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Opened 12 months ago

Last modified 12 months ago

#16457 assigned defect

ChimeraX bug report submission — at Initial Version

Reported by:	chimerax-bug-report@…	Owned by:
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:	chimera-programmers
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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_review2.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  
Opened 2xMotB.mrc as #37, grid size 240,240,240, pixel 2.1, shown at level
0.000313, step 1, values float32  
Log from Wed Dec 11 17:58:52 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/Fig4_After_review2.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  
Opened 2xMotB.mrc as #37, grid size 240,240,240, pixel 2.1, shown at level
0.000313, step 1, values float32  
Log from Wed Dec 11 17:05:13 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/Fig4_After_review2.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  
Opened 2xMotB.mrc as #37, grid size 240,240,240, pixel 2.1, shown at level
0.000313, step 1, values float32  
Log from Wed Dec 4 21:50:17 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/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

> ui mousemode right "translate selected atoms"

> select clear

> select # 2.1:580-end

1758 atoms, 1792 bonds, 212 residues, 1 model selected  

> select clear

> hide #!1 models

> select #2.1/A:581

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #2.1/A:581

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2.1/A:580

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> show #!1 models

> view orient

> sym #2.1 C18 center #1.1 copies true

Made 18 copies for pflA symmetry C18  

> rename #12 "pflA FlgY"

> show #!9 models

> hide #!1 models

> hide #!3 models

> close #12.3,7,10,14,18

> rename #12.1 id #9.1

> rename #12.2 id #9.2

> rename #12.4 id #9.4

> rename #12.5 id #9.5

> rename #12.6 id #9.6

> rename #12.8 id #9.8

> rename #12.9 id #9.9

> rename #12.11 id #9.11

> rename #12.12 id #9.12

> rename #12.13 id #9.13

> rename #12.15 id #9.15

> rename #12.16 id #9.16

> rename #12.17 id #9.17

> close #12

> rename #9 "pflA "

> show #!7 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 3 14:11:08 2024 ———

opened ChimeraX session  
Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces  

> color #2.2 mediumslateblue

> color #2.1 #ff5500ff

> color #9 #ff5500ff models

> color #7 deeppink models

> hide #!4 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

> select #7.1.1:116-end

643 atoms, 657 bonds, 84 residues, 1 model selected  

> select #7.1.1-2:116-end

1286 atoms, 1314 bonds, 168 residues, 2 models selected  

> view orient

> undo

[Repeated 1 time(s)]

> select #7.1.1:116-end, #7.1.2:102-end

Expected an objects specifier or a keyword  

> select #7.1.1:116-end

643 atoms, 657 bonds, 84 residues, 1 model selected  

> select #7.1.2:102-end

752 atoms, 767 bonds, 98 residues, 1 model selected  

> select #7.1.1-2:116-end

1286 atoms, 1314 bonds, 168 residues, 2 models selected  

> select add #7.1.2/B:115

1295 atoms, 1322 bonds, 169 residues, 2 models selected  

> select add #7.1.2/B:114

1303 atoms, 1329 bonds, 170 residues, 2 models selected  

> select add #7.1.2/B:113

1312 atoms, 1337 bonds, 171 residues, 2 models selected  

> select add #7.1.2/B:112

1318 atoms, 1342 bonds, 172 residues, 2 models selected  

> select add #7.1.2/B:111

1330 atoms, 1354 bonds, 173 residues, 2 models selected  

> select add #7.1.2/B:110

1337 atoms, 1360 bonds, 174 residues, 2 models selected  

> select add #7.1.2/B:109

1346 atoms, 1368 bonds, 175 residues, 2 models selected  

> select add #7.1.2/B:108

1350 atoms, 1371 bonds, 176 residues, 2 models selected  

> select add #7.1.2/B:107

1358 atoms, 1378 bonds, 177 residues, 2 models selected  

> select add #7.1.2/B:106

1367 atoms, 1386 bonds, 178 residues, 2 models selected  

> select add #7.1.2/B:105

1373 atoms, 1391 bonds, 179 residues, 2 models selected  

> select add #7.1.2/B:104

1381 atoms, 1398 bonds, 180 residues, 2 models selected  

> select add #7.1.2/B:103

1390 atoms, 1406 bonds, 181 residues, 2 models selected  

> select add #7.1.2/B:102

1395 atoms, 1410 bonds, 182 residues, 2 models selected  

> view orient

> select clear

> view orient

[Repeated 1 time(s)]

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 3 14:21:22 2024 ———

opened ChimeraX session  
Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces  

> hide #!4 models

> select #7.12.1-2:114-end

1320 atoms, 1348 bonds, 172 residues, 2 models selected  

> select add #7.12.2/B:113

1329 atoms, 1356 bonds, 173 residues, 2 models selected  

> select add #7.12.2/B:111

1341 atoms, 1368 bonds, 174 residues, 2 models selected  

> select add #7.12.2/B:112

1347 atoms, 1373 bonds, 175 residues, 2 models selected  

> select add #7.12.2/B:110

1354 atoms, 1379 bonds, 176 residues, 2 models selected  

> select subtract #7.12.2/B:110

1347 atoms, 1373 bonds, 175 residues, 2 models selected  

> select add #7.12.2/B:109

1356 atoms, 1381 bonds, 176 residues, 2 models selected  

> select add #7.12.2/B:110

1363 atoms, 1387 bonds, 177 residues, 2 models selected  

> select add #7.12.2/B:107

1371 atoms, 1394 bonds, 178 residues, 2 models selected  

> select add #7.12.2/B:108

1375 atoms, 1397 bonds, 179 residues, 2 models selected  

> select add #7.12.2/B:106

1384 atoms, 1405 bonds, 180 residues, 2 models selected  

> select add #7.12.2/B:105

1390 atoms, 1410 bonds, 181 residues, 2 models selected  

> view orient

> select clear

> view orient

> select #9.*:1-180

25848 atoms, 26424 bonds, 3240 residues, 18 models selected  

> split sel

Did not split pflA, has only one piece  
[Repeated 17 time(s)]

> split #9.* atoms :180-end

Split pflA (#9.1) into 2 models  
Split pflA (#9.2) into 2 models  
Split pflA (#9.3) into 2 models  
Split pflA (#9.4) into 2 models  
Split pflA (#9.5) into 2 models  
Split pflA (#9.6) into 2 models  
Split pflA (#9.7) into 2 models  
Split pflA (#9.8) into 2 models  
Split pflA (#9.9) into 2 models  
Split pflA (#9.10) into 2 models  
Split pflA (#9.11) into 2 models  
Split pflA (#9.12) into 2 models  
Split pflA (#9.13) into 2 models  
Split pflA (#9.14) into 2 models  
Split pflA (#9.15) into 2 models  
Split pflA (#9.16) into 2 models  
Split pflA (#9.17) into 2 models  
Split pflA (#9.18) into 2 models  
Chain information for pflA 1 #9.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.1.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.2.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.3.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.4.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.5.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.5.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.6.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.6.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.7.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.7.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.8.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.8.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.9.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.9.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.10.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.10.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.11.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.11.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.12.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.12.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.13.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.13.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.14.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.14.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.15.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.15.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.16.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.16.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.17.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.17.2  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 1 #9.18.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pflA 2 #9.18.2  
---  
Chain | Description  
A | No description available  
  

> hide #9.*.2 cartoons

> view orient

> show #2.2 cartoons

> split #2.2 atoms :1-137

Split pflB (#2.2) into 2 models  
Chain information for pflB 1 #2.2.1  
---  
Chain | Description  
B | No description available  
  
Chain information for pflB 2 #2.2.2  
---  
Chain | Description  
B | No description available  
  

> view orient

> hide #2.2.2 models

> show #2.2.2 models

> close #2.2.1

> sym #2.2 C18 center #1.1

Invalid "center" argument: Center argument has no object bounds  

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> sym #2.2 C18 center #1.1

Made 18 graphical clones for pflB 2 symmetry C18  

> hide #!1 models

> show
> #2.2.2#7.1.1-3#7.2.1-3#7.3.1-3#7.4.1-3#7.5.1-3#7.6.1-3#7.7.1-3#7.8.1-3#7.9.1-3#7.10.1-3#7.11.1-3#7.12.1-3#7.13.1-3#7.14.1-3#7.15.1-3#7.16.1-3#7.17.1-3#7.18.1-3#9.1.1-2#9.2.1-2#9.3.1-2#9.4.1-2#9.5.1-2#9.6.1-2#9.7.1-2#9.8.1-2#9.9.1-2#9.10.1-2#9.11.1-2#9.12.1-2#9.13.1-2#9.14.1-2#9.15.1-2#9.16.1-2#9.17.1-2#9.18.1-2
> surfaces

