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Opened 11 months ago
Closed 11 months ago
#16420 closed defect (fixed)
Combine: Cannot set polymeric chain ID directly from Residue
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-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/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.0379, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32
Opened 1xPflAB-New.mrc as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 1xPflAB-New-no-cyt-cage.mrc as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 2xFliL.mrc as #21, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits_imasked as #24, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 3xOnly-PflAB.mrc as #25, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 3xOnly-PflAB.mrc as #26, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 1xOnly-PflAB.mrc as #27, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened Rod.mrc as #31, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened PflA-2.1A-230911_imasked as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 3xOnly-PflAB.mrc as #34, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Log from Wed Dec 4 20:28:30 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Wed Sep 18 14:12:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB_Sep2024.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at level 0.185, step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32
Opened 1xPflAB-New.mrc as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 1xPflAB-New-no-cyt-cage.mrc as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 2xFliL.mrc as #21, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Log from Wed Sep 4 20:03:04 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB_Sep2024.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at level 0.185, step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32
Opened 1xPflAB-New.mrc as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 1xPflAB-New-no-cyt-cage.mrc as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Log from Wed Sep 4 18:57:11 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at level 0.185, step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Log from Thu Aug 22 11:39:22 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at level 0.185, step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Log from Fri Jul 26 17:21:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Fri Jul 26 15:41:13 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/Segment2-local-PflAB.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
at level 0.0467, step 1, values float32
Opened 1x_Cage-units.mrc as #4, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened MotB_PG.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.0467, step 1, values float32
Opened PflA.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.0467, step 1, values float32
Opened Cage.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at level 0.0467, step 1, values float32
Opened PflB.mrc as #12, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened PflA-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
240,240,240, pixel 2.1, shown at level 0.0467, step 1, values float32
Opened FliL.mrc as #14, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Other_Cage.mrc as #15, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Log from Tue Jun 11 23:04:54 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/Segment-local-PflAB.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
at level 0.0467, step 1, values float32
Opened 1x_Cage-units.mrc as #4, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Log from Tue Jun 11 18:45:39 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/H.pylori-univ-G/PflA-
> PflB/Manuscript-Start2023/Start/New_Start_June2024/For-
> Figures/HP_Modeling_June_2024/pylori flgY model.cxs"
Error opening map "/Users/shoichitachiyama/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Project-documents/H.pylori-univ-G/PflA-
PflB/Manuscript-Start2023/Start/New_Start_June2024/For-
Figures/HP_Modeling_June_2024/pylori flgY model.cxs": File pylori flgY
model.cxs, format mrc
MRC data value type (119742531) is not 8 or 16 bit integers or 16 or 32 bit
floats
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Error opening map "/Users/shoichitachiyama/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Project-documents/H.pylori-univ-G/PflA-
PflB/Manuscript-Start2023/Start/New_Start_June2024/For-
Figures/HP_Modeling_June_2024/pylori flgY model.cxs": File pylori flgY
model.cxs, format mrc
MRC data value type (119742531) is not 8 or 16 bit integers or 16 or 32 bit
floats
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
Log from Mon Jun 10 09:14:27 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened FlgY-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Opened IM_1.mrc as #13, grid size 121,121,39, pixel 4.2,4.2,4.2, shown at
level 0.00101, step 1, values float32
Opened IM_2.mrc as #14, grid size 207,207,129, pixel 5,5,0.6, shown at level
0.00211, step 1, values float32
Log from Fri Jun 7 16:12:49 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved Sessions\pylori flgY
> pflA pflB.cxs" format session
Opened FlgY-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Thu Jun 6 10:26:44 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened FlgY-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Wed Jun 5 14:36:12 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened FlgY-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Tue Jun 4 16:15:45 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved Sessions\pylori flgY
> pflA pflB.cxs" format session
Opened FlgY-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Tue Jun 4 11:39:36 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved Sessions\pylori flgY
> pflA pflB.cxs" format session
Opened FlgY-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Tue Jun 4 09:30:10 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved Sessions\pylori flgY
> pflA pflB.cxs" format session
Opened PflB-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Mon Jun 3 16:15:41 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Mon Jun 3 15:19:25 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Log from Mon Jun 3 15:09:09 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc copy as #10, grid size 240,240,240, pixel 2.14,
shown at level 0.783, step 1, values float32
Log from Mon Jun 3 14:56:25 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc copy as #10, grid size 240,240,240, pixel 2.14,
shown at level 0.783, step 1, values float32
Log from Mon Jun 3 14:21:22 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1.1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc as #1.2, grid size 240,240,240, pixel 2.14, shown
at level 0.783, step 1, values float32
Opened HP-PflA-PflB-2.1A.mrc copy as #10, grid size 240,240,240, pixel 2.14,
shown at level 0.783, step 1, values float32
Log from Mon Jun 3 14:11:08 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Log from Fri May 31 16:05:16 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Log from Wed May 22 11:24:28 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Log from Wed May 22 11:16:21 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Log from Tue May 21 11:25:20 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
Opened PflB-sym13-2.1A.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Log from Mon May 20 15:39:18 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Jack Botting\Documents\Chimera\Saved Sessions\pylori flgY
> pflA pflB.cxs" format session
Opened PflB-sym13-2.1A.mrc as #1, grid size 256,256,256, pixel 2.1, shown at
level 0.998, step 1, values float32
Log from Mon May 20 11:38:56 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 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Jack Botting/Documents/C jejuni/CJcyt0.18.mrc"
Opened CJcyt0.18.mrc as #1, grid size 250,250,130, pixel 4.3,4.3,4.3, shown at
level 0.245, step 1, values float32
> view orient
[Repeated 1 time(s)]
> volume #1 level 0.1233
> view orient
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_campy_flgy_pfla/fold_campy_flgy_pfla_model_0.cif"
Chain information for fold_campy_flgy_pfla_model_0.cif #2
---
Chain | Description
A B | .
C | .
> transparency 50
> select add #2
9359 atoms, 9495 bonds, 1158 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,468.67,0,1,0,555.43,0,0,1,0
> view matrix models #2,1,0,0,465.19,0,1,0,460.66,0,0,1,337.33
> view matrix models #2,1,0,0,459.06,0,1,0,494.38,0,0,1,455.89
> view matrix models
> #2,-0.058647,-0.26294,0.96303,440.1,-0.96652,0.25634,0.01113,494.08,-0.24979,-0.93014,-0.26917,480.73
> view matrix models
> #2,-0.058647,-0.26294,0.96303,350.26,-0.96652,0.25634,0.01113,468.82,-0.24979,-0.93014,-0.26917,455.76
> view matrix models
> #2,-0.058647,-0.26294,0.96303,348.33,-0.96652,0.25634,0.01113,469.91,-0.24979,-0.93014,-0.26917,525.68
> view matrix models
> #2,-0.058647,-0.26294,0.96303,350.98,-0.96652,0.25634,0.01113,437.19,-0.24979,-0.93014,-0.26917,519.65
> view matrix models
> #2,-0.021053,-0.26611,0.96371,351.44,-0.96746,0.24854,0.047493,436.89,-0.25216,-0.93135,-0.26268,519.57
> view matrix models
> #2,-0.021053,-0.26611,0.96371,356.43,-0.96746,0.24854,0.047493,431.78,-0.25216,-0.93135,-0.26268,518.36
> view matrix models
> #2,-0.021053,-0.26611,0.96371,353.06,-0.96746,0.24854,0.047493,436.24,-0.25216,-0.93135,-0.26268,518.63
> view matrix models
> #2,-0.021053,-0.26611,0.96371,352.62,-0.96746,0.24854,0.047493,435.53,-0.25216,-0.93135,-0.26268,518.62
> view matrix models
> #2,-0.021053,-0.26611,0.96371,355.19,-0.96746,0.24854,0.047493,435.84,-0.25216,-0.93135,-0.26268,508.52
> fitmap #2 inMap #1
Fit molecule fold_campy_flgy_pfla_model_0.cif (#2) to map CJcyt0.18.mrc (#1)
using 9359 atoms
average map value = 0.1651, steps = 168
shifted from previous position = 12.6
rotated from previous position = 17.7 degrees
atoms outside contour = 3490, contour level = 0.1233
Position of fold_campy_flgy_pfla_model_0.cif (#2) relative to CJcyt0.18.mrc
(#1) coordinates:
Matrix rotation and translation
0.22883482 -0.30556811 0.92426336 363.52150520
-0.96973887 0.01144057 0.24387626 427.21113380
-0.08509491 -0.95210149 -0.29370327 510.90386625
Axis -0.70348107 0.59371040 -0.39066911
Axis point 0.00000000 538.00471694 -61.93335664
Rotation angle (degrees) 121.78369664
Shift along axis -201.68515813
> select /A:101
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /B:103
18 atoms, 16 bonds, 2 residues, 1 model selected
> select up
1606 atoms, 1616 bonds, 195 residues, 1 model selected
> select up
2946 atoms, 2966 bonds, 370 residues, 1 model selected
> split #1/C
> split #1
> split #2
Split fold_campy_flgy_pfla_model_0.cif (#2) into 3 models
Chain information for fold_campy_flgy_pfla_model_0.cif A #2.1
---
Chain | Description
A | No description available
Chain information for fold_campy_flgy_pfla_model_0.cif B #2.2
---
Chain | Description
B | No description available
Chain information for fold_campy_flgy_pfla_model_0.cif C #2.3
---
Chain | Description
C | No description available
> hide #2.1 models
> show #2.1 models
> hide #2.3 models
> show #2.3 models
> color #2.3 #ff5500ff
> merge #2.1,2.2
Unknown command: merge #2.1,2.2
> combine #2.1,2.2
No structures specified
> rename #2.1 id #3
> rename #2.2 id #4
> rename #3 id #3.1
> rename #4 id #3.2
> combine #3
> close #3
> rename #4 flgY
> rename #2 pflA
> rename #2.3 id #2
> rename #2.3 id #3
> hide #2 models
> show #2 models
> close #2
> rename #3 pflA
> ui tool show "Side View"
> view orient
> sym #3 C17 center #1
Made 17 graphical clones for pflA symmetry C17
> fitmap #4 inMap #1
Fit molecule flgY (#4) to map CJcyt0.18.mrc (#1) using 2946 atoms
average map value = 0.2043, steps = 216
shifted from previous position = 12.9
rotated from previous position = 22.7 degrees
atoms outside contour = 763, contour level = 0.1233
Position of flgY (#4) relative to CJcyt0.18.mrc (#1) coordinates:
Matrix rotation and translation
0.04829257 -0.57287363 0.81821980 359.62988709
-0.94493865 0.23924451 0.22327789 422.30484875
-0.32366461 -0.78395017 -0.52977670 522.34964209
Axis -0.64259792 0.72850685 -0.23737247
Axis point 535.64808240 0.00000000 220.76366516
Rotation angle (degrees) 128.39795497
Shift along axis -47.43686528
> select add #4
2946 atoms, 2966 bonds, 370 residues, 1 model selected
> view matrix models
> #4,-0.0045306,-0.55863,0.82941,357.19,-0.94616,0.27085,0.17726,425.35,-0.32366,-0.78395,-0.52978,522.35
> view matrix models
> #4,-0.0045306,-0.55863,0.82941,354.93,-0.94616,0.27085,0.17726,430.31,-0.32366,-0.78395,-0.52978,522.35
> view matrix models
> #4,-0.10538,-0.52656,0.84358,350.75,-0.94029,0.32886,0.087818,436.49,-0.32366,-0.78395,-0.52978,522.35
> view matrix models
> #4,-0.10538,-0.52656,0.84358,349.85,-0.94029,0.32886,0.087818,436.94,-0.32366,-0.78395,-0.52978,522.35
> sym #4 C13 center #1
Made 13 graphical clones for flgY symmetry C13
> view orient
> sym clear #4
> sym #4 C10 center #1
Made 10 copies for flgY symmetry C10
> sym clear #4
> close #2
> show #4 models
> view orient
> sym #4 C11 center #1
Made 11 copies for flgY symmetry C11
> view orient
> close #2
> sym #4 C12 center #1
Made 12 copies for flgY symmetry C12
> sym #4 C13 center #1
Made 13 graphical clones for flgY symmetry C13
> show #4 models
> hide #!2 models
> view orient
> select clear
> select add #4
2946 atoms, 2966 bonds, 370 residues, 1 model selected
> view orient
> view matrix models
> #4,-0.10538,-0.52656,0.84358,343.64,-0.94029,0.32886,0.087818,438.5,-0.32366,-0.78395,-0.52978,522.35
> view matrix models
> #4,-0.10538,-0.52656,0.84358,342,-0.94029,0.32886,0.087818,438.17,-0.32366,-0.78395,-0.52978,522.35
> view matrix models
> #4,-0.10538,-0.52656,0.84358,342.99,-0.94029,0.32886,0.087818,420.8,-0.32366,-0.78395,-0.52978,522.35
> view matrix models
> #4,-0.10538,-0.52656,0.84358,343.98,-0.94029,0.32886,0.087818,424.4,-0.32366,-0.78395,-0.52978,522.31
> select clear
> view orient
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/c jejuni
> flgY/pflA.cxs"
[Errno 20] Not a directory: 'C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/c jejuni flgY'
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/c jejuni flgY
> pflA pflB.cxs"
> close session
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_pfla_257/fold_pylori_pfla_257_model_0.cif"
Chain information for fold_pylori_pfla_257_model_0.cif #1
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_pfla_pflb/fold_pylori_pfla_pflb_model_0.cif"
Chain information for fold_pylori_pfla_pflb_model_0.cif #2
---
Chain | Description
A | .
B | .
> open "C:/Users/Jack Botting/Documents/H pylori/pylori maps/PflB-
> sym13-2.1A.mrc"
Opened PflB-sym13-2.1A.mrc as #3, grid size 256,256,256, pixel 2.1, shown at
level 4.37, step 1, values float32
> view orient
> volume #3 level 0.9978
> transparency 50
> select add #1
9846 atoms, 10009 bonds, 1221 residues, 1 model selected
> view matrix models #1,1,0,0,-278.93,0,1,0,17.256,0,0,1,0
> view matrix models
> #1,0.6463,0.76309,0,-280.63,-0.76309,0.6463,0,16.811,0,0,1,0
> view matrix models
> #1,-0.11896,0.9929,0,-282.03,-0.9929,-0.11896,0,17.744,0,0,1,0
> view matrix models
> #1,0.14157,-0.38638,0.91141,-301.58,-0.92851,-0.37108,-0.013089,18.556,0.34326,-0.8444,-0.41129,36.104
> view matrix models
> #1,-0.35885,-0.52258,0.77339,-298.68,-0.86799,-0.11788,-0.4824,29.625,0.34326,-0.8444,-0.41129,36.104
> view matrix models
> #1,0.063714,-0.71249,0.69879,-295.99,-0.14846,-0.69919,-0.69936,36.797,0.98686,-0.059184,-0.15032,29.352
> view matrix models
> #1,0.11498,-0.39632,0.91088,-301.59,-0.11349,-0.9162,-0.38431,29.543,0.98686,-0.059184,-0.15032,29.352
> view matrix models
> #1,0.12631,-0.38427,0.91454,-301.68,-0.55545,-0.79124,-0.25575,25.628,0.8219,-0.47568,-0.31339,33.767
> view matrix models
> #1,0.12631,-0.38427,0.91454,-216.95,-0.55545,-0.79124,-0.25575,7.8571,0.8219,-0.47568,-0.31339,33.767
> view matrix models
> #1,0.086434,-0.35998,0.92895,-217.39,-0.56686,-0.78456,-0.25128,7.7226,0.81927,-0.50486,-0.27187,32.803
> view matrix models
> #1,-0.13233,-0.19773,0.97128,-218.97,-0.54489,-0.80404,-0.23792,7.459,0.828,-0.56073,-0.0013384,26.334
> view matrix models
> #1,-0.13233,-0.19773,0.97128,-210.24,-0.54489,-0.80404,-0.23792,5.656,0.828,-0.56073,-0.0013384,11.67
> view matrix models
> #1,-0.13233,-0.19773,0.97128,-209.91,-0.54489,-0.80404,-0.23792,5.732,0.828,-0.56073,-0.0013384,9.4921
> split #1
Split fold_pylori_pfla_257_model_0.cif (#1) into 3 models
Chain information for fold_pylori_pfla_257_model_0.cif A #1.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_pfla_257_model_0.cif B #1.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_pfla_257_model_0.cif C #1.3
---
Chain | Description
C | No description available
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> rename #1.1 id #4.1
> rename #1.2 id #4.2
> combine #4
> close #4
> rename #5 flgY
> view orient
> sym #5 C13 center #3
Made 13 graphical clones for flgY symmetry C13
> sym clear
> rename #1.3 id #4
> close #1
> rename #4 id #1
> rename #1 id #4
> rename #3 id #1
> rename #5 id #3
> rename #4 pflA
> close #3-4
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_pfla_257/fold_pylori_pfla_257_model_0.cif"
Chain information for fold_pylori_pfla_257_model_0.cif #3
---
Chain | Description
A B | .
C | .
