.00087442,-0.99985,84.773,#5,0.99989,-0.014603,0.001138,20.316,0.014599,0.99989,0.0034711,-2.039,-0.0011886,-0.0034541,0.99999,4.276
> ui tool show "Fit in Map"
> fitmap #2 inMap #1 metric correlation envelope false
Fit map NE-NPC_IR in map NE-NPC_SUpadded.em using 175616 points
correlation = 0.8048, correlation about mean = 0.8127, overlap = 2490
steps = 68, shift = 3.93, angle = 0.0142 degrees
Position of NE-NPC_IR (#2) relative to NE-NPC_SUpadded.em (#1) coordinates:
Matrix rotation and translation
0.99997539 0.00452305 -0.00536266 16.16147685
-0.00454545 0.99998096 -0.00417294 20.20345669
0.00534368 0.00419722 0.99997691 48.71652885
Axis 0.51231930 -0.65531186 -0.55506332
Axis point -5766.33623300 0.00000000 6097.31935316
Rotation angle (degrees) 0.46804814
Shift along axis -32.00048669
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select clear
[Repeated 1 time(s)]
> view all
> volume #1 level -0.1518
> select subtract #2
Nothing selected
> select subtract #3
Nothing selected
> select subtract #4
Nothing selected
> select subtract #5
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> fitmap #3 inMap #1 metric correlation envelope false
Fit map NE-NPC_CR in map NE-NPC_SUpadded.em using 287496 points
correlation = 0.7026, correlation about mean = 0.7042, overlap = 2192
steps = 60, shift = 3.92, angle = 0.0229 degrees
Position of NE-NPC_CR (#3) relative to NE-NPC_SUpadded.em (#1) coordinates:
Matrix rotation and translation
0.99996602 0.00037438 0.00823480 13.75151465
-0.00032757 0.99998379 -0.00568485 3.20586226
-0.00823679 0.00568196 0.99994993 68.12820269
Axis 0.56762407 0.82254129 -0.03505336
Axis point 8312.05153565 0.00000000 -1080.43454403
Rotation angle (degrees) 0.57369049
Shift along axis 8.05452253
> hide #!3 models
> show #!4 models
> fitmap #4 inMap #1 metric correlation envelope false
Fit map NE-NPC_NR in map NE-NPC_SUpadded.em using 287496 points
correlation = 0.5919, correlation about mean = 0.5925, overlap = 1674
steps = 60, shift = 3.91, angle = 0.0302 degrees
Position of NE-NPC_NR (#4) relative to NE-NPC_SUpadded.em (#1) coordinates:
Matrix rotation and translation
0.95171846 -0.30647957 -0.01738544 27.93560986
-0.30644771 -0.95187670 0.00453360 91.51071855
-0.01793825 0.00101302 -0.99983858 84.17390223
Axis -0.98785586 0.15511569 0.00893946
Axis point 0.00000000 47.98663036 42.17119821
Rotation angle (degrees) 179.89790270
Shift along axis -12.64913849
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!1 models
> fitmap #5 inMap #4 metric correlation envelope false
Fit map NE-NPC_NB in map NE-NPC_NR using 287496 points
correlation = 0.6933, correlation about mean = 0.6944, overlap = 1263
steps = 88, shift = 3.88, angle = 0.616 degrees
Position of NE-NPC_NB (#5) relative to NE-NPC_NR (#4) coordinates:
Matrix rotation and translation
0.94618590 -0.32341105 -0.01172732 26.36798494
-0.32336661 -0.94625744 0.00555874 89.69264711
-0.01289482 -0.00146738 -0.99991578 80.27018964
Axis -0.98645469 0.16391521 0.00624006
Axis point 0.00000000 47.10956354 40.13594207
Rotation angle (degrees) 179.79595222
Shift along axis -10.80794260
> volume resample #2-5 onGrid #1
Opened NE-NPC_IR resampled as #6, grid size 100,100,150, pixel 1, shown at
step 1, values float32
Opened NE-NPC_CR resampled as #7, grid size 100,100,150, pixel 1, shown at
step 1, values float32
Opened NE-NPC_NR resampled as #8, grid size 100,100,150, pixel 1, shown at
step 1, values float32
Opened NE-NPC_NB resampled as #9, grid size 100,100,150, pixel 1, shown at
step 1, values float32
> info #1
2 models
#1, NE-NPC_SUpadded.em, hidden size 100,100,150, step 1, voxel size 1, level
-0.1518, value range -0.58591 - 0.50854, value type float32, 0 symmetry
operators
#1.1, surface, shown, 121670 triangles
> info path #1
Expected one of 'all', 'system', or 'user' or a keyword
> info path
system versioned config directory: /Library/Application Support/ChimeraX/1.7
system versioned data directory: /Library/Application Support/ChimeraX/1.7
system unversioned config directory: /Library/Application Support/ChimeraX
system unversioned data directory: /Library/Application Support/ChimeraX
user versioned cache directory: /Users/jenny/Library/Caches/ChimeraX/1.7
user versioned config directory: /Users/jenny/Library/Application
Support/ChimeraX/1.7
user versioned data directory: /Users/jenny/Library/Application
Support/ChimeraX/1.7
user versioned log directory: /Users/jenny/Library/Logs/ChimeraX/1.7
user versioned state directory: /Users/jenny/Library/Application
Support/ChimeraX/1.7
user unversioned cache directory: /Users/jenny/Library/Caches/ChimeraX
user unversioned config directory: /Users/jenny/Library/Application
Support/ChimeraX
user unversioned data directory: /Users/jenny/Library/Application
Support/ChimeraX
user unversioned log directory: /Users/jenny/Library/Logs/ChimeraX
user unversioned state directory: /Users/jenny/Library/Application
Support/ChimeraX
> log #1
Expected a keyword
> log metadata #1
No models had metadata
> ui tool show "Selection Inspector"
> save #6 SUposition_NE-NPC_IR.mrc
Cannot determine format for '#6'
> save SUposition_NE-NPC_IR.mrc #6
> save SUposition_NE-NPC_CR.mrc #7
[Repeated 2 time(s)]
> save SUposition_NE-NPC_NR.mrc #8
> save SUposition_NE-NPC_NB.mrc #9
> save 240501_NE-NPC_fitting.cxs
> view all
> save 240501_NE-NPC_fitting.cxs
——— End of log from Wed May 1 14:54:08 2024 ———
opened ChimeraX session
> close
> open cNPC_*.em
Opened cNPC_CRmap_ring.em as #1.1, grid size 150,150,150, pixel 1, shown at
level 0.339, step 1, values float32
Opened cNPC_IRmap_ring.em as #1.2, grid size 150,150,150, pixel 1, shown at
level 0.338, step 1, values float32
Opened cNPC_NRmap_ring.em as #1.3, grid size 150,150,150, pixel 1, shown at
level 0.346, step 1, values float32
Opened cNPC_ring.em as #1.4, grid size 150,150,150, pixel 1, shown at level
0.52, step 1, values float32
> ui tool show "Color Zone"
> volume #1.4 level 0.1847
> volume #1.2 level 0.2169
> volume #1.2 style image region 0,0,74,149,149,74 step 1 showOutlineBox true
> open NE-NPC_ring
'NE-NPC_ring' has no suffix
> open NE-NPC_ring.em
Opened NE-NPC_ring.em as #2, grid size 150,150,150, pixel 1, shown at level
0.514, step 1, values float32
> volume #2 level 0.2812
> ui tool show "Fit in Map"
> fitmap #1.4 inMap #2 metric correlation envelope false
Fit map cNPC_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.2652, correlation about mean = 0.2613, overlap = 1.311e+04
steps = 84, shift = 4.57, angle = 4.34 degrees
Position of cNPC_ring.em (#1.4) relative to NE-NPC_ring.em (#2) coordinates:
Matrix rotation and translation
0.99713185 -0.07568402 -0.00000221 5.89106961
0.07568402 0.99713185 -0.00000270 -5.46159990
0.00000241 0.00000252 1.00000000 -4.57285254
Axis 0.00003450 -0.00003055 1.00000000
Axis point 75.00715046 74.99727702 0.00000000
Rotation angle (degrees) 4.34052567
Shift along axis -4.57248248
> fitmap #1.2 inMap #2 metric correlation envelope false
Fit map cNPC_IRmap_ring.em in map NE-NPC_ring.em using 22500 points
correlation = 0.1833, correlation about mean = 0.2277, overlap = 65
steps = 2000, shift = 3.94, angle = 0.598 degrees
Position of cNPC_IRmap_ring.em (#1.2) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99994760 0.01017351 -0.00113986 -0.72558439
-0.01017581 0.99994615 -0.00203596 0.79518427
0.00111909 0.00204745 0.99999728 3.69959058
Axis 0.19558840 -0.10820001 -0.97469889
Axis point 37.38963215 -2.19500339 0.00000000
Rotation angle (degrees) 0.59810850
Shift along axis -3.83394169
> volume #1.2 level -0.1243,0 level 0.5041,0.8 level 0.7795,1
> volume #1.2 region 0,0,0,149,149,149 step 1
> volume #1.2 style surface region 0,0,0,149,149,149 step 1
> fitmap #1.2 inMap #2 metric correlation envelope false
Fit map cNPC_IRmap_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.05593, correlation about mean = 0.05203, overlap = 1675
steps = 80, shift = 1.43, angle = 2.13 degrees
Position of cNPC_IRmap_ring.em (#1.2) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99963654 -0.02695897 0.00003538 2.04711233
0.02695897 0.99963654 0.00004763 -1.99715428
-0.00003666 -0.00004666 1.00000000 5.36214728
Axis -0.00174890 0.00133608 0.99999758
Axis point 75.36141716 75.26578814 0.00000000
Rotation angle (degrees) 1.54482626
Shift along axis 5.35588573
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #1.2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.2,0.99964,-0.026959,3.5384e-05,6.8012,0.026959,0.99964,4.7634e-05,-1.8336,-3.6655e-05,-4.6663e-05,1,-0.5867
> view matrix models
> #1.2,0.99964,-0.026959,3.5384e-05,4.8188,0.026959,0.99964,4.7634e-05,-2.3365,-3.6655e-05,-4.6663e-05,1,-1.0773
> fitmap #1.2 inMap #2 metric correlation envelope false
Fit map cNPC_IRmap_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.116, correlation about mean = 0.1124, overlap = 3505
steps = 152, shift = 4.53, angle = 5.21 degrees
Position of cNPC_IRmap_ring.em (#1.2) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99486688 -0.06336891 -0.07889406 17.63437767
0.06548273 0.99755293 0.02449816 -6.80487632
0.07714858 -0.02953861 0.99658194 -6.73671096
Axis -0.25798566 -0.74498833 0.61517134
Axis point 67.60633696 0.00000000 207.27011635
Rotation angle (degrees) 6.01151002
Shift along axis -3.62409469
> fitmap #1.1 inMap #2 metric correlation envelope false
Fit map cNPC_CRmap_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.4264, correlation about mean = 0.4246, overlap = 1.187e+04
steps = 80, shift = 4.46, angle = 4.35 degrees
Position of cNPC_CRmap_ring.em (#1.1) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99712324 -0.07579744 -0.00000146 5.90001422
0.07579744 0.99712324 -0.00000165 -5.46913000
0.00000158 0.00000153 1.00000000 -4.45561456
Axis 0.00002097 -0.00002000 1.00000000
Axis point 75.00198640 74.99388360 0.00000000
Rotation angle (degrees) 4.34704288
Shift along axis -4.45538143
> jview position #1 sameAsModel 1.1
Unknown command: jview position #1 sameAsModel 1.1
> view position #1 sameAsModels 1.1
Invalid "sameAsModels" argument: invalid models specifier
> view position #1 sameAsModels #1.1
> fitmap #1.1 inMap #2 metric correlation envelope false
Fit map cNPC_CRmap_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.4264, correlation about mean = 0.4246, overlap = 1.187e+04
steps = 96, shift = 4.45, angle = 4.34 degrees
Position of cNPC_CRmap_ring.em (#1.1) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
1.00000000 -0.00006959 0.00000176 0.00465854
0.00006959 1.00000000 -0.00000098 -0.00542114
-0.00000176 0.00000098 1.00000000 -0.01043725
Axis 0.01406980 0.02526632 0.99958174
Axis point 74.08601048 69.06041615 0.00000000
Rotation angle (degrees) 0.00398908
Shift along axis -0.01050431
> view position #1.2-1.4 sameAsModels #1.1
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> hide #!1.3 models
> hide #!2 models
> show #!1.3 models
> view position #1.2 sameAsModels #1.1
> view position #1.3 sameAsModels #1.1
> view position #1.4 sameAsModels #1.1
> ui mousemode right select
> select clear
> show #!2 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1 models
> volume #2 level 0.1455
> dust #2 diameter 2
Unknown command: dust #2 diameter 2
> volume dust #2 diameter 2
Expected a density maps specifier or a keyword
> volume dust #2 radius 10
Expected a density maps specifier or a keyword
> ui tool show "Hide Dust"
> surface dust #2 size 6
> surface dust #2 radius 10
Expected a keyword
> volume #1.4 level 0.0644
> view all
No displayed objects specified.
> volume #1.4 level 0.09248
> view all
No displayed objects specified.