> hide #9.*.2 surfaces

> hide #7.*.3 surfaces

> show #!3 models

> color #3 #01543fff models

> show
> #3.1-42#!3.43-81#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.4.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.8.1-3#!7.9.1-3#!7.10.1-3#!7.11.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.15.1-3#!7.16.1-3#!7.17.1-3#!7.18.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
> surfaces

> hide #7.*.3 surfaces

> hide #9.*.2 surfaces

> view orient

> lighting soft

> lighting simple

> hide
> #!3.1-81#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.4.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.8.1-3#!7.9.1-3#!7.10.1-3#!7.11.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.15.1-3#!7.16.1-3#!7.17.1-3#!7.18.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
> surfaces

> view orient

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 3 14:56:25 2024 ———

opened ChimeraX session  
Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces  

> hide #!4 models

> open "C:/Users/Jack Botting/Documents/Chimera/PDB/stator.pdb"

Summary of feedback from opening C:/Users/Jack
Botting/Documents/Chimera/PDB/stator.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 85 VAL A 87 1 3  
Start residue of secondary structure not found: HELIX 2 2 ARG A 88 LYS A 107 1
20  
Start residue of secondary structure not found: HELIX 3 3 ALA A 128 ALA A 130
1 3  
Start residue of secondary structure not found: HELIX 4 4 LEU A 141 ALA A 152
1 12  
Start residue of secondary structure not found: HELIX 5 5 PHE A 154 PHE A 157
1 4  
247 messages similar to the above omitted  
  
Chain information for stator.pdb  
---  
Chain | Description  
12.3/? | No description available  
12.14/? 12.15/? 12.16/? 12.17/? 12.18/? 12.19/? 12.20/? 12.21/? 12.22/? 12.23/? | No description available  
12.1/A 12.2/A | No description available  
12.4/B 12.5/B 12.6/B 12.7/B 12.8/B 12.9/B 12.10/B 12.11/B 12.12/B 12.13/B | No description available  
  

> select add #12

24669 atoms, 24971 bonds, 2802 residues, 24 models selected  

> ui mousemode right "translate selected models"

> view matrix models #12,1,0,0,-578.91,0,1,0,28.461,0,0,1,-3.6162

> view matrix models #12,1,0,0,-563.77,0,1,0,48.676,0,0,1,-486.31

> view matrix models #12,1,0,0,-585.84,0,1,0,-392.56,0,0,1,-568.02

> view matrix models #12,1,0,0,-625.19,0,1,0,-401.85,0,0,1,-452.6

> show #!1 models

> hide #!2.2 models

> hide #!3 models

> hide #!7 models

> hide #!9 models

> hide #!1.1 models

> view matrix models #12,1,0,0,-595.83,0,1,0,-407.42,0,0,1,-449.38

> view matrix models #12,1,0,0,-589.75,0,1,0,-408.62,0,0,1,-485.85

> select clear

> view orient

> color #12 #00aa00ff models

> color #12 #008600ff models

> show #!1.1 models

> view orient

> show #!2.2 models

> show #2.1 models

> hide #2.1 models

> show #!9 models

> show #!7 models

> view orient

> hide #!1.2 models

> view orient

> sym #12 C18 center #1.1

Made 18 graphical clones for stator.pdb, stator.pdb, stator.pdb, stator.pdb,
stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb,
stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb,
stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb,
stator.pdb symmetry C18  

> select clear

[Repeated 1 time(s)]

> color #12 #005400ff models

> color #12 #004f00ff models

> view orient

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_piln_pilo_pflb/fold_pylori_piln_pilo_pflb_model_0.cif"

Chain information for fold_pylori_piln_pilo_pflb_model_0.cif #13  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #13 to #2.2

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 pflB 2, chain B (#2.2.2) with
fold_pylori_piln_pilo_pflb_model_0.cif, chain B (#13), sequence alignment
score = 3635.5  
RMSD between 608 pruned atom pairs is 0.697 angstroms; (across all 707 pairs:
6.109)  
  

> hide #!12 models

> hide #!9 models

> hide #!7 models

> hide #!1.1 models

> show #!1.2 models

> select add #13

9256 atoms, 9455 bonds, 1136 residues, 1 model selected  

> view matrix models
> #13,-0.63411,0.028196,-0.77273,298.14,-0.66839,0.48249,0.56609,10.698,0.38879,0.87545,-0.2871,-43.281

> view matrix models
> #13,-0.65422,0.035133,-0.75549,297.83,-0.56433,0.64236,0.51856,11.914,0.50351,0.7656,-0.40042,-41.315

> view matrix models
> #13,-0.65422,0.035133,-0.75549,315.66,-0.56433,0.64236,0.51856,-322.03,0.50351,0.7656,-0.40042,-56.272

> split #13 atoms /B

Split fold_pylori_piln_pilo_pflb_model_0.cif (#13) into 2 models  
Chain information for fold_pylori_piln_pilo_pflb_model_0.cif 1 #13.1  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_pylori_piln_pilo_pflb_model_0.cif 2 #13.2  
---  
Chain | Description  
A | No description available  
C | No description available  
  

> hide #13.1 models

> close #13.1

> select add #13.2

2418 atoms, 2473 bonds, 292 residues, 1 model selected  

> view matrix models
> #13.2,-0.65422,0.035133,-0.75549,298.03,-0.56433,0.64236,0.51856,-2.1929,0.50351,0.7656,-0.40042,-37.817

> view matrix models
> #13.2,-0.65734,0.03675,-0.7527,298.07,-0.54523,0.6663,0.50869,-2.4932,0.52022,0.74477,-0.41795,-37.968

> view orient

> turn x -90

> view matrix models
> #13.2,-0.65734,0.03675,-0.7527,298.08,-0.54523,0.6663,0.50869,1.2039,0.52022,0.74477,-0.41795,-13.096

> view matrix models
> #13.2,-0.65734,0.03675,-0.7527,360.28,-0.54523,0.6663,0.50869,13.702,0.52022,0.74477,-0.41795,-17.781

> view matrix models
> #13.2,-0.65734,0.03675,-0.7527,360.09,-0.54523,0.6663,0.50869,3.9914,0.52022,0.74477,-0.41795,-24.544

> fitmap #13.2 inMap #1.2

Fit molecule fold_pylori_piln_pilo_pflb_model_0.cif 2 (#13.2) to map HP-PflA-
PflB-2.1A.mrc (#1.2) using 2418 atoms  
average map value = 5.318, steps = 244  
shifted from previous position = 9.27  
rotated from previous position = 20.2 degrees  
atoms outside contour = 513, contour level = 0.78314  
  
Position of fold_pylori_piln_pilo_pflb_model_0.cif 2 (#13.2) relative to HP-
PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.38190509 0.03803185 -0.92341869 130.64005158  
-0.57941091 0.76856187 0.27128518 5.36319709  
0.72002188 0.63864406 -0.27148162 -93.36724892  
Axis 0.20481382 -0.91626845 -0.34424325  
Axis point 91.29210272 0.00000000 -7.11876351  
Rotation angle (degrees) 116.25790439  
Shift along axis 53.98380587  
  

> combine #13

> select add #14

4836 atoms, 4946 bonds, 584 residues, 2 models selected  

> view matrix models
> #13.2,-0.38191,0.038032,-0.92342,343.93,-0.57941,0.76856,0.27129,3.1769,0.72002,0.63864,-0.27148,-29.695,#14,-0.38191,0.038032,-0.92342,343.93,-0.57941,0.76856,0.27129,3.1769,0.72002,0.63864,-0.27148,-29.695

> undo

> select subtract #13.2

2418 atoms, 2473 bonds, 292 residues, 1 model selected  

> view matrix models
> #14,-0.38191,0.038032,-0.92342,340.37,-0.57941,0.76856,0.27129,54.359,0.72002,0.63864,-0.27148,-44.455

> select up

34274 atoms, 34866 bonds, 4224 residues, 15 models selected  

> select clear

> fitmap #14 inMap #1.2

Fit molecule copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 (#14) to map HP-
PflA-PflB-2.1A.mrc (#1.2) using 2418 atoms  
average map value = 4.763, steps = 536  
shifted from previous position = 11.3  
rotated from previous position = 26.7 degrees  
atoms outside contour = 656, contour level = 0.78314  
  
Position of copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 (#14) relative to
HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.67020056 0.24615531 -0.70017053 144.21435003  
-0.23151960 0.82698178 0.51234736 47.22202715  
0.70514530 0.50547868 -0.49725387 -115.16981588  
Axis -0.00462757 -0.94678980 -0.32181928  
Axis point 99.64464218 0.00000000 -31.77890818  
Rotation angle (degrees) 132.08530707  
Shift along axis -8.31282746  
  