> select add #3
9846 atoms, 10009 bonds, 1221 residues, 1 model selected
> view matrix models #3,1,0,0,-146.21,0,1,0,-39.837,0,0,1,-39.423
> view matrix models
> #3,-0.089603,0.36193,0.92789,-170.79,-0.25033,-0.90991,0.33074,-45.111,0.96401,-0.20264,0.17213,-17.701
> view matrix models
> #3,0.16511,0.39253,0.9048,-169.93,-0.70613,-0.59342,0.3863,-47.581,0.68856,-0.70269,0.1792,-17.431
> view matrix models
> #3,0.15385,0.18203,0.97118,-171.22,-0.73257,-0.63857,0.23573,-43.886,0.66308,-0.74773,0.035104,-13.892
> view matrix models
> #3,0.067635,-0.7754,0.62784,-161.45,0.76035,0.4475,0.47077,-49.362,-0.64599,0.44553,0.61984,-31.773
> view matrix models
> #3,0.067635,-0.7754,0.62784,-193.21,0.76035,0.4475,0.47077,-40.825,-0.64599,0.44553,0.61984,-23.825
> view matrix models
> #3,0.067635,-0.7754,0.62784,-215.9,0.76035,0.4475,0.47077,-47.205,-0.64599,0.44553,0.61984,39.867
> view matrix models
> #3,-0.1912,-0.55983,0.80624,-220.93,0.66845,0.52722,0.52461,-48.764,-0.71876,0.63924,0.27341,47.87
> view orient
> view matrix models
> #3,-0.1912,-0.55983,0.80624,-202.83,0.66845,0.52722,0.52461,-78.575,-0.71876,0.63924,0.27341,47.87
> view matrix models
> #3,-0.32718,-0.65798,0.67824,-199.74,0.61346,0.39804,0.68208,-82.264,-0.71876,0.63924,0.27341,47.87
> view matrix models
> #3,-0.32718,-0.65798,0.67824,-189.63,0.61346,0.39804,0.68208,-97.968,-0.71876,0.63924,0.27341,47.87
> view matrix models
> #3,-0.31859,-0.65236,0.6877,-189.86,0.61797,0.40718,0.67255,-97.745,-0.71876,0.63924,0.27341,47.87
> view matrix models
> #3,-0.31859,-0.65236,0.6877,-189.14,0.61797,0.40718,0.67255,-97.614,-0.71876,0.63924,0.27341,56.128
> view matrix models
> #3,-0.28019,-0.70127,0.65553,-188.22,0.64275,0.37016,0.67071,-97.477,-0.713,0.60927,0.34702,54.396
> view matrix models
> #3,-0.28019,-0.70127,0.65553,-192.97,0.64275,0.37016,0.67071,-101.06,-0.713,0.60927,0.34702,51.557
> view matrix models
> #3,-0.27277,-0.68671,0.67381,-193.43,0.64864,0.38599,0.65596,-100.71,-0.71054,0.61599,0.34014,51.716
> view matrix models
> #3,-0.27277,-0.68671,0.67381,-195.06,0.64864,0.38599,0.65596,-101.65,-0.71054,0.61599,0.34014,51.332
> ui tool show Matchmaker
> matchmaker #2 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_257_model_0.cif, chain C (#3) with
fold_pylori_pfla_pflb_model_0.cif, chain A (#2), sequence alignment score =
4054.5
RMSD between 185 pruned atom pairs is 1.209 angstroms; (across all 791 pairs:
24.299)
> view matrix models
> #3,-0.24896,-0.71711,0.65098,-194.43,0.62826,0.39197,0.67205,-102.08,-0.7371,0.57629,0.35294,51.05
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
——— End of log from Mon May 20 11:38:56 2024 ———
opened ChimeraX session
> select clear
> view orient
> fitmap #3/A,B inMap #1
Fit molecule fold_pylori_pfla_257_model_0.cif (#3) to map PflB-sym13-2.1A.mrc
(#1) using 3422 atoms
average map value = 3.591, steps = 212
shifted from previous position = 18.7
rotated from previous position = 11 degrees
atoms outside contour = 1101, contour level = 0.99777
Position of fold_pylori_pfla_257_model_0.cif (#3) relative to PflB-
sym13-2.1A.mrc (#1) coordinates:
Matrix rotation and translation
-0.40323251 -0.62044246 0.67264753 -174.38478967
0.65257932 0.32033624 0.68667673 -96.03572898
-0.64151677 0.71584625 0.27571794 61.65368808
Axis 0.01594067 0.71816941 0.69568570
Axis point -49.03487710 0.00000000 156.27417577
Rotation angle (degrees) 113.80274736
Shift along axis -28.85814446
> undo
> fitmap #3/A,B inMap #1
Fit molecule fold_pylori_pfla_257_model_0.cif (#3) to map PflB-sym13-2.1A.mrc
(#1) using 3422 atoms
average map value = 3.591, steps = 212
shifted from previous position = 18.7
rotated from previous position = 11 degrees
atoms outside contour = 1101, contour level = 0.99777
Position of fold_pylori_pfla_257_model_0.cif (#3) relative to PflB-
sym13-2.1A.mrc (#1) coordinates:
Matrix rotation and translation
-0.40323251 -0.62044246 0.67264753 -174.38478967
0.65257932 0.32033624 0.68667673 -96.03572898
-0.64151677 0.71584625 0.27571794 61.65368808
Axis 0.01594067 0.71816941 0.69568570
Axis point -49.03487710 0.00000000 156.27417577
Rotation angle (degrees) 113.80274736
Shift along axis -28.85814446
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.40323,-0.62044,0.67265,-192.12,0.65258,0.32034,0.68668,-107.71,-0.64152,0.71585,0.27572,60.959
> hide #3 cartoons
> show #3/A,B cartoons
> hide #2 models
> view matrix models
> #3,-0.40323,-0.62044,0.67265,-189.83,0.65258,0.32034,0.68668,-104.33,-0.64152,0.71585,0.27572,61.876
> view matrix models
> #3,0.45698,0.09403,0.8845,-216.54,-0.23727,-0.94548,0.2231,-72.189,0.85725,-0.31182,-0.40975,34.767
> view matrix models
> #3,0.49593,0.30772,0.81201,-209.81,-0.018111,-0.93124,0.36396,-86.972,0.86817,-0.19521,-0.45626,39.169
> view matrix models
> #3,0.022927,0.46495,0.88504,-196.07,-0.013164,-0.88505,0.4653,-92.09,0.99965,-0.022318,-0.014171,12.824
> view matrix models
> #3,0.022927,0.46495,0.88504,-164.08,-0.013164,-0.88505,0.4653,-118.64,0.99965,-0.022318,-0.014171,28.001
> view matrix models
> #3,0.37793,-0.048472,0.92456,-186.89,-0.64175,-0.73351,0.22387,-82.077,0.66732,-0.67795,-0.30832,43.633
> view matrix models
> #3,0.37793,-0.048472,0.92456,-191.37,-0.64175,-0.73351,0.22387,-84.722,0.66732,-0.67795,-0.30832,37.75
> select up
23108 atoms, 23540 bonds, 2856 residues, 4 models selected
> select up
23108 atoms, 23540 bonds, 2856 residues, 4 models selected
> fitmap #3/A,B inMap #1
Fit molecule fold_pylori_pfla_257_model_0.cif (#3) to map PflB-sym13-2.1A.mrc
(#1) using 3422 atoms
average map value = 3.74, steps = 288
shifted from previous position = 9.03
rotated from previous position = 50.2 degrees
atoms outside contour = 905, contour level = 0.99777
Position of fold_pylori_pfla_257_model_0.cif (#3) relative to PflB-
sym13-2.1A.mrc (#1) coordinates:
Matrix rotation and translation
0.00303202 0.17420050 0.98470554 -174.53082090
0.04016037 -0.98393685 0.17394085 -97.31238614
0.99918865 0.03901875 -0.00997927 29.28003318
Axis -0.70737358 -0.07593247 -0.70274951
Axis point -0.00000000 -35.68174025 104.33952870
Rotation angle (degrees) 174.52747882
Shift along axis 110.27113304
> select subtract #3
13262 atoms, 13531 bonds, 1635 residues, 3 models selected
> select add #3
23108 atoms, 23540 bonds, 2856 residues, 4 models selected
> select subtract #2
9846 atoms, 10009 bonds, 1221 residues, 3 models selected
> select subtract #1
9846 atoms, 10009 bonds, 1221 residues, 1 model selected
> view matrix models
> #3,0.003032,0.1742,0.98471,-185.78,0.04016,-0.98394,0.17394,-101.51,0.99919,0.039019,-0.0099793,28.417
> view matrix models
> #3,-0.048264,0.15173,0.98724,-184.69,0.11868,-0.98052,0.1565,-102.96,0.99176,0.12472,0.029317,27.948
> undo
> view matrix models
> #3,-0.051196,0.1838,0.98163,-183.7,0.0061068,-0.98284,0.18434,-101,0.99867,0.015432,0.049196,24.63
> view matrix models
> #3,-0.051196,0.1838,0.98163,-187.78,0.0061068,-0.98284,0.18434,-103.92,0.99867,0.015432,0.049196,22.829
> view matrix models
> #3,-0.051196,0.1838,0.98163,-188.94,0.0061068,-0.98284,0.18434,-104.47,0.99867,0.015432,0.049196,23.135
> view orient
> sym #3 C13 center #1
Made 13 graphical clones for fold_pylori_pfla_257_model_0.cif symmetry C13
> select clear
> lighting soft
> save "C:/Users/Jack Botting/Documents/Chimera/Images/hp flgY.jpg" width 2861
> height 1180 supersample 3
> ui tool show "Segment Map"
Segmenting PflB-sym13-2.1A.mrc, density threshold 0.997772
Showing 229 region surfaces
2534 watershed regions, grouped to 229 regions
Showing PflB-sym13-2.1A.seg - 229 regions, 229 surfaces
> select #4.21
1 model selected
> select add #4.22
2 models selected
> select add #4.18
3 models selected
> select add #3
9846 atoms, 10009 bonds, 1221 residues, 4 models selected
> view matrix models
> #3,-0.043957,0.14667,0.98821,-192.81,0.0047676,-0.98912,0.14702,-97.177,0.99902,0.011174,0.04278,24.174,#4.18,0.99926,0.037744,0.0069802,-0.22958,-0.037722,0.99928,-0.0032704,0.17058,-0.0070986,0.0030047,0.99997,0.012734,#4.21,0.99926,0.037744,0.0069802,-0.22958,-0.037722,0.99928,-0.0032704,0.17058,-0.0070986,0.0030047,0.99997,0.012734,#4.22,0.99926,0.037744,0.0069802,-0.22958,-0.037722,0.99928,-0.0032704,0.17058,-0.0070986,0.0030047,0.99997,0.012734
> undo
> select #4.20
1 model selected
> select add #4
230 models selected
> select subtract #4
Nothing selected
> select add #3
9846 atoms, 10009 bonds, 1221 residues, 1 model selected
> view matrix models
> #3,-0.044248,0.14818,0.98797,-190.17,0.0048269,-0.9889,0.14853,-102.5,0.99901,0.011341,0.043042,23.402
> view orient
> sym #3 C13 center #1
Made 13 graphical clones for fold_pylori_pfla_257_model_0.cif symmetry C13
> select #4.21
1 model selected
> select add #4.22
2 models selected
> hide #!1 models
Ungrouped to 6 regions
Ungrouped to 16 regions
Ungrouped to 8 regions
[Repeated 1 time(s)]Ungrouped to 0 regions
> select #4.242
1 model selected
> select add #4.243
2 models selected
> select add #4.244
3 models selected
> select add #4.248
4 models selected
> select add #4.22
5 models selected
> select add #4.249
6 models selected
Region has 13 adjacent regions
> select #4.22
1 model selected
> select add #4.249
2 models selected
Ungrouped to 0 regions
> select clear
> select #4.242
1 model selected
Region has 2 adjacent regions
> select #4.12
1 model selected
Ungrouped to 2 regions
Ungrouped to 9 regions
Ungrouped to 14 regions
Ungrouped to 0 regions
> select #4.267
1 model selected
> select add #4.266
2 models selected
> select add #4.265
3 models selected
> select #4.242
1 model selected
> select add #4.243
2 models selected
> select add #4.244
3 models selected
> select add #4.248
4 models selected
> select add #4.249
5 models selected
> select add #4.22
6 models selected
Region has 13 adjacent regions
Grouped 6 regions
Region has 8 adjacent regions
> select add #4.267
2 models selected
Region has 11 adjacent regions
> select #4.267
1 model selected
> select add #4.265
2 models selected
> select add #4.234
3 models selected
Region has 11 adjacent regions
> select #3/A:75
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
942 atoms, 945 bonds, 115 residues, 1 model selected
> select up
1711 atoms, 1730 bonds, 215 residues, 1 model selected
Overlapping 1711 atoms with 261 regions
Selected 0 regions
> select clear
> select #4.267
1 model selected
> select add #4.266
2 models selected
> select add #4.22
3 models selected
> select add #4.265
4 models selected
> select add #4.264
5 models selected
> select add #4.231
6 models selected
> select add #4.269
7 models selected
> select add #4.52
8 models selected
> select add #4.262
9 models selected
Grouped 9 regions
Ungrouped to 9 regions
> select subtract #4.231
8 models selected
Grouped 8 regions
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Images/hp flgY seg.jpg" width
> 2848 height 1180 supersample 3
> view orient
> hide #!4 models
> show #!1 models
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
——— End of log from Mon May 20 15:39:18 2024 ———
opened ChimeraX session
Showing PflB-sym13-2.1A.seg - 254 regions, 254 surfaces
> hide #!4 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_0.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif #5
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_1.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_1.cif #6
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_2.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_2.cif #7
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_3.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_3.cif #8
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_4.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_4.cif #9
---
Chain | Description
A B | .
C | .
> hide #3 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #6-9 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#5) with
fold_pylori_flgy_pfla_nosig_model_1.cif, chain C (#6), sequence alignment
score = 4006.4
RMSD between 558 pruned atom pairs is 1.120 angstroms; (across all 781 pairs:
20.180)
Matchmaker fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#5) with
fold_pylori_flgy_pfla_nosig_model_2.cif, chain C (#7), sequence alignment
score = 4036.4
RMSD between 373 pruned atom pairs is 1.217 angstroms; (across all 781 pairs:
17.109)
Matchmaker fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#5) with
fold_pylori_flgy_pfla_nosig_model_3.cif, chain C (#8), sequence alignment
score = 4031.6
RMSD between 481 pruned atom pairs is 1.053 angstroms; (across all 781 pairs:
22.829)
Matchmaker fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#5) with
fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#9), sequence alignment
score = 4040
RMSD between 606 pruned atom pairs is 1.093 angstroms; (across all 781 pairs:
7.682)
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #2 models
> show #3 models
> hide #3 models
> close #6-9
> hide #2 models
> show #3 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_257_model_0.cif, chain C (#3) with
fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#5), sequence alignment
score = 4001.6
RMSD between 355 pruned atom pairs is 0.650 angstroms; (across all 781 pairs:
28.335)
> show #5 models
> hide #3 models
> hide #!1 models
> show #3 models
> ui tool show Matchmaker
> matchmaker #5 to #3/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_257_model_0.cif, chain A (#3) with
fold_pylori_flgy_pfla_nosig_model_0.cif, chain B (#5), sequence alignment
score = 1009.9
RMSD between 142 pruned atom pairs is 0.978 angstroms; (across all 199 pairs:
9.403)
> show #!1 models
> hide #5/C cartoons
> view orient
> sym #5 C13 center #1
Made 13 graphical clones for fold_pylori_flgy_pfla_nosig_model_0.cif symmetry
C13
> hide #3 models
> close #3
> transparency #1 70
> lighting soft
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
——— End of log from Tue May 21 11:25:20 2024 ———
opened ChimeraX session
Showing PflB-sym13-2.1A.seg - 254 regions, 254 surfaces
> hide #!4 models
> select add #5
9525 atoms, 9685 bonds, 1179 residues, 1 model selected
> show sel surfaces
> hide #5/C surfaces
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Images/hp flgY4.jpg" width
> 2160 height 905 supersample 3
> color #5 #55ffffff
> color #5 #0055ffff
> color #5 blue
> color #5 #00aaffff
> color #5 #55aaffff
> color #5 #5555ffff
> color #5 #5500ffff
> color #5 #00aaffff
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
——— End of log from Wed May 22 11:16:21 2024 ———
opened ChimeraX session
Showing PflB-sym13-2.1A.seg - 254 regions, 254 surfaces
> hide #!4 models
> color #5 dodgerblue
> save "C:/Users/Jack Botting/Documents/Chimera/Images/hp flgY4.jpg" width
> 2160 height 905 supersample 3
> open "C:/Users/Jack Botting/Documents/Chimera/PDB/MS_pylori.pdb"
Summary of feedback from opening C:/Users/Jack
Botting/Documents/Chimera/PDB/MS_pylori.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS A 19 PHE A 44 1 26
Start residue of secondary structure not found: HELIX 2 2 PRO A 63 GLN A 75 1
13
Start residue of secondary structure not found: HELIX 3 3 LYS A 92 LYS A 94 1
3
Start residue of secondary structure not found: HELIX 4 4 TYR A 96 SER A 104 1
9
Start residue of secondary structure not found: SHEET 1 1 1 TYR A 54 GLU A 59
0
355 messages similar to the above omitted
Chain information for MS_pylori.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A 3.21/A | No description available
3.22/A 3.23/A 3.24/A 3.25/A 3.26/A 3.27/A 3.28/A 3.29/A 3.30/A 3.31/A 3.32/A 3.33/A 3.34/A 3.35/A 3.36/A 3.37/A 3.38/A 3.39/A 3.40/A 3.41/A 3.42/A | No description available
3.43/A 3.44/A 3.45/A 3.46/A 3.47/A 3.48/A 3.49/A 3.50/A 3.51/A 3.52/A 3.53/A 3.54/A 3.55/A 3.56/A 3.57/A 3.58/A 3.59/A 3.60/A 3.61/A 3.62/A 3.63/A 3.64/A 3.65/A 3.66/A 3.67/A 3.68/A 3.69/A 3.70/A 3.71/A 3.72/A 3.73/A 3.74/A 3.75/A 3.76/A 3.77/A 3.78/A 3.79/A 3.80/A 3.81/A | No description available
> view orient
> lighting simple
> turn x -90
> select add #3
112125 atoms, 113781 bonds, 14157 residues, 82 models selected
> view matrix models #3,1,0,0,8.6778,0,1,0,1.0711e-14,0,0,1,96.477
> view matrix models #3,1,0,0,2.7747,0,1,0,1.0793e-14,0,0,1,97.215
> select clear
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
——— End of log from Wed May 22 11:24:28 2024 ———
opened ChimeraX session
Showing PflB-sym13-2.1A.seg - 254 regions, 254 surfaces
> hide #!4 models
> hide #3.1-42#!5#!3.43-81 surfaces
> hide #!3 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_pflc/fold_pylori_pflc_model_0.cif"
Chain information for fold_pylori_pflc_model_0.cif #6
---
Chain | Description
A | .