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> volume showOutlineBox false
> volume showOutlineBox true
> hide #!2 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!2 models
> hide #!1.3 models
> hide #!1.2 models
> fitmap #1.1 inMap #2 metric correlation envelope false rotate false
Fit map cNPC_CRmap_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.2197, correlation about mean = 0.2173, overlap = 6343
steps = 88, shift = 4.48, angle = 0 degrees
Position of cNPC_CRmap_ring.em (#1.1) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99712324 -0.07579744 -0.00000146 3.74804252
0.07579744 0.99712324 -0.00000165 -5.64074692
0.00000158 0.00000153 1.00000000 -0.53570458
Axis 0.00002097 -0.00002000 1.00000000
Axis point 76.18582182 46.55678289 0.00000000
Rotation angle (degrees) 4.34704288
Shift along axis -0.53551315
> fitmap #1.1 inMap #2 metric correlation envelope false shift false
Fit map cNPC_CRmap_ring.em in map NE-NPC_ring.em using 3375000 points
correlation = 0.3423, correlation about mean = 0.3402, overlap = 9663
steps = 68, shift = 7.78e-14, angle = 4.44 degrees
Position of cNPC_CRmap_ring.em (#1.1) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99975777 -0.00178825 0.02193636 -3.59628264
0.00168033 0.99998640 0.00493703 -0.70025920
-0.02194489 -0.00489897 0.99974718 1.48322998
Axis -0.21807531 0.97289732 0.07690232
Axis point 64.95612195 0.00000000 162.50119919
Rotation angle (degrees) 1.29223492
Shift along axis 0.21704397
> fitmap #1.1 inMap #2 metric correlation
Fit map cNPC_CRmap_ring.em in map NE-NPC_ring.em using 33748 points
correlation = 0.8422, correlation about mean = 0.3073, overlap = 5685
steps = 56, shift = 1.58, angle = 1.29 degrees
Position of cNPC_CRmap_ring.em (#1.1) relative to NE-NPC_ring.em (#2)
coordinates:
Matrix rotation and translation
0.99999998 0.00018900 0.00000158 -0.01363227
-0.00018900 0.99999998 0.00000140 0.01423846
-0.00000158 -0.00000140 1.00000000 0.08040417
Axis -0.00740882 0.00835330 -0.99993766
Axis point 78.87211275 75.27866747 0.00000000
Rotation angle (degrees) 0.01082961
Shift along axis -0.08017922
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240501_alignedCompositeMaps.cxs
> view position #1.2 sameAsModels #1.1
> view position #1.3 sameAsModels #1.1
> view position #1.4 sameAsModels #1.1
> show #!1.4 models
> hide #!1.1 models
> volume #!2#!1.4 showOutlineBox false
> view orient
> turn x -90
> ui tool show "Side View"
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240501_alignedCompositeMaps.cxs
——— End of log from Thu May 2 17:14:30 2024 ———
opened ChimeraX session
> hide #!2 models
> color #1.1 #ffa405ff models
> color #1.2 #aaaaaaff models
> color #1.3 #039d91ff models
> hide #!1.4 models
> hide #2.1 models
> set bgColor white
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> view all
> graphics silhouettes true
> graphics silhouettes false
> volume #!1.1-3 showOutlineBox false
> view orient
> turn x 90
> view orient
> volume #!1.1-3 showOutlineBox true
> volume #!1.1-3 showOutlineBox false
> volume #!1.1-3 showOutlineBox true
> set bgColor black
> show #!2 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #2.1 models
> color #2.1 #aaaaaaff
> color #1.3 #ffa405ff models
> color #1.2 #777777ff models
> show #!1.2 models
> set bgColor white
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/NE-
> NPC_CRmap_ring.em
Opened NE-NPC_CRmap_ring.em as #3, grid size 150,150,150, pixel 1, shown at
level 0.322, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/NE-
> NPC_NRmap_ring.em
Opened NE-NPC_NRmap_ring.em as #4, grid size 150,150,150, pixel 1, shown at
level 0.282, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/NE-
> NPC_IRmap_ring.em
Opened NE-NPC_IRmap_ring.em as #5, grid size 150,150,150, pixel 1, shown at
level 0.329, step 1, values float32
> hide #!1.2 models
> hide #!2 models
> hide #2.1 models
> color #3 #ffa405ff models
> color #4 #aaaaaaff models
> color #4 #039d91ff models
> color #5 #aaaaaaff models
> volume #3 level 0.2777
> volume #4 level 0.249
> volume #5 level 0.2359
> volume #3 level 0.15
> volume #3 level 0.12
> volume #3 level 0.2
> volume #4 level 0.2
> volume #5 level 0.2
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps.cxs
> view orient
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NE_CR_box66_ref_16.em
Opened NE_CR_box66_ref_16.em as #6, grid size 66,66,66, pixel 1, shown at
level 0.285, step 1, values float32
> volume #6 level 0.1555
> close #6
> rename #5 id #6
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/NE-
> NPC_NBmap_ring.em
Opened NE-NPC_NBmap_ring.em as #5, grid size 150,150,150, pixel 1, shown at
level 0.175, step 1, values float32
> color #6 #039d91ff models
> color #6 #aaaaaaff models
> color #5 #039d91ff models
> volume all hide dust size 10
Expected a keyword
> ui tool show "Hide Dust"
> surface dust #5 size 6
> surface dust all size 10
> view orient
> turn x 90
[Repeated 4 time(s)]
> view orient
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting soft
> volume #5 level 0.2
> turn x 90
[Repeated 3 time(s)]
> turn x 45
> turn x -45
[Repeated 1 time(s)]
> turn x 180
> view orient
> turn x -90
> ui tool show "Side View"
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> view orient
> volume #1.1 level 0.2
> volume #1.2 level 0.2
> volume #1.2 level -0.0005483
> volume #1.2 level 0.2
> volume #1.2 level 0.2562
> volume #1.2 level 0.2963
> volume #1.3 level 0.2
> volume #!1.1-3 showOutlineBox false
> view orient
> turn x -45
> turn x 180
> view orient
> turn x -90
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps.cxs
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_2.cxs
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NE_CR_box66_ref_16.em
Opened NE_CR_box66_ref_16.em as #7, grid size 66,66,66, pixel 1, shown at
level 0.285, step 1, values float32
> volume scale #7 factor -1
Opened NE_CR_box66_ref_16.em scaled as #8, grid size 66,66,66, pixel 1, shown
at step 1, values float32
> hide #!4 models
> hide #!5 models
> hide #!6 models
> close #7
> rename #8 id #7
> volume #7 level 0.3144
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-12.478,0,1,0,85.661,0,0,1,36.741
> view matrix models #7,1,0,0,-14.25,0,1,0,83.515,0,0,1,71.924
> view orient
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.99866,-0.051671,0,49.422,0.051671,-0.99866,0,147.02,0,0,1,71.924
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.99866,-0.051671,0,67.042,0.051671,-0.99866,0,121.26,0,0,1,71.924
> ui tool show "Fit in Map"
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 6483
points
correlation = 0.9869, correlation about mean = 0.8125, overlap = 1603
steps = 72, shift = 4.07, angle = 2.96 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.99997356 -0.00071421 -0.00723606 65.23213625
0.00068811 -0.99999325 0.00360859 121.84661176
-0.00723859 0.00360351 0.99996731 68.16969873
Axis -0.00361869 0.00180304 0.99999183
Axis point 32.71807435 60.87332707 0.00000000
Rotation angle (degrees) 179.95982603
Shift along axis 68.15278071
> marker #9 position 10.8, 40.5, 31 color red radius 1 coordinateSystem #7
> volume #7 level 0.1923
> view matrix models
> #7,-0.99997,-0.00071421,-0.0072361,157.38,0.00068811,-0.99999,0.0036086,91.742,-0.0072386,0.0036035,0.99997,68.17
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99723,-0.074039,0.0074856,93.104,0.074063,0.99725,-0.0030576,24.546,-0.0072386,0.0036035,0.99997,68.17
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99723,-0.074039,0.0074856,87.254,0.074063,0.99725,-0.0030576,25.912,-0.0072386,0.0036035,0.99997,68.17
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.9652, correlation about mean = 0.832, overlap = 2190
steps = 72, shift = 0.473, angle = 4.29 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.99996125 0.00074255 0.00877249 84.68525785
-0.00069999 0.99998797 -0.00485439 28.20400661
-0.00877599 0.00484806 0.99994974 68.20425170
Axis 0.48261528 0.87288822 -0.07175404
Axis point 8303.11491116 0.00000000 -6283.18948171
Rotation angle (degrees) 0.57594454
Shift along axis 60.59541408
> marker #9 position 10.8, 40.5, 31 color red radius 1 coordinateSystem #7
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99996,0.00074255,0.0087725,88.529,-0.00069999,0.99999,-0.0048544,57.287,-0.008776,0.0048481,0.99995,68.204
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.79922,-0.60096,0.0099279,114.72,0.60098,0.79927,0.0013993,43.686,-0.008776,0.0048481,0.99995,68.204
> view matrix models
> #7,0.90575,-0.4237,0.010003,105.42,0.42373,0.90579,-0.00067269,46.158,-0.008776,0.0048481,0.99995,68.204
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.4797, correlation about mean = 0.02075, overlap = 738.1
steps = 76, shift = 2.08, angle = 6.24 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.87050541 -0.48437266 0.08719777 107.19803227
0.48818063 0.87229007 -0.02810190 46.45336987
-0.06244996 0.06703112 0.99579457 70.12561377
Axis 0.09623129 0.15137534 0.98378099
Axis point -13.99688728 207.90259804 0.00000000
Rotation angle (degrees) 29.62317988
Shift along axis 86.33594573
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.87051,-0.48437,0.087198,101.54,0.48818,0.87229,-0.028102,48.181,-0.06245,0.067031,0.99579,70.126
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.965, correlation about mean = 0.8247, overlap = 2128
steps = 132, shift = 5.06, angle = 16.5 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.70761517 -0.70653502 0.00943538 114.93580698
0.70654499 0.70766258 0.00280271 48.74858821
-0.00865728 0.00468328 0.99995156 68.20753711
Axis 0.00133072 0.01280264 0.99991716
Axis point -0.41977543 162.71911209 0.00000000
Rotation angle (degrees) 44.95883281
Shift along axis 68.97894431
> marker #9 position 10.8, 40.5, 31 color red radius 1 coordinateSystem #7
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.70422,0.70992,-0.0094218,116.22,-0.70993,-0.70427,-0.0028479,141.81,-0.0086573,0.0046833,0.99995,68.208
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.70422,0.70992,-0.0094218,34.1,-0.70993,-0.70427,-0.0028479,100.98,-0.0086573,0.0046833,0.99995,68.208
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.965, correlation about mean = 0.8249, overlap = 2129
steps = 68, shift = 0.777, angle = 0.276 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.70762534 0.70652423 -0.00948126 35.05931349
-0.70653368 -0.70767353 -0.00288540 101.25130747
-0.00874824 0.00465705 0.99995089 68.20926177
Axis 0.00533760 -0.00051874 -0.99998562
Axis point 38.65073034 43.27990720 0.00000000
Rotation angle (degrees) 135.04597869
Shift along axis -68.07367150
> marker #9 position 10.8, 40.5, 31 color red radius 1 coordinateSystem #7
> ui mousemode right "delete markers"
> marker delete #9:3
> marker delete #9:4
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.70763,0.70652,-0.0094813,46.574,-0.70653,-0.70767,-0.0028854,158.15,-0.0087482,0.0046571,0.99995,68.209
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.80115,-0.59845,-0.0042219,91.973,0.5984,-0.80115,0.0089664,117.58,-0.0087482,0.0046571,0.99995,68.209
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.80115,-0.59845,-0.0042219,98.889,0.5984,-0.80115,0.0089664,120.28,-0.0087482,0.0046571,0.99995,68.209
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.9649, correlation about mean = 0.8249, overlap = 2130
steps = 104, shift = 3.04, angle = 8.29 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.70645873 -0.70774765 -0.00305348 101.25141936
0.70769963 -0.70645124 0.00937411 114.94041654
-0.00879164 0.00446147 0.99995140 68.20107381
Axis -0.00347068 0.00405390 0.99998576
Axis point 26.96634614 78.37759801 0.00000000
Rotation angle (degrees) 134.94917739
Shift along axis 68.31464771
> open
> /Users/jenny/Desktop/TempDocuments/PaperNPCasymmetry/Data&Figures/Figures/DrosophilaNPCstructures/DrosophilaNPCstructure/240506_DifferenceMap.mrc
Opened 240506_DifferenceMap.mrc as #8, grid size 66,66,66, pixel 9.66, shown
at level 0.228, step 1, values float32
> ui tool show "Map Coordinates"
> view position #8 sameAsModels #7
> volume #8 level -0.2544
> volume all capFaces false
> volume #8 level -0.2585
> volume #8 color #ff7205
> volume #8 level -0.1761
> volume #8 level -0.3698
> volume #8 level -0.1926
> close #8
> open
> /Users/jenny/Desktop/TempDocuments/PaperNPCasymmetry/Data&Figures/Figures/DrosophilaNPCstructures/DrosophilaNPCstructure/240506_OnMyCR_CR-
> InnerY.cif
Chain information for 240506_OnMyCR_CR-InnerY.cif #8
---
Chain | Description
K0 | Nuclear pore complex protein Nup133
L0 | Nuclear pore complex protein Nup107
M0 | Nuclear pore complex protein Nup96
N0 | Protein SEC13 homolog
O0 | Nucleoporin SEH1
P0 | Nuclear pore complex protein Nup85
Q0 | Nucleoporin Nup43
R0 | Nuclear pore complex protein Nup160
S0 | Nucleoporin Nup37
240506_OnMyCR_CR-InnerY.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close #8
> rename #9 id #8
> rename #8 CRmarkers
> hide #8 models
> select subtract #7
Nothing selected
> show #!2 models
> show #2.1 models
> show #!4 models
> show #!5 models
> show all
> volume show all
Expected a keyword
> show #!6 models
> show #!7 models
> show #!1.4 models
> show #!1.3 models
> show #!1.2 models
> show #!1.1 models
> view all
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_correctScale.cxs
> hide #2.1 models
> hide #!2 models
> hide #!1.4 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!7 models
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.1447, correlation about mean = -0.05131, overlap = 179.9
steps = 164, shift = 28.3, angle = 14.3 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.67690812 -0.73559124 0.02647510 111.12985417
0.71121963 -0.66290077 -0.23394275 174.52794005
0.18963660 -0.13952813 0.97188984 30.44384948
Axis 0.06471010 -0.11182799 0.99161843
Axis point 16.01146719 113.00323751 0.00000000
Rotation angle (degrees) 133.15383437
Shift along axis 17.86279740
> view orient
> ui mousemode right select
> select #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.95651,-0.25901,0.13416,27.645,0.2033,-0.92178,-0.33014,439.72,0.20918,-0.28851,0.93435,79.154
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.95651,-0.25901,0.13416,102.27,0.2033,-0.92178,-0.33014,659.49,0.20918,-0.28851,0.93435,79.154
> fitmap #7 inMap #3
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 16659
points
correlation = 0.4084, correlation about mean = -0.002186, overlap = 594.5
steps = 172, shift = 115, angle = 22.1 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.95862175 -0.24261508 -0.14893714 151.53310119
0.25597472 -0.96353240 -0.07798888 632.89017942
-0.12458448 -0.11288598 0.98576644 29.81790247
Axis -0.06973806 -0.04866614 0.99637754
Axis point 36.47277975 326.78805681 0.00000000
Rotation angle (degrees) 165.51057895
Shift along axis -11.65806035
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.8124,-0.57447,-0.099954,198.06,0.54099,-0.80654,0.2384,422.92,-0.21757,0.1396,0.96601,-15.272
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.8124,-0.57447,-0.099954,277.3,0.54099,-0.80654,0.2384,377.28,-0.21757,0.1396,0.96601,-6.5013
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8548, correlation about mean = 0.8565, overlap = 3409
steps = 132, shift = 32.7, angle = 17.9 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.70638746 -0.70782261 -0.00197291 257.91277936
0.70779143 -0.70637815 0.00782288 391.10128855
-0.00693083 0.00412958 0.99996745 -61.28729399
Axis -0.00260895 0.00350228 0.99999046
Axis point 47.71731383 249.11676058 0.00000000
Rotation angle (degrees) 134.94268477
Shift along axis -60.58984517
> open
> /Users/jenny/Desktop/TempDocuments/PaperNPCasymmetry/Data&Figures/Figures/DrosophilaNPCstructures/DrosophilaNPCstructure/240506_OnMyCR_CR-
> InnerY.cif
Chain information for 240506_OnMyCR_CR-InnerY.cif #9
---
Chain | Description
K0 | Nuclear pore complex protein Nup133
L0 | Nuclear pore complex protein Nup107
M0 | Nuclear pore complex protein Nup96
N0 | Protein SEC13 homolog
O0 | Nucleoporin SEH1
P0 | Nuclear pore complex protein Nup85
Q0 | Nucleoporin Nup43
R0 | Nuclear pore complex protein Nup160
S0 | Nucleoporin Nup37
240506_OnMyCR_CR-InnerY.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> view position #9 sameAsModels #7
> hide #!5 models
> hide #!3 models
> hide #!7 models
> show #!7 models
> open
> /Users/jenny/Desktop/TempDocuments/PaperNPCasymmetry/Data&Figures/Figures/DrosophilaNPCstructures/DrosophilaNPCstructure/240506_OnMyCR_CR-