> combine #13.2,14

> hide #14 models

> hide #!13 models

> show #!13 models

> show #14 models

> close #15

> combine #13.2 #14

Remapping chain ID 'A' in copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 #14
to 'B'  
Remapping chain ID 'C' in copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 #14
to 'D'  

> hide #13.2 models

> hide #14 models

> hide #15 models

> show #15 models

> view orient

> hide #!1.2 models

> show #!1.1 models

> show #!12 models

> close #14#13

> rename #15 pilNO

> show #!9 models

> close #10

> show #!7 models

> show #!3 models

> view orient

> sym #15 C18 center #1.1

Made 18 graphical clones for pilNO symmetry C18  

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 3 15:09:09 2024 ———

opened ChimeraX session  
Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces  

> hide #!4 models

> color #12 #356a00ff models

> color #15 #003600ff

> hide #!1.1 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

> lighting soft

> show
> #15#12.1-23#!3.1-81#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.4.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.8.1-3#!7.9.1-3#!7.10.1-3#!7.11.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.15.1-3#!7.16.1-3#!7.17.1-3#!7.18.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
> surfaces

> hide #9.*.2 surfaces

> hide #17.*.3 surfaces

[Repeated 1 time(s)]

> hide #7.*.3 surfaces

> view orient

> hide #!7.4 models

> hide #!7.18 models

> hide #!7.15 models

> hide #!7.11 models

> hide #!7.8 models

> save "C:/Users/Jack Botting/Documents/Chimera/Images/pylori FlgY system.jpg"
> width 2848 height 1180 supersample 3

> lighting simple

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 3 15:19:25 2024 ———

opened ChimeraX session  
Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces  

> hide
> #!15#!3.1-81#!12.1-23#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.9.1-3#!7.10.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.16.1-3#!7.17.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
> surfaces

> hide #!4 models

> show #!1.2 models

> color #1.2 #00000080 models

> color #1.2 #a8a8a880 models

> color #1.2 #adadad80 models

> view orient

> hide #!12 models

> hide #!15 models

> hide #!3 models

> view orient

> hide #!1.2 models

> show #!1.1 models

> view orient

[Repeated 1 time(s)]

> close #4

> rename #3 id #13

> rename #2.2 id #3

> rename #5 id #16

> rename #8 id #17

> rename #11 id #18

> close #2

> hide #!1 models

> show #!12 models

> show #!13 models

> show #!15 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

> turn x -90

> view orient

> close #7.*.3

> select #7.*:164-end

9864 atoms, 10188 bonds, 1296 residues, 36 models selected  

> view orient

[Repeated 2 time(s)]

> hide #7.*:164-end cartoons

> view orient

> turn x -90

> show #!1 models

> hide #!7 models

> hide #!3 models

> hide #!9 models

> hide #!12 models

> hide #!15 models

> select add #13

121989 atoms, 123969 bonds, 15453 residues, 154 models selected  

> view matrix models
> #7.1.1,0.32864,0.93245,-0.15009,-186.67,-0.75761,0.35516,0.54762,-94.364,0.56394,-0.066262,0.82315,30.867,#7.1.2,0.32864,0.93245,-0.15009,-186.67,-0.75761,0.35516,0.54762,-94.364,0.56394,-0.066262,0.82315,30.867,#7.2.1,0.52473,0.79843,-0.29522,-145.29,-0.63767,0.59842,0.48504,-154.11,0.56394,-0.066262,0.82315,30.867,#7.2.2,0.52473,0.79843,-0.29522,-145.29,-0.63767,0.59842,0.48504,-154.11,0.56394,-0.066262,0.82315,30.867,#7.3.1,0.69449,0.57738,-0.42932,-81.712,-0.44682,0.81378,0.37163,-197.51,0.56394,-0.066262,0.82315,30.867,#7.3.2,0.69449,0.57738,-0.42932,-81.712,-0.44682,0.81378,0.37163,-197.51,0.56394,-0.066262,0.82315,30.867,#7.4.1,0.81186,0.22698,-0.53793,-13.526,-0.15119,0.97164,0.1818,-211.13,0.56394,-0.066262,0.82315,30.867,#7.4.2,0.81186,0.22698,-0.53793,-13.526,-0.15119,0.97164,0.1818,-211.13,0.56394,-0.066262,0.82315,30.867,#7.5.1,0.82059,-0.067022,-0.56758,45.023,0.092778,0.99555,0.016577,-207.23,0.56394,-0.066262,0.82315,30.867,#7.5.2,0.82059,-0.067022,-0.56758,45.023,0.092778,0.99555,0.016577,-207.23,0.56394,-0.066262,0.82315,30.867,#7.6.1,0.7191,-0.45069,-0.52894,124.06,0.40603,0.89022,-0.20651,-170.12,0.56394,-0.066262,0.82315,30.867,#7.6.2,0.7191,-0.45069,-0.52894,124.06,0.40603,0.89022,-0.20651,-170.12,0.56394,-0.066262,0.82315,30.867,#7.7.1,0.56372,-0.69752,-0.44236,175.15,0.60348,0.71349,-0.35601,-114.52,0.56394,-0.066262,0.82315,30.867,#7.7.2,0.56372,-0.69752,-0.44236,175.15,0.60348,0.71349,-0.35601,-114.52,0.56394,-0.066262,0.82315,30.867,#7.8.1,0.28987,-0.91747,-0.27245,203.1,0.77327,0.39225,-0.49819,-50.258,0.56394,-0.066262,0.82315,30.867,#7.8.2,0.28987,-0.91747,-0.27245,203.1,0.77327,0.39225,-0.49819,-50.258,0.56394,-0.066262,0.82315,30.867,#7.9.1,-0.0013443,-0.99685,-0.079323,204.97,0.82581,0.043627,-0.56225,16.669,0.56394,-0.066262,0.82315,30.867,#7.9.2,-0.0013443,-0.99685,-0.079323,204.97,0.82581,0.043627,-0.56225,16.669,0.56394,-0.066262,0.82315,30.867,#7.10.1,-0.26136,-0.95986,0.10179,182.41,0.78337,-0.27254,-0.55862,91.475,0.56394,-0.066262,0.82315,30.867,#7.10.2,-0.26136,-0.95986,0.10179,182.41,0.78337,-0.27254,-0.55862,91.475,0.56394,-0.066262,0.82315,30.867,#7.11.1,-0.52473,-0.79843,0.29522,143.14,0.63767,-0.59842,-0.48504,150.89,0.56394,-0.066262,0.82315,30.867,#7.11.2,-0.52473,-0.79843,0.29522,143.14,0.63767,-0.59842,-0.48504,150.89,0.56394,-0.066262,0.82315,30.867,#7.12.1,-0.74397,-0.47341,0.47159,80.282,0.35844,-0.87835,-0.31627,186.09,0.56394,-0.066262,0.82315,30.867,#7.12.2,-0.74397,-0.47341,0.47159,80.282,0.35844,-0.87835,-0.31627,186.09,0.56394,-0.066262,0.82315,30.867,#7.13.1,-0.81186,-0.22698,0.53793,11.377,0.15119,-0.97164,-0.1818,207.91,0.56394,-0.066262,0.82315,30.867,#7.13.2,-0.81186,-0.22698,0.53793,11.377,0.15119,-0.97164,-0.1818,207.91,0.56394,-0.066262,0.82315,30.867,#7.14.1,-0.82059,0.067022,0.56758,-65.836,-0.092778,-0.99555,-0.016577,197.58,0.56394,-0.066262,0.82315,30.867,#7.14.2,-0.82059,0.067022,0.56758,-65.836,-0.092778,-0.99555,-0.016577,197.58,0.56394,-0.066262,0.82315,30.867,#7.15.1,-0.7191,0.45069,0.52894,-126.21,-0.40603,-0.89022,0.20651,166.89,0.56394,-0.066262,0.82315,30.867,#7.15.2,-0.7191,0.45069,0.52894,-126.21,-0.40603,-0.89022,0.20651,166.89,0.56394,-0.066262,0.82315,30.867,#7.16.1,-0.50663,0.7594,0.40822,-175.3,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,30.867,#7.16.2,-0.50663,0.7594,0.40822,-175.3,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,30.867,#7.17.1,-0.32333,0.89948,0.29392,-205.34,-0.75989,-0.4319,0.48583,47.002,0.56394,-0.066262,0.82315,30.867,#7.17.2,-0.32333,0.89948,0.29392,-205.34,-0.75989,-0.4319,0.48583,47.002,0.56394,-0.066262,0.82315,30.867,#7.18.1,-0.0079177,0.9963,0.085624,-209.57,-0.82578,-0.054804,0.56133,-25.733,0.56394,-0.066262,0.82315,30.867,#7.18.2,-0.0079177,0.9963,0.085624,-209.57,-0.82578,-0.054804,0.56133,-25.733,0.56394,-0.066262,0.82315,30.867,#13,1,0,0,-40.813,0,1,0,-1.5052,0,0,1,70.377