> select add #6
2710 atoms, 2772 bonds, 331 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-228.19,0,1,0,-6.544,0,0,1,11.619
> view orient
> view matrix models #6,1,0,0,-283.01,0,1,0,-4.7165,0,0,1,11.619
> view matrix models
> #6,-0.15005,0.98854,0.016767,-304.06,-0.96193,-0.14989,0.22853,14.913,0.22842,0.018161,0.97339,11.76
> view matrix models
> #6,0.39162,0.91949,-0.034162,-301.61,-0.90542,0.39171,0.16366,4.8305,0.16387,-0.033163,0.98593,12.59
> view matrix models
> #6,-0.7677,0.62901,0.1224,-298.59,-0.58812,-0.76745,0.25522,27.336,0.25447,0.12395,0.9591,9.8218
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-272.96,-0.91985,0.28263,-0.27202,3.5384,-0.10749,-0.84852,-0.51814,15.399
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-200.13,-0.91985,0.28263,-0.27202,9.2651,-0.10749,-0.84852,-0.51814,6.9232
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-188.1,-0.91985,0.28263,-0.27202,33.788,-0.10749,-0.84852,-0.51814,62.568
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-191.37,-0.91985,0.28263,-0.27202,26.787,-0.10749,-0.84852,-0.51814,64.69
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-190.95,-0.91985,0.28263,-0.27202,27.194,-0.10749,-0.84852,-0.51814,65.29
> show cartoons #5
Expected ',' or a keyword
> show #5 cartoons
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-192.67,-0.91985,0.28263,-0.27202,25.266,-0.10749,-0.84852,-0.51814,72.198
> select clear
> hide #!5 models
> hide #!1 models
Alignment identifier is 2/A
Alignment identifier is 2/B
Alignment identifier is 1
Alignment identifier is 5/C
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 6/A
> select #6/A:5
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:5-19
111 atoms, 112 bonds, 15 residues, 1 model selected
> color sel red
> show #!1 models
> show sel surfaces
> mlp sel
Map values for surface "fold_pylori_pflc_model_0.cif_A SES surface": minimum
-26.88, mean -3.187, maximum 24.6
To also show corresponding color key, enter the above mlp command and add key
true
> select up
168 atoms, 172 bonds, 21 residues, 2 models selected
> select up
2710 atoms, 2772 bonds, 331 residues, 2 models selected
> view matrix models
> #6,-0.37725,-0.44737,0.81089,-242.3,-0.91985,0.28263,-0.27202,50.86,-0.10749,-0.84852,-0.51814,35.178
> undo
> hide #!1 models
> select clear
> view orient
> show #!1 models
> hide #!6 models
> show #!5 models
> view orient
> sym clear
> sym #5 C18 center #1 copies true
Made 18 copies for fold_pylori_flgy_pfla_nosig_model_0.cif symmetry C18
> split #7
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.1) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.2) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.3) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.4) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.5) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.6) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.7) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.8) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.9) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.10) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.11) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.12) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.13) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.14) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.15) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.16) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.17) into 3 models
Split fold_pylori_flgy_pfla_nosig_model_0.cif (#7.18) into 3 models
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.1.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.1.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.1.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.2.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.2.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.2.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.3.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.3.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.3.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.4.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.4.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.4.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.5.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.5.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.5.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.6.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.6.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.6.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.7.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.7.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.7.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.8.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.8.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.8.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.9.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.9.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.9.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.10.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.10.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.10.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.11.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.11.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.11.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.12.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.12.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.12.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.13.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.13.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.13.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.14.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.14.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.14.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.15.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.15.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.15.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.16.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.16.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.16.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.17.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.17.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.17.3
---
Chain | Description
C | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif A #7.18.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif B #7.18.2
---
Chain | Description
B | No description available
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif C #7.18.3
---
Chain | Description
C | No description available
> hide #7.1,4,8,11,14.1-2
> hide #7.1,4,8,11,14.1-2 cartoons
> hide #!1 models
> view orient
> show #!1 models
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
> hide #7.18.1-2 cartoons
> show #7.1.1-2 cartoons
> show #7.14.1-2 cartoons
> hide #7.15.1-2 cartoons
> select #7.16.2/B:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.16.1/A:60
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view orient
> view matrix models
> #7.16.1,-0.50663,0.7594,0.40822,-176.19,-0.65215,-0.64725,0.39468,111.67,0.56394,-0.066262,0.82315,57.704,#7.16.2,-0.50663,0.7594,0.40822,-176.19,-0.65215,-0.64725,0.39468,111.67,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.16.1,-0.50663,0.7594,0.40822,-175.61,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,57.704,#7.16.2,-0.50663,0.7594,0.40822,-175.61,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.16.1,-0.50663,0.7594,0.40822,-173.86,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,57.704,#7.16.2,-0.50663,0.7594,0.40822,-173.86,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,57.704
> select #7.17.1/A:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #7.17.1/A:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7.17.2/B:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.17.1/A:66
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.17.1,-0.32333,0.89948,0.29392,-203.31,-0.75989,-0.4319,0.48583,49.335,0.56394,-0.066262,0.82315,57.704,#7.17.2,-0.32333,0.89948,0.29392,-203.31,-0.75989,-0.4319,0.48583,49.335,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.17.1,-0.32333,0.89948,0.29392,-203.9,-0.75989,-0.4319,0.48583,47.002,0.56394,-0.066262,0.82315,57.704,#7.17.2,-0.32333,0.89948,0.29392,-203.9,-0.75989,-0.4319,0.48583,47.002,0.56394,-0.066262,0.82315,57.704
> select #1
2 models selected
> select clear
> hide #!1 models
> select #7.1.2/B:84
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #7.1.1/A:86
19 atoms, 18 bonds, 2 residues, 2 models selected
> view matrix models
> #7.1.1,0.34181,0.92611,-0.15963,-184.68,-0.75176,0.37138,0.54492,-99.874,0.56394,-0.066262,0.82315,57.704,#7.1.2,0.34181,0.92611,-0.15963,-184.68,-0.75176,0.37138,0.54492,-99.874,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.1.1,0.34181,0.92611,-0.15963,-182.34,-0.75176,0.37138,0.54492,-96.958,0.56394,-0.066262,0.82315,57.704,#7.1.2,0.34181,0.92611,-0.15963,-182.34,-0.75176,0.37138,0.54492,-96.958,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.1.1,0.32864,0.93245,-0.15009,-182.9,-0.75761,0.35516,0.54762,-96.113,0.56394,-0.066262,0.82315,57.704,#7.1.2,0.32864,0.93245,-0.15009,-182.9,-0.75761,0.35516,0.54762,-96.113,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.1.1,0.32864,0.93245,-0.15009,-185.23,-0.75761,0.35516,0.54762,-94.364,0.56394,-0.066262,0.82315,57.704,#7.1.2,0.32864,0.93245,-0.15009,-185.23,-0.75761,0.35516,0.54762,-94.364,0.56394,-0.066262,0.82315,57.704
> select clear
> select add #7.3.2/B:80
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.3.1/A:85
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.3.1,0.69057,0.58446,-0.42606,-85.374,-0.45287,0.80871,0.37536,-193.23,0.56394,-0.066262,0.82315,57.704,#7.3.2,0.69057,0.58446,-0.42606,-85.374,-0.45287,0.80871,0.37536,-193.23,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.3.1,0.69057,0.58446,-0.42606,-81.291,-0.45287,0.80871,0.37536,-194.39,0.56394,-0.066262,0.82315,57.704,#7.3.2,0.69057,0.58446,-0.42606,-81.291,-0.45287,0.80871,0.37536,-194.39,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.3.1,0.70219,0.56309,-0.43574,-79.975,-0.43463,0.82374,0.36408,-194.97,0.56394,-0.066262,0.82315,57.704,#7.3.2,0.70219,0.56309,-0.43574,-79.975,-0.43463,0.82374,0.36408,-194.97,0.56394,-0.066262,0.82315,57.704
> select #7.5.2/B:86
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.5.1/A:86
18 atoms, 16 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.5.1,0.82059,-0.067022,-0.56758,57.548,0.092778,0.99555,0.016577,-203.73,0.56394,-0.066262,0.82315,57.704,#7.5.2,0.82059,-0.067022,-0.56758,57.548,0.092778,0.99555,0.016577,-203.73,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.5.1,0.82059,-0.067022,-0.56758,49.966,0.092778,0.99555,0.016577,-206.64,0.56394,-0.066262,0.82315,57.704,#7.5.2,0.82059,-0.067022,-0.56758,49.966,0.092778,0.99555,0.016577,-206.64,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.5.1,0.82059,-0.067022,-0.56758,46.466,0.092778,0.99555,0.016577,-207.23,0.56394,-0.066262,0.82315,57.704,#7.5.2,0.82059,-0.067022,-0.56758,46.466,0.092778,0.99555,0.016577,-207.23,0.56394,-0.066262,0.82315,57.704
> select clear
[Repeated 1 time(s)]
> select add #7.3.2/B:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #7.3.1/A:82
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.3.1,0.69449,0.57738,-0.42932,-80.853,-0.44682,0.81378,0.37163,-194.59,0.56394,-0.066262,0.82315,57.704,#7.3.2,0.69449,0.57738,-0.42932,-80.853,-0.44682,0.81378,0.37163,-194.59,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.3.1,0.69449,0.57738,-0.42932,-80.269,-0.44682,0.81378,0.37163,-197.51,0.56394,-0.066262,0.82315,57.704,#7.3.2,0.69449,0.57738,-0.42932,-80.269,-0.44682,0.81378,0.37163,-197.51,0.56394,-0.066262,0.82315,57.704
[Repeated 1 time(s)]
> select #7.7.1/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #7.7.2/B:92
19 atoms, 17 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.7.1,0.55311,-0.70987,-0.43607,174.8,0.61322,0.70121,-0.36367,-118.38,0.56394,-0.066262,0.82315,57.704,#7.7.2,0.55311,-0.70987,-0.43607,174.8,0.61322,0.70121,-0.36367,-118.38,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.7.1,0.55311,-0.70987,-0.43607,177.14,0.61322,0.70121,-0.36367,-113.71,0.56394,-0.066262,0.82315,57.704,#7.7.2,0.55311,-0.70987,-0.43607,177.14,0.61322,0.70121,-0.36367,-113.71,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.7.1,0.56372,-0.69752,-0.44236,176.59,0.60348,0.71349,-0.35601,-114.52,0.56394,-0.066262,0.82315,57.704,#7.7.2,0.56372,-0.69752,-0.44236,176.59,0.60348,0.71349,-0.35601,-114.52,0.56394,-0.066262,0.82315,57.704
> select clear
> select #7.9.2/B:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.9.1/A:86
18 atoms, 16 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.9.1,-0.035311,-0.9978,-0.056129,208.23,0.82506,0.0025871,-0.56504,25.324,0.56394,-0.066262,0.82315,57.704,#7.9.2,-0.035311,-0.9978,-0.056129,208.23,0.82506,0.0025871,-0.56504,25.324,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,-0.035311,-0.9978,-0.056129,204.74,0.82506,0.0025871,-0.56504,21.241,0.56394,-0.066262,0.82315,57.704,#7.9.2,-0.035311,-0.9978,-0.056129,204.74,0.82506,0.0025871,-0.56504,21.241,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,0.029531,-0.99452,-0.10029,205.63,0.82529,0.080866,-0.55889,17.009,0.56394,-0.066262,0.82315,57.704,#7.9.2,0.029531,-0.99452,-0.10029,205.63,0.82529,0.080866,-0.55889,17.009,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,0.029531,-0.99452,-0.10029,206.21,0.82529,0.080866,-0.55889,10.009,0.56394,-0.066262,0.82315,57.704,#7.9.2,0.029531,-0.99452,-0.10029,206.21,0.82529,0.080866,-0.55889,10.009,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,0.15706,-0.96998,-0.18568,206.91,0.81074,0.234,-0.5366,1.6385,0.56394,-0.066262,0.82315,57.704,#7.9.2,0.15706,-0.96998,-0.18568,206.91,0.81074,0.234,-0.5366,1.6385,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,0.15706,-0.96998,-0.18568,208.66,0.81074,0.234,-0.5366,-11.777,0.56394,-0.066262,0.82315,57.704,#7.9.2,0.15706,-0.96998,-0.18568,208.66,0.81074,0.234,-0.5366,-11.777,0.56394,-0.066262,0.82315,57.704
> undo
[Repeated 4 time(s)]
> view matrix models
> #7.9.1,-0.015757,-0.99746,-0.069498,208.54,0.82567,0.026223,-0.56355,24.025,0.56394,-0.066262,0.82315,57.704,#7.9.2,-0.015757,-0.99746,-0.069498,208.54,0.82567,0.026223,-0.56355,24.025,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,-0.015757,-0.99746,-0.069498,206.79,0.82567,0.026223,-0.56355,19.942,0.56394,-0.066262,0.82315,57.704,#7.9.2,-0.015757,-0.99746,-0.069498,206.79,0.82567,0.026223,-0.56355,19.942,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,-0.0013443,-0.99685,-0.079323,206.99,0.82581,0.043627,-0.56225,19.002,0.56394,-0.066262,0.82315,57.704,#7.9.2,-0.0013443,-0.99685,-0.079323,206.99,0.82581,0.043627,-0.56225,19.002,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.9.1,-0.0013443,-0.99685,-0.079323,206.41,0.82581,0.043627,-0.56225,16.669,0.56394,-0.066262,0.82315,57.704,#7.9.2,-0.0013443,-0.99685,-0.079323,206.41,0.82581,0.043627,-0.56225,16.669,0.56394,-0.066262,0.82315,57.704
> select #7.10.1/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.10.2/B:88
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.10.1,-0.31813,-0.93728,0.1425,186.4,0.76208,-0.34223,-0.54965,95.132,0.56394,-0.066262,0.82315,57.704,#7.10.2,-0.31813,-0.93728,0.1425,186.4,0.76208,-0.34223,-0.54965,95.132,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.10.1,-0.31813,-0.93728,0.1425,175.9,0.76208,-0.34223,-0.54965,103.3,0.56394,-0.066262,0.82315,57.704,#7.10.2,-0.31813,-0.93728,0.1425,175.9,0.76208,-0.34223,-0.54965,103.3,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.10.1,-0.21305,-0.97471,0.067498,179.61,0.79786,-0.21344,-0.56379,96.53,0.56394,-0.066262,0.82315,57.704,#7.10.2,-0.21305,-0.97471,0.067498,179.61,0.79786,-0.21344,-0.56379,96.53,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.10.1,-0.21305,-0.97471,0.067498,183.11,0.79786,-0.21344,-0.56379,91.281,0.56394,-0.066262,0.82315,57.704,#7.10.2,-0.21305,-0.97471,0.067498,183.11,0.79786,-0.21344,-0.56379,91.281,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.10.1,-0.21305,-0.97471,0.067498,185.44,0.79786,-0.21344,-0.56379,88.364,0.56394,-0.066262,0.82315,57.704,#7.10.2,-0.21305,-0.97471,0.067498,185.44,0.79786,-0.21344,-0.56379,88.364,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.10.1,-0.26136,-0.95986,0.10179,183.86,0.78337,-0.27254,-0.55862,91.475,0.56394,-0.066262,0.82315,57.704,#7.10.2,-0.26136,-0.95986,0.10179,183.86,0.78337,-0.27254,-0.55862,91.475,0.56394,-0.066262,0.82315,57.704