> OuterY.cif
Chain information for 240506_OnMyCR_CR-OuterY.cif #10
---
Chain | Description
K1 | Nuclear pore complex protein Nup133
L1 | Nuclear pore complex protein Nup107
M1 | Nuclear pore complex protein Nup96
N1 | Protein SEC13 homolog
O1 | Nucleoporin SEH1
P1 | Nuclear pore complex protein Nup85
Q1 | Nucleoporin Nup43
R1 | Nuclear pore complex protein Nup160
S1 | Nucleoporin Nup37
240506_OnMyCR_CR-OuterY.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> view position #10 sameAsModels #7
> hide #!7 models
> hide #!4 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> color #9 #ff7205ff
> color #10 #df4400ff
> color #3 #ffa40580 models
> color #3 #ffa405cc models
> view orient
> ui tool show "Segment Map"
> color #3 #ffa405ff models
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #9 distance 57.94
> surface unzone #3
> surface zone #3 nearAtoms #9 distance 57.94
> surface zone #3 nearAtoms #9 distance 59.32
> surface zone #3 nearAtoms #9 distance 798.72
> surface unzone #3
> ui tool show "Segment Map"
> ui tool show "Surface Color"
> ui tool show "Segment Map"
> ui tool show "Color Zone"
> color zone #3 near #9 distance 57.94
> color zone #3 near #9 distance 59.48
> color zone #3 near #9 distance 34.78
> color zone #3 near #9 distance 30
[Repeated 1 time(s)]
> color zone #3 near #10 distance 30
[Repeated 1 time(s)]
> combine #9-10
> color zone #3 near #11 distance 30
> color zone #3 near #11 distance 29.42
> color zone #3 near #11 distance 15.65
> show #8 models
> hide #8 models
> show #!7 models
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.70639,-0.70782,-0.0019729,620.31,0.70779,-0.70638,0.0078229,389.74,-0.0069308,0.0041296,0.99997,-61.287
> view matrix models
> #7,-0.70639,-0.70782,-0.0019729,589.67,0.70779,-0.70638,0.0078229,390.57,-0.0069308,0.0041296,0.99997,-61.287
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.83121,-0.53022,0.16721,536.9,0.52635,-0.84735,-0.070389,510.12,0.17901,0.029506,0.9834,-125.25
> view matrix models
> #7,-0.0079175,-0.88434,0.46677,318.41,0.96253,-0.13327,-0.23617,182.47,0.27107,0.44741,0.85226,-257.19
> view matrix models
> #7,-0.092423,-0.98996,0.10691,457.47,0.98483,-0.10672,-0.13683,145.23,0.14686,0.092644,0.98481,-135.06
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.092423,-0.98996,0.10691,432.93,0.98483,-0.10672,-0.13683,187.96,0.14686,0.092644,0.98481,-135.06
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8536, correlation about mean = 0.8553, overlap = 3513
steps = 92, shift = 18.8, angle = 11.7 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.00099892 -0.99999135 0.00403628 456.97748713
0.99997431 0.00102753 0.00709351 98.96278640
-0.00709759 0.00402910 0.99996669 -61.35034788
Axis -0.00153221 0.00556694 0.99998333
Axis point 178.73883400 278.32537520 0.00000000
Rotation angle (degrees) 89.94290086
Shift along axis -61.49858924
> rename #11 combination_1
> select up
187770 atoms, 191968 bonds, 23546 residues, 17 models selected
> select up
187770 atoms, 191968 bonds, 23546 residues, 17 models selected
> select up
187770 atoms, 191968 bonds, 23546 residues, 17 models selected
> view position #9-10 sameAsModels #7
> hide #!7 models
> color #9 #ff7205cc
> color #9 #ff7205ff
> combine #9-10
> color zone #3 near #12 distance 15.65
> combine 11-12
Expected a keyword
> combine #11-12
Remapping chain ID 'K0' in combination #12 to 'LA'
Remapping chain ID 'K1' in combination #12 to 'K2'
Remapping chain ID 'L0' in combination #12 to 'MA'
Remapping chain ID 'L1' in combination #12 to 'L2'
Remapping chain ID 'M0' in combination #12 to 'NA'
Remapping chain ID 'M1' in combination #12 to 'M2'
Remapping chain ID 'N0' in combination #12 to 'OA'
Remapping chain ID 'N1' in combination #12 to 'N2'
Remapping chain ID 'O0' in combination #12 to 'PA'
Remapping chain ID 'O1' in combination #12 to 'O2'
Remapping chain ID 'P0' in combination #12 to 'QA'
Remapping chain ID 'P1' in combination #12 to 'P2'
Remapping chain ID 'Q0' in combination #12 to 'RA'
Remapping chain ID 'Q1' in combination #12 to 'Q2'
Remapping chain ID 'R0' in combination #12 to 'SA'
Remapping chain ID 'R1' in combination #12 to 'R2'
Remapping chain ID 'S0' in combination #12 to 'TA'
Remapping chain ID 'S1' in combination #12 to 'S2'
> color zone #3 near #13 distance 15.65
> hide #!11 models
> hide #!10 models
> hide #!9 models
> ui mousemode right select
> select clear
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_correctScale.cxs
> close #12
> close #13
> show #!11 models
> hide #!11 models
> hide #11.1 models
> show #!10 models
> show #!9 models
> color single #3
No atoms chosen for color zoning
> color zone #3 near #11 distance 15.65
> color #8 #999999ff
> color #9 #999999ff
> color #9 #333333ff
> color #9 #555555ff
> color #10 #777777ff
> color #10 #aaaaaaff
> color #10 #ddddddff
> combine #9-10
> color zone #3 near #12 distance 15.65
> color #9 #777777ff
> combine #9-10
> color zone #3 near #13 distance 15.65
> color #9 #ddddddff
> color #10 #777777ff
> close #13
> combine #9-10
> color zone #3 near #13 distance 15.65
> color #10 #999999ff
> combine #9-10
> color zone #3 near #14 distance 15.65
> color #9 white
> close #14
> combine #9-10
> color zone #3 near #14 distance 15.65
> close #11#12-14
> combine #9-10
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!10 models
> hide #!9 models
> select #11/K0,L0,M0,N0,O0,P0,Q0,R0,S0
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> select #11/K1,L1,M1,N1,O1,P1,Q1,R1,S1
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> name frozen CR-outerY sel
> color #11 #006d40ff
> select CR-outerY
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> color sel grey
> ui tool show Log
> select #11/K0,L0,M0,N0,O0,P0,Q0,R0,S0
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> name frozen CR-innerY sel
> color CR-innerY white
> show #!1.1 models
> hide #!1.1 models
> show #!3 models
> view orient
> close #9-11
> open
> /Users/jenny/Desktop/TempDocuments/PaperNPCasymmetry/Data&Figures/Figures/DrosophilaNPCstructures/DrosophilaNPCstructure/240506_OnMyCR_CR-
> BothY.cif
Chain information for 240506_OnMyCR_CR-BothY.cif #9
---
Chain | Description
K0 K1 | Nuclear pore complex protein Nup133
L0 L1 | Nuclear pore complex protein Nup107
M0 M1 | Nuclear pore complex protein Nup96
N0 N1 | Protein SEC13 homolog
O0 O1 | Nucleoporin SEH1
P0 P1 | Nuclear pore complex protein Nup85
Q0 Q1 | Nucleoporin Nup43
R0 R1 | Nuclear pore complex protein Nup160
S0 S1 | Nucleoporin Nup37
240506_OnMyCR_CR-BothY.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> view position #9 sameAsModels #7
> hide #!3 models
> select #9/K0,L0,M0,N0,O0,P0,Q0,R0,S0
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> name frozen CR-innerY sel
> color CR-innerY white
> color CR-innerY #FFFFFF
> select #9/K0,L0,M0,N0,O0,P0,Q0,R0,S0
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> select #9/K1,L1,M1,N1,O1,P1,Q1,R1,S1
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> name frozen CR-outerY sel
> color CR-outerY #999999
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_withYcomplexes.cxs
> show #!3 models
> show #!7 models
> ui mousemode right select
> select #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.00099892,-0.99999,0.0040363,756.42,0.99997,0.0010275,0.0070935,-115.24,-0.0070976,0.0040291,0.99997,-61.35
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8547, correlation about mean = 0.8565, overlap = 3409
steps = 224, shift = 50.4, angle = 45 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.70775181 -0.70641785 0.00782295 391.12758546
0.70642746 0.70778282 0.00193083 -248.23999409
-0.00690092 0.00415980 0.99996753 -61.30021626
Axis 0.00157755 0.01042085 0.99994446
Axis point 494.87082021 349.08841924 0.00000000
Rotation angle (degrees) 44.94776945
Shift along axis -63.26665924
> combine #9
> view position #10 sameAsModels #7
> combine #9-10
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'LA'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'K2'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'MA'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'L2'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'NA'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'M2'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'OA'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'N2'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'PA'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'O2'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'QA'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'P2'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'RA'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'Q2'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'SA'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'R2'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'TA'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'S2'
> color zone #3 near #11 distance 15.65
> hide #!7 models
> show #!7 models
> view matrix models
> #7,0.70775,-0.70642,0.0078229,397.04,0.70643,0.70778,0.0019308,-576.82,-0.0069009,0.0041598,0.99997,-61.3
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8533, correlation about mean = 0.855, overlap = 3513
steps = 264, shift = 15.6, angle = 45 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.99997568 0.00103419 0.00689667 99.01691417
-0.00100517 0.99999063 -0.00420980 -447.29069849
-0.00690096 0.00420277 0.99996735 -61.54479501
Axis 0.51648275 0.84709465 -0.12520468
Axis point -14543.47986413 0.00000000 -38376.71859605
Rotation angle (degrees) 0.46662711
Shift along axis -320.05133473
> close #11
> combine #9
> view position #11 sameAsModels #7
> view matrix models
> #7,0.99998,0.0010342,0.0068967,-56.991,-0.0010052,0.99999,-0.0042098,-670.28,-0.006901,0.0042028,0.99997,-61.545
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.2202, correlation about mean = 0.2208, overlap = 858.6
steps = 136, shift = 40.2, angle = 15.2 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.97034065 0.20589796 0.12666905 -116.56101949
-0.21849554 0.97119087 0.09512099 -643.42716707
-0.10343461 -0.11997638 0.98737376 24.12280309
Axis -0.40698711 0.43538060 -0.80299765
Axis point -2534.72559469 699.23424993 0.00000000
Rotation angle (degrees) 15.32273419
Shift along axis -252.06742845
> view matrix models
> #7,0.97034,0.2059,0.12667,-164.52,-0.2185,0.97119,0.095121,-605.59,-0.10343,-0.11998,0.98737,24.123
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8544, correlation about mean = 0.8562, overlap = 3412
steps = 192, shift = 67, angle = 33.9 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.70644385 0.70776628 0.00199675 -248.31178337
-0.70773724 0.70643601 -0.00749447 -381.62110383
-0.00671491 0.00388125 0.99996992 -61.48492658
Axis 0.00803610 0.00615415 -0.99994877
Axis point -584.88064105 108.89984361 0.00000000
Rotation angle (degrees) 45.05522618
Shift along axis 57.13776604
> combine #9
> view position #12 sameAsModels #7
> view matrix models
> #7,0.70644,0.70777,0.0019968,-519.21,-0.70774,0.70644,-0.0074945,-430.38,-0.0067149,0.0038812,0.99997,-61.485
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.2202, correlation about mean = 0.2208, overlap = 858.9
steps = 136, shift = 39.8, angle = 15.3 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.53111146 0.83240205 0.15820061 -538.94897153
-0.84092817 0.54070523 -0.02185549 -367.40348278
-0.10373245 -0.12142765 0.98716508 24.90714303
Axis -0.05868816 0.15438420 -0.98626630
Axis point -599.02985888 313.53236034 0.00000000
Rotation angle (degrees) 58.02893751
Shift along axis -49.65644791
> view matrix models
> #7,0.53111,0.8324,0.1582,-570.48,-0.84093,0.54071,-0.021855,-342.34,-0.10373,-0.12143,0.98717,24.907
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.2202, correlation about mean = 0.2208, overlap = 858.8
steps = 60, shift = 40.3, angle = 0.0338 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
0.53139977 0.83231275 0.15770148 -538.85972742
-0.84078820 0.54092798 -0.02172838 -367.61016543
-0.10338995 -0.12104709 0.98724775 24.45280492
Axis -0.05855157 0.15392178 -0.98634669
Axis point -599.35995394 313.43672916 0.00000000
Rotation angle (degrees) 58.00888498
Shift along axis -49.15107311
> view matrix models
> #7,0.5314,0.83231,0.1577,-548.13,-0.84079,0.54093,-0.021728,-305.84,-0.10339,-0.12105,0.98725,24.453
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8539, correlation about mean = 0.8556, overlap = 3509
steps = 188, shift = 65.5, angle = 34 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.00097863 0.99999132 -0.00405050 -447.30403838
-0.99997314 -0.00100801 -0.00725977 -89.33503142
-0.00726379 0.00404329 0.99996544 -61.10742814
Axis 0.00565153 0.00160664 -0.99998274
Axis point -268.49476065 178.87832148 0.00000000
Rotation angle (degrees) 90.05790302
Shift along axis 58.43489062
> combine #9
> view position #13 sameAsModels #7
> view matrix models
> #7,-0.00097863,0.99999,-0.0040505,-693.2,-0.99997,-0.001008,-0.0072598,101.44,-0.0072638,0.0040433,0.99997,-61.107
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8548, correlation about mean = 0.8566, overlap = 3408
steps = 240, shift = 28.6, angle = 45 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.70778535 0.70638297 -0.00793711 -381.41418500
-0.70639258 -0.70781744 -0.00199802 257.91269428
-0.00702939 0.00419255 0.99996650 -61.23706291
Axis 0.00438181 -0.00064250 -0.99999019
Axis point -137.49339230 207.91166724 0.00000000
Rotation angle (degrees) 135.05766964
Shift along axis 59.39947079
> combine #9
> view position #14 sameAsModels #7
> view matrix models
> #7,-0.70779,0.70638,-0.0079371,-450.56,-0.70639,-0.70782,-0.001998,528.58,-0.0070294,0.0041925,0.99997,-61.237
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.2202, correlation about mean = 0.2208, overlap = 858.9
steps = 128, shift = 23.4, angle = 15.3 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.84091107 0.54073367 -0.02180978 -367.43292451
-0.53114658 -0.83238218 -0.15818728 548.60117122
-0.10369126 -0.12143724 0.98716823 24.90290550
Axis 0.03416602 0.07612412 -0.99651282
Axis point -103.01601805 329.07078404 0.00000000
Rotation angle (degrees) 147.46494013
Shift along axis 4.39199803
> view matrix models
> #7,-0.84091,0.54073,-0.02181,-310.38,-0.53115,-0.83238,-0.15819,603.41,-0.10369,-0.12144,0.98717,24.903
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8535, correlation about mean = 0.8552, overlap = 3513
steps = 180, shift = 23.4, angle = 33.9 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.99997493 -0.00104284 -0.00700359 -89.32867115
0.00101476 -0.99999143 0.00401224 456.98742840
-0.00700771 0.00400504 0.99996742 -61.41799284
Axis -0.00350150 0.00200360 0.99999186
Axis point -44.88943379 228.53221331 0.00000000
Rotation angle (degrees) 179.94105372
Shift along axis -60.18908983
> combine #9
> view position #15 sameAsModels #7
> view matrix models
> #7,-0.99997,-0.0010428,-0.0070036,95.636,0.0010148,-0.99999,0.0040122,674.48,-0.0070077,0.004005,0.99997,-61.418
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8547, correlation about mean = 0.8565, overlap = 3410
steps = 216, shift = 46.7, angle = 45 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.70641080 -0.70779947 -0.00191786 257.90353860
0.70776905 -0.70640143 0.00774547 391.14449759
-0.00683702 0.00411408 0.99996816 -61.34779427
Axis -0.00256530 0.00347500 0.99999067
Axis point 47.70902734 249.13377429 0.00000000
Rotation angle (degrees) 134.94454284
Shift along axis -60.64959219
> view matrix models
> #7,-0.70641,-0.7078,-0.0019179,315.8,0.70777,-0.7064,0.0077455,398.82,-0.006837,0.0041141,0.99997,-61.348
> fitmap #7 inMap #3 metric correlation envelope false
Fit map NE_CR_box66_ref_16.em scaled in map NE-NPC_CRmap_ring.em using 287496
points
correlation = 0.8544, correlation about mean = 0.8562, overlap = 3412
steps = 72, shift = 58.4, angle = 0.0161 degrees
Position of NE_CR_box66_ref_16.em scaled (#7) relative to NE-NPC_CRmap_ring.em
(#3) coordinates:
Matrix rotation and translation
-0.70642271 -0.70778736 -0.00200153 257.97003117
0.70775842 -0.70641497 0.00747707 391.25695857
-0.00670608 0.00386538 0.99997004 -61.49067026
Axis -0.00255143 0.00332346 0.99999122
Axis point 47.72291702 249.19816615 0.00000000
Rotation angle (degrees) 134.94549673
Shift along axis -60.84799381
> combine #9
> view position #16 sameAsModels #7
> combine #9-16