> select clear

> select add #13

112125 atoms, 113781 bonds, 14157 residues, 82 models selected  

> view matrix models #13,1,0,0,-38.504,0,1,0,-1.5052,0,0,1,70.089

> select clear

> view orient

> show #!3 models

> show #!6 models

> show #!7 models

> hide #!6 models

> show #!9 models

> show #!12 models

> show #!15 models

> view orient

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

> turn x -90

> select add #1.1

4 models selected  

> select clear

> select add #7

57096 atoms, 57744 bonds, 7164 residues, 55 models selected  

> view matrix models #7,1,0,0,-39.329,0,1,0,-3.6426,0,0,1,8.9225

> view orient

> hide #!1 models

> show #!1.2 models

> hide #!1.1 models

> view orient

> select clear

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 3 16:15:41 2024 ———

opened ChimeraX session  

> hide #!1 models

> show #18 models

> hide #18/A,B cartoon'

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

> hide #18/A,B cartoons

> view orient

[Repeated 1 time(s)]

> show #!1 models

> show #!6 models

> hide #18 models

> select add #6

2710 atoms, 2772 bonds, 331 residues, 1 model selected  

> hide #!15 models

> hide #!13 models

> hide #!12 models

> hide #!3 models

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.37725,-0.44737,0.81089,24.268,-0.91985,0.28263,-0.27202,170.26,-0.10749,-0.84852,-0.51814,187.19

> view matrix models
> #6,-0.37725,-0.44737,0.81089,107.06,-0.91985,0.28263,-0.27202,188.71,-0.10749,-0.84852,-0.51814,107.82

> hide sel surfaces

> view matrix models
> #6,-0.37725,-0.44737,0.81089,166.96,-0.91985,0.28263,-0.27202,14.919,-0.10749,-0.84852,-0.51814,85.961

> view matrix models
> #6,-0.37725,-0.44737,0.81089,165.76,-0.91985,0.28263,-0.27202,12.248,-0.10749,-0.84852,-0.51814,92.284

> view matrix models
> #6,-0.37725,-0.44737,0.81089,165.55,-0.91985,0.28263,-0.27202,14.538,-0.10749,-0.84852,-0.51814,65.62

> view matrix models
> #6,-0.37725,-0.44737,0.81089,178.07,-0.91985,0.28263,-0.27202,1.4718,-0.10749,-0.84852,-0.51814,52.601

> open "C:/Users/Jack Botting/Documents/alphafold
> results/pflAB/fold_pylori_pfla_pflc/fold_pylori_pfla_pflc_model_0.cif"

Chain information for fold_pylori_pfla_pflc_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> mmaker #2 to #9.18.1

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 pflA 1, chain A (#9.18.1) with fold_pylori_pfla_pflc_model_0.cif,
chain A (#2), sequence alignment score = 3183.5  
RMSD between 89 pruned atom pairs is 0.293 angstroms; (across all 612 pairs:
25.225)  
  

> close #2

> view orient

> ui tool show "Side View"

> view matrix models
> #6,-0.37725,-0.44737,0.81089,178.41,-0.91985,0.28263,-0.27202,0.90513,-0.10749,-0.84852,-0.51814,52.601

> view matrix models
> #6,-0.37725,-0.44737,0.81089,178.38,-0.91985,0.28263,-0.27202,2.9904,-0.10749,-0.84852,-0.51814,52.808

> view matrix models
> #6,-0.37725,-0.44737,0.81089,178.85,-0.91985,0.28263,-0.27202,3.2499,-0.10749,-0.84852,-0.51814,53.36

> view matrix models
> #6,-0.37725,-0.44737,0.81089,182.4,-0.91985,0.28263,-0.27202,-78.627,-0.10749,-0.84852,-0.51814,44.028

> view matrix models
> #6,-0.37725,-0.44737,0.81089,161.35,-0.91985,0.28263,-0.27202,-73.059,-0.10749,-0.84852,-0.51814,40.963

> view matrix models
> #6,-0.37725,-0.44737,0.81089,162,-0.91985,0.28263,-0.27202,-73.712,-0.10749,-0.84852,-0.51814,42.155

> view matrix models
> #6,-0.37725,-0.44737,0.81089,165.22,-0.91985,0.28263,-0.27202,-74.73,-0.10749,-0.84852,-0.51814,46.859

> select clear

> fitmap #6 inMap #1.2 shift false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 0.7647, steps = 64  
shifted from previous position = 5.68e-14  
rotated from previous position = 16.9 degrees  
atoms outside contour = 1781, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.30285245 -0.68737158 0.66015204 -48.52526860  
-0.95285864 0.23180699 -0.19577011 -67.98025203  
-0.01846105 -0.68832103 -0.72517127 -19.67829116  
Axis -0.56000429 0.77154712 -0.30184472  
Axis point -52.76429963 0.00000000 -14.22503516  
Rotation angle (degrees) 153.91052268  
Shift along axis -19.33582070  
  

> fitmap #6 inMap #1.2 rotate false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 0.8716, steps = 44  
shifted from previous position = 5.91  
rotated from previous position = 0 degrees  
atoms outside contour = 1645, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.30285245 -0.68737158 0.66015204 -46.93764496  
-0.95285864 0.23180699 -0.19577011 -68.13717407  
-0.01846105 -0.68832103 -0.72517127 -25.36694166  
Axis -0.56000429 0.77154712 -0.30184472  
Axis point -52.84953027 0.00000000 -17.39787428  
Rotation angle (degrees) 153.91052268  
Shift along axis -18.62888040  
  

> fitmap #6 inMap #1.2

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 2.92, steps = 368  
shifted from previous position = 22.4  
rotated from previous position = 81.3 degrees  
atoms outside contour = 555, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.94371631 0.25400702 0.21184892 -46.09255130  
0.14453894 0.89281185 -0.42660932 -54.17654056  
-0.29750298 -0.37197775 -0.87927501 -41.60541004  
Axis 0.10429077 0.97234449 -0.20897278  
Axis point -23.69126255 0.00000000 -23.81405425  
Rotation angle (degrees) 164.81601291  
Shift along axis -48.79089015  
  

> view matrix models
> #6,-0.96972,-0.024248,-0.24302,169.11,0.048713,0.95586,-0.28975,-61.215,0.23932,-0.29282,-0.92573,24.399

> view matrix models
> #6,-0.83191,0.48147,0.27588,164.23,0.43122,0.24802,0.86749,-38.79,0.34924,0.84064,-0.41395,8.0546

> view matrix models
> #6,-0.87725,-0.48004,-0.0014224,179.39,-0.12758,0.236,-0.96334,-53.719,0.46278,-0.84491,-0.26827,39.861

> view matrix models
> #6,-0.87725,-0.48004,-0.0014224,177.67,-0.12758,0.236,-0.96334,-75.32,0.46278,-0.84491,-0.26827,44.313

> fitmap #6 inMap #1.2 rotate false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 1.722, steps = 60  
shifted from previous position = 11.8  
rotated from previous position = 0 degrees  
atoms outside contour = 1307, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.87724573 -0.48003942 -0.00142242 -31.82690333  
-0.12757774 0.23599581 -0.96334306 -63.00722732  
0.46277834 -0.84490715 -0.26826866 -31.44548340  
Axis 0.19913251 -0.78048505 0.59261229  
Axis point -19.48872547 0.00000000 -43.21458388  
Rotation angle (degrees) 162.69971271  
Shift along axis 24.20344831  
  

> fitmap #6 inMap #1.2 shift false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 1.796, steps = 56  
shifted from previous position = 3.26e-14  
rotated from previous position = 9.35 degrees  
atoms outside contour = 1250, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.85554718 -0.51036300 -0.08699756 -31.91291532  
-0.13260657 0.37845086 -0.91607336 -63.01025522  
0.50045426 -0.77220756 -0.39146005 -31.61608246  
Axis 0.20174994 -0.82381195 0.52974601  
Axis point -18.43270312 0.00000000 -40.28574201  
Rotation angle (degrees) 159.11184496  
Shift along axis 28.72167879  
  

> view matrix models
> #6,-0.85555,-0.51036,-0.086998,180.5,-0.13261,0.37845,-0.91607,-80.249,0.50045,-0.77221,-0.39146,36.14