> select #7.12.2/B:128
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #7.12.1/A:104
15 atoms, 13 bonds, 2 residues, 2 models selected
> select up
992 atoms, 994 bonds, 122 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.12.1,-0.72193,-0.52355,0.45245,82.393,0.40099,-0.84941,-0.34309,191.52,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.72193,-0.52355,0.45245,82.393,0.40099,-0.84941,-0.34309,191.52,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.72193,-0.52355,0.45245,84.143,0.40099,-0.84941,-0.34309,187.44,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.72193,-0.52355,0.45245,84.143,0.40099,-0.84941,-0.34309,187.44,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.73873,-0.48601,0.46698,81.892,0.36911,-0.87144,-0.32303,188.2,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.73873,-0.48601,0.46698,81.892,0.36911,-0.87144,-0.32303,188.2,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.73873,-0.48601,0.46698,81.892,0.36911,-0.87144,-0.32303,185.28,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.73873,-0.48601,0.46698,81.892,0.36911,-0.87144,-0.32303,185.28,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.73548,-0.49359,0.46415,82.344,0.37555,-0.86717,-0.32709,185.14,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.73548,-0.49359,0.46415,82.344,0.37555,-0.86717,-0.32709,185.14,0.56394,-0.066262,0.82315,57.704
> undo
[Repeated 4 time(s)]
> view matrix models
> #7.12.1,-0.7531,-0.45025,0.4797,78.025,0.33884,-0.89044,-0.30382,192.89,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.7531,-0.45025,0.4797,78.025,0.33884,-0.89044,-0.30382,192.89,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.7531,-0.45025,0.4797,77.442,0.33884,-0.89044,-0.30382,188.23,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.7531,-0.45025,0.4797,77.442,0.33884,-0.89044,-0.30382,188.23,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.7531,-0.45025,0.4797,80.358,0.33884,-0.89044,-0.30382,186.48,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.7531,-0.45025,0.4797,80.358,0.33884,-0.89044,-0.30382,186.48,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.12.1,-0.74397,-0.47341,0.47159,81.725,0.35844,-0.87835,-0.31627,186.09,0.56394,-0.066262,0.82315,57.704,#7.12.2,-0.74397,-0.47341,0.47159,81.725,0.35844,-0.87835,-0.31627,186.09,0.56394,-0.066262,0.82315,57.704
> select #7.14.1/A:93
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7.14.2/B:88
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
1733 atoms, 1738 bonds, 211 residues, 2 models selected
> select up
3172 atoms, 3208 bonds, 398 residues, 2 models selected
> view matrix models
> #7.14.1,-0.82059,0.067022,0.56758,-56.811,-0.092778,-0.99555,-0.016577,200.5,0.56394,-0.066262,0.82315,57.704,#7.14.2,-0.82059,0.067022,0.56758,-56.811,-0.092778,-0.99555,-0.016577,200.5,0.56394,-0.066262,0.82315,57.704
> view matrix models
> #7.14.1,-0.82059,0.067022,0.56758,-64.393,-0.092778,-0.99555,-0.016577,197.58,0.56394,-0.066262,0.82315,57.704,#7.14.2,-0.82059,0.067022,0.56758,-64.393,-0.092778,-0.99555,-0.016577,197.58,0.56394,-0.066262,0.82315,57.704
> select clear
> show #!1 models
> view orient
[Repeated 1 time(s)]
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
> view orient
[Repeated 2 time(s)]
> color #7.*.1-2 orchid
> color #7.*.2 magenta
> ui tool show "Color Actions"
> color #7.*.1 sandy brown
> color #7.*.1 orchid
> color #7.*.3 sandy brown
> color #7.*.3 dark orange
> view orient
> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"
——— End of log from Fri May 31 16:05:16 2024 ———
opened ChimeraX session
Showing PflB-sym13-2.1A.seg - 254 regions, 254 surfaces
> hide #!4 models
> select clear
> open "C:/Users/Jack Botting/Documents/H pylori/pylori maps/HP-PflA-
> PflB-2.1A.mrc"
Opened HP-PflA-PflB-2.1A.mrc as #8, grid size 240,240,240, pixel 2.14, shown
at level 4.32, step 1, values float32
> select add #8
2 models selected
> view matrix models #8,1,0,0,-382.21,0,1,0,47.267,0,0,1,0
> volume #8 level 0.7831
> view matrix models #8,1,0,0,-80.204,0,1,0,24.141,0,0,1,0
> view matrix models
> #8,0.99942,-0.019563,0.027776,-80.177,-0.014797,0.48529,0.87423,25.193,-0.030582,-0.87413,0.48473,-3.2117
> undo
> view matrix models #8,1,0,0,198.59,0,1,0,1.4983,0,0,1,0
> view matrix models #8,1,0,0,206.1,0,1,0,-1.4758,0,0,1,95.369
> view matrix models #8,1,0,0,213.9,0,1,0,-6.7695,0,0,1,94.677
> view matrix models #8,1,0,0,213.62,0,1,0,-6.6337,0,0,1,66.214
> hide #!1 models
> transparency sel 50
> rename #1 id #1.1
> rename #8 id #1.2
> hide #!7 models
> show #!7 models
> hide #7.*.3 cartoons
> show #!5 models
> select add #5
9525 atoms, 9685 bonds, 1179 residues, 3 models selected
> view matrix models
> #5,0.27499,0.95496,-0.11152,-12.733,-0.77869,0.28925,0.55676,34.045,0.56394,-0.066262,0.82315,43.677,#1.2,1,0,0,388.2,0,1,0,123,0,0,1,52.187
> undo
> select clear
> select add #5
9525 atoms, 9685 bonds, 1179 residues, 1 model selected
> view matrix models
> #5,0.27499,0.95496,-0.11152,123.3,-0.77869,0.28925,0.55676,127.15,0.56394,-0.066262,0.82315,17.37
> view matrix models
> #5,-0.11429,-0.96183,0.24864,167.61,0.76069,-0.24571,-0.60081,117.82,0.63897,0.12047,0.75974,12.565
> view matrix models
> #5,-0.11429,-0.96183,0.24864,164.39,0.76069,-0.24571,-0.60081,128.97,0.63897,0.12047,0.75974,39.177
> fitmap #5 inMap #1.2
Fit molecule fold_pylori_flgy_pfla_nosig_model_0.cif (#5) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 9525 atoms
average map value = 1.127, steps = 268
shifted from previous position = 38.9
rotated from previous position = 21.5 degrees
atoms outside contour = 5886, contour level = 0.78314
Position of fold_pylori_flgy_pfla_nosig_model_0.cif (#5) relative to HP-PflA-
PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.02521049 -0.98608204 0.16433715 -27.82436458
0.94304020 -0.07800748 -0.32340389 108.34635925
0.33172227 0.14682335 0.93188163 -44.06798496
Axis 0.23598114 -0.08400137 0.96812017
Axis point -57.57114322 45.59766919 0.00000000
Rotation angle (degrees) 94.91444810
Shift along axis -58.33037327
> view matrix models
> #5,-0.02521,-0.98608,0.16434,192.46,0.94304,-0.078007,-0.3234,111.39,0.33172,0.14682,0.93188,49.608
> view matrix models
> #5,-0.18375,-0.9808,-0.065334,193.61,0.85773,-0.12752,-0.49803,112.95,0.48013,-0.14755,0.8647,53.759
> fitmap #5 inMap #1.2
Fit molecule fold_pylori_flgy_pfla_nosig_model_0.cif (#5) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 9525 atoms
average map value = 1.078, steps = 108
shifted from previous position = 10.5
rotated from previous position = 11.2 degrees
atoms outside contour = 5941, contour level = 0.78314
Position of fold_pylori_flgy_pfla_nosig_model_0.cif (#5) relative to HP-PflA-
PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.36736330 -0.92501009 -0.09695664 -17.62002977
0.80656333 -0.26493153 -0.52845714 129.60882241
0.46314129 -0.27233742 0.84340536 -11.95872231
Axis 0.13935915 -0.30475891 0.94217888
Axis point -47.57926437 59.30217548 0.00000000
Rotation angle (degrees) 113.23134771
Shift along axis -53.22221173
> fitmap #5 inMap #1.2
Fit molecule fold_pylori_flgy_pfla_nosig_model_0.cif (#5) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 9525 atoms
average map value = 1.078, steps = 28
shifted from previous position = 0.0173
rotated from previous position = 0.00972 degrees
atoms outside contour = 5941, contour level = 0.78314
Position of fold_pylori_flgy_pfla_nosig_model_0.cif (#5) relative to HP-PflA-
PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.36741876 -0.92499815 -0.09686034 -17.60596407
0.80646791 -0.26498815 -0.52857438 129.60288482
0.46326345 -0.27232288 0.84334296 -11.96700745
Axis 0.13943653 -0.30478541 0.94215886
Axis point -47.56436905 59.30472786 0.00000000
Rotation angle (degrees) 113.23678734
Shift along axis -53.23080486
> select clear
Segmenting HP-PflA-PflB-2.1A.mrc, density threshold 0.783137
Showing 283 region surfaces
3344 watershed regions, grouped to 283 regions
Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces
> select add #4
284 models selected
> view matrix models #4,1,0,0,157.17,0,1,0,84.184,0,0,1,57.089
> view matrix models #4,1,0,0,198.06,0,1,0,-2.3089,0,0,1,81.691
> view matrix models #4,1,0,0,205.87,0,1,0,-3.1302,0,0,1,83.687
> view matrix models #4,1,0,0,211.59,0,1,0,-1.8374,0,0,1,65.383
> view matrix models #4,1,0,0,213.69,0,1,0,-3.7356,0,0,1,65.355
> select clear
> select #4.31
1 model selected
> hide #!1.2 models
Region has 6 adjacent regions
> select add #4.37
2 models selected
Region has 8 adjacent regions
> select add #5
9525 atoms, 9685 bonds, 1179 residues, 3 models selected
> select add #4
9525 atoms, 9685 bonds, 1179 residues, 288 models selected
> select subtract #4
9525 atoms, 9685 bonds, 1179 residues, 4 models selected
> view matrix models
> #5,-0.36742,-0.925,-0.09686,198.93,0.80647,-0.26499,-0.52857,84.228,0.46326,-0.27232,0.84334,88.995
> view matrix models
> #5,-0.36742,-0.925,-0.09686,220.29,0.80647,-0.26499,-0.52857,44.111,0.46326,-0.27232,0.84334,92.112
> view matrix models
> #5,-0.36742,-0.925,-0.09686,214.56,0.80647,-0.26499,-0.52857,47.605,0.46326,-0.27232,0.84334,74.21
> view matrix models
> #5,-0.36004,-0.93042,-0.06848,214.65,0.80649,-0.2735,-0.52419,47.789,0.46898,-0.24396,0.84885,73.581
> view matrix models
> #5,-0.15733,-0.97903,-0.1294,213.2,0.87224,-0.07632,-0.48309,43.125,0.46309,-0.18887,0.86596,72.567
> view matrix models
> #5,-0.15733,-0.97903,-0.1294,220.63,0.87224,-0.07632,-0.48309,47.18,0.46309,-0.18887,0.86596,62.868
> view matrix models
> #5,-0.15733,-0.97903,-0.1294,220.46,0.87224,-0.07632,-0.48309,33.63,0.46309,-0.18887,0.86596,63.031
> view matrix models
> #5,-0.14568,-0.98358,-0.10649,220.48,0.87576,-0.078132,-0.47637,33.642,0.46023,-0.16266,0.87277,62.545
> view matrix models
> #5,-0.071909,-0.99323,-0.091178,219.87,0.78655,-0.00025665,-0.61753,32.733,0.61333,-0.11612,0.78125,59.642
> view matrix models
> #5,-0.071909,-0.99323,-0.091178,208.77,0.78655,-0.00025665,-0.61753,30.137,0.61333,-0.11612,0.78125,63.781
> select clear
> show #!1.2 models
> hide #!4 models
> show #!4 models
> show #2 models
> mmaker #2 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#5) with
fold_pylori_pfla_pflb_model_0.cif, chain A (#2), sequence alignment score =
4008.2
RMSD between 229 pruned atom pairs is 0.623 angstroms; (across all 781 pairs:
35.568)
> open "C:/Users/Jack Botting/Documents/alphafold
> results/HpyloripflB_4cab4/HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #8
---
Chain | Description
A | No description available
> select add #8
13645 atoms, 13789 bonds, 844 residues, 1 model selected
> view matrix models #8,1,0,0,272.6,0,1,0,193.28,0,0,1,106.96
> mm#8 to #2
Unknown command: mm#8 to #2
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_pflb_model_0.cif, chain B (#2) with
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#8), sequence alignment score = 4154.7
RMSD between 469 pruned atom pairs is 1.009 angstroms; (across all 844 pairs:
37.462)
> select clear
> hide #!7 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #2 models
> select add #8
13645 atoms, 13789 bonds, 844 residues, 1 model selected
> view matrix models
> #8,0.86454,0.19195,-0.46446,365.26,-0.26591,-0.60951,-0.74685,128.72,-0.42645,0.76919,-0.47591,157.92
> view matrix models
> #8,0.86454,0.19195,-0.46446,464.56,-0.26591,-0.60951,-0.74685,111.48,-0.42645,0.76919,-0.47591,138.25
> select clear
> select add #8
13645 atoms, 13789 bonds, 844 residues, 1 model selected
> hide #!1.2 models
> hide #8:1-139 cartoons
> show #!1.2 models
> view matrix models
> #8,0.86454,0.19195,-0.46446,432.07,-0.26591,-0.60951,-0.74685,37.067,-0.42645,0.76919,-0.47591,190.09
> view matrix models
> #8,0.86454,0.19195,-0.46446,459.79,-0.26591,-0.60951,-0.74685,38.389,-0.42645,0.76919,-0.47591,122.59
> view matrix models
> #8,0.86454,0.19195,-0.46446,404.96,-0.26591,-0.60951,-0.74685,28.685,-0.42645,0.76919,-0.47591,173.23
> view matrix models
> #8,0.86454,0.19195,-0.46446,375.64,-0.26591,-0.60951,-0.74685,14.489,-0.42645,0.76919,-0.47591,65.039
> view matrix models
> #8,0.86454,0.19195,-0.46446,347.36,-0.26591,-0.60951,-0.74685,0.82137,-0.42645,0.76919,-0.47591,99.58
> view matrix models
> #8,0.86454,0.19195,-0.46446,340.7,-0.26591,-0.60951,-0.74685,6.5606,-0.42645,0.76919,-0.47591,54.682
> view matrix models
> #8,0.17733,0.96804,-0.17737,348.8,0.60959,-0.24953,-0.75242,-1.306,-0.77263,0.025304,-0.63435,56.701
> view matrix models
> #8,0.17733,0.96804,-0.17737,336.6,0.60959,-0.24953,-0.75242,-0.81076,-0.77263,0.025304,-0.63435,75.718
> view matrix models
> #8,0.17733,0.96804,-0.17737,336.97,0.60959,-0.24953,-0.75242,0.61613,-0.77263,0.025304,-0.63435,35.703
> view matrix models
> #8,0.17733,0.96804,-0.17737,325.64,0.60959,-0.24953,-0.75242,2.8599,-0.77263,0.025304,-0.63435,53.799
> fitmap #8 inMap #1.2
Fit molecule
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
map HP-PflA-PflB-2.1A.mrc (#1.2) using 13645 atoms
average map value = 2.335, steps = 132
shifted from previous position = 14.6
rotated from previous position = 29.1 degrees
atoms outside contour = 6619, contour level = 0.78314
Position of
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
0.51693560 0.85248881 0.07772002 110.01758939
0.42404505 -0.17614508 -0.88834605 10.73960757
-0.74361507 0.49217449 -0.45254933 -26.69334503
Axis 0.83037536 0.49402845 -0.25770652
Axis point 0.00000000 -27.35415678 -9.27560321
Rotation angle (degrees) 123.77130733
Shift along axis 103.54061629
> ui mousemode right "map eraser"
> volume erase #1.2 center 317.75,1.859,29.775 radius 119.84 outside true
Opened HP-PflA-PflB-2.1A.mrc copy as #10, grid size 240,240,240, pixel 2.14,
shown at step 1, values float32
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.51694,0.85249,0.07772,306.22,0.42405,-0.17615,-0.88835,-13.583,-0.74362,0.49217,-0.45255,58.805
> view matrix models
> #8,0.22368,0.92359,0.31136,308.3,0.78261,0.020213,-0.62218,-17.985,-0.58094,0.38284,-0.71829,58.105
> view matrix models
> #8,0.22368,0.92359,0.31136,297.98,0.78261,0.020213,-0.62218,-18.329,-0.58094,0.38284,-0.71829,57.274
> view matrix models
> #8,0.22368,0.92359,0.31136,295.24,0.78261,0.020213,-0.62218,-13.91,-0.58094,0.38284,-0.71829,40.522
> view matrix models
> #8,0.2224,0.92287,0.31441,295.23,0.77889,0.025782,-0.62663,-13.832,-0.5864,0.38425,-0.71308,40.557
> view matrix models
> #8,-0.42673,-0.89901,0.098408,297.27,0.66694,-0.38631,-0.63715,-13.921,0.61082,-0.20626,0.76443,19.018
> view matrix models
> #8,-0.42673,-0.89901,0.098408,300.7,0.66694,-0.38631,-0.63715,-5.4296,0.61082,-0.20626,0.76443,32.784
> view matrix models
> #8,-0.3792,-0.92128,0.086361,300.2,0.60758,-0.31829,-0.72769,-4.1541,0.69789,-0.22346,0.68045,32.249
> view matrix models
> #8,-0.3792,-0.92128,0.086361,301.94,0.60758,-0.31829,-0.72769,-8.0865,0.69789,-0.22346,0.68045,34.402
> fitmap #8 inMap #1.2
Fit molecule
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
map HP-PflA-PflB-2.1A.mrc (#1.2) using 13645 atoms
average map value = 2.931, steps = 204
shifted from previous position = 19.7
rotated from previous position = 32.2 degrees
atoms outside contour = 5607, contour level = 0.78314
Position of
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.70152979 -0.65999558 -0.26881549 105.06052909
0.55369055 -0.26731897 -0.78864905 12.50644863
0.44864541 -0.70210141 0.55296555 -31.48315593
Axis 0.06127085 -0.50792185 0.85922132
Axis point 53.93921062 22.62680834 0.00000000
Rotation angle (degrees) 135.06768532
Shift along axis -26.96614953
> fitmap #8 inMap #10
Fit molecule
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
map HP-PflA-PflB-2.1A.mrc copy (#10) using 13645 atoms
average map value = 2.931, steps = 44
shifted from previous position = 0.0338
rotated from previous position = 0.0357 degrees
atoms outside contour = 5604, contour level = 0.78314
Position of
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
relative to HP-PflA-PflB-2.1A.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.70195513 -0.65967480 -0.26849233 105.07939828
0.55330098 -0.26772213 -0.78878569 12.47918353
0.44846071 -0.70224924 0.55292764 -31.47645998
Axis 0.06130064 -0.50787475 0.85924703
Axis point 53.95202121 22.59760397 0.00000000
Rotation angle (degrees) 135.10283915
Shift along axis -26.94248276
> fitmap #8 inMap #10 search 50
Found 35 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (35 of 50).