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'LA'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'K2'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'MA'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'L2'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'NA'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'M2'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'OA'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'N2'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'PA'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'O2'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'QA'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'P2'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'RA'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'Q2'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'SA'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'R2'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'TA'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #10 to 'S2'
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'LB'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'K3'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'MB'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'L3'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'NB'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'M3'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'OB'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'N3'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'PB'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'O3'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'QB'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'P3'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'RB'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'Q3'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'SB'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'R3'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'TB'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #11 to 'S3'
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'LC'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'K4'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'MC'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'L4'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'NC'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'M4'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'OC'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'N4'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'PC'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'O4'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'QC'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'P4'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'RC'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'Q4'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'SC'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'R4'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'TC'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #12 to 'S4'
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'LD'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'K5'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'MD'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'L5'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'ND'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'M5'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'OD'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'N5'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'PD'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'O5'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'QD'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'P5'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'RD'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'Q5'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'SD'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'R5'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'TD'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #13 to 'S5'
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'LE'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'K6'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'ME'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'L6'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'NE'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'M6'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'OE'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'N6'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'PE'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'O6'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'QE'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'P6'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'RE'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'Q6'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'SE'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'R6'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'TE'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #14 to 'S6'
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'LF'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'K7'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'MF'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'L7'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'NF'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'M7'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'OF'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'N7'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'PF'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'O7'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'QF'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'P7'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'RF'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'Q7'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'SF'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'R7'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'TF'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #15 to 'S7'
Remapping chain ID 'K0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'LG'
Remapping chain ID 'K1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'K8'
Remapping chain ID 'L0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'MG'
Remapping chain ID 'L1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'L8'
Remapping chain ID 'M0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'NG'
Remapping chain ID 'M1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'M8'
Remapping chain ID 'N0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'OG'
Remapping chain ID 'N1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'N8'
Remapping chain ID 'O0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'PG'
Remapping chain ID 'O1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'O8'
Remapping chain ID 'P0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'QG'
Remapping chain ID 'P1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'P8'
Remapping chain ID 'Q0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'RG'
Remapping chain ID 'Q1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'Q8'
Remapping chain ID 'R0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'SG'
Remapping chain ID 'R1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'R8'
Remapping chain ID 'S0' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'TG'
Remapping chain ID 'S1' in copy of 240506_OnMyCR_CR-BothY.cif #16 to 'S8'
> hide #!7 models
> select subtract #7
Nothing selected
> color zone #3 near #17 distance 15.65
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> color zone #3 near #17 distance 20
[Repeated 1 time(s)]
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_withYcomplexes.cxs
> show #!4 models
> show #!5 models
> show #!6 models
> rename #17 AllCR_Ycomplexes
> show #!17 models
> hide #!3 models
> show #!1.1 models
> hide #!1.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> sym #9
240506_OnMyCR_CR-BothY.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1, 1 copy of chains
K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1
> log metadata #9
No models had metadata
> log chains #9
Chain information for 240506_OnMyCR_CR-BothY.cif #9
---
Chain | Description
K0 K1 | Nuclear pore complex protein Nup133
L0 L1 | Nuclear pore complex protein Nup107
M0 M1 | Nuclear pore complex protein Nup96
N0 N1 | Protein SEC13 homolog
O0 O1 | Nucleoporin SEH1
P0 P1 | Nuclear pore complex protein Nup85
Q0 Q1 | Nucleoporin Nup43
R0 R1 | Nuclear pore complex protein Nup160
S0 S1 | Nucleoporin Nup37
> sym #10
copy of 240506_OnMyCR_CR-BothY.cif mmCIF Assemblies
---
> log metadata #10
No models had metadata
> log chains #10
Chain information for copy of 240506_OnMyCR_CR-BothY.cif #10
---
Chain | Description
K0 K1 | Nuclear pore complex protein Nup133
L0 L1 | Nuclear pore complex protein Nup107
M0 M1 | Nuclear pore complex protein Nup96
N0 N1 | Protein SEC13 homolog
O0 O1 | Nucleoporin SEH1
P0 P1 | Nuclear pore complex protein Nup85
Q0 Q1 | Nucleoporin Nup43
R0 R1 | Nuclear pore complex protein Nup160
S0 S1 | Nucleoporin Nup37
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NE_NRrotatedshifted_ref_16.em
Opened NE_NRrotatedshifted_ref_16.em as #18, grid size 66,66,66, pixel 1,
shown at level 0.244, step 1, values float32
> volume scale #18 factor -1
Opened NE_NRrotatedshifted_ref_16.em scaled as #19, grid size 66,66,66, pixel
1, shown at step 1, values float32
> ui tool show "Map Coordinates"
> close #18
> rename #19 id #18
> hide #!17 models
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select #18
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.15377,-0.93241,-0.32707,658.18,0.8368,0.29891,-0.45871,108.09,0.52547,-0.20316,0.8262,-42.985
> view matrix models
> #18,-0.92122,-0.059266,0.3845,491.7,-0.027381,0.99575,0.087883,-16.507,-0.38808,0.070432,-0.91893,669.07
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.92122,-0.059266,0.3845,661.72,-0.027381,0.99575,0.087883,20.096,-0.38808,0.070432,-0.91893,-308.67
> view matrix models
> #18,-0.92122,-0.059266,0.3845,28.484,-0.027381,0.99575,0.087883,-601.58,-0.38808,0.070432,-0.91893,-345.13
> hide #!5 models
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.92122,-0.059266,0.3845,-49.03,-0.027381,0.99575,0.087883,-619.23,-0.38808,0.070432,-0.91893,186.85
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.7939, correlation about mean = 0.7962, overlap = 2380
steps = 224, shift = 63.7, angle = 33 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
-0.88913499 -0.45736891 0.01589574 124.65640623
-0.45722920 0.88927141 0.01174007 -442.30720303
-0.01950517 0.00317052 -0.99980474 93.34254103
Axis -0.23527468 0.97192135 0.00383566
Axis point 9.23871324 0.00000000 47.46581626
Rotation angle (degrees) 178.95648216
Shift along axis -458.85827991
> volume #18 level 0.161
> open
> /Users/jenny/Desktop/TempDocuments/PaperNPCasymmetry/Data&Figures/Figures/DrosophilaNPCstructures/DrosophilaNPCstructure/240506_OnMyNR_NR-
> BothY.cif
Chain information for 240506_OnMyNR_NR-BothY.cif #19
---
Chain | Description
K2 K3 | Nuclear pore complex protein Nup133
L2 L3 | Nuclear pore complex protein Nup107
M2 M3 | Nuclear pore complex protein Nup96
N2 N3 | Protein SEC13 homolog
O2 O3 | Nucleoporin SEH1
P2 P3 | Nuclear pore complex protein Nup85
Q2 Q3 | Nucleoporin Nup43
R2 R3 | Nuclear pore complex protein Nup160
S2 S3 | Nucleoporin Nup37
240506_OnMyNR_NR-BothY.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> view position #19 sameAsModels #18
> view all
> hide #!4 models
> hide #!3 models
> hide #!6 models
> hide #!18 models
> select #19/K2,L2,M2,N2,O2,P2,Q2,R2,S2
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> name frozen NR-innerY sel
> color NR-innerY #FFFFFF
> select #19/K3,L3,M3,N3,O3,P3,Q3,R3,S3
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> name frozen NR-outerY sel
> color NR-outerY #999999
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/NE-
> NPC_NRNBmap_ring.em
Opened NE-NPC_NRNBmap_ring.em as #5, grid size 150,150,150, pixel 1, shown at
level 0.293, step 1, values float32
> color #5 #039d91ff models
> color zone #5 near #17 distance 57.94
> color zone #5 near #19 distance 57.94
> color zone #5 near #19 distance 20
[Repeated 1 time(s)]
> color zone #5 near #19 distance 19.2
> color zone #5 near #19 distance 12.76
> volume #5 level 0.1653
> volume #5 level 0.2
> color zone #5 near #19 distance 20
[Repeated 1 time(s)]
> color zone #5 near #19 distance 25
[Repeated 1 time(s)]
> combine #19
> show #!18 models
> ui mousemode right select
> select #18
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.88913,-0.45737,0.015896,514.13,-0.45723,0.88927,0.01174,-519.17,-0.019505,0.0031705,-0.9998,81.201
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.1542, correlation about mean = 0.1542, overlap = 466.3
steps = 256, shift = 34.4, angle = 13.7 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
-0.93175762 -0.32324040 -0.16535839 545.18166403
-0.34011303 0.93645363 0.08589382 -626.17975441
0.12708611 0.13627277 -0.98248607 -0.10291210
Axis 0.16949401 -0.98389502 -0.05676598
Axis point 217.13201576 0.00000000 34.15438236
Rotation angle (degrees) 171.45328711
Shift along axis 708.50600931
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.3196,-0.41138,0.85359,89.435,0.010739,0.89921,0.43738,-829.08,-0.94749,0.14895,-0.28297,175.92
> view matrix models
> #18,-0.4793,-0.8757,0.058465,503.48,-0.76729,0.38576,-0.51231,-146.35,0.42608,-0.29041,-0.85681,-2.3501
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.794, correlation about mean = 0.7964, overlap = 2380
steps = 196, shift = 84.7, angle = 33.6 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
-0.30551624 -0.95218252 0.00287501 405.77326214
-0.95198701 0.30551258 0.01956473 -226.64773344
-0.01950754 0.00324037 -0.99980445 93.22120537
Axis -0.58924579 0.80792301 0.00705706
Axis point 120.64801446 0.00000000 46.92588982
Rotation angle (degrees) 179.20631873
Shift along axis -421.55623995
> view position #20 sameAsModels #18
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.30552,-0.95218,0.002875,704.74,-0.95199,0.30551,0.019565,-99.322,-0.019508,0.0032404,-0.9998,97.43
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.067937,-0.97714,0.20145,531.34,-0.9713,-0.018647,0.23711,-49.434,-0.22793,-0.21178,-0.95037,222.99
> view matrix models
> #18,0.04095,-0.99806,-0.046933,613.88,-0.98836,-0.047351,0.14458,-9.7228,-0.14652,0.040466,-0.98838,126.17
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.7939, correlation about mean = 0.7963, overlap = 2380
steps = 180, shift = 16.6, angle = 25.8 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
0.45722006 -0.88927668 -0.01169625 451.98245922
-0.88914139 -0.45735871 0.01583037 124.65245508
-0.01942696 0.00316165 -0.99980628 93.18513264
Axis -0.85358439 0.52087485 0.00911532
Axis point 0.00000000 200.43962733 48.37266059
Rotation angle (degrees) 179.57481000
Shift along axis -320.02742875
> combine #19
> view position #21 sameAsModels #18
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.45722,-0.88928,-0.011696,550.28,-0.88914,-0.45736,0.01583,352.24,-0.019427,0.0031617,-0.99981,108.05
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.282, correlation about mean = 0.2826, overlap = 864.6
steps = 156, shift = 87.2, angle = 23.6 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
0.77545682 -0.63139576 -0.00246990 357.90319136
-0.63137872 -0.77545658 0.00529177 289.19882851
-0.00525650 -0.00254410 -0.99998295 89.53845568
Axis -0.94219314 0.33506401 0.00204964
Axis point 0.00000000 208.33776245 44.75065060
Rotation angle (degrees) 179.76174551
Shift along axis -240.13028838
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.77211,-0.63531,-0.015312,363.73,-0.62968,-0.76807,0.11646,256.43,-0.085751,-0.080281,-0.99308,139.64
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.77211,-0.63531,-0.015312,408.72,-0.62968,-0.76807,0.11646,453.82,-0.085751,-0.080281,-0.99308,153.22
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.794, correlation about mean = 0.7964, overlap = 2380
steps = 148, shift = 44.7, angle = 22.5 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
0.95198573 -0.30552261 -0.01947051 236.29522133
-0.30552617 -0.95217937 0.00286470 405.78219279