> fitmap #6 inMap #1.2 shift false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 1.261, steps = 88  
shifted from previous position = 1.03e-13  
rotated from previous position = 21.5 degrees  
atoms outside contour = 1495, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.80394309 -0.58905015 -0.08182530 -33.13685232  
-0.35908216 0.59047996 -0.72276786 -73.30860251  
0.47406272 -0.55168224 -0.68622969 -30.39146180  
Axis 0.27354726 -0.88880436 0.36769376  
Axis point -23.61741436 0.00000000 -34.45768777  
Rotation angle (degrees) 161.77696883  
Shift along axis 44.91775978  
  

> fitmap #6 inMap #1.2 rotate false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 1.655, steps = 72  
shifted from previous position = 12.3  
rotated from previous position = 0 degrees  
atoms outside contour = 1246, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.80394309 -0.58905015 -0.08182530 -30.97954999  
-0.35908216 0.59047996 -0.72276786 -62.45119875  
0.47406272 -0.55168224 -0.68622969 -35.68542061  
Axis 0.27354726 -0.88880436 0.36769376  
Axis point -20.75547151 0.00000000 -34.39256177  
Rotation angle (degrees) 161.77696883  
Shift along axis 33.91122049  
  

> view matrix models
> #6,-0.92898,0.17022,0.32866,171.62,-0.1264,0.68868,-0.71396,-70.114,-0.34787,-0.7048,-0.61826,31.402

> view matrix models
> #6,-0.92898,0.17022,0.32866,167.27,-0.1264,0.68868,-0.71396,-78.744,-0.34787,-0.7048,-0.61826,59.742

> view matrix models
> #6,-0.892,0.21544,0.39738,167.07,-0.26509,0.46276,-0.84592,-76.047,-0.36614,-0.8599,-0.35568,64.425

> view matrix models
> #6,-0.892,0.21544,0.39738,165.74,-0.26509,0.46276,-0.84592,-76.153,-0.36614,-0.8599,-0.35568,60.256

> fitmap #6 inMap #1.2 rotate false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 1.498, steps = 76  
shifted from previous position = 30.9  
rotated from previous position = 0 degrees  
atoms outside contour = 1347, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.89200350 0.21544120 0.39738494 -49.29839561  
-0.26508574 0.46276321 -0.84591945 -60.14427182  
-0.36614104 -0.85990422 -0.35567603 -35.38181210  
Axis -0.01549970 0.84623693 -0.53258127  
Axis point -32.53055108 0.00000000 -29.60494458  
Rotation angle (degrees) 153.18378369  
Shift along axis -31.28850345  
  

> view matrix models
> #6,-0.892,0.21544,0.39738,164.74,-0.26509,0.46276,-0.84592,-74.836,-0.36614,-0.8599,-0.35568,55.972

> fitmap #6 inMap #1.2 shift false

Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms  
average map value = 0.963, steps = 60  
shifted from previous position = 8.56e-14  
rotated from previous position = 23.7 degrees  
atoms outside contour = 1815, contour level = 0.78314  
  
Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.92577832 0.29237105 0.23969485 -49.01968455  
-0.22793582 0.07418241 -0.97084612 -68.21238874  
-0.30162844 -0.95342336 -0.00203464 -9.95055506  
Axis 0.02319834 0.72076965 -0.69278637  
Axis point -28.82316026 0.00000000 -31.26620913  
Rotation angle (degrees) 157.94369601  
Shift along axis -43.40898577  
  

> select clear

> view orient

[Repeated 2 time(s)]

> hide #!1 models

> hide #!1.2 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> show #7 cartoons

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.2 models

> view orient

> rename #1.1 FlgY-sym13-2.1A.mrc

> hide #!1.2 models

> view orient

> show #!1.1 models

> sym #6 C18 center #1.1

Made 18 graphical clones for pflC symmetry C18  

> hide #!1.1 models

> show #!1.2 models

> hide #!6 models

> view orient

> hide #!1 models

> show #!6 models

> show #!3 models

> show #!12 models

> show #!13 models

> show #!15 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Tue Jun 4 09:30:10 2024 ———

opened ChimeraX session  

> color #6 #aa0000ff

> color #6 #aa007fff

> color #6 #aa0003ff

> color #6 #004daaff

> color #6 #6300aaff

> color #6 #001aaaff

> color #6 #00158aff

> view orient

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

> set bgColor white

> set bgColor black

> set bgColor gray

> set bgColor black

> view orient

> show #!1 models

> ui tool show "Side View"

> hide #!6 models

> hide #!7 models

> hide #!9 models

> hide #!12 models

> hide #!13 models

> hide #!15 models

> fitmap #3.2 inMap #1.2

Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
atoms  
average map value = 3.673, steps = 132  
shifted from previous position = 2.15  
rotated from previous position = 21.6 degrees  
atoms outside contour = 1634, contour level = 0.78314  
  
Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
0.80291160 -0.52157229 0.28860930 60.18065259  
-0.56854588 -0.81555340 0.10783445 40.94646428  
0.17913284 -0.25066916 -0.95135505 -40.20640584  
Axis -0.94897880 0.28979025 -0.12434167  
Axis point 0.00000000 27.39177205 -26.68750735  
Rotation angle (degrees) 169.11203642  
Shift along axis -40.24494598  
  

> fitmap #3.2 inMap #1.2

Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
atoms  
average map value = 3.673, steps = 80  
shifted from previous position = 0.0367  
rotated from previous position = 0.0746 degrees  
atoms outside contour = 1631, contour level = 0.78314  
  
Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
0.80327839 -0.52166751 0.28741411 60.12735411  
-0.56827441 -0.81577700 0.10757370 40.95182051  
0.17834811 -0.24974171 -0.95174632 -40.19180750  
Axis -0.94907957 0.28969450 -0.12379444  
Axis point 0.00000000 27.39239640 -26.64929415  
Rotation angle (degrees) 169.14972727  
Shift along axis -40.22660404  
  

> fitmap #3.2 inMap #1.2

Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
atoms  
average map value = 3.673, steps = 80  
shifted from previous position = 0.024  
rotated from previous position = 0.0303 degrees  
atoms outside contour = 1631, contour level = 0.78314  
  
Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
0.80354108 -0.52137777 0.28720546 60.10572930  
-0.56799800 -0.81591769 0.10796587 40.96659533  
0.17804501 -0.24988714 -0.95176490 -40.18454753  
Axis -0.94914803 0.28953069 -0.12365273  
Axis point 0.00000000 27.38819739 -26.64343560  
Rotation angle (degrees) 169.13399735  
Shift along axis -40.21921879  
  

> fitmap #3.2 inMap #1.2

Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
atoms  
average map value = 3.673, steps = 64  
shifted from previous position = 0.0348  
rotated from previous position = 0.0278 degrees  
atoms outside contour = 1636, contour level = 0.78314  
  
Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
0.80346674 -0.52137448 0.28741934 60.14388335  
-0.56797181 -0.81599222 0.10753953 40.96691971  
0.17846358 -0.24965051 -0.95174860 -40.19178707  
Axis -0.94913002 0.28951867 -0.12381903  
Axis point 0.00000000 27.39728385 -26.65040903  
Rotation angle (degrees) 169.15416414  
Shift along axis -40.24716905  
  

> fitmap #3.2 inMap #1.2

Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
atoms  
average map value = 3.673, steps = 76  
shifted from previous position = 0.0336  
rotated from previous position = 0.0166 degrees  
atoms outside contour = 1633, contour level = 0.78314  
  
Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
0.80342788 -0.52130240 0.28765860 60.12353808  
-0.56798849 -0.81596225 0.10767872 40.95156780  
0.17858538 -0.24989885 -0.95166058 -40.21197705  
Axis -0.94911865 0.28951319 -0.12391895  
Axis point 0.00000000 27.38281428 -26.66426324  
Rotation angle (degrees) 169.14212239  
Shift along axis -40.22532595  
  

> fitmap #3.2 inMap #1.2

Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
atoms  
average map value = 3.673, steps = 84  
shifted from previous position = 0.0115  
rotated from previous position = 0.0325 degrees  
atoms outside contour = 1631, contour level = 0.78314  
  
Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
0.80325146 -0.52136987 0.28802878 60.12732889  
-0.56821419 -0.81576401 0.10798956 40.95545529  
0.17866101 -0.25040481 -0.95151337 -40.20604415  
Axis -0.94906953 0.28961845 -0.12404915  
Axis point 0.00000000 27.38373734 -26.67254520  
Rotation angle (degrees) 169.11644776  
Shift along axis -40.21603469  
  

> show #!9 models

> view orient

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!6 models

> show #!7 models

> show #!12 models

> show #!13 models

> show #!15 models

> view orient

[Repeated 1 time(s)]

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_0.cif"

Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif #2  
---  
Chain | Description  
A B | .  
C D | .  
  