Average map values and times found:
3.851 (1), 2.961 (1), 2.594 (1), 2.425 (1), 2.356 (1), 2.26 (1), 2.159 (1),
1.872 (1), 1.623 (1), 1.592 (1), 1.492 (1), 1.476 (1), 1.456 (1), 1.412 (1),
1.394 (1), 1.345 (1), 1.335 (1), 1.334 (1), 1.319 (1), 1.279 (1), 1.186 (1),
1.169 (1), 1.051 (1), 1.015 (1), 0.8287 (1), 0.7675 (1), 0.759 (1), 0.7321
(1), 0.6918 (1), 0.6119 (1), 0.5938 (1), 0.4862 (1), 0.4109 (1), 0.2699 (1),
0.2429 (1)
Best fit found:
Fit molecule
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
map HP-PflA-PflB-2.1A.mrc copy (#10) using 13645 atoms
average map value = 3.851, steps = 540
shifted from previous position = 69.3
rotated from previous position = 120 degrees
atoms outside contour = 4739, contour level = 0.78314
Position of
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
relative to HP-PflA-PflB-2.1A.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.80517259 -0.56616117 0.17651803 86.11498047
-0.47565094 0.43875097 -0.76239999 -59.93436147
0.35419384 -0.69782455 -0.62256533 -8.26114267
Axis 0.30809375 -0.84770323 0.43183038
Axis point 33.40937783 0.00000000 -17.43174535
Rotation angle (degrees) 173.98445054
Shift along axis 73.77062645
Found 35 fits.
> hide #!10 models
> close #9#10
> show #!1.2 models
> view orient
> view matrix models
> #8,-0.80517,-0.56616,0.17652,269.26,-0.47565,0.43875,-0.7624,6.6873,0.35419,-0.69782,-0.62257,57.953
> view matrix models
> #8,-0.82927,0.029704,0.55806,269.48,-0.53528,0.24472,-0.80845,6.9213,-0.16058,-0.96914,-0.18704,60.243
> view matrix models
> #8,-0.82927,0.029704,0.55806,266.56,-0.53528,0.24472,-0.80845,-24.857,-0.16058,-0.96914,-0.18704,-54.386
> view matrix models
> #8,-0.82927,0.029704,0.55806,281.94,-0.53528,0.24472,-0.80845,-12.145,-0.16058,-0.96914,-0.18704,-12.041
> view matrix models
> #8,-0.84124,0.18697,-0.5073,287.85,0.53436,0.14474,-0.83277,-23.365,-0.082277,-0.97164,-0.22167,-12.684
> view matrix models
> #8,-0.84124,0.18697,-0.5073,311.12,0.53436,0.14474,-0.83277,-16.792,-0.082277,-0.97164,-0.22167,-11.483
> view matrix models
> #8,-0.84124,0.18697,-0.5073,309.52,0.53436,0.14474,-0.83277,-5.0068,-0.082277,-0.97164,-0.22167,34.71
> view matrix models
> #8,-0.84124,0.18697,-0.5073,309.25,0.53436,0.14474,-0.83277,-14.836,-0.082277,-0.97164,-0.22167,34.72
> fitmap #8 inMap #1.2
Fit molecule
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
map HP-PflA-PflB-2.1A.mrc (#1.2) using 13645 atoms
average map value = 2.741, steps = 180
shifted from previous position = 21.9
rotated from previous position = 11.2 degrees
atoms outside contour = 5878, contour level = 0.78314
Position of
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.92150179 0.19288374 -0.33709094 111.18331880
0.36424268 0.12804289 -0.92245989 8.00867933
-0.13476540 -0.97283137 -0.18824822 -36.62916278
Axis -0.18664195 -0.74967890 0.63493805
Axis point 54.81507538 0.00000000 -10.31888937
Rotation angle (degrees) 172.24476469
Shift along axis -50.01265912
> fitmap #8 inMap #1.2
Fit molecule
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
map HP-PflA-PflB-2.1A.mrc (#1.2) using 13645 atoms
average map value = 2.741, steps = 120
shifted from previous position = 0.00193
rotated from previous position = 0.0173 degrees
atoms outside contour = 5880, contour level = 0.78314
Position of
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.92139865 0.19310067 -0.33724865 111.18287890
0.36444926 0.12809101 -0.92237161 8.00909646
-0.13491205 -0.97278200 -0.18839825 -36.62878465
Axis -0.18677990 -0.74969493 0.63487856
Axis point 54.81382704 0.00000000 -10.31930172
Rotation angle (degrees) 172.24450516
Shift along axis -50.02593564
> close #8
> show #2 models
> split #2
Split fold_pylori_pfla_pflb_model_0.cif (#2) into 2 models
Chain information for fold_pylori_pfla_pflb_model_0.cif A #2.1
---
Chain | Description
A | No description available
Chain information for fold_pylori_pfla_pflb_model_0.cif B #2.2
---
Chain | Description
B | No description available
> hide #2.2 models
> show #2.2 models
> color #2.2 blue
> select add #2.2
6838 atoms, 6982 bonds, 844 residues, 1 model selected
> view matrix models
> #2.2,-0.52349,-0.78607,0.3287,441.45,-0.079043,-0.33932,-0.93735,88.749,0.84836,-0.51668,0.1155,131.88
> view orient
> select add #2.1
13262 atoms, 13531 bonds, 1635 residues, 2 models selected
> view matrix models
> #2.1,-0.52349,-0.78607,0.3287,189.48,-0.079043,-0.33932,-0.93735,59.679,0.84836,-0.51668,0.1155,109.44,#2.2,-0.52349,-0.78607,0.3287,397.44,-0.079043,-0.33932,-0.93735,80.831,0.84836,-0.51668,0.1155,134.41
> view matrix models
> #2.1,-0.45963,-0.81134,0.36121,189.78,-0.11115,-0.35096,-0.92977,56.989,0.88113,-0.4675,0.07113,116.18,#2.2,-0.45963,-0.81134,0.36121,398.34,-0.11115,-0.35096,-0.92977,83.537,0.88113,-0.4675,0.07113,126.92
> view matrix models
> #2.1,-0.45963,-0.81134,0.36121,190.86,-0.11115,-0.35096,-0.92977,52.509,0.88113,-0.4675,0.07113,113.4,#2.2,-0.45963,-0.81134,0.36121,399.43,-0.11115,-0.35096,-0.92977,79.057,0.88113,-0.4675,0.07113,124.14
> view matrix models
> #2.1,-0.45963,-0.81134,0.36121,191.15,-0.11115,-0.35096,-0.92977,58.876,0.88113,-0.4675,0.07113,105.18,#2.2,-0.45963,-0.81134,0.36121,399.71,-0.11115,-0.35096,-0.92977,85.424,0.88113,-0.4675,0.07113,115.92
> view matrix models
> #2.1,-0.51826,-0.8512,-0.082782,192.38,0.098322,0.03685,-0.99447,104.57,0.84955,-0.52354,0.064594,98.777,#2.2,-0.51826,-0.8512,-0.082782,390.67,0.098322,0.03685,-0.99447,37.89,0.84955,-0.52354,0.064594,122.29
> view matrix models
> #2.1,-0.51826,-0.8512,-0.082782,192.2,0.098322,0.03685,-0.99447,37.197,0.84955,-0.52354,0.064594,107.46,#2.2,-0.51826,-0.8512,-0.082782,390.5,0.098322,0.03685,-0.99447,-29.483,0.84955,-0.52354,0.064594,130.97
> select clear
> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_pflanob_pflc_flgy/fold_pylori_pflanob_pflc_flgy_model_0.cif"
Chain information for fold_pylori_pflanob_pflc_flgy_model_0.cif #8
---
Chain | Description
A | .
B | .
C D | .
> hide #!2 models
> select add #8
10870 atoms, 11060 bonds, 1340 residues, 1 model selected
> view matrix models #8,1,0,0,158.15,0,1,0,-73.011,0,0,1,67.312
> view matrix models
> #8,-0.27447,-0.61292,-0.74094,165.59,0.69203,-0.6609,0.29036,-41.748,-0.66766,-0.43306,0.60556,73.191
> view matrix models
> #8,-0.27447,-0.61292,-0.74094,181.29,0.69203,-0.6609,0.29036,-7.4341,-0.66766,-0.43306,0.60556,62.004
> view matrix models
> #8,-0.28898,-0.6768,-0.67708,181.33,0.68329,-0.64118,0.34929,-8.6805,-0.67053,-0.3617,0.64774,60.179
> view matrix models
> #8,-0.057524,-0.39642,-0.91627,182.33,0.028772,-0.91806,0.39539,-11.45,-0.99793,-0.0036181,0.064217,58.847
> view matrix models
> #8,-0.057524,-0.39642,-0.91627,161.09,0.028772,-0.91806,0.39539,-5.1111,-0.99793,-0.0036181,0.064217,56.584
> view matrix models
> #8,-0.057524,-0.39642,-0.91627,161.28,0.028772,-0.91806,0.39539,-9.74,-0.99793,-0.0036181,0.064217,56.41
> view matrix models
> #8,-0.057524,-0.39642,-0.91627,163.28,0.028772,-0.91806,0.39539,-7.9025,-0.99793,-0.0036181,0.064217,49.2
> view matrix models
> #8,-0.031343,-0.16412,-0.98594,160.59,-0.033496,-0.9857,0.16514,-4.1959,-0.99895,0.038201,0.025398,49.023
> view matrix models
> #8,-0.20143,0.098503,-0.97454,154.22,-0.2213,-0.97378,-0.052687,-3.3154,-0.95418,0.20505,0.21795,43.981
> view matrix models
> #8,-0.20143,0.098503,-0.97454,163.38,-0.2213,-0.97378,-0.052687,-1.2369,-0.95418,0.20505,0.21795,48.39
> view matrix models
> #8,-0.33179,0.08528,-0.93949,161.76,-0.10075,-0.99341,-0.054594,0.37659,-0.93796,0.076541,0.33819,49.057
> view matrix models
> #8,-0.33179,0.08528,-0.93949,166.1,-0.10075,-0.99341,-0.054594,2.6668,-0.93796,0.076541,0.33819,50.041
> view matrix models
> #8,-0.28587,0.019868,-0.95806,167.95,-0.041422,-0.99911,-0.0083591,2.736,-0.95737,0.037295,0.28644,51.224
> fitmap #8 inMap #1.2
Fit molecule fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 10870 atoms
average map value = 1.073, steps = 276
shifted from previous position = 36.4
rotated from previous position = 25.3 degrees
atoms outside contour = 8297, contour level = 0.78314
Position of fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) relative to HP-
PflA-PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.05996141 -0.25908761 -0.96399080 -20.57711302
-0.24506312 -0.93235181 0.26582736 36.34047063
-0.96765113 0.25217797 -0.00758769 -18.26006028
Axis -0.68556995 0.18384827 0.70441015
Axis point -19.29764091 20.49963346 0.00000000
Rotation angle (degrees) 179.42962414
Shift along axis 7.92561143
> view matrix models
> #8,-0.059961,-0.25909,-0.96399,196.77,-0.24506,-0.93235,0.26583,-2.5626,-0.96765,0.25218,-0.0075877,50.483
> view matrix models
> #8,-0.059961,-0.25909,-0.96399,160.39,-0.24506,-0.93235,0.26583,-10.563,-0.96765,0.25218,-0.0075877,49.163
> show #!4 models
> hide #!1.2 models
> select #4.104
1 model selected
> select add #4.28
2 models selected
Region has 13 adjacent regions
> select clear
> show #!1.2 models
> select #4.90
1 model selected
> select add #4.141
2 models selected
> select clear
> select #4.86
1 model selected
> select clear
> hide #!1.2 models
> show #!2 models
> select add #2.2
6838 atoms, 6982 bonds, 844 residues, 1 model selected
> hide #2.1 models
> view matrix models
> #2.2,-0.51826,-0.8512,-0.082782,354.56,0.098322,0.03685,-0.99447,-9.004,0.84955,-0.52354,0.064594,140.23
> view matrix models
> #2.2,-0.51826,-0.8512,-0.082782,339.3,0.098322,0.03685,-0.99447,23.329,0.84955,-0.52354,0.064594,0.18441
> view matrix models
> #2.2,-0.51826,-0.8512,-0.082782,303.88,0.098322,0.03685,-0.99447,23.934,0.84955,-0.52354,0.064594,-5.5463
> view matrix models
> #2.2,-0.2848,-0.95285,-0.10473,300.45,-0.64725,0.27174,-0.7122,37.798,0.70708,-0.13505,-0.69412,-14.044
> select clear
> select #4.46
1 model selected
> select add #4.50
2 models selected
> select add #4.28
3 models selected
> select add #4.104
4 models selected
> select add #4.31
5 models selected
> select add #4.12
6 models selected
> select add #4.126
7 models selected
> select add #4.66
8 models selected
> select clear
> select #4.62
1 model selected
> select add #4.228
2 models selected
> select add #4.261
3 models selected
> select clear
> select add #2.2
6838 atoms, 6982 bonds, 844 residues, 1 model selected
> view matrix models
> #2.2,-0.2848,-0.95285,-0.10473,294.39,-0.64725,0.27174,-0.7122,36.123,0.70708,-0.13505,-0.69412,-14.728
> view matrix models
> #2.2,-0.2848,-0.95285,-0.10473,291.95,-0.64725,0.27174,-0.7122,37.261,0.70708,-0.13505,-0.69412,14.333
> view matrix models
> #2.2,0.82698,-0.26986,0.49323,319.88,-0.44589,-0.84917,0.283,33.917,0.34246,-0.45396,-0.82258,4.5328
> view matrix models
> #2.2,0.82698,-0.26986,0.49323,278.14,-0.44589,-0.84917,0.283,45.567,0.34246,-0.45396,-0.82258,19.687
> view matrix models
> #2.2,0.82698,-0.26986,0.49323,278.02,-0.44589,-0.84917,0.283,44.078,0.34246,-0.45396,-0.82258,20.378
> view matrix models
> #2.2,0.82698,-0.26986,0.49323,277.26,-0.44589,-0.84917,0.283,43.474,0.34246,-0.45396,-0.82258,19.847
> select clear
> hide #!4 models
> hide #2.2:1-137
> hide #2.2:1-137 cartoons
> show #!1.2 models
> fitmap #2.2 inMap #1.2
Fit molecule fold_pylori_pfla_pflb_model_0.cif B (#2.2) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 6838 atoms
average map value = 3.316, steps = 96
shifted from previous position = 12.2
rotated from previous position = 12.6 degrees
atoms outside contour = 2362, contour level = 0.78314
Position of fold_pylori_pfla_pflb_model_0.cif B (#2.2) relative to HP-PflA-
PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
0.72134562 -0.34120996 0.60269087 64.14730073
-0.48947677 -0.86681514 0.09510009 36.86395482
0.48997247 -0.36360321 -0.79228765 -49.34849803
Axis -0.92653683 0.22768040 -0.29948477
Axis point 0.00000000 22.22858053 -38.10267412
Rotation angle (degrees) 165.66821959
Shift along axis -36.26251320
> select #8:1-275
7645 atoms, 7771 bonds, 948 residues, 1 model selected
> select #8:1-276
7663 atoms, 7790 bonds, 950 residues, 1 model selected
> view matrix models
> #8,-0.081803,-0.39746,-0.91397,161.81,-0.42733,-0.81448,0.39244,-16.22,-0.90039,0.42267,-0.10322,48.311
> undo
> ui mousemode right "translate selected atoms"
> undo
> select clear
> select #8:1-276
7663 atoms, 7790 bonds, 950 residues, 1 model selected
> show #2.1 models
> hide #8 models
> select add #2.1
14087 atoms, 14339 bonds, 1741 residues, 2 models selected
> select clear
> select #2.1/A:720
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
97 atoms, 97 bonds, 12 residues, 1 model selected
> select up
6424 atoms, 6549 bonds, 791 residues, 1 model selected
> select up
13262 atoms, 13531 bonds, 1635 residues, 2 models selected
> select down
6424 atoms, 6549 bonds, 791 residues, 1 model selected
> ui mousemode right "map eraser"
> volume erase #1.2 center 238.91,8.9647,40.719 radius 119.7 outside true
Opened HP-PflA-PflB-2.1A.mrc copy as #10, grid size 240,240,240, pixel 2.14,
shown at step 1, values float32
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.22265,-0.97427,-0.035071,211.1,0.21968,0.085187,-0.97185,38.401,0.94982,0.20868,0.233,89.342
> view matrix models
> #2.1,0.22265,-0.97427,-0.035071,225.87,0.21968,0.085187,-0.97185,40.116,0.94982,0.20868,0.233,83.644
> view matrix models
> #2.1,0.28295,-0.85523,-0.43419,217.62,0.14836,0.48626,-0.86113,27.999,0.94759,0.17924,0.26447,84.959
> view matrix models
> #2.1,0.28295,-0.85523,-0.43419,240.58,0.14836,0.48626,-0.86113,31.095,0.94759,0.17924,0.26447,82.712
> view matrix models
> #2.1,0.30516,-0.84748,-0.43434,240.77,0.090483,0.47983,-0.87268,29.999,0.94799,0.22701,0.22311,80.654
> fitmap #2.1 inMap #1.2
Fit molecule fold_pylori_pfla_pflb_model_0.cif A (#2.1) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 6424 atoms
average map value = 3.025, steps = 108
shifted from previous position = 12.2
rotated from previous position = 18 degrees
atoms outside contour = 2660, contour level = 0.78314
Position of fold_pylori_pfla_pflb_model_0.cif A (#2.1) relative to HP-PflA-
PflB-2.1A.mrc (#1.2) coordinates:
Matrix rotation and translation
0.11845427 -0.79763237 -0.59139765 13.21575514
-0.13127716 0.57778284 -0.80556396 21.63069805
0.98424331 0.17305950 -0.03627007 6.60123598
Axis 0.49654076 -0.79945964 0.33809993
Axis point 8.33436068 0.00000000 17.05899800
Rotation angle (degrees) 99.78877722
Shift along axis -8.49883154
> view matrix models
> #2.1,0.11845,-0.79763,-0.5914,227.47,-0.13128,0.57778,-0.80556,18.659,0.98424,0.17306,-0.03627,74.679
> show #!1.2 models
> hide #!10 models
> hide #!1.2 models
> show #!10 models
> show #8 models
> mmaker #8 to #2.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_pylori_pflanob_pflc_flgy_model_0.cif, chain A (#8), sequence alignment
score = 3176.4
RMSD between 188 pruned atom pairs is 0.565 angstroms; (across all 611 pairs:
11.355)
> fitmap #8 inMap #10
Fit molecule fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) to map HP-PflA-
PflB-2.1A.mrc copy (#10) using 10870 atoms
average map value = 1.325, steps = 448
shifted from previous position = 5.63
rotated from previous position = 12.7 degrees
atoms outside contour = 7827, contour level = 0.78314
Position of fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) relative to HP-
PflA-PflB-2.1A.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.73780364 -0.29797262 -0.60568814 -40.97742596
-0.67013134 0.43107792 0.60423160 58.29804599
0.08105431 0.85169487 -0.51773165 -26.16309988
Axis 0.30201917 -0.83814211 -0.45420505
Axis point -3.77609840 0.00000000 -32.21009413
Rotation angle (degrees) 155.81517811
Shift along axis -49.35460328
> hide #8 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_campy_flgy_pfla_nosig/fold_campy_flgy_pfla_nosig_model_0.cif"
Chain information for fold_campy_flgy_pfla_nosig_model_0.cif #11
---
Chain | Description
A B | .