-0.01941465 0.00322160 -0.99980633 93.18084063
Axis 0.98792368 -0.15462790 -0.00985017
Axis point 0.00000000 221.37899539 47.78816827
Rotation angle (degrees) 179.98965069
Shift along axis 169.77854973
> combine #19
> view position #22 sameAsModels #18
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.95199,-0.30552,-0.019471,96.577,-0.30553,-0.95218,0.0028647,753.78,-0.019415,0.0032216,-0.99981,120.8
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.8268,0.55985,-0.0546,-122.69,0.55971,-0.80914,0.17892,365.31,0.055987,-0.17849,-0.98235,147.32
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.8268,0.55985,-0.0546,-116.12,0.55971,-0.80914,0.17892,371.03,0.055987,-0.17849,-0.98235,80.568
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.7939, correlation about mean = 0.7963, overlap = 2380
steps = 128, shift = 54.3, angle = 13.3 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
0.88912930 0.45737859 -0.01593465 -114.97097090
0.45724055 -0.88926677 -0.01164840 451.97043844
-0.01949789 0.00307097 -0.99980518 93.28274511
Axis 0.97188673 0.23527241 -0.00911459
Axis point 0.00000000 239.71959398 46.98553370
Rotation angle (degrees) 179.56611926
Shift along axis -6.25281957
> combine #19
> view position #23 sameAsModels #18
> view matrix models
> #18,0.88913,0.45738,-0.015935,-481.23,0.45724,-0.88927,-0.011648,614.28,-0.019498,0.003071,-0.99981,63.963
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.293,0.91968,-0.26143,-356.21,0.8237,-0.38163,-0.41937,439.05,-0.48546,-0.092462,-0.86936,218.45
> view matrix models
> #18,0.27047,0.89846,-0.34586,-319.15,0.89746,-0.36532,-0.24718,362.41,-0.34843,-0.24354,-0.90514,228.55
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.794, correlation about mean = 0.7964, overlap = 2380
steps = 212, shift = 63.4, angle = 24.4 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
0.30568907 0.95212696 -0.00290616 -396.16938846
0.95193273 -0.30568620 -0.01949428 236.42194740
-0.01944940 0.00319272 -0.99980574 93.26249490
Axis 0.80797734 0.58917295 -0.00691743
Axis point -0.00000000 262.25362289 46.42683995
Rotation angle (degrees) 179.19557654
Shift along axis -181.44760888
> combine #19
> view position #24 sameAsModels #18
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.30569,0.95213,-0.0029062,-672.46,0.95193,-0.30569,-0.019494,150.59,-0.019449,0.0031927,-0.99981,55.883
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.25529,0.95974,-0.11715,-452.06,0.96411,0.26183,0.044078,-48.761,0.072977,-0.10169,-0.99214,55.089
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.7938, correlation about mean = 0.7962, overlap = 2380
steps = 112, shift = 71.1, angle = 14.6 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
-0.45727114 0.88925344 0.01146333 -442.14426073
0.88911962 0.45740494 -0.01571720 -115.09298088
-0.01921996 0.00300525 -0.99981076 93.29926696
Axis 0.52086999 0.85362790 -0.00372312
Axis point -185.47351473 0.00000000 47.82429005
Rotation angle (degrees) 178.97020849
Shift along axis -328.89361972
> combine #19
> view position #25 sameAsModels #18
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.45727,0.88925,0.011463,-550.18,0.88912,0.4574,-0.015717,-408.83,-0.01922,0.0030052,-0.99981,86.269
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.76121,0.64842,-0.010276,-364.69,0.64462,0.75829,0.097277,-449.9,0.070868,0.067425,-0.9952,33.967
> fitmap #18 inMap #4 metric correlation envelope false
Fit map NE_NRrotatedshifted_ref_16.em scaled in map NE-NPC_NRmap_ring.em using
287496 points
correlation = 0.794, correlation about mean = 0.7963, overlap = 2381
steps = 160, shift = 32, angle = 23.4 degrees
Position of NE_NRrotatedshifted_ref_16.em scaled (#18) relative to NE-
NPC_NRmap_ring.em (#4) coordinates:
Matrix rotation and translation
-0.95199623 0.30548557 0.01953824 -226.54186816
0.30548672 0.95219161 -0.00299941 -396.05057196
-0.01952042 0.00311325 -0.99980461 93.38742151
Axis 0.15461732 0.98797443 0.00002890
Axis point -81.81289012 0.00000000 47.50302167
Rotation angle (degrees) 178.86735823
Shift along axis -426.31243754
> combine #19
> view position #26 sameAsModels #18
> hide #!18 models
> combine #19-26
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'K4'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'K5'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'L4'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'L5'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'M4'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'M5'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'N4'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'N5'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'O4'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'O5'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'P4'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'P5'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'Q4'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'Q5'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'R4'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'R5'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'S4'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #20 to 'S5'
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'K6'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'K7'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'L6'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'L7'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'M6'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'M7'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'N6'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'N7'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'O6'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'O7'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'P6'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'P7'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'Q6'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'Q7'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'R6'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'R7'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'S6'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #21 to 'S7'
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'K8'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'K9'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'L8'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'L9'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'M8'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'M9'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'N8'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'N9'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'O8'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'O9'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'P8'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'P9'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'Q8'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'Q9'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'R8'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'R9'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'S8'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #22 to 'S9'
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'K0'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'LA'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'L0'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'MA'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'M0'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'NA'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'N0'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'OA'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'O0'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'PA'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'P0'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'QA'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'Q0'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'RA'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'R0'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'SA'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'S0'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #23 to 'TA'
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'LB'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'LC'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'MB'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'MC'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'NB'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'NC'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'OB'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'OC'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'PB'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'PC'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'QB'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'QC'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'RB'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'RC'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'SB'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'SC'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'TB'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #24 to 'TC'
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'LD'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'LE'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'MD'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'ME'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'ND'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'NE'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'OD'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'OE'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'PD'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'PE'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'QD'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'QE'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'RD'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'RE'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'SD'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'SE'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'TD'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #25 to 'TE'
Remapping chain ID 'K2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'LF'
Remapping chain ID 'K3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'LG'
Remapping chain ID 'L2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'MF'
Remapping chain ID 'L3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'MG'
Remapping chain ID 'M2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'NF'
Remapping chain ID 'M3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'NG'
Remapping chain ID 'N2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'OF'
Remapping chain ID 'N3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'OG'
Remapping chain ID 'O2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'PF'
Remapping chain ID 'O3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'PG'
Remapping chain ID 'P2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'QF'
Remapping chain ID 'P3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'QG'
Remapping chain ID 'Q2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'RF'
Remapping chain ID 'Q3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'RG'
Remapping chain ID 'R2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'SF'
Remapping chain ID 'R3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'SG'
Remapping chain ID 'S2' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'TF'
Remapping chain ID 'S3' in copy of 240506_OnMyNR_NR-BothY.cif #26 to 'TG'
> rename #27 AllNR_Ycomplexes
> color zone #5 near #27 distance 25
> show #!3 models
> color zone #3 near #17 distance 25
> show #!6 models
> show #!17 models
> color zone #3 near #17 distance 20
> color zone #5 near #27 distance 20
> color zone #5 near #27 distance 22
> color zone #5 near #27 distance 20
[Repeated 1 time(s)]
> color zone #3 near #17 distance 20
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_withYcomplexes.cxs
> close #20-26
> hide #!3 models
> hide #!5 models
> hide #!6 models
> close #10-16
> hide #!19 models
> view matrix models
> #18,-0.952,0.30549,0.019538,-226.54,0.30549,0.95219,-0.0029994,-396.05,-0.01952,0.0031132,-0.9998,93.387
> ui mousemode right select
Drag select of 2747 atoms
> select up
2845 atoms, 2896 bonds, 370 residues, 1 model selected
> select up
3212 atoms, 3275 bonds, 421 residues, 1 model selected
> select up
8574 atoms, 8740 bonds, 1086 residues, 1 model selected
> hide #!27 models
> show #!27 models
> show #!5 models
> show #!3 models
> hide #!3 models
Drag select of 2632 atoms
> select up
2768 atoms, 2813 bonds, 363 residues, 1 model selected
> select up
3075 atoms, 3132 bonds, 405 residues, 1 model selected
> select up
8574 atoms, 8740 bonds, 1086 residues, 1 model selected
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> sym #27
AllNR_Ycomplexes mmCIF Assemblies
---
> log metadata #27
No models had metadata
> log chains #27
Chain information for AllNR_Ycomplexes #27
---
Chain | Description
K0 K2 K3 K4 K5 K6 K7 K8 K9 LA LB LC LD LE LF LG | Nuclear pore complex protein Nup133
L0 L2 L3 L4 L5 L6 L7 L8 L9 MA MB MC MD ME MF MG | Nuclear pore complex protein Nup107
M0 M2 M3 M4 M5 M6 M7 M8 M9 NA NB NC ND NE NF NG | Nuclear pore complex protein Nup96
N0 N2 N3 N4 N5 N6 N7 N8 N9 OA OB OC OD OE OF OG | Protein SEC13 homolog
O0 O2 O3 O4 O5 O6 O7 O8 O9 PA PB PC PD PE PF PG | Nucleoporin SEH1
P0 P2 P3 P4 P5 P6 P7 P8 P9 QA QB QC QD QE QF QG | Nuclear pore complex protein Nup85
Q0 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 RA RB RC RD RE RF RG | Nucleoporin Nup43
R0 R2 R3 R4 R5 R6 R7 R8 R9 SA SB SC SD SE SF SG | Nuclear pore complex protein Nup160
S0 S2 S3 S4 S5 S6 S7 S8 S9 TA TB TC TD TE TF TG | Nucleoporin Nup37
> view orient
> turn x 90
> show #!3 models
> show #!6 models
> turn x -90
[Repeated 1 time(s)]
> select clear
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_withYcomplexes.cxs
> surface dust all size 10
> surface dust all size 20
> surface dust all size 50
> view orient
> turn x -90
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240506_alignedCompositeMaps_withYcomplexes.cxs
——— End of log from Mon May 6 17:54:25 2024 ———
opened ChimeraX session
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240507_alignedCompositeMaps_withYcomplexes.cxs
> hide #!17 models
> hide #!27 models
> show #!17 models
> hide #!3 models
> show #!3 models
> color #3 #ffa40580 models
> color #3 #ffa405ff models
> color #6 #333333ff models
> ui tool show "Side View"
> color #6 #555555ff models
> show #!1.2 models
> color #1.2 #333333ff models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240507_alignedCompositeMaps_withYcomplexes.cxs
——— End of log from Tue May 7 09:28:01 2024 ———
opened ChimeraX session
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240609_alignedCompositeMaps_newColors.cxs
> ui tool show "Side View"
> hide #!5 models
> hide #!1.2 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!5 models
> rename #1 cNPC
> show #8 models
> hide #8 models
> hide #!1 models
> show #8 models
> hide #8 models
> hide #!17 models
> ui tool show "Color Zone"
> color single #3
> color single #5
> color #1.2 #555555ff models
> view orient
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4 models
> show #!1 models
> rename #2 id #2.1
> rename #2 NE-NPC
> rename #3 id #2.2
> rename #4 id #2.3
> rename #5 id #2.4
> rename #6 id #2.5
> hide #!2.3 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!7 models
> show #!18 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!7 models
> show #!2.1 models
> hide #!2.1 models
> show #!1 models
> hide #!18 models
> view orient
> turn x 45
> turn x -45
[Repeated 1 time(s)]
> view all
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!9 models
> turn x -45
> turn x -135
> hide #!2 models
> show #!1 models
> volume #2.5 level 0.25
> volume #2.5 level 0.2
> volume #1.2 level 0.2
> turn x 135
> turn x 45
> view orient
> view name topview
> turn x -45
> show #!2 models
> hide #!1 models
> view name sidetopview
> turn x -45
> view name sideview
> turn x -135
> view name sidebottomview
> turn x -45
> turn x 45
[Repeated 1 time(s)]
> view name bottomview
> view list