> hide #2,A,B,C cartoon

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

> hide #2/A,B,C cartoons

> mmaker #2/D to #9.10.1

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 pflA 1, chain A (#9.10.1) with
fold_pylori_flgy_pfla2_nosig_model_0.cif, chain D (#2), sequence alignment
score = 3174.5  
RMSD between 277 pruned atom pairs is 0.741 angstroms; (across all 612 pairs:
11.168)  
  

> mmaker #2/D to #9.9.1

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 pflA 1, chain A (#9.9.1) with
fold_pylori_flgy_pfla2_nosig_model_0.cif, chain D (#2), sequence alignment
score = 3170.9  
RMSD between 292 pruned atom pairs is 0.771 angstroms; (across all 612 pairs:
7.930)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> mmaker #2/D to #9.1.1

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 pflA 1, chain A (#9.1.1) with
fold_pylori_flgy_pfla2_nosig_model_0.cif, chain D (#2), sequence alignment
score = 3170.9  
RMSD between 292 pruned atom pairs is 0.771 angstroms; (across all 612 pairs:
7.930)  
  

> close #2

> hide #!1 models

> hide #!3.2 models

> hide #!6 models

> hide #!3 models

> hide #!7 models

> hide #!9 models

> hide #!12 models

> hide #!13 models

> hide #!15 models

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_4.cif"

Chain information for fold_pylori_flgy_pfla2_nosig_model_4.cif #2  
---  
Chain | Description  
A B | .  
C D | .  
  

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_0.cif"

Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif #4  
---  
Chain | Description  
A B | .  
C D | .  
  

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_1.cif"

Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif #5  
---  
Chain | Description  
A B | .  
C D | .  
  

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_2.cif"

Chain information for fold_pylori_flgy_pfla2_nosig_model_2.cif #8  
---  
Chain | Description  
A B | .  
C D | .  
  

> open "C:/Users/Jack Botting/Documents/alphafold
> results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_3.cif"

Chain information for fold_pylori_flgy_pfla2_nosig_model_3.cif #10  
---  
Chain | Description  
A B | .  
C D | .  
  

> mmaker #4,5,8,10 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_flgy_pfla2_nosig_model_4.cif, chain C (#2) with
fold_pylori_flgy_pfla2_nosig_model_0.cif, chain C (#4), sequence alignment
score = 4034.6  
RMSD between 143 pruned atom pairs is 1.084 angstroms; (across all 781 pairs:
15.051)  
  
Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain D (#2) with
fold_pylori_flgy_pfla2_nosig_model_1.cif, chain C (#5), sequence alignment
score = 4037.6  
RMSD between 491 pruned atom pairs is 0.943 angstroms; (across all 781 pairs:
22.995)  
  
Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain D (#2) with
fold_pylori_flgy_pfla2_nosig_model_2.cif, chain C (#8), sequence alignment
score = 4026.2  
RMSD between 473 pruned atom pairs is 1.081 angstroms; (across all 781 pairs:
3.295)  
  
Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain D (#2) with
fold_pylori_flgy_pfla2_nosig_model_3.cif, chain D (#10), sequence alignment
score = 4011.8  
RMSD between 455 pruned atom pairs is 1.046 angstroms; (across all 781 pairs:
7.826)  
  

> hide #2 models

> hide #8 models

> hide #10 models

> hide #5 models

> show #5 models

> show #2 models

> hide #4 models

> show #8 models

> show #10 models

> show #4 models

> select add #4

15878 atoms, 16162 bonds, 1960 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.48287,0.82725,0.2872,-23.127,-0.86081,-0.50862,0.017761,-16.209,0.16077,-0.23865,0.9577,-76.601

> select clear

> mmaker #4/D to #4/C

Must use different reference and match structures  

> split #4

Split fold_pylori_flgy_pfla2_nosig_model_0.cif (#4) into 4 models  
Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif A #4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif B #4.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif C #4.3  
---  
Chain | Description  
C | No description available  
  
Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif D #4.4  
---  
Chain | Description  
D | No description available  
  

> mmaker #4.3 to #4.4

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_pfla2_nosig_model_0.cif D, chain D (#4.4) with
fold_pylori_flgy_pfla2_nosig_model_0.cif C, chain C (#4.3), sequence alignment
score = 4058  
RMSD between 624 pruned atom pairs is 0.804 angstroms; (across all 781 pairs:
1.684)  
  

> close #4

> split #5

Split fold_pylori_flgy_pfla2_nosig_model_1.cif (#5) into 4 models  
Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif A #5.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif B #5.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif C #5.3  
---  
Chain | Description  
C | No description available  
  
Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif D #5.4  
---  
Chain | Description  
D | No description available  
  

> mmaker #5e.3 to #5.4

> matchmaker #5e.3 to #5.4

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> hide #8 models

> hide #10 models

> hide #2 models

> mmaker #5.3 to #5.4

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_pfla2_nosig_model_1.cif D, chain D (#5.4) with
fold_pylori_flgy_pfla2_nosig_model_1.cif C, chain C (#5.3), sequence alignment
score = 4058.6  
RMSD between 553 pruned atom pairs is 0.951 angstroms; (across all 781 pairs:
4.311)  
  

> show #!9 models

> select ~sel & ##selected

Nothing selected  

> mmaker #5.3 to #9.1.1

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 pflA 1, chain A (#9.1.1) with
fold_pylori_flgy_pfla2_nosig_model_1.cif C, chain C (#5.3), sequence alignment
score = 3184.1  
RMSD between 177 pruned atom pairs is 0.625 angstroms; (across all 612 pairs:
18.352)  
  

> hide #5.1 models

> hide #5.2 models

> hide #5.4 models

> show #!1 models

> close #2,8,10#5

> view orient

[Repeated 1 time(s)]

> show #!6 models

> view orient

> show #!3 models

> show #!3.2 models

> rename #3.2 id #4

> close #3

> rename #9 id #2

> rename #7 id #3

> rename #12 id #7

> rename #13 id #8

> rename #15 id #9

> rename #4 "pflB "

> show #!7 models

> show #!8 models

> show #!9 models

> show #!3 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Tue Jun 4 11:39:36 2024 ———

opened ChimeraX session  

> color #3.*.1 orchid

> color #7 yellow

> color #8 forest green

> color #8 green

> color #2 #7b68ee

> color #2 mediumslateblue models

> color #2 #6152bdff models

> color #2 #40377eff models

> color #2 #5a4db1ff models

> color #2 #5f51baff models

> hide #!6 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

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 #5

284 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,209.3,0,1,0,-34.119,0,0,1,69.594

> view matrix models #5,1,0,0,208.49,0,1,0,-8.9177,0,0,1,64.454

> view matrix models #5,1,0,0,211.45,0,1,0,-9.0965,0,0,1,64.729

> select clear

> show #!6 models

> select #5.190

1 model selected  

> select add #5.104

2 models selected  
Ungrouped to 4 regions  
Ungrouped to 12 regions  
Ungrouped to 7 regions  
Ungrouped to 0 regions  

> select add #5

299 models selected  

> view matrix models #5,1,0,0,212.19,0,1,0,-8.3139,0,0,1,65.137

> select clear

> show #!2 models

> select #5.37

1 model selected  

> close #5

> view orient

> select clear

> hide #!6 models

> view orient

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Tue Jun 4 16:15:45 2024 ———

opened ChimeraX session  
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 #5

284 models selected  

> view matrix models #5,1,0,0,213.13,0,1,0,-12.179,0,0,1,64.138

> view matrix models #5,1,0,0,214.02,0,1,0,-6.5896,0,0,1,64.448

> select clear

> ui tool show "Side View"

> view orient

> hide #!1.2 models

> select #5.248

1 model selected  

> select add #5.37

2 models selected  

> select add #5.31

3 models selected  

> show #!4 models

> select clear

> show #!9 models

> select #5.248

1 model selected  

> select add #5.37

2 models selected  

> select add #5.31

3 models selected  

> select add #5.90

4 models selected  

> select add #5.141

5 models selected  

> select add #5.104

6 models selected  

> view orient

> sym clear #4

> select add #5.28

7 models selected  

> select add #5.12

8 models selected  

> select add #5.62

9 models selected  

> select add #5.42

10 models selected  

> show #!7 models

> hide #!7 models

Region has 27 adjacent regions  
[Repeated 1 time(s)]

> select add #5.75

11 models selected  

> select add #5.228

12 models selected  
Region has 27 adjacent regions  
[Repeated 1 time(s)]Grouped 12 regions  

> select clear

Showing 272 region surfaces  

> select #5.12

1 model selected  

> select add #5.174

2 models selected  

> select add #5.169

3 models selected  

> select add #5.46

4 models selected  
Grouped 4 regions  
Ungrouped to 4 regions  
Ungrouped to 19 regions  
Ungrouped to 50 regions  
Ungrouped to 58 regions  
Ungrouped to 25 regions  
Ungrouped to 2 regions  
Ungrouped to 0 regions  