C | .
> select clear
> mmaker #11 to #2.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_campy_flgy_pfla_nosig_model_0.cif, chain C (#11), sequence alignment
score = 1295.3
RMSD between 75 pruned atom pairs is 1.084 angstroms; (across all 744 pairs:
42.656)
> hide #11 models
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_4.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_4.cif #12
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_0.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif #13
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_1.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_1.cif #14
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_2.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_2.cif #15
---
Chain | Description
A B | .
C | .
> open "C:/Users/Jack Botting/Documents/alphafold
> results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_3.cif"
Chain information for fold_pylori_flgy_pfla_nosig_model_3.cif #16
---
Chain | Description
A B | .
C | .
> mmaker #13-16 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#13), sequence alignment
score = 4040
RMSD between 606 pruned atom pairs is 1.093 angstroms; (across all 781 pairs:
7.682)
Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
fold_pylori_flgy_pfla_nosig_model_1.cif, chain C (#14), sequence alignment
score = 4023.2
RMSD between 546 pruned atom pairs is 0.909 angstroms; (across all 781 pairs:
20.883)
Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
fold_pylori_flgy_pfla_nosig_model_2.cif, chain C (#15), sequence alignment
score = 4033.4
RMSD between 390 pruned atom pairs is 1.016 angstroms; (across all 781 pairs:
15.670)
Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
fold_pylori_flgy_pfla_nosig_model_3.cif, chain C (#16), sequence alignment
score = 4035.2
RMSD between 425 pruned atom pairs is 0.845 angstroms; (across all 781 pairs:
26.988)
> mmaker #12-16 to #2.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12), sequence alignment
score = 4005.2
RMSD between 146 pruned atom pairs is 1.357 angstroms; (across all 781 pairs:
31.332)
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#13), sequence alignment
score = 4008.2
RMSD between 229 pruned atom pairs is 0.623 angstroms; (across all 781 pairs:
35.568)
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_pylori_flgy_pfla_nosig_model_1.cif, chain C (#14), sequence alignment
score = 4004.6
RMSD between 116 pruned atom pairs is 0.461 angstroms; (across all 781 pairs:
23.485)
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_pylori_flgy_pfla_nosig_model_2.cif, chain C (#15), sequence alignment
score = 4001.6
RMSD between 269 pruned atom pairs is 0.619 angstroms; (across all 781 pairs:
20.809)
Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
fold_pylori_flgy_pfla_nosig_model_3.cif, chain C (#16), sequence alignment
score = 4003.4
RMSD between 186 pruned atom pairs is 0.631 angstroms; (across all 781 pairs:
25.936)
> close #12-16
> show #11 models
> hide #11 models
> hide #!1 models
> show #!1.1 models
> hide #!1 models
> hide #!1.1 models
> show #!1.2 models
> hide #!10 models
> view orient
> show #!1.1 models
> select add #1.1
2 models selected
> show #!5 models
> hide #!5 models
> show #!7 models
> select add #7
171450 atoms, 174330 bonds, 21222 residues, 75 models selected
> view orient
> view matrix models
> #7,1,0,0,-40.839,0,1,0,-3.0251,0,0,1,0,#1.1,1,0,0,-40.839,0,1,0,-3.0251,0,0,1,0
> view matrix models
> #7,1,0,0,-41.712,0,1,0,-3.6426,0,0,1,-18.652,#1.1,1,0,0,-41.712,0,1,0,-3.6426,0,0,1,-18.652
> ui tool show "Side View"
> view orient
> view matrix models
> #7,-0.96983,-0.24379,0,-41.379,0.24379,-0.96983,0,-6.9085,0,0,1,-18.652,#1.1,-0.96983,-0.24379,0,-41.379,0.24379,-0.96983,0,-6.9085,0,0,1,-18.652
> undo
> view orient
> select clear
> syn #2 C18 center #1.1
Unknown command: syn #2 C18 center #1.1
> sym #2 C18 center #1.1
Made 18 graphical clones for fold_pylori_pfla_pflb_model_0.cif A,
fold_pylori_pfla_pflb_model_0.cif B symmetry C18
> hide #!7 models
> show #!7 models
> rename #7 FlgY
> rename #6 pflC
> rename #2.1 pflA
> rename #2.2 pflB
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
112125 atoms, 113781 bonds, 14157 residues, 82 models selected
> view orient
> view matrix models #3,1,0,0,-36.359,0,1,0,0.75258,0,0,1,97.215
> view matrix models #3,1,0,0,-38.617,0,1,0,0.75258,0,0,1,97.215
> hide #!1.2 models
> view matrix models #3,1,0,0,-39.37,0,1,0,-1.5052,0,0,1,97.215
> select clear
> view orient
> hide #!1.1 models
> show #!1.2 models
> sym clear #2.1
> sym #2.1 C18 center #1.1 copies true
Made 18 copies for pflA symmetry C18
> rename #9 "pflA no FlgY"
> hide #!1 models
> rename #1 maps
> hide #9.1-18 target m
> show #9.18 models
> show #9.17 models
> hide #9.17 models
> show #9.14 models
> show #9.10 models
> show #9.7 models
> show #9.3 models
> close #9.1-2,4-6,8-9,11-13,15-17
> show #2.1 models
> hide #!9 models
> show #!1 models
> hide #!7 models
> hide #!1 models
> select # 2.1 1-580
Expected a keyword
> select # 2.1:1-580
4671 atoms, 4761 bonds, 580 residues, 1 model selected
> select clear
> select # 2.1:580-end
1758 atoms, 1792 bonds, 212 residues, 1 model selected
> show #!1 models
> view matrix models
> #2.1,0.12292,-0.74376,-0.65705,224.95,-0.3617,0.58296,-0.72755,15.14,0.92415,0.32709,-0.19736,66.449
> undo
[deleted to fit within ticket limits]
> select subtract #29.7
Nothing selected
> select add #29.7
1 model selected
> select add #29.83
2 models selected
> select add #29.42
3 models selected
> select add #29.82
4 models selected
> select add #29.115
5 models selected
> select add #29.61
6 models selected
> select add #29.111
7 models selected
> select add #29.92
8 models selected
> select add #29.100
9 models selected
> select add #29.10
10 models selected
> select subtract #29.7
9 models selected
> select add #29.7
10 models selected
> select add #29.103
11 models selected
> select add #29.96
12 models selected
> select add #29.101
13 models selected
> select add #29.9
14 models selected
> select add #29.77
15 models selected
> select add #29.98
16 models selected
> select add #29.124
17 models selected
> select add #29.25
18 models selected
Grouped 18 regions
> select add #29.18
2 models selected
> select add #29.65
3 models selected
> select add #29.67
4 models selected
> select add #29.79
5 models selected
> select add #29.27
6 models selected
> select add #29.47
7 models selected
> select add #29.64
8 models selected
> select add #29.146
9 models selected
> select add #29.122
10 models selected
Grouped 10 regions
> select add #29.123
2 models selected
Grouped 2 regions
> select clear
> select #29.58
1 model selected
> select add #29.7
2 models selected
Grouped 2 regions
> select clear
> select #29.7
1 model selected
> select add #29.127
2 models selected
Grouped 2 regions
Opened PflA-2_imasked as #34, grid size 240,240,240, pixel 2.1, shown at step
1, values float32
> select add #32
19762 atoms, 20168 bonds, 2435 residues, 94 models selected
> select subtract #32
92 models selected
> show #!32 models
> show #!33 models
> hide #!33 models
Opened PflA-2_imasked as #35, grid size 240,240,240, pixel 2.1, shown at step
1, values float32
Segmenting PflA-2_imasked, density threshold 0.184695
Showing 69 region surfaces
415 watershed regions, grouped to 69 regions
Showing PflA-2_imasked.seg - 69 regions, 69 surfaces
> hide #!32 models
> close #35
> show #!32 models
> show #!33 models
> select #29.57
1 model selected
> select add #29.65
2 models selected
> select add #29.10
3 models selected
> select add #29.43
4 models selected
> select add #29.1
5 models selected
> select add #29.46
6 models selected
> select add #29.17
7 models selected
> select add #29.45
8 models selected
> select add #29.26
9 models selected
> select subtract #29.26
8 models selected
> select add #29.26
9 models selected
> select subtract #29.26
8 models selected
> select add #29.24
9 models selected
> select add #29.25
10 models selected
> show #!28 models
> select add #29.52
11 models selected
> select add #29.15
12 models selected
> select add #29.39
13 models selected
> select add #29.29
14 models selected
> select add #28.2
4995 atoms, 5088 bonds, 612 residues, 15 models selected
> select subtract #28.2
15 models selected
Grouped 14 regions
> select clear
> select #29.1
1 model selected
> select clear
> select add #28.2
4995 atoms, 5088 bonds, 612 residues, 1 model selected
> select add #28.4
11824 atoms, 12060 bonds, 1455 residues, 3 models selected
> select add #28.6
18653 atoms, 19032 bonds, 2298 residues, 5 models selected
> select add #28.7
19762 atoms, 20168 bonds, 2435 residues, 7 models selected
> show sel surfaces
> select add #28
38799 atoms, 39588 bonds, 4776 residues, 14 models selected
> select subtract #28
4 models selected
Showing 56 region surfaces
> select #29.1
1 model selected
> select add #29.19
2 models selected
> select add #29.23
3 models selected
> select add #29.49
4 models selected
> select add #29.18
5 models selected
> select add #29.33
6 models selected
> select add #29.20
7 models selected
> select add #29.27
8 models selected
> select add #29.6
9 models selected
> select add #29.21
10 models selected
> select add #29.4
11 models selected
> select add #29.30
12 models selected
> select add #29.50
13 models selected
> select add #29.62
14 models selected
> select add #29.36
15 models selected
> select add #29.22
16 models selected
> select add #29.11
17 models selected
> select add #29.47
18 models selected
> select add #29.61
19 models selected
> select add #29.12
20 models selected
> select add #29.41
21 models selected
> select add #29.64
22 models selected
> select add #29.34
23 models selected
> select add #29.53
24 models selected
> select add #29.40
25 models selected
> select add #29.55
26 models selected
> select add #29.51
27 models selected
> select add #29.32
28 models selected
> select add #29.56
29 models selected
> select subtract #29.32
28 models selected
> select subtract #29.56
27 models selected
Grouped 27 regions
> select #29.32
1 model selected
> select add #29.56
2 models selected
> select add #29.48
3 models selected
> select add #29.54
4 models selected
> select add #29.35
5 models selected
> select add #29.59
6 models selected
> select add #29.44
7 models selected
> select add #29.60
8 models selected
> select add #29.28
9 models selected
> select add #29.1
10 models selected
> select add #32
19762 atoms, 20168 bonds, 2435 residues, 15 models selected
> select subtract #32
13 models selected
> select add #30
12 models selected
> select subtract #30
10 models selected
> select add #30
12 models selected
> select subtract #30
10 models selected
> select clear
> hide #!30 models
> hide #!29 models
> show #!11 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!11 models
> show #!11 models
> close #11
> close #34
Segmenting PflA-2.1A-230911.mrc, density threshold 0.184695
Showing 295 region surfaces
3349 watershed regions, grouped to 295 regions
Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces
Drag select of 4907, 27032 of 27220 triangles, 4951, 22300 of 23188 triangles,
4720, 4945, 4668, 15469 of 19220 triangles, 4957, 4679, 20000 of 20372
triangles, 4765, 2043 of 18048 triangles, 4933, 4931, 15275 of 19404
triangles, 4666, 18478 of 18596 triangles, 4903, 17730 of 18084 triangles,
4921, 13998 of 18508 triangles, 4922, 15563 of 16240 triangles, 4902, 4721,
4913, 11549 of 15704 triangles, 4896, 4956, 4898, 4958, 13764 of 18276
triangles, 4919, 4784, 3146 of 14912 triangles, 4946, 4719, 13132 of 16136
triangles, 4763, 3540 of 14720 triangles, 4953, 4938, 4891, 15577 of 16352
triangles, 4966, 4673, 4892, 4795, 4793, 4914, 4889, 4928, 4776, 9889 of 12868
triangles, 4909, 4916, 12248 of 13012 triangles, 4759, 12515 of 12864
triangles, 4860, 4934, 4965, 4963, 4739, 10306 of 13180 triangles, 4814, 4927,
4948, 4830, 12374 of 12536 triangles, 4875, 10999 of 12580 triangles, 4910,
4778, 11924 of 12092 triangles, 4835, 12818 of 12820 triangles, 4943, 4761,
4941, 4917, 4936, 4783, 774 of 10748 triangles, 4856, 9392 of 11748 triangles,
4838, 4662, 4695, 4920, 4833, 4901, 9358 of 10760 triangles, 4935, 4753, 4952,
4096, 9615 of 9676 triangles, 4961, 4742, 4722, 4915, 4710, 8928 of 9776
triangles, 4817, 6437 of 8508 triangles, 4735, 4746, 4877, 4791, 9178 of 9200
triangles, 4754, 4713, 8651 of 8944 triangles, 4467, 6529 of 8108 triangles,
4699, 7813 of 7876 triangles, 4857, 6662 of 9600 triangles, 4714, 4749, 4809,
7878 of 7880 triangles, 4290, 7135 of 8912 triangles, 4700, 4319, 4874, 4282,
4832, 6638 of 7408 triangles, 4866, 4845, 7538 of 7556 triangles, 4522, 7676
of 7912 triangles, 4844, 7211 of 7216 triangles, 4750, 1129 of 5968 triangles,
4546, 4885 of 6700 triangles, 4327, 4140, 4876, 4769 of 6004 triangles, 4634,
3407, 4459, 4627
> select add #11.145
109 models selected
> select add #11.4
110 models selected
> select add #11.3
111 models selected
> select add #11.139
112 models selected
> select add #11.256
113 models selected
> select add #11.179
114 models selected
> select add #11.224
115 models selected
> select add #11.232
116 models selected
> select add #11.147
117 models selected
> select add #11.198
118 models selected
> select add #11.230
119 models selected
> select add #11.233
120 models selected
> select add #11.158
121 models selected
> select add #11.114
122 models selected
> select add #11.201
123 models selected
> select add #11.97
124 models selected
> select add #11.281
125 models selected
> select add #11.289
126 models selected
Drag select of 4767, 9531 of 11416 triangles, 4829, 10271 of 10404 triangles,
4855, 6857 of 10016 triangles, 4824, 4501, 4316, 4799, 5684 of 8332 triangles,
4110, 4486 of 7504 triangles, 3420, 4692 of 5904 triangles, 4519, 4404, 791 of
6452 triangles, 4139, 3370, 4294, 1508 of 4868 triangles, 4159, 1394 of 4036
triangles, 160, 2191 of 2876 triangles
> select add #11.1
143 models selected
> select add #11.113
144 models selected
> select add #11.100
145 models selected
> select add #11.130
146 models selected
> select add #11.191
147 models selected
> select add #11.129
148 models selected
> select add #11.106
149 models selected
> select add #11.119
150 models selected
> select add #11.254
151 models selected
> select add #11.140
152 models selected
> select add #11.6
153 models selected
> select add #11.105
154 models selected
> select add #11.287
155 models selected
> select add #11.2
156 models selected
> select add #11.195
157 models selected
> select add #11.101
158 models selected
> select add #11.213
159 models selected
> select add #11.286
160 models selected
> select add #11.150
161 models selected
> select add #11.243
162 models selected
> select add #11.199
163 models selected
> select add #11.95
164 models selected
> select add #11.197
165 models selected
> select add #11.48
166 models selected
> select add #11.177
167 models selected
> select add #11.265
168 models selected
> select add #11.54
169 models selected
> select add #11.20
170 models selected
> select add #11.8
171 models selected
> select add #11.53
172 models selected
> select add #11.10
173 models selected
> select add #11.27
174 models selected
> select add #11.117
175 models selected
> select add #11.205
176 models selected
> select add #11.173
177 models selected
> select add #11.168
178 models selected
> select add #11.262
179 models selected
> select add #11.169
180 models selected
> select add #11.141
181 models selected
> select add #11.204
182 models selected
> select add #11.273
183 models selected
> select add #11.103
184 models selected
> select add #11.186
185 models selected
> select add #11.290
186 models selected
> select add #11.245
187 models selected
> select add #11.151
188 models selected
> select add #11.11
189 models selected
> select add #11.133
190 models selected
> select add #11.284
191 models selected
> select add #11.208
192 models selected
> select add #11.170
193 models selected
> select add #11.217
194 models selected
> select add #11.268
195 models selected
> select add #11.43
196 models selected
> select add #11.248
197 models selected
> select add #11.162
198 models selected