Named views: bottomview, sidebottomview, sidetopview, sideview, topview
> view topview
> view sideview
> view sidetopview
> view sidebottomview
> view bottomview
[Repeated 1 time(s)]
> view sidebottomview
> view bottomview
[Repeated 1 time(s)]
> view sidebottomview
> view sidetopview
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240609_alignedCompositeMaps_newColors.cxs
> view list
Named views: bottomview, sidebottomview, sidetopview, sideview, topview
> view sideview
> view name sidecutview
> view sideview
> view sidecutview
> hide #!2 models
> show #!1 models
> view sidetopview
> show #!2 models
> hide #!1 models
> view sidetopview
> volume copy #2.1
Opened NE-NPC_ring.em copy as #3, grid size 150,150,150, pixel 9.66, shown at
step 1, values float32
> hide #!2 models
> hide #!3 models
> show #!3 models
> close #3
> volume copy #2.2
Opened NE-NPC_CRmap_ring.em copy as #3, grid size 150,150,150, pixel 9.66,
shown at step 1, values float32
> rename #3 id #10
> volume copy #2.4
Opened NE-NPC_NRNBmap_ring.em copy as #3, grid size 150,150,150, pixel 9.66,
shown at step 1, values float32
> rename #3 id #11
> color zone #10 near #17 distance 57.94
> color zone #10 near #17 distance 57.42
> color zone #10 near #17 distance 14.27
> color zone #10 near #17 distance 10
[Repeated 1 time(s)]
> color zone #10 near #17 distance 12
[Repeated 1 time(s)]
> view topview
> hide #!11 models
> view topview
> view sidetopview
> view topview
> color zone #10 near #17 distance 12
[Repeated 2 time(s)]
> color zone #10 near #17 distance 11
> color zone #10 near #17 distance 10
> color zone #10 near #17 distance 9.9
> color zone #10 near #17 distance 9.8
> color zone #10 near #17 distance 9.7
> color zone #10 near #17 distance 9.66
> color zone #10 near #17 distance 10
[Repeated 1 time(s)]
> color zone #10 near #17 distance 12
[Repeated 1 time(s)]
> color zone #10 near #17 distance 15
[Repeated 1 time(s)]
> view sidetopview
> view sidebottomview
> hide #!10 models
> show #!11 models
> color zone #11 near #19 distance 15
> color zone #11 near #27 distance 15
> show #!10 models
> view sidetopview
> hide #!10 models
> show #!10 models
> hide #!11 models
> volume copy #11
Opened NE-NPC_NRNBmap_ring.em copy as #3, grid size 150,150,150, pixel 9.66,
shown at step 1, values float32
> rename #3 id #12
> rename #12 "NE-NPC_NRNBmap_ring.em copy_rotated"
> hide #!10 models
> show #!10 models
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select #12
2 models selected
> select #12
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.43873,-0.87494,0.20493,68.623,-0.84216,-0.32077,0.43345,140.92,-0.3135,-0.36275,-0.87757,-561.93
> view matrix models
> #12,0.44049,-0.89665,-0.04453,-6.3744,-0.8965,-0.44196,0.031056,20.639,-0.047527,0.026241,-0.99853,-601.5
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.44049,-0.89665,-0.04453,115.34,-0.8965,-0.44196,0.031056,134.36,-0.047527,0.026241,-0.99853,-76.283
> view matrix models
> #12,0.44049,-0.89665,-0.04453,39.858,-0.8965,-0.44196,0.031056,28.401,-0.047527,0.026241,-0.99853,-70.59
> view matrix models
> #12,0.44049,-0.89665,-0.04453,11.768,-0.8965,-0.44196,0.031056,34.012,-0.047527,0.026241,-0.99853,39.537
> ui tool show "Fit in Map"
> fitmap #12 inMap #10 metric correlation
Fit map NE-NPC_NRNBmap_ring.em copy_rotated in map NE-NPC_CRmap_ring.em copy
using 68780 points
correlation = 0.8489, correlation about mean = 0.525, overlap = 7147
steps = 60, shift = 26.3, angle = 3.24 degrees
Position of NE-NPC_NRNBmap_ring.em copy_rotated (#12) relative to NE-
NPC_CRmap_ring.em copy (#10) coordinates:
Matrix rotation and translation
0.45586360 -0.89004965 -0.00000001 6.92425789
-0.89004965 -0.45586360 0.00000002 11.32612510
-0.00000002 0.00000000 -1.00000000 23.88241251
Axis -0.85368542 0.51972909 0.03320967
Axis point -0.00000000 7.77082864 12.07588834
Rotation angle (degrees) 179.99999960
Shift along axis 0.76850569
> volume copy #27 #28
> combine #27 #28
> rename #3 id #28
> view position #28 sameAsModels #12
> show #!27 models
> view position #27
Missing required "same_as_models" argument
> ui mousemode right select
> select #28/TF:160@CA
1 atom, 1 residue, 1 model selected
> select add #28
751072 atoms, 767872 bonds, 32 pseudobonds, 94176 residues, 2 models selected
> select subtract #28
Nothing selected
> ui mousemode right "rotate selected models"
> select add #28
751072 atoms, 767872 bonds, 32 pseudobonds, 94176 residues, 2 models selected
> select subtract #28
Nothing selected
> select add #28
751072 atoms, 767872 bonds, 32 pseudobonds, 94176 residues, 2 models selected
> view matrix models
> #28,-0.74184,0.58119,-0.3345,-661.29,-0.66432,-0.56898,0.48471,-68.887,0.091379,0.58179,0.80819,-796.68
> view matrix models
> #28,-0.16211,0.95816,-0.23592,-809.5,-0.98668,-0.15415,0.051921,-149.89,0.01338,0.2412,0.97038,-700.88
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.16211,0.95816,-0.23592,-344.07,-0.98668,-0.15415,0.051921,-94.158,0.01338,0.2412,0.97038,-129.92
> hide #!27 models
> ui tool show "Fit in Map"
> fitmap #28 inMap #12
Fit molecule copy of AllNR_Ycomplexes (#28) to map NE-NPC_NRNBmap_ring.em
copy_rotated (#12) using 751072 atoms
average map value = 0.4207, steps = 136
shifted from previous position = 76.1
rotated from previous position = 16.8 degrees
atoms outside contour = 104432, contour level = 0.2
Position of copy of AllNR_Ycomplexes (#28) relative to NE-NPC_NRNBmap_ring.em
copy_rotated (#12) coordinates:
Matrix rotation and translation
0.88999440 0.45568899 -0.01604440 -114.08739617
0.45555053 -0.89013378 -0.01163916 452.17052081
-0.01958550 0.00304975 -0.99980349 93.09261523
Axis 0.97210931 0.23434914 -0.00916319
Axis point 0.00000000 239.65616911 46.88981931
Rotation angle (degrees) 179.56711621
Shift along axis -5.79267167
> hide #!10 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> color zone #12 near #28 distance 57.94
> color zone #12 near #28 distance 15
[Repeated 1 time(s)]
> view position #27
Missing required "same_as_models" argument
> view sidetopview
> show #!10 models
> hide #!28 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!12 models
> ui mousemode right "map eraser"
> view sidetopview
> ui mousemode right "crop volume"
> volume #!10,12 showOutlineBox true
> ui mousemode right select
> ui mousemode right "pick blobs"
[Repeated 1 time(s)]
> ui mousemode right "map eraser"
> color zone #12 near #28 distance 15
[Repeated 1 time(s)]
> volume #!10,12 showOutlineBox false
> view sidetopview
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> view sidetopview
> view topview
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> view sidetopview
> view sideview
> view orient
> turn x -60
> turn x 60
> turn x -70
> show #!10 models
> hide #!10 models
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> show #!10 models
> view sideview
> view sidetopview
> hide #!10 models
> show #!10 models
> view sidetopview
> turn x -10
> view sidetopview
> turn x -10
[Repeated 1 time(s)]
> hide #!10 models
> show #!10 models
> view sidetopview
> hide #!10 models
> show #!10 models
> hide #!12 models
> hide #!10 models
> show #!17 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!17 models
> show #!17 models
> select subtract #28
Nothing selected
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!28 models
> show #!12 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!12 models
> show #!12 models
> hide #!10 models
> view orient
> turn z 10
> turn x -45
> show #!10 models
> view orient
> hide #!10 models
> show #!10 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> view sidetopview
> show #!12 models
> hide #!10 models
> show #!10 models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240709_alignedCompositeMaps_newColors.cxs
> view sidetopview
> show #!1 models
> hide #!12 models
> hide #!10 models
> show #!2.2 models
> show #!2.4 models
> hide #!1 models
> view sidetopview
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true pixelSize
> 0.2
> save 240709_Snapshots/NE-NPC_top_1.png transparentBackground true pixelSize
> 0.5
> save 240709_Snapshots/NE-NPC_top_2.png transparentBackground true pixelSize
> 1
> save 240709_Snapshots/NE-NPC_top_3.png transparentBackground true pixelSize
> 10
> save 240709_Snapshots/NE-NPC_top_3.png transparentBackground true pixelSize
> 5
> save 240709_Snapshots/NE-NPC_top_3.png transparentBackground true pixelSize
> 1
> save 240709_Snapshots/NE-NPC_top_3.png transparentBackground true pixelSize
> 2
> save 240709_Snapshots/NE-NPC_top_3.png transparentBackground true pixelSize
> 1
> save 240709_Snapshots/NE-NPC_top_3.png transparentBackground true pixelSize
> 2
> view sidetopview
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true pixelSize 2
> hide #!2 models
> show #!1 models
> save 240709_Snapshots/cNPC_top.png transparentBackground true pixelSize 2
> view sideview
> save 240709_Snapshots/cNPC_side.png transparentBackground true pixelSize 2
> show #!2 models
> hide #!1 models
> save 240709_Snapshots/NE-NPC_side.png transparentBackground true pixelSize 2
> view sidebottomview
> save 240709_Snapshots/NE-NPC_bottom.png transparentBackground true pixelSize
> 2
> hide #!2 models
> show #!1 models
> save 240709_Snapshots/cNPC_bottom.png transparentBackground true pixelSize 2
> view sidetopview
> hide #!1 models
> show #!10 models
> save 240709_Snapshots/NE-NPC_CR.png transparentBackground true pixelSize 2
> show #!12 models
> hide #!10 models
> save 240709_Snapshots/NE-NPC_NR.png transparentBackground true pixelSize 2
> surface dust all size 30
> view sidetopview
> show #!2.1 models
> hide #!12 models
> save 240709_Snapshots/NE-NPC_top2.png transparentBackground true pixelSize 2
> turn x 180
> save 240709_Snapshots/NE-NPC_bottom2.png transparentBackground true
> pixelSize 2
> view list
Named views: bottomview, sidebottomview, sidecutview, sidetopview, sideview,
topview
> view name bottomview
> turn x -135
> turn x -90
> view name sideview
> turn x 45
> view name sidetopview
> turn x 180
> view name sidebottomview
> view sidetopview
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true pixelSize 2
> hide #!2 models
> show #!1 models
> save 240709_Snapshots/cNPC_top.png transparentBackground true pixelSize 2
> hide #!1 models
> turn x 180
> show #!2 models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240709_alignedCompositeMaps_newColors.cxs
——— End of log from Tue Jul 9 15:24:43 2024 ———
opened ChimeraX session
> view list
Named views: bottomview, sidebottomview, sidecutview, sidetopview, sideview,
topview
> view sidetopview
> view sidetview
Expected an objects specifier or a view name or a keyword
> view sideview
> view topview
> view bottomview
> view topview
> turn x 180
> view name bottomview
> view sidetopview
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true
> hide #!2 models
> show #!1 models
> save 240709_Snapshots/cNPC_top.png transparentBackground true
> view sideview
> save 240709_Snapshots/cNPC_side.png transparentBackground true
> show #!2 models
> hide #!1 models
> save 240709_Snapshots/NE-NPC_side.png transparentBackground true
> view sideview
> view sidebottomview
> save 240709_Snapshots/NE-NPC_bottom.png transparentBackground true
> hide #!2 models
> show #!1 models
> save 240709_Snapshots/cNPC_bottom.png transparentBackground true
> view sidetopview
> show #!10 models
> show #!12 models
> close #11
> hide #!1 models
> hide #!10 models
> save 240709_Snapshots/NE-NPC_NR.png transparentBackground true
> show #!10 models
> hide #!12 models
> save 240709_Snapshots/NE-NPC_CR.png transparentBackground true
> show #!27 models
> hide #!27 models
> show #!28 models
> hide #!10 models
> view sidetopview
> show #!17 models
> hide #!28 models
> save 240709_Snapshots/NE-NPC_CRmodels.png transparentBackground true
> hide #!17 models
> show #!27 models
> hide #!27 models
> show #!28 models
> save 240709_Snapshots/NE-NPC_NRmodels.png transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> hide #!28 models
> show #!2 models
> show #!1 models
> lighting soft
> save 240709_Snapshots/test_both_2PX.png transparentBackground true pixelSize
> 2
> hide #!2 models
> save 240709_Snapshots/test_cNPC_2PX.png transparentBackground true pixelSize
> 2
> show #!2 models
> hide #!1 models
> save 240709_Snapshots/test_NE-NPC_2PX.png transparentBackground true
> pixelSize 2
> camera ortho
> save 240709_Snapshots/test_NE-NPC_1PX.png transparentBackground true
> pixelSize 1
> hide #!2 models
> show #!1 models
> save 240709_Snapshots/test_cNPC_1PX.png transparentBackground true pixelSize
> 1
> view sidetopview
> show #!2 models
> hide #!1 models
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true pixelSize 2
Cannot save '240709_Snapshots/NE-NPC_top.png': [Errno 2] No such file or
directory
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true pixelSize 2
> show #!1 models
> hide #!2 models
> save 240709_Snapshots/cNPC_top.png transparentBackground true pixelSize 2
> lighting depthCue false
> lighting depthCue true
> lighting depthCue false
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting shadows true intensity 0.5
> lighting depthCue false
> lighting depthCue true
> lighting depthCue flase
Invalid "depthCue" argument: Expected true or false (or 1 or 0)
> graphics silhouettes false
> lighting depthCue false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting depthCue true
> save 240709_Snapshots/cNPC_top_SS3png transparentBackground true pixelSize 2
> supersample 3
Cannot determine format for '240709_Snapshots/cNPC_top_SS3png'
> save 240709_Snapshots/cNPC_top_SS3.png transparentBackground true pixelSize
> 2 supersample 3
> save 240709_Snapshots/cNPC_top_SS1.png transparentBackground true pixelSize
> 2 supersample 1
> volume all colorMode rgb8
> save 240709_Snapshots/cNPC_top_SS1_rgb8.png transparentBackground true
> pixelSize 2 supersample 1
> hide #!2 models
> hide #!1 models
> show #!2 models
> view sidetopview
> save 240709_Snapshots/NE-NPC_top.png transparentBackground true pixelSize 2
> show #!1 models
> hide #!2 models
> save 240709_Snapshots/cNPC_top.png transparentBackground true pixelSize 2
> view sideview
> save 240709_Snapshots/cNPC_side.png transparentBackground true pixelSize 2
> show #!2 models
> hide #!1 models
> save 240709_Snapshots/NE-NPC_side.png transparentBackground true pixelSize 2
> view sidebottomview
> save 240709_Snapshots/NE-NPC_bottom.png transparentBackground true pixelSize
> 2
> show #!1 models
> hide #!2 models
> save 240709_Snapshots/cNPC_bottom.png transparentBackground true pixelSize 2
> view sidetopview
> hide #!1 models
> show #!10 models
> save 240709_Snapshots/NE-NPC_CR.png transparentBackground true pixelSize 2
> show #!12 models
> hide #!10 models
> save 240709_Snapshots/NE-NPC_NR.png transparentBackground true pixelSize 2
> show #!17 models
> hide #!12 models
> save 240709_Snapshots/NE-NPC_CRmodels.png transparentBackground true
> pixelSize 2
> cartoon #17
> surface hidePatches #17
> hide #!17 models
> show #!17 models
> hide #17 target a
> cartoon hide #17
> surface #17
> surface style #17 solid
> surface hidePatches #17
> cartoon #17
> view sidetopview
> save 240709_Snapshots/NE-NPC_CRcartoons.png transparentBackground true
> pixelSize 2
Directory "240709_Snapshots" does not exist
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps
> save 240709_Snapshots/NE-NPC_CRcartoons.png transparentBackground true
> pixelSize 2
> view sidetopview
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240709_alignedCompositeMaps_newColors.cxs
——— End of log from Wed Jul 10 08:49:01 2024 ———
opened ChimeraX session
> hide #!17 models
> show #!12 models
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps
> save 240709_Snapshots/NE-NPC_NRpx1.png transparentBackground true pixelSize
> 1
> show #!17 models
> ui tool show "Color Zone"
> color zone #12 near #17 distance 9.66
> color zone #12 near #17 distance 15
[Repeated 1 time(s)]
> show #!10 models
> hide #!12 models
> color zone #10 near #17 distance 15
> hide #!10 models
> cartoon hide #17
> surface #17
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> show #!12 models
> lighting soft
> hide #!12 models
> show #!12 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> lighting flat
> lighting soft
> show #!10 models
> hide #!12 models
> hide #!17 models
> lighting soft
> save 240709_Snapshots/NE-NPC_CRpx1.png transparentBackground true pixelSize
> 1
> show #!12 models
> hide #!10 models