> select #5.320

1 model selected  

> select add #5.364

2 models selected  

> select add #5.363

3 models selected  

> select add #5.291

4 models selected  

> select add #5.340

5 models selected  

> select add #5.324

6 models selected  

> select add #5.326

7 models selected  

> select add #5.339

8 models selected  

> select add #5.31

9 models selected  

> select add #5.28

10 models selected  

> select add #5.368

11 models selected  

> select add #5.369

12 models selected  

> select add #5.322

13 models selected  

> select add #5.367

14 models selected  

> select add #5.290

15 models selected  

> select add #5.321

16 models selected  

> select add #5.169

17 models selected  

> select add #5.141

18 models selected  

> select subtract #5.321

17 models selected  

> select subtract #5.169

16 models selected  

> select subtract #5.141

15 models selected  
Grouped 15 regions  

> select clear

> select add #5.321

1 model selected  

> select add #5.169

2 models selected  

> select add #5.141

3 models selected  

> select add #5.349

4 models selected  

> select add #5.348

5 models selected  

> select add #5.342

6 models selected  

> select add #5.316

7 models selected  

> select add #5.344

8 models selected  

> select add #5.62

9 models selected  

> select add #5.104

10 models selected  

> select add #5.305

11 models selected  

> select subtract #5.62

10 models selected  

> select subtract #5.104

9 models selected  

> select add #5.297

10 models selected  

> select add #5.62

11 models selected  
Region has 38 adjacent regions  

> select add #5.104

12 models selected  
Region has 38 adjacent regions  
Grouped 12 regions  
Region has 27 adjacent regions  

> select add #5.314

2 models selected  
Grouped 2 regions  

> hide #!2 models

Region has 26 adjacent regions  

> select add #5.347

2 models selected  
Region has 26 adjacent regions  
[Repeated 4 time(s)]

> select add #5.295

3 models selected  
Grouped 3 regions  
Region has 25 adjacent regions  
[Repeated 1 time(s)]

> select clear

> select #5.310

1 model selected  

> select add #5.330

2 models selected  

> select add #5.350

3 models selected  

> select add #5.351

4 models selected  

> select add #5.379

5 models selected  
Grouped 5 regions  
Region has 10 adjacent regions  

> select add #5.293

2 models selected  

> select add #5.378

3 models selected  

> select add #5.292

4 models selected  

> select add #5.380

5 models selected  

> select add #5.46

6 models selected  
Grouped 6 regions  
Region has 7 adjacent regions  

> select add #5.288

2 models selected  

> select add #5.309

3 models selected  
Grouped 3 regions  
Region has 13 adjacent regions  

> select add #5.304

2 models selected  
Grouped 2 regions  

> select add #5.303

2 models selected  

> select add #5.302

3 models selected  
Grouped 3 regions  
Region has 12 adjacent regions  
[Repeated 1 time(s)]

> select add #5.31

2 models selected  
Region has 29 adjacent regions  

> select add #5.28

3 models selected  
Region has 38 adjacent regions  
[Repeated 1 time(s)]

> select add #5.360

4 models selected  
Region has 41 adjacent regions  

> select #5.28

1 model selected  

> select add #5.31

2 models selected  

> select add #5.42

3 models selected  

> select clear

> select #5.31

1 model selected  
Ungrouped to 3 regions  
Ungrouped to 2 regions  
Ungrouped to 12 regions  
Ungrouped to 0 regions  

> select #5.169

1 model selected  

> select add #5.291

2 models selected  

> select add #5.293

3 models selected  

> select add #5.31

4 models selected  

> select add #5.287

5 models selected  

> select add #5.302

6 models selected  

> select add #5.288

7 models selected  

> select add #5.104

8 models selected  

> select add #5.62

9 models selected  

> select add #5.297

10 models selected  

> select add #5.303

11 models selected  

> select add #5.46

12 models selected  

> select add #5.295

13 models selected  

> select add #5.290

14 models selected  

> select add #5.292

15 models selected  
Grouped 15 regions  
Showing 329 region surfaces  

> select #5.360

1 model selected  

> select add #5.359

2 models selected  

> select add #5.306

3 models selected  

> select add #5.318

4 models selected  
Region has 13 adjacent regions  

> select add #5.319

5 models selected  

> select add #5.371

6 models selected  

> select add #5.370

7 models selected  

> select add #5.374

8 models selected  

> select add #5.365

9 models selected  

> select add #5.354

10 models selected  

> select add #5.353

11 models selected  
Grouped 11 regions  
Region has 11 adjacent regions  

> select add #5.329

2 models selected  

> select add #5.328

3 models selected  

> select add #5.375

4 models selected  

> select add #5.327

5 models selected  

> select add #5.335

6 models selected  

> select add #5.336

7 models selected  

> select add #5.337

8 models selected  

> select add #5.334

9 models selected  
Grouped 9 regions  
Region has 6 adjacent regions  

> select add #5.312

2 models selected  

> select add #5.313

3 models selected  

> select add #5.343

4 models selected  

> select subtract #5.343

3 models selected  
Grouped 3 regions  
Region has 4 adjacent regions  
[Repeated 1 time(s)]

> select clear

Showing 264 grouped regions  

> select #5.28

1 model selected  

> select add #5.31

2 models selected  

> select add #5.46

3 models selected  

> select add #5.42

4 models selected  
Deleted 305 regions  

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg" models #5

> view orient

[Repeated 1 time(s)]

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> rename #10 id #30

> rename #11 id #31

> rename #12 id #32

> rename #13 id #33

> rename #14 id #34

> rename #15 id #35

> rename #16 id #10

> rename #17 id #11

> rename #18 id #12

> rename #5 id #36

> select #19-35

85 models selected  

> view matrix models
> #19,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#20,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#21,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#22,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#23,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#24,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#25,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#26,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#27,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#28,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#29,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#30,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#31,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#32,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#33,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#34,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#35,1,0,0,216.49,0,1,0,-5.851,0,0,1,0

> view matrix models
> #19,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#20,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#21,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#22,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#23,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#24,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#25,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#26,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#27,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#28,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#29,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#30,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#31,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#32,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#33,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#34,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#35,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137

> hide #!9 models

> view matrix models
> #19,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#20,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#21,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#22,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#23,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#24,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#25,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#26,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#27,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#28,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#29,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#30,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#31,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#32,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#33,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#34,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#35,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952

> view matrix models
> #19,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#20,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#21,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#22,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#23,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#24,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#25,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#26,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#27,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#28,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#29,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#30,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#31,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#32,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#33,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#34,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#35,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403

> view orient

> show #!1.1 models

> view orient

> view matrix models
> #19,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#20,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#21,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#22,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#23,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#24,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#25,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#26,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#27,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#28,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#29,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#30,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#31,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#32,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#33,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#34,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#35,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403

> undo

> select clear

> turn z 20 1 models #19 center #1.1

> turn z 20 2 models #20 center #1.1

> turn z 20 3 models #21 center #1.1

> turn z 20 4 models #22 center #1.1

> turn z 20 5 models #23 center #1.1

> turn z 20 6 models #24 center #1.1

> turn z 20 7 models #25 center #1.1

> turn z 20 8 models #26 center #1.1

> turn z 20 9 models #27 center #1.1

> turn z 20 10 models #28 center #1.1

> turn z 20 11 models #29 center #1.1

> turn z 20 12 models #30 center #1.1

> turn z 20 13 models #31 center #1.1

> turn z 20 14 models #32 center #1.1

> turn z 20 15 models #33 center #1.1

> turn z 20 16 models #34 center #1.1

> turn z 20 17 models #35 center #1.1

> view orient

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> view orient

> color #19-35.4 #5f51ba

> color #19-35.1 #7b68ee

> color #19-35.2 yellow

> color #19-35.3 #003600

> color #36.42 #003600

> color #36.31 #7b68ee

> color #36.28 #5f51ba

> color #36.46 yellow

Segmenting FlgY-sym13-2.1A.mrc, density threshold 0.997772  
Showing 229 region surfaces  
2534 watershed regions, grouped to 229 regions  