> select add #11.138
199 models selected
> select add #11.266
200 models selected
> select add #11.291
201 models selected
> select add #11.50
202 models selected
> select add #11.90
203 models selected
> select add #11.255
204 models selected
> select add #11.148
205 models selected
> select add #11.52
206 models selected
> select add #11.222
207 models selected
> select add #11.267
208 models selected
> select add #11.74
209 models selected
> select add #11.270
210 models selected
> select add #11.178
211 models selected
> select add #11.278
212 models selected
> select add #11.57
213 models selected
Grouped 213 regions
> select #11.1
1 model selected
> hide #!26 models
> select clear
> select #11.1
1 model selected
Opened PflA-2.1A-230911_imasked as #29, grid size 240,240,240, pixel 2.1,
shown at step 1, values float32
Segmenting PflA-2.1A-230911_imasked, density threshold 0.184695
Showing 81 region surfaces
463 watershed regions, grouped to 81 regions
Showing PflA-2.seg - 81 regions, 81 surfaces
> hide #!29 models
> select add #11.64
1 model selected
> select add #11.79
2 models selected
> select add #11.50
3 models selected
> select add #11.4
4 models selected
> select add #11.29
5 models selected
> select add #11.20
6 models selected
> select add #11.6
7 models selected
> select add #11.21
8 models selected
> select add #11.36
9 models selected
> select add #11.11
10 models selected
> select add #11.66
11 models selected
> select add #11.76
12 models selected
> select add #11.80
13 models selected
> select add #11.81
14 models selected
> select add #11.49
15 models selected
> select add #11.17
16 models selected
> select add #11.32
17 models selected
> select add #11.26
18 models selected
> select add #11.19
19 models selected
> select add #11.41
20 models selected
> select add #11.18
21 models selected
> select add #11.22
22 models selected
> select add #11.52
23 models selected
> select add #11.14
24 models selected
> select add #11.39
25 models selected
> select add #11.28
26 models selected
> select add #11.47
27 models selected
> select add #11.46
28 models selected
> select add #11.25
29 models selected
> select add #11.23
30 models selected
> select add #11.24
31 models selected
> select add #11.16
32 models selected
> select add #11.1
33 models selected
> select add #11.44
34 models selected
> select add #11.34
35 models selected
> select add #11.57
36 models selected
> select add #11.69
37 models selected
> select add #11.72
38 models selected
Grouped 38 regions
> select #11.42
1 model selected
> select add #11.68
2 models selected
> select add #11.70
3 models selected
> select add #11.33
4 models selected
> select add #11.53
5 models selected
> select add #11.60
6 models selected
> select add #11.9
7 models selected
> select add #11.51
8 models selected
> select add #11.55
9 models selected
> select add #11.31
10 models selected
> select add #11.56
11 models selected
> select add #11.75
12 models selected
> select add #11.48
13 models selected
> select add #11.54
14 models selected
> select add #11.78
15 models selected
> select add #11.35
16 models selected
> select add #11.59
17 models selected
> select add #11.62
18 models selected
> select add #11.73
19 models selected
> select add #11.45
20 models selected
> select add #11.61
21 models selected
> select add #11.63
22 models selected
> select add #11.27
23 models selected
> select add #11.65
24 models selected
> select subtract #11.27
23 models selected
Grouped 23 regions
> select clear
> select #11.27
1 model selected
Ungrouped to 6 regions
Ungrouped to 9 regions
Ungrouped to 0 regions
> select #11.4
1 model selected
> select add #11.20
2 models selected
> select add #11.19
3 models selected
> select add #11.16
4 models selected
> select add #11.26
5 models selected
> select add #11.25
6 models selected
Grouped 6 regions
> select add #11.1
2 models selected
Opened PflA-2_imasked as #34, grid size 240,240,240, pixel 2.1, shown at step
1, values float32
> hide #!11 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3xOnly-PflAB.mrc
> models #34
> view orient
> select add #11
28 models selected
> select subtract #11
Nothing selected
> select add #28
38799 atoms, 39588 bonds, 4776 residues, 10 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #28.4/Ch:1-3 #28.6/Cj:1-3 #28.8/Cl:1-3
72 atoms, 69 bonds, 9 residues, 3 models selected
> select #28.4/Ch:1-135 #28.6/Cj:1-135 #28.8/Cl:1-135
3153 atoms, 3177 bonds, 405 residues, 3 models selected
2 [ID: 2] region chains Ch,Cj,Cl [1-135] RMSD: 178.301
> hide sel & #!28.4,6 surfaces
> hide sel & #!28.4,6 cartoons
> select add #28
38799 atoms, 39588 bonds, 4776 residues, 12 models selected
> select subtract #28
4 models selected
> select add #32
19762 atoms, 20168 bonds, 2435 residues, 5 models selected
Alignment identifier is 32.1/BJ
Alignment identifier is 1
Alignment identifier is 32.4/Ck
> select #32.2/Ch:1-2 #32.3/Cj:1-2
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #32.2/Ch:1-135 #32.3/Cj:1-135
2102 atoms, 2118 bonds, 270 residues, 2 models selected
1 [ID: 1] region chains Ch,Cj [1-135] RMSD: 127.364
> hide sel & #!32.3 surfaces
> hide sel & #!32.3 cartoons
> select add #32
19762 atoms, 20168 bonds, 2435 residues, 6 models selected
> select subtract #32
3 models selected
> select add #33
19762 atoms, 20168 bonds, 2435 residues, 5 models selected
Alignment identifier is 33.1/BJ
Alignment identifier is 1
Alignment identifier is 33.4/Ck
> select #33.2/Ch:1-4 #33.3/Cj:1-4
66 atoms, 64 bonds, 8 residues, 2 models selected
> select #33.2/Ch:1-135 #33.3/Cj:1-135
2102 atoms, 2118 bonds, 270 residues, 2 models selected
1 [ID: 1] region chains Ch,Cj [1-135] RMSD: 127.364
> hide sel & #!33.2 surfaces
> hide sel & #!33.2 cartoons
> select add #33
19762 atoms, 20168 bonds, 2435 residues, 6 models selected
> select subtract #33
3 models selected
> show #!19 models
> hide #!19 models
> color #34 #72727233 models
> save /Users/shoichi/Desktop/HP-Fig4C1_09172024.png supersample 2
> transparentBackground true
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Sep18-2024_Figure4_PflAB.cxs includeMaps true
——— End of log from Wed Sep 18 14:12:12 2024 ———
opened ChimeraX session
Showing PflA-2.seg - 27 regions, 27 surfaces
> open /Users/shoichitachiyama/Desktop/PflAB-working/PilNO_BasedonJack.pdb
Summary of feedback from opening /Users/shoichitachiyama/Desktop/PflAB-
working/PilNO_BasedonJack.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10
End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
1 9
Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
1 4
Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
1 3
2 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
0
Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
0
Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
107 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
133 0
Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
145 0
9 messages similar to the above omitted
Chain information for PilNO_BasedonJack.pdb
---
Chain | Description
35.1/A 35.2/A 35.3/A 35.4/A 35.5/A 35.6/A 35.7/A 35.8/A 35.9/A 35.10/A 35.11/A 35.12/A 35.13/A 35.14/A 35.15/A 35.16/A 35.17/A 35.18/A 35.19/A 35.20/A 35.21/A 35.22/A 35.23/A 35.24/A 35.25/A 35.26/A 35.27/A 35.28/A 35.29/A 35.30/A 35.31/A 35.32/A 35.33/A 35.34/A 35.35/A 35.36/A | No description available
35.1/B 35.2/B 35.3/B 35.4/B 35.5/B 35.6/B 35.7/B 35.8/B 35.9/B 35.10/B 35.11/B 35.12/B 35.13/B 35.14/B 35.15/B 35.16/B 35.17/B 35.18/B 35.19/B 35.20/B 35.21/B 35.22/B 35.23/B 35.24/B 35.25/B 35.26/B 35.27/B 35.28/B 35.29/B 35.30/B 35.31/B 35.32/B 35.33/B 35.34/B 35.35/B 35.36/B | No description available
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!34 models
> select add #35
99720 atoms, 101844 bonds, 12096 residues, 37 models selected
> view matrix models #35,1,0,0,-194.18,0,1,0,-6.2337,0,0,1,91.174
> view matrix models #35,1,0,0,-285.64,0,1,0,-11.679,0,0,1,-43.763
> view matrix models #35,1,0,0,-214.82,0,1,0,-18.415,0,0,1,-85.478
> view orient
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.99774,-0.067158,0,-215.16,0.067158,0.99774,0,-15.677,0,0,1,-85.478
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 2 time(s)]
> turn y -5
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.99774,-0.067158,0,-214.96,0.067158,0.99774,0,-16.788,0,0,1,-85.493
> undo
[Repeated 1 time(s)]
> view matrix models
> #35,0.99774,-0.067158,0,-215.17,0.067158,0.99774,0,-15.572,0,0,1,-83.066
> undo
> select subtract #35
Nothing selected
Drag select of 21 residues
> select add #35
99720 atoms, 101844 bonds, 12096 residues, 37 models selected
> select subtract #35
Nothing selected
> select add #35.1
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> view matrix models
> #35.1,1,-4.5797e-16,0,-0.024183,-3.1919e-16,1,0,1.2055,0,0,1,11.442
> select add #35.3
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> undo
[Repeated 1 time(s)]
> select add #35.3
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> view matrix models
> #35.1,1,-4.5797e-16,0,-0.020861,-3.1919e-16,1,0,1.0399,0,0,1,12.824,#35.3,1,-4.5797e-16,0,-0.020861,-3.1919e-16,1,0,1.0399,0,0,1,12.824
> ui mousemode right "rotate selected models"
> select add #35.2
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select add #35.4
11080 atoms, 11316 bonds, 1344 residues, 4 models selected
> select subtract #35.4
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select add #35.36
11080 atoms, 11316 bonds, 1344 residues, 4 models selected
> select subtract #35.1
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select subtract #35.3
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> view matrix models
> #35.2,0.99902,0.0443,0.0021133,1.0714,-0.044301,0.99902,2.5893e-05,14.147,-0.0021101,-0.00011949,1,0.67259,#35.36,0.99902,0.0443,0.0021133,1.0714,-0.044301,0.99902,2.5893e-05,14.147,-0.0021101,-0.00011949,1,0.67259
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,1,-4.5797e-16,0,0.13308,-3.1919e-16,1,0,-6.6339,0,0,1,0.0024963,#35.36,1,-4.5797e-16,0,0.13308,-3.1919e-16,1,0,-6.6339,0,0,1,0.0024963
> select add #35.1
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select add #35.3
11080 atoms, 11316 bonds, 1344 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #35.1,1,2.1533e-05,-0.00092923,-0.044253,2.1533e-05,0.99893,0.046321,2.2059,0.00092923,-0.046321,0.99893,13.094,#35.2,1,2.1533e-05,-0.00092923,0.12144,2.1533e-05,0.99893,0.046321,-6.0535,0.00092923,-0.046321,0.99893,0.64234,#35.3,1,2.1533e-05,-0.00092923,-0.044253,2.1533e-05,0.99893,0.046321,2.2059,0.00092923,-0.046321,0.99893,13.094,#35.36,1,2.1533e-05,-0.00092923,0.12144,2.1533e-05,0.99893,0.046321,-6.0535,0.00092923,-0.046321,0.99893,0.64234
> ui mousemode right "translate selected models"
> view matrix models
> #35.1,1,2.1533e-05,-0.00092923,0.03946,2.1533e-05,0.99893,0.046321,-1.9671,0.00092923,-0.046321,0.99893,13.14,#35.2,1,2.1533e-05,-0.00092923,0.20515,2.1533e-05,0.99893,0.046321,-10.226,0.00092923,-0.046321,0.99893,0.68811,#35.3,1,2.1533e-05,-0.00092923,0.03946,2.1533e-05,0.99893,0.046321,-1.9671,0.00092923,-0.046321,0.99893,13.14,#35.36,1,2.1533e-05,-0.00092923,0.20515,2.1533e-05,0.99893,0.046321,-10.226,0.00092923,-0.046321,0.99893,0.68811
> select subtract #35.1
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select add #35.1
11080 atoms, 11316 bonds, 1344 residues, 4 models selected
> select subtract #35.2
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select subtract #35.3
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> select subtract #35.36
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> view matrix models
> #35.1,1,2.1533e-05,-0.00092923,-0.019077,2.1533e-05,0.99893,0.046321,0.95098,0.00092923,-0.046321,0.99893,12.86
> ui mousemode right "rotate selected models"
> view matrix models
> #35.1,1,0.00021329,-0.0029175,-0.051694,0.00021329,0.98937,0.14543,2.5769,0.0029175,-0.14543,0.98936,10.424
> ui mousemode right "translate selected models"
> view matrix models
> #35.1,1,0.00021329,-0.0029175,0.092404,0.00021329,0.98937,0.14543,-4.6062,0.0029175,-0.14543,0.98936,10.55
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> select add #35.36
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> select add #35.2
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select subtract #35.1
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> view matrix models
> #35.2,1,2.1533e-05,-0.00092923,0.21989,2.1533e-05,0.99893,0.046321,-10.961,0.00092923,-0.046321,0.99893,-3.0682,#35.36,1,2.1533e-05,-0.00092923,0.21989,2.1533e-05,0.99893,0.046321,-10.961,0.00092923,-0.046321,0.99893,-3.0682
> ui mousemode right "rotate selected models"
> view matrix models
> #35.2,1,4.9594e-05,-0.0014097,0.21159,4.9594e-05,0.99753,0.070273,-10.547,0.0014097,-0.070273,0.99753,-3.6353,#35.36,1,4.9594e-05,-0.0014097,0.21159,4.9594e-05,0.99753,0.070273,-10.547,0.0014097,-0.070273,0.99753,-3.6353
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,1,4.9594e-05,-0.0014097,0.24923,4.9594e-05,0.99753,0.070273,-12.424,0.0014097,-0.070273,0.99753,-3.2204,#35.36,1,4.9594e-05,-0.0014097,0.24923,4.9594e-05,0.99753,0.070273,-12.424,0.0014097,-0.070273,0.99753,-3.2204
> ui mousemode right "rotate selected models"
> view matrix models
> #35.2,1,3.1046e-05,-0.0011156,0.25428,3.1046e-05,0.99845,0.055613,-12.676,0.0011156,-0.055613,0.99845,-2.872,#35.36,1,3.1046e-05,-0.0011156,0.25428,3.1046e-05,0.99845,0.055613,-12.676,0.0011156,-0.055613,0.99845,-2.872
> select clear
> view orient
> select add #35.36
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> view matrix models
> #35.36,0.98258,0.18562,0.0092411,20.981,-0.18585,0.98105,0.054851,45.312,0.0011156,-0.055613,0.99845,-2.872
> ui mousemode right "translate selected models"
> view matrix models
> #35.36,0.98258,0.18562,0.0092411,18.323,-0.18585,0.98105,0.054851,52.797,0.0011156,-0.055613,0.99845,-2.872
> view orient
> turn x 90
[Repeated 2 time(s)]
> ui mousemode right "rotate selected models"
> view matrix models
> #35.36,0.97614,0.19112,-0.10312,18.735,-0.18541,0.98068,0.062414,52.77,0.11305,-0.041806,0.99271,-37.639
> ui mousemode right "translate selected models"
> view matrix models
> #35.36,0.97614,0.19112,-0.10312,22.709,-0.18541,0.98068,0.062414,52.502,0.11305,-0.041806,0.99271,-38.602
> ui mousemode right "rotate selected models"
> view matrix models
> #35.36,0.96838,0.22992,-0.096834,28.434,-0.22377,0.9721,0.070386,64.217,0.11032,-0.046492,0.99281,-38.104
> select clear
> view orient
> select add #35.1
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> view matrix models
> #35.1,0.99979,-0.0031958,0.020403,0.53893,0.00022735,0.9896,0.14386,-4.6363,-0.020651,-0.14383,0.98939,18.256
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #35.1,1,0.00021329,-0.0029175,4.4471,0.00021329,0.98937,0.14543,-4.7021,0.0029175,-0.14543,0.98936,10.55
> ui mousemode right "rotate selected models"
> view matrix models
> #35.1,0.99926,0.0054454,-0.038076,4.1178,0.00041041,0.98836,0.15212,-4.6582,0.038461,-0.15203,0.98763,-1.1709
> select clear
> view orient
> select add #35.2
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,1,3.1046e-05,-0.0011156,1.8164,3.1046e-05,0.99845,0.055613,-10.884,0.0011156,-0.055613,0.99845,-2.872
> view matrix models
> #35.2,1,3.1046e-05,-0.0011156,2.5229,3.1046e-05,0.99845,0.055613,-9.4142,0.0011156,-0.055613,0.99845,-2.872
> ui mousemode right "rotate selected models"
> view matrix models
> #35.2,0.99952,0.001647,-0.031015,2.0382,-5.4393e-05,0.99868,0.051281,-9.4793,0.031058,-0.051255,0.9982,-12.711
> view orient
> turn x 90
[Repeated 1 time(s)]
> view matrix models
> #35.2,0.9562,0.022538,-0.29185,10.014,0.035394,0.98081,0.19171,-17.324,0.29057,-0.19364,0.93706,-89.809
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,0.99952,0.001647,-0.031015,11.277,-5.4393e-05,0.99868,0.051281,-9.0099,0.031058,-0.051255,0.9982,-12.711
> ui mousemode right "rotate selected models"
> view matrix models
> #35.2,0.98158,0.010537,-0.19077,13.606,0.0010351,0.99817,0.06046,-9.1624,0.19106,-0.059544,0.97977,-63.98
> view matrix models
> #35.2,0.98094,0.0036026,-0.19427,14.102,0.020936,0.99205,0.12411,-14.05,0.19317,-0.12581,0.97307,-61.37