> save 240709_Snapshots/NE-NPC_NRpx1.png transparentBackground true pixelSize
> 1
> show #!17 models
> hide #!12 models
> save 240709_Snapshots/NE-NPC_CRmodels.png transparentBackground true
> pixelSize 1
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240501_CompositeMaps/240709_alignedCompositeMaps_newColors.cxs
——— End of log from Wed Jul 10 10:30:24 2024 ———
opened ChimeraX session
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/cNPC_membranemap_ring.em
Opened cNPC_membranemap_ring.em as #3, grid size 150,150,150, pixel 1, shown
at level 0.282, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/NE-
> NPC_membranemap_ring.em
Opened NE-NPC_membranemap_ring.em as #4, grid size 150,150,150, pixel 1, shown
at level 0.272, step 1, values float32
> hide #!4 models
> rename #3 id #1.5
> show #!1 models
> hide #!17 models
> ui tool show "Map Coordinates"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1.2 models
> hide #!1.1 models
> hide #!1.3 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> volume #1.5 level 0.1996
> hide #!1.5 models
> show #!1.5 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.5 models
> show #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.5 models
> hide #!2.4 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!2.2 models
> volume #1.5 level 0.1805
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Volume Viewer"
> volume #1.5 level 0.04393
> hide #!1.2 models
> show #!1.2 models
> volume #2.5 level -0.1731
> volume #2.5 level 0.4247
> volume #2.5 level 0.2
> volume #1.2 level 0.3685
> volume #1.5 level 0.15
> volume #1.2 level 0.25
> volume #1.2 level 0.266
> volume #1.2 level 0.2139
> volume #1.5 color #555555
> volume #1.5 color #b2b2b2
> volume #1.2 level 0.22
> volume #1.2 level 0.25
> volume #1.2 level 0.26
> ui tool show "Side View"
> volume #1.2 color #b2b2b2
> hide #!1 models
> hide #!2 models
> show #!2 models
> rename #4 id #2.6
> color #2.6 #b2b2b2ff models
> show #!2.6 models
> show #!2.5 models
> volume #2.6 level 0.2215
> volume #2.6 level 0.1723
> volume #2.6 level 0.18
> volume #1.5 level 0.18
> show #!1 models
> hide #!1.1 models
> hide #!1.3 models
> volume #1.5 level 0.15
> hide #!1.2 models
> show #!1.5 models
> volume #2.6 level 0.1497
> volume #1.5 level 0.123
> volume #1.5 level 0.15
> volume #2.6 level 0.18
> volume #2.6 level 0.2
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> hide #!2 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1 models
> show #!2 models
> volume #2.6 level 0.21
> volume #2.6 level 0.19
> volume #2.6 level 0.18
> volume #2.6 level 0.15
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_alignedCompositeMaps.cxs
> volume #10 level 0.21
> volume #2.2 level 0.21
> volume #2.2 level 0.25
> volume #2.2 level 0.23
> volume #2.2 level 0.18
> volume #2.2 level 0.2204
> volume #2.2 level 0.2
> volume #2.6 level 0.14
> volume #2.6 level 0.13
> volume #2.6 level 0.12
> volume #2.6 level 0.11
> show #!2.5 models
> color #2.5 #b2b2b2ff models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> surface dust all size 30
> surface dust all size 50
> volume #1.2 level 0.252
> volume #1.2 level 0.3081
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> volume #1.2 level 0.2
> volume #1.2 level 0.25
> volume #1.2 level 0.26
> volume #1.2 level 0.28
> hide #!2 models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_alignedCompositeMaps.cxs
> close #28
> show #!2 models
> hide #!1.2 models
> hide #!2 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2.3 models
> show #!1.2 models
> hide #!1.2 models
> hide #!2 models
> show #!1.2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!9 models
> hide #!2 models
> show #!2 models
> measure symmetry #10
Symmetry NE-NPC_CRmap_ring.em copy: C8, center 75 75 96
> sym #9 symmetry #10
Made 8 copies for 240506_OnMyCR_CR-BothY.cif symmetry #10
> close #3#3.1-8
> close #17-19,27
> show #!9 models
> hide #!2 models
> show #!10 models
> select #11/K0,L0,M0,N0,O0,P0,Q0,R0,S0
Nothing selected
> select #9/K0,L0,M0,N0,O0,P0,Q0,R0,S0
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #10 id #10.1
> rename #12 id #10.2
> rename #10 YcomplexSegmentation
> close #8
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #7
> rename #9 id #9.1
> rename #9.1 id #10.1
> rename #10.2 id #10.3
> rename #10.1.2 id #10.1
> rename #10.1 id #10.2
> rename #10.2.2 id #10.1
> close #9
> rename #10 id #3
> volume copy #2.6
Opened NE-NPC_membranemap_ring.em copy as #4, grid size 150,150,150, pixel
9.66, shown at step 1, values float32
> rename #4 id #3.2
> rename #3.3 id #3.4
> rename #3.2.2 id #3.3
> hide #!3.1 models
> hide #3.1.1 models
> hide #!3.2 models
> hide #!3.3 models
> show #3.1.1 models
> select color white
Expected an objects specifier or a keyword
> color (#!3.1 & sel) orange red
> color sel red
> color sel 999999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #999999
> color sel #333333
> color #3.1 #929292ff
> color #3.1 #797979ff
> color #3.1 #424242ff
> color #3.1 #d6d6d6ff
> color #3.1 #941751ff
> color #3.1 white
> color #3.1 #858585ff
> color #3.1 #bcbcbcff
> color sel #999999
> select #11/K1,L1,M1,N1,O1,P1,Q1,R1,S1
Nothing selected
> select #3.1/K1,L1,M1,N1,O1,P1,Q1,R1,S1
46942 atoms, 47992 bonds, 2 pseudobonds, 5886 residues, 2 models selected
> color sel #555555
> color sel #FFFFFF
> ~select
Nothing selected
> sym #3.1 symmetry #3.2
Made 8 copies for 240506_OnMyCR_CR-BothY.cif symmetry #3.2
> show #!3.3 models
> view sidetopview
> show #!3.2 models
> hide #!4 models
> ui tool show "Surface Color"
> ui tool show "Surface Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4 models
> show #!4 models
> combine #4.1-4.8
No structures specified
> combine #4.1,4.2,4.3, 4.4, 4.5, 4.6, 4.7 4.8
Expected a keyword
> combine #4.1,4.2,4.3, 4.4, 4.5, 4.6, 4.7,4.8
No structures specified
> combine #4.1,4.2
No structures specified
> combine #4
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'LA'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'K2'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'MA'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'L2'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'NA'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'M2'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'OA'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'N2'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'PA'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'O2'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'QA'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'P2'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'RA'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'Q2'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'SA'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'R2'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'TA'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.2 to 'S2'
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'LB'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'K3'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'MB'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'L3'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'NB'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'M3'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'OB'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'N3'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'PB'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'O3'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'QB'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'P3'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'RB'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'Q3'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'SB'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'R3'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'TB'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.3 to 'S3'
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'LC'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'K4'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'MC'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'L4'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'NC'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'M4'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'OC'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'N4'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'PC'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'O4'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'QC'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'P4'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'RC'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'Q4'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'SC'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'R4'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'TC'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.4 to 'S4'
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'LD'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'K5'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'MD'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'L5'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'ND'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'M5'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'OD'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'N5'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'PD'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'O5'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'QD'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'P5'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'RD'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'Q5'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'SD'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'R5'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'TD'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.5 to 'S5'
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'LE'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'K6'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'ME'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'L6'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'NE'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'M6'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'OE'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'N6'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'PE'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'O6'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'QE'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'P6'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'RE'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'Q6'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'SE'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'R6'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'TE'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.6 to 'S6'
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'LF'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'K7'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'MF'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'L7'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'NF'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'M7'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'OF'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'N7'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'PF'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'O7'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'QF'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'P7'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'RF'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'Q7'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'SF'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'R7'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'TF'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.7 to 'S7'
Remapping chain ID 'K0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'LG'
Remapping chain ID 'K1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'K8'
Remapping chain ID 'L0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'MG'
Remapping chain ID 'L1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'L8'
Remapping chain ID 'M0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'NG'
Remapping chain ID 'M1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'M8'
Remapping chain ID 'N0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'OG'
Remapping chain ID 'N1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'N8'
Remapping chain ID 'O0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'PG'
Remapping chain ID 'O1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'O8'
Remapping chain ID 'P0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'QG'
Remapping chain ID 'P1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'P8'
Remapping chain ID 'Q0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'RG'
Remapping chain ID 'Q1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'Q8'
Remapping chain ID 'R0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'SG'
Remapping chain ID 'R1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'R8'
Remapping chain ID 'S0' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'TG'
Remapping chain ID 'S1' in 240506_OnMyCR_CR-BothY.cif #4.8 to 'S8'
> close #4#4.1-8
> rename #5 id #3.5
> rename #3.5 YcomplexRing
> surface zone #3.2 nearAtoms #3.5 distance 15
> hide #!3.2 models
> show #!3.2 models
> hide #!3 models
> show #!3 models
> surface unzone #3.2
> ui tool show "Surface Color"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Surface Color"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #!3.3 models
> ui tool show "Segment Map"
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color zone #3.2 near #3.5 distance 9.66
> color zone #3.2 near #3.5 distance 15
[Repeated 1 time(s)]
> show #!3.3 models
> show #!3.4 models
> hide #!3.2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #3.4 near #3.5 distance 15
> hide #!3.5 models
> copy #3.3
Unknown command: copy #3.3
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume copy #3.3
Opened NE-NPC_membranemap_ring.em copy as #4, grid size 150,150,150, pixel
9.66, shown at step 1, values float32
> rename #4 NE-NPC_membranemap_ring_reoriented
> rename #3.1 id #4
> rename #3.5 id #3.1
> show #!3.1 models
> rename #4 id #3.5
> view position #3.5 sameAsModels #3.4
> hide #!3.4 models
> hide #!3.5 models
> show #!3.5 models
> show #!3.4 models
> save
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_alignedCompositeMaps.cxs
> hide #!3.1 models
> view list
Named views: bottomview, sidebottomview, sidecutview, sidetopview, sideview,
topview
> view sidecutview
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2.6 models
> hide #!2.6 models
> show #!2.6 models
> hide #!2.6 models
> show #!2.6 models
> hide #!2.6 models
> show #!2.6 models
> hide #!2.6 models
> show #!2.6 models
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_Snapshots/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_Snapshots
> hide all
> hide #!2 models
> show #!2 models
> hide !all
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show all
> hide all
> view sidetopview
> save NE-NPC_top.png transparentBackground true
> view sidecutview
> save NE-NPC_side.png transparentBackground true
> view sidebottomview
> save NE-NPC_bottom.png transparentBackground true
> view orient
> view sidebottomview
> view all
> view sidecutview
> show #2
> view sidetopview
> save NE-NPC_top.png transparentBackground true
> view sidecutview
> save NE-NPC_side.png transparentBackground true
> view sidebottomview
> save NE-NPC_bottom.png transparentBackground true
> hide #2
> show #2
> hide #2.1
> hide all
[Repeated 1 time(s)]
> hide
> hide #2
> show all
> show
> show #2.1
> show #2.2
> hide #2.1
> sidetopview
Unknown command: sidetopview
> view sidetopview
> show #2.1-2.3
> show #2.3
> show #2.1,2.2,2.3
> show #!2.4 models
> hide models
> show models
> hide models
> show #2
> hide models
> show #2.2 show 2.4 show 2.5 show 2.6
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show models #2.2-2.4
Expected ',' or a keyword
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> view all
No displayed objects specified.