> show #!19-28,30-36 target m

> hide #!36 models

> show #!36 models

> hide #!5 models

> show #!1.1 models

> show #!5 models

> select add #5

230 models selected  

> view orient

> view matrix models #5,1,0,0,-41.306,0,1,0,-6.6385,0,0,1,0

> view matrix models #5,1,0,0,-40.707,0,1,0,-6.0357,0,0,1,-14.746

> hide #!19-28,30-36 target m

> select clear

> select #5.22

1 model selected  

> select add #5.20

2 models selected  

> select add #5.19

3 models selected  

> select add #5.23

4 models selected  

> select add #5.40

5 models selected  

> select add #5.1

6 models selected  

> select add #5.42

7 models selected  

> select add #5.2

8 models selected  

> select add #5.37

9 models selected  

> select add #5.3

10 models selected  

> select add #5.17

11 models selected  

> select add #5.18

12 models selected  

> select add #5.21

13 models selected  
Ungrouped to 39 regions  

> select #5.266

1 model selected  
Ungrouped to 3 regions  

> select #5.245

1 model selected  

> select #5.259

1 model selected  
Ungrouped to 3 regions  

> select #5.249

1 model selected  
Ungrouped to 3 regions  

> select #5.240

1 model selected  

> select #5.21

1 model selected  

> select #5.240

1 model selected  
Ungrouped to 3 regions  

> select #5.251

1 model selected  

> select add #5.242

2 models selected  

> select add #5.254

3 models selected  

> select add #5.234

4 models selected  

> select add #5.2

5 models selected  

> select add #5.3

6 models selected  

> select add #5.245

7 models selected  

> select add #5.263

8 models selected  

> select add #5.231

9 models selected  

> select add #5.18

10 models selected  

> select add #5.19

11 models selected  

> select add #5.261

12 models selected  

> select add #5.22

13 models selected  

> select add #5.236

14 models selected  

> select add #5.37

15 models selected  

> select add #5.40

16 models selected  
Grouped 16 regions  

> select add #5.241

2 models selected  

> select add #5.253

3 models selected  

> select add #5.244

4 models selected  

> select add #5.256

5 models selected  

> select add #5.235

6 models selected  

> select add #5.268

7 models selected  

> select add #5.246

8 models selected  

> select add #5.265

9 models selected  

> select add #5.232

10 models selected  

> select add #5.258

11 models selected  

> select add #5.262

12 models selected  

> select add #5.250

13 models selected  

> select add #5.238

14 models selected  

> select subtract #5.241

13 models selected  
Grouped 13 regions  

> show #!19-28,30-36 target m

Region has 32 adjacent regions  

> select add #5.241

2 models selected  
Grouped 2 regions  

> hide #!1.1 models

> select clear

> open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
> asymm.seg"

Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
Sessions/pylori pfla asymm.seg  
---  
note | Showing 4 region surfaces  
  
Opened pylori pfla asymm.seg  

> hide #!13 models

> show #!13 models

> select add #13

5 models selected  

> view orient

> view matrix models #13,1,0,0,202.16,0,1,0,50.908,0,0,1,0

> view matrix models #13,1,0,0,191.22,0,1,0,45.673,0,0,1,70.544

> view matrix models #13,1,0,0,213.1,0,1,0,-5.5216,0,0,1,69.695

> hide #!19-28,30-35 target m

> view matrix models #13,1,0,0,214.22,0,1,0,-5.9712,0,0,1,64.639

> view matrix models #13,1,0,0,214.33,0,1,0,-6.6974,0,0,1,64.637

> show #!19-28,30-35 target m

> view orient

> turn z 11 20 models #13

> select clear

> rename #13 id #29

> color #29.4 #5f51ba

> color #29.1 #7b68ee

> color #29.3 #003600

> color #29.2 yellow

> view orient

> show #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> hide #!6 models

> show #!3 models

> show #!2 models

> transparency #19-36 50

> transparency #5 50

> color #5 magenta

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Wed Jun 5 14:36:12 2024 ———

opened ChimeraX session  

> hide #!5 models

> show #!5 models

> hide #5.1-234 target m

> close #5.1-234

> view orient

[Repeated 1 time(s)]

> sym #4 C18 center #1.1

Invalid "center" argument: Center argument has no object bounds  

> show #!1.1 models

> sym #4 C18 center #1.1

Made 18 graphical clones for pflB symmetry C18  

> hide #!1.1 models

> view orient

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Thu Jun 6 10:26:44 2024 ———

opened ChimeraX session  

> open "C:/Users/Jack Botting/Documents/B burgdorferi/borrelia maps/IM_1.mrc"

Opened IM_1.mrc as #13, grid size 121,121,39, pixel 4.2,4.2,4.2, shown at
level 0.0419, step 1, values float32  

> open "C:/Users/Jack Botting/Documents/B burgdorferi/borrelia maps/IM_2.mrc"

Opened IM_2.mrc as #14, grid size 207,207,129, pixel 5,5,0.6, shown at level
0.0708, step 1, values float32  

> select add #13

2 models selected  

> select add #14

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #13,1,0,0,-533.4,0,1,0,-492.94,0,0,1,8.0147,#14,1,0,0,-533.4,0,1,0,-492.94,0,0,1,8.0147

> volume #13 level 0.001013

> volume #14 level 0.002112

> color #13,14 dark gray

> view matrix models
> #13,1,0,0,-546.92,0,1,0,-487.29,0,0,1,-68.732,#14,1,0,0,-546.92,0,1,0,-487.29,0,0,1,-68.732

> select subtract #13

2 models selected  

> select add #13

4 models selected  

> select subtract #14

2 models selected  

> view matrix models #13,1,0,0,-518.11,0,1,0,-451.13,0,0,1,-533.27

> view matrix models #13,1,0,0,-499.41,0,1,0,-444.88,0,0,1,-531.97

> view orient

> select add #14

4 models selected  

> view matrix models
> #13,1,0,0,-509.51,0,1,0,-465.08,0,0,1,-531.97,#14,1,0,0,-557.01,0,1,0,-507.49,0,0,1,-68.732

> select clear

> view orient

> select add #13

2 models selected  

> select add #14

4 models selected  

> view matrix models
> #13,1,0,0,-505.87,0,1,0,-468.72,0,0,1,-531.97,#14,1,0,0,-553.37,0,1,0,-511.13,0,0,1,-68.732

> select clear

> show #!1.2 models

> ui tool show "Side View"

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> view orient

> turn x -90

> select add #13

2 models selected  

> select add #14

4 models selected  

> view matrix models
> #13,1,0,0,-505.29,0,1,0,-468.72,0,0,1,-530.21,#14,1,0,0,-552.79,0,1,0,-511.13,0,0,1,-66.974

> select clear

> view orient

> hide #!1.2 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Fri Jun 7 16:12:49 2024 ———

opened ChimeraX session  

> hide #!2-3,5,7-9 target m

> hide #19-36.1

> hide #19-36.2

> hide #19-36.4

> sym clear #4

> show #4 cartoons

> show #!7 models

> hide #!7 models

> select #4/B:325

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

127 atoms, 131 bonds, 14 residues, 2 models selected  

> select up

5767 atoms, 5902 bonds, 707 residues, 2 models selected  
Alignment identifier is 4/B  

> show #4/A cartoons

> select #4/B:138

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/B

5767 atoms, 5902 bonds, 707 residues, 1 model selected  

> 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 #15  
---  
Chain | Description  
A | No description available  
  

> mmaker #15 to #4

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 pflB , chain B (#4) with
HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#15), sequence alignment score = 3570.7  
RMSD between 467 pruned atom pairs is 1.012 angstroms; (across all 707 pairs:
6.069)  
  

> open "C:/Users/Jack Botting/Documents/alphafold
> results/pflAB/fold_pylori_pfla_pflb/fold_pylori_pfla_pflb_model_0.cif"

Chain information for fold_pylori_pfla_pflb_model_0.cif #16  
---  
Chain | Description  
A | .  
B | .  
  

> mmaker #16 to #4

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 pflB , chain B (#4) with fold_pylori_pfla_pflb_model_0.cif, chain B
(#16), sequence alignment score = 3709.9  
RMSD between 707 pruned atom pairs is 0.000 angstroms; (across all 707 pairs:
0.000)  
  

> hide #15 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!1.2 models

> hide #!1.2 models

> hide #16 models

> show #!4 models

> rename #4 "pflB (from pflA-pflB)"

> view orient

> sym #4 C18 center #1.1

Invalid "center" argument: Center argument has no object bounds  

> show #!1.1 models

> sym #4 C18 center #1.1

Made 18 graphical clones for pflB (from pflA-pflB) symmetry C18  

> select clear

> show #19-36

> close #15-16

> show #!9 models

> show #!8 models

> show #!7 models

> show #!3 models

> show #!2 models

> save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
> pflA pflB.cxs"

——— End of log from Mon Jun 10 09:14:27 2024 ———

opened ChimeraX session  

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/PflA-2.1A-230911.mrc

Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 4.29, step 1, values float32  

> volume #1 level 0.04668

> ui tool show "Segment Map"

Segmenting PflA-2.1A-230911.mrc, density threshold 0.046682  
Showing 295 region surfaces  
3353 watershed regions, grouped