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,0.98094,0.0036026,-0.19427,14.426,0.020936,0.99205,0.12411,-13.996,0.19317,-0.12581,0.97307,-58.362
> ui mousemode right "rotate selected models"
> view matrix models
> #35.2,0.98062,0.00071125,-0.19589,14.647,0.029482,0.98807,0.15117,-16.031,0.19366,-0.15402,0.9689,-57.147
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,0.98062,0.00071125,-0.19589,15.024,0.029482,0.98807,0.15117,-17.691,0.19366,-0.15402,0.9689,-54.342
> ui mousemode right "rotate selected models"
> view matrix models
> #35.2,0.98017,-0.0029887,-0.19814,15.318,0.040647,0.98166,0.18627,-20.292,0.19394,-0.19063,0.96231,-52.669
> ui mousemode right "translate selected models"
> view matrix models
> #35.2,0.98017,-0.0029887,-0.19814,15.438,0.040647,0.98166,0.18627,-20.68,0.19394,-0.19063,0.96231,-51.725
> select clear
> select add #35.1
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> view matrix models
> #35.1,0.99926,0.0054454,-0.038076,7.3317,0.00041041,0.98836,0.15212,-5.6519,0.038461,-0.15203,0.98763,-2.0768
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #35.1,0.99399,0.0011476,-0.10945,7.6508,0.016586,0.98682,0.16098,-10.783,0.10819,-0.16183,0.98087,-25.082
> ui mousemode right "translate selected models"
> view matrix models
> #35.1,0.99399,0.0011476,-0.10945,8.2279,0.016586,0.98682,0.16098,-10.799,0.10819,-0.16183,0.98087,-25.272
> select subtract #35.1
Nothing selected
> select add #35.3
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #35.3,0.99599,-0.010439,-0.088891,0.83153,0.013601,0.99929,0.035045,-6.3675,0.088462,-0.036113,0.99542,-14.84
> ui mousemode right "translate selected models"
> view matrix models
> #35.3,0.99599,-0.010439,-0.088891,8.0585,0.013601,0.99929,0.035045,-3.6041,0.088462,-0.036113,0.99542,-16.656
> ui mousemode right "rotate selected models"
> view matrix models
> #35.3,0.98573,-0.032695,-0.16512,12.332,0.051335,0.99261,0.10992,-12.972,0.1603,-0.11683,0.98013,-29.611
> ui mousemode right "translate selected models"
> view matrix models
> #35.3,0.98573,-0.032695,-0.16512,15.715,0.051335,0.99261,0.10992,-19.238,0.1603,-0.11683,0.98013,-29.068
> view matrix models
> #35.3,0.98573,-0.032695,-0.16512,19.72,0.051335,0.99261,0.10992,-20.301,0.1603,-0.11683,0.98013,-29.236
> view matrix models
> #35.3,0.98573,-0.032695,-0.16512,24.649,0.051335,0.99261,0.10992,-19.666,0.1603,-0.11683,0.98013,-24.674
> view matrix models
> #35.3,0.98573,-0.032695,-0.16512,23.586,0.051335,0.99261,0.10992,-17.105,0.1603,-0.11683,0.98013,-23.963
> ui mousemode right "rotate selected models"
> view matrix models
> #35.3,0.98449,-0.036221,-0.17167,24.249,0.057551,0.99099,0.12095,-18.612,0.16574,-0.12895,0.9777,-24.276
> ui mousemode right "translate selected models"
> view matrix models
> #35.3,0.98449,-0.036221,-0.17167,23.824,0.057551,0.99099,0.12095,-17.343,0.16574,-0.12895,0.9777,-23.641
> select clear
> select add #35.1
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> select add #35.2
5540 atoms, 5658 bonds, 672 residues, 2 models selected
> select add #35.3
8310 atoms, 8487 bonds, 1008 residues, 3 models selected
> select add #35.36
11080 atoms, 11316 bonds, 1344 residues, 4 models selected
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Four_Cage-
> based_Jack.pdb selectedOnly true
> select add #35
99720 atoms, 101844 bonds, 12096 residues, 37 models selected
> select subtract #35
Nothing selected
> hide #!35 models
> show #!35 models
> hide #!35 models
> open /Users/shoichitachiyama/Desktop/PflAB-working/Four_Cage-based_Jack.pdb
Summary of feedback from opening /Users/shoichitachiyama/Desktop/PflAB-
working/Four_Cage-based_Jack.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14
Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
1 14
Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
1 15
Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
1 14
Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
1 14
163 messages similar to the above omitted
Chain information for Four_Cage-based_Jack.pdb
---
Chain | Description
36.1/A 36.2/A 36.3/A 36.4/A | No description available
36.1/B 36.2/B 36.3/B 36.4/B | No description available
> color #36 #6c93d5ff models
> color #36 #4a9ed2ff models
> color #36 #0071bfff models
> color #36 #23a0d0ff models
Cell requested for row 0 is out of bounds for table with 40 rows! Resizing
table model.
> select clear
> select add #36
11080 atoms, 11316 bonds, 1344 residues, 5 models selected
> show sel surfaces
> select clear
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review.cxs includeMaps true
> show #!1 models
> show #!22 models
> hide #!1 models
> select add #28.2
4995 atoms, 5088 bonds, 612 residues, 1 model selected
> hide #!32 models
> hide #!33 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #28.2,0.99197,0.041941,0.11934,-7.0023,-0.0085891,0.96359,-0.26725,-10.025,-0.12621,0.26407,0.95621,-8.352
> ui mousemode right "rotate selected models"
> view matrix models
> #28.2,0.99703,0.028694,0.071415,-8.4791,-0.0085891,0.96359,-0.26725,-10.025,-0.076483,0.26584,0.96098,-7.9347
> ui mousemode right "translate selected models"
> view matrix models
> #28.2,0.99703,0.028694,0.071415,-8.4494,-0.0085891,0.96359,-0.26725,-10.025,-0.076483,0.26584,0.96098,-8.2276
> select clear
> select add #28.7
1109 atoms, 1136 bonds, 137 residues, 1 model selected
> hide sel surfaces
> view orient
> view matrix models
> #28.7,0.99197,0.041941,0.11934,-8.4438,-0.0085891,0.96359,-0.26725,-17.049,-0.12621,0.26407,0.95621,-12.202
> ui mousemode right "rotate selected models"
> view matrix models
> #28.7,0.9694,-0.17177,0.17539,16.725,0.21056,0.94908,-0.23431,-36.827,-0.12621,0.26407,0.95621,-12.202
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #28.7,0.9694,-0.17177,0.17539,16.054,0.21056,0.94908,-0.23431,-36.403,-0.12621,0.26407,0.95621,-12.202
> select clear
> select add #28.7
1109 atoms, 1136 bonds, 137 residues, 1 model selected
> show sel surfaces
> select clear
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review.cxs includeMaps true
——— End of log from Wed Dec 4 20:28:30 2024 ———
opened ChimeraX session
Showing PflA-2.seg - 27 regions, 27 surfaces
> hide #!11 models
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/2xMotB.mrc
Opened 2xMotB.mrc as #37, grid size 240,240,240, pixel 2.1, shown at level
0.000313, step 1, values float32
> surface dust #37 size 12.6
> surface dust #37 size 50
> color #37 #b2b2b2ff models
> hide #!22 models
> show #!22 models
> hide #!19 models
> show #!19 models
> color #37 #72727233 models
> select clear
> show #!21 models
> select add #22
21694 atoms, 22006 bonds, 2748 residues, 13 models selected
> select subtract #22
13 models selected
> select add #19
2 models selected
> select subtract #19
Nothing selected
> select add #22.1
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> select add #22.2
10404 atoms, 10572 bonds, 1348 residues, 3 models selected
> select subtract #22.2
9605 atoms, 9765 bonds, 1250 residues, 3 models selected
> select subtract #22.1
1 model selected
> select add #22.22
4099 atoms, 4171 bonds, 518 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select add #22
21694 atoms, 22006 bonds, 2748 residues, 15 models selected
> ombine #22 modelId #38 name Modified_Stator
Unknown command: ombine #22 modelId #38 name Modified_Stator
> select subtract #22
13 models selected
> hide #!22 models
> show #!22 models
> combine #22 modelId #38 name Modified_Stator
Remapping chain ID 'K' in Stator-complexb.pdb #22.22 to 'M'
Remapping chain ID 'L' in Stator-complexb.pdb #22.22 to 'N'
Remapping chain ID ' ' in Stator-complexb.pdb #22.1 to 'A'
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/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> select add #22
21694 atoms, 22006 bonds, 2748 residues, 13 models selected
> select subtract #22
13 models selected
> select add #22.22
4099 atoms, 4171 bonds, 518 residues, 1 model selected
> select add #22.1
13704 atoms, 13936 bonds, 1768 residues, 4 models selected
> select add #22.2
14503 atoms, 14743 bonds, 1866 residues, 6 models selected
> select add #22.3
15302 atoms, 15550 bonds, 1964 residues, 8 models selected
> select add #22.4
16101 atoms, 16357 bonds, 2062 residues, 10 models selected
> select add #22.5
16900 atoms, 17164 bonds, 2160 residues, 12 models selected
> select add #22.6
17699 atoms, 17971 bonds, 2258 residues, 14 models selected
> select add #22.7
18498 atoms, 18778 bonds, 2356 residues, 16 models selected
> select add #22.8
19297 atoms, 19585 bonds, 2454 residues, 18 models selected
> select add #22.9
20096 atoms, 20392 bonds, 2552 residues, 20 models selected
> select add #22.10
20895 atoms, 21199 bonds, 2650 residues, 22 models selected
> select add #22
21694 atoms, 22006 bonds, 2748 residues, 25 models selected
> select subtract #22
13 models selected
> select add #22
21694 atoms, 22006 bonds, 2748 residues, 13 models selected
> hide sel surfaces
> show sel cartoons
> view orient
> view matrix models #22,1,0,0,-14.544,0,1,0,106.39,0,0,1,-1.9686
> undo
> select subtract #22
13 models selected
> select add #22.1
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> select subtract #22.1
1 model selected
> select add #22.2
799 atoms, 807 bonds, 98 residues, 1 model selected
> select add #22.3
1598 atoms, 1614 bonds, 196 residues, 3 models selected
> select add #22.4
2397 atoms, 2421 bonds, 294 residues, 5 models selected
> select add #22.5
3196 atoms, 3228 bonds, 392 residues, 7 models selected
> select add #22.6
3995 atoms, 4035 bonds, 490 residues, 9 models selected
> select add #22.7
4794 atoms, 4842 bonds, 588 residues, 11 models selected
> select add #22.8
5593 atoms, 5649 bonds, 686 residues, 13 models selected
> select add #22.9
6392 atoms, 6456 bonds, 784 residues, 15 models selected
> select add #22.10
7191 atoms, 7263 bonds, 882 residues, 17 models selected
> select add #22.11
7990 atoms, 8070 bonds, 980 residues, 19 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models
> #22.2,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.3,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.4,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.5,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.6,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.7,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.8,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.9,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.10,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0,#22.11,1,0,0,0.22417,0,1,0,0.25293,0,0,1,0
> undo
> ui mousemode right "rotate selected models"
> view matrix models
> #22.2,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.3,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.4,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.5,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.6,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.7,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.8,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.9,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.10,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0,#22.11,0.9442,0.32938,0,7.8451,-0.32938,0.9442,0,13.404,0,0,1,0
> ui mousemode right "translate selected models"
> select add #22.1
17595 atoms, 17835 bonds, 2230 residues, 21 models selected
> view matrix models
> #22.1,1,0,0,3.0986,0,1,0,0.97304,0,0,1,0,#22.2,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.3,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.4,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.5,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.6,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.7,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.8,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.9,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.10,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0,#22.11,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.377,0,0,1,0
> select add #22
21694 atoms, 22006 bonds, 2748 residues, 24 models selected
> select subtract #22
13 models selected
> select add #22.22
4099 atoms, 4171 bonds, 518 residues, 1 model selected
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 1 time(s)]
> view matrix models #22.22,1,0,0,-0.0088343,0,1,0,0,0,0,1,-3.6724
> ui mousemode right "rotate selected models"
> view matrix models
> #22.22,0.99951,1.0299e-17,-0.031246,-1.801,-1.0516e-17,1,-6.7754e-18,1.256e-17,0.031246,7.1007e-18,0.99951,-5.2852
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> undo
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models #22.22,1,0,0,-0.42241,0,1,0,0,0,0,1,-3.8301
> select clear
> select add #22.2
799 atoms, 807 bonds, 98 residues, 1 model selected
> select add #22.3
1598 atoms, 1614 bonds, 196 residues, 3 models selected
> select add #22.4
2397 atoms, 2421 bonds, 294 residues, 5 models selected
> select add #22.5
3196 atoms, 3228 bonds, 392 residues, 7 models selected
> select add #22.6
3995 atoms, 4035 bonds, 490 residues, 9 models selected
> select add #22.7
4794 atoms, 4842 bonds, 588 residues, 11 models selected
> select add #22.8
5593 atoms, 5649 bonds, 686 residues, 13 models selected
> select add #22.9
6392 atoms, 6456 bonds, 784 residues, 15 models selected
> select add #22.10
7191 atoms, 7263 bonds, 882 residues, 17 models selected
> select add #22.11
7990 atoms, 8070 bonds, 980 residues, 19 models selected
> turn x 90
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 4 time(s)]
> view matrix models
> #22.2,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.3,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.4,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.5,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.6,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.7,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.8,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.9,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.10,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504,#22.11,0.9442,0.32938,0,10.944,-0.32938,0.9442,0,14.451,0,0,1,0.02504
> ui mousemode right "rotate selected models"
> view matrix models
> #22.2,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.3,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.4,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.5,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.6,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.7,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.8,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.9,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.10,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157,#22.11,0.9442,0.32938,-9.1275e-17,10.944,-0.3259,0.93422,0.145,23.507,0.047759,-0.13691,0.98943,-5.0157
> select clear
> combine #22 modelId #38 name Modified_Stator
Remapping chain ID 'K' in Stator-complexb.pdb #22.22 to 'M'
Remapping chain ID 'L' in Stator-complexb.pdb #22.22 to 'N'
Remapping chain ID ' ' in Stator-complexb.pdb #22.1 to 'A'
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/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)
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.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
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: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000E1LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 31 days, 55 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Q24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
ASUS PA279:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
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-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
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
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
pycollada: 0.8
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
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 , 11 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Combine: Cannot set polymeric chain ID directly from Residue |
comment:2 by , 11 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Fix: https://github.com/RBVI/ChimeraX/commit/7cf35a002c5a0010b2256cbf60b4ea2bc5fe25d8