> show models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> close #1.2.2
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.4 models
> hide #!1 models
> hide #!2.1 models
> hide #!2.3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> rename #3.5.2 id #4
> hide #!4 models
> hide all
> hide #1-4
> show #!4 models
> hide #!1-4
> hide #!4 models
> show #!1 models
> hide #!1-4 models
> show #!1 models
> hide #!1-4 models
> show #!2 models
> view sidetopview
> save NE-NPC_top.png transparentBackground true
> view sidecutview
> save NE-NPC_side.png transparentBackground true
> view sidebottomview
> save NE-NPC_bottom.png transparentBackground true
> hide #!2 models
> show #!1 models
> view sidetopview
> save cNPC_top.png transparentBackground true
> view sidecutview
> save cNPC_side.png transparentBackground true
> view sidebottomview
> save cNPC_bottom.png transparentBackground true
> hide #!1 models
> show #!3 models
> view sidetopview
> hide #!3.1-3.4 models
> show #!3.1,3.3 models
> hide #!3.1-3.4 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> hide #!3.3 models
> show #!3 models
> hide #!3 models
> show #!3.1,3.3 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
[Repeated 1 time(s)]
> show #!3.2 models
> hide #!3.1,3.2 models
> hide #!3.1
> hide #3 models
> show #!3.1 models
> show #3 models
> hide #!3.1 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> show #!3.1 models
[Repeated 1 time(s)]
> show #!3.2 models
> hide #!3.1 models
> show #!3.1 models
> show #!3.1
> show #3 models
> hide #!3.1
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> show #!3.1
> show #!3.3 models
> save NE-NPC_CRmodels.png transparentBackground true
> hide #!3.1 models
> show #!3.2 models
> save NE-NPC_CR.png transparentBackground true
> hide #!3.2 models
> hide #!3.3 models
> show #!3.4 models
> show #!3.5 models
> save NE-NPC_MR.png transparentBackground true
> runScript TakeSnapshots.cxc
Unknown command: runScript TakeSnapshots.cxc
> runscript TakeSnapshots.cxc
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_Snapshots/
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_Snapshots
> hide #!1-4 models
> show #!2 models
> view sidetopview
> save NE-NPC_top.png transparentBackground true
> view sidecutview
> save NE-NPC_side.png transparentBackground true
> view sidebottomview
> save NE-NPC_bottom.png transparentBackground true
> hide #!2 models
> show #!1 models
> view sidetopview
> save cNPC_top.png transparentBackground true
> view sidecutview
> save cNPC_side.png transparentBackground true
> view sidebottomview
> save cNPC_bottom.png transparentBackground true
> hide #!1 models
> show #!3 models
> view sidetopview
> show #3 models
> hide #!3.1
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> show #!3.1
> show #!3.3 models
> save NE-NPC_CRmodels.png transparentBackground true
> hide #!3.1 models
> show #!3.2 models
> save NE-NPC_CR.png transparentBackground true
> hide #!3.2 models
> hide #!3.3 models
> show #!3.4 models
> show #!3.5 models
> save NE-NPC_NR.png transparentBackground true
> pwd
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps/240711_Snapshots
> cd ..
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps
> pwd
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240711_CompositeMaps
> save 240711_ChimeraXForFigures.cxs
——— End of log from Thu Jul 11 18:12:06 2024 ———
opened ChimeraX session
> hide #!3 models
> show #!2 models
> show #!1 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_IR/run2/NE_IR_ref_21.em
Opened NE_IR_ref_21.em as #5, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> rename #5 NE_IR
> volume scale #5 factor -1
Opened NE_IR scaled as #6, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> hide #!2 models
> hide #!1 models
> ui tool show "Map Coordinates"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #5 voxelSize 9.656
No volumes specified
> volume #6 voxelSize 9.656
> volume #6 voxelSize 1
> volume #6 voxelSize 9.656
> close #6
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_IR/run2/NE_IR_ref_21.em
Opened NE_IR_ref_21.em as #5, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> rename #5 NE_IR
> volume scale #5 factor -1
Opened NE_IR scaled as #6, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoIR/run2/AligntoNENPC_IR/run2_checkShiftAfterRotation/ref_1.em
Opened ref_1.em as #5, grid size 56,56,56, pixel 1, shown at level 0.406, step
1, values float32
> rename #5 cNPC_IR
> volume scale #5 factor -1
Opened cNPC_IR scaled as #7, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> open
> /STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NEMotl_CR_16.em
No such file/path:
/STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NEMotl_CR_16.em
> rename #5 NE_CR
> volume scale #5 factor -1
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoCR/run2/AligntoNENPC_CR/run3_checkrotationTransposeShift/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.31, step
1, values float32
> rename #5 cNPC_CR
> volume scale #5 factor -1
Opened cNPC_CR scaled as #8, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NEMotl_NRrotatedshifted_16.em
No such file/path:
/STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NEMotl_NRrotatedshifted_16.em
> rename #5 NE_NR
> volume scale #5 factor -1
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.326, step
1, values float32
> rename #5 cNPC_NR
> volume scale #5 factor -1
Opened cNPC_NR scaled as #9, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> volume #6-11 voxelSize 9.656
> open
> /STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NEMotl_CR_16.em
No such file/path:
/STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NEMotl_CR_16.em
> rename #5 NE_CR
> volume scale #5 factor -1
> close #7-9
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NEMotl_CR_16.em
Opened NEMotl_CR_16.em as #5, grid size 20,1627,1, pixel 1, shown at step 1,
values float32
> rename #5 NE_CR
> volume scale #5 factor -1
Opened NE_CR scaled as #7, grid size 20,1627,1, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoCR/run2/AligntoNENPC_CR/run3_checkrotationTransposeShift/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.31, step
1, values float32
> rename #5 cNPC_CR
> volume scale #5 factor -1
Opened cNPC_CR scaled as #8, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NEMotl_NRrotatedshifted_16.em
No such file/path:
/STORAGE/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NEMotl_NRrotatedshifted_16.em
> rename #5 NE_NR
> volume scale #5 factor -1
> close #5
> open
> /Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
No such file/path:
/Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
> rename #5 cNPC_NR
> volume scale #5 factor -1
> close #5
>
> SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_CR_16.em
Unknown command:
SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_CR_16.em
>
> SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_16.em
Unknown command:
SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_16.em
> open open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_CR_16.em
'open' has no suffix
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_CR_16.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_CR_16.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_16.em
No such file/path:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/ref_16.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NE_CR_box66_ref_16.em
Opened NE_CR_box66_ref_16.em as #5, grid size 66,66,66, pixel 1, shown at
level 0.285, step 1, values float32
> rename #5 NE_CR
> volume scale #5 factor -1
Opened NE_CR scaled as #9, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> close #6-9
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NE_NRrotatedshifted_ref_16.em
Opened NE_NRrotatedshifted_ref_16.em as #5, grid size 66,66,66, pixel 1, shown
at level 0.244, step 1, values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_IR/run2/NE_IR_ref_21.em
Opened NE_IR_ref_21.em as #5, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> rename #5 NE_IR
> volume scale #5 factor -1
Opened NE_IR scaled as #6, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoIR/run2/AligntoNENPC_IR/run2_checkShiftAfterRotation/ref_1.em
Opened ref_1.em as #5, grid size 56,56,56, pixel 1, shown at level 0.406, step
1, values float32
> rename #5 cNPC_IR
> volume scale #5 factor -1
Opened cNPC_IR scaled as #7, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NE_CR_box66_ref_16.em
Opened NE_CR_box66_ref_16.em as #5, grid size 66,66,66, pixel 1, shown at
level 0.285, step 1, values float32
> rename #5 NE_CR
> volume scale #5 factor -1
Opened NE_CR scaled as #8, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoCR/run2/AligntoNENPC_CR/run3_checkrotationTransposeShift/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.31, step
1, values float32
> rename #5 cNPC_CR
> volume scale #5 factor -1
Opened cNPC_CR scaled as #9, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NE_NRrotatedshifted_ref_16.em
Opened NE_NRrotatedshifted_ref_16.em as #5, grid size 66,66,66, pixel 1, shown
at level 0.244, step 1, values float32
> rename #5 NE_NR
> volume scale #5 factor -1
Opened NE_NR scaled as #10, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
No such file/path:
/Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
> rename #5 cNPC_NR
> volume scale #5 factor -1
> close #5
> volume #6-11 voxelSize 9.656
> open
> /Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
No such file/path:
/Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
> open
> /Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
No such file/path:
/Volumes/msdata/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.326, step
1, values float32
> rename #5 cNPC_NR
> volume scale #5 factor -1
Opened cNPC_NR scaled as #11, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> close #6-11
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_IR/run2/NE_IR_ref_21.em
Opened NE_IR_ref_21.em as #5, grid size 56,56,56, pixel 1, shown at level
0.372, step 1, values float32
> rename #5 NE_IR
> volume scale #5 factor -1
Opened NE_IR scaled as #6, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoIR/run2/AligntoNENPC_IR/run2_checkShiftAfterRotation/ref_1.em
Opened ref_1.em as #5, grid size 56,56,56, pixel 1, shown at level 0.406, step
1, values float32
> rename #5 cNPC_IR
> volume scale #5 factor -1
Opened cNPC_IR scaled as #7, grid size 56,56,56, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_CR/run2b_box66/NE_CR_box66_ref_16.em
Opened NE_CR_box66_ref_16.em as #5, grid size 66,66,66, pixel 1, shown at
level 0.285, step 1, values float32
> rename #5 NE_CR
> volume scale #5 factor -1
Opened NE_CR scaled as #8, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoCR/run2/AligntoNENPC_CR/run3_checkrotationTransposeShift/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.31, step
1, values float32
> rename #5 cNPC_CR
> volume scale #5 factor -1
Opened cNPC_CR scaled as #9, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NormalNPCs_bin8/run_1/SUaverage/run2_box100/NE_NR/run2/240103_NRinCRposition/run3_refineWithCRmask/tobox66/run1_extract66/NE_NRrotatedshifted_ref_16.em
Opened NE_NRrotatedshifted_ref_16.em as #5, grid size 66,66,66, pixel 1, shown
at level 0.244, step 1, values float32
> rename #5 NE_NR
> volume scale #5 factor -1
Opened NE_NR scaled as #10, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/CytoNPCs_bin8/run_2_noFSC/SUaverage/run3/CytoNR/run2/AlgintoNENPC_CR/run2_checkShiftAfterRotation/ref_1.em
Opened ref_1.em as #5, grid size 66,66,66, pixel 1, shown at level 0.326, step
1, values float32
> rename #5 cNPC_NR
> volume scale #5 factor -1
Opened cNPC_NR scaled as #11, grid size 66,66,66, pixel 1, shown at step 1,
values float32
> close #5
> volume #6-11 voxelSize 9.656
> pwd
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/pwd.py", line 28, in pwd
directory = os.getcwd()
^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/pwd.py", line 28, in pwd
directory = os.getcwd()
^^^^^^^^^^^
See log for complete Python traceback.
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> pwd
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/pwd.py", line 28, in pwd
directory = os.getcwd()
^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory
FileNotFoundError: [Errno 2] No such file or directory
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/pwd.py", line 28, in pwd
directory = os.getcwd()
^^^^^^^^^^^
See log for complete Python traceback.
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> cd
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_DiameterComparison
Current working directory is:
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/FlyNPCs_Krios3ForProcessing/SA_DrosophilaNPC/NPCcomparison/240429_DiameterComparison
> save 240716_FlyNPCDiameterFigure.cxs
> select ~sel & ##selected
Nothing selected
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3D/A
Chip: Unknown
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 13 days, 3 hours, 39 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2721DE:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.7
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 16.1.0
pycollada: 0.8
pydantic: 2.8.2
pydantic-core: 2.20.1
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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
starfile: 0.5.8
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'pwd' failure when working directory removed |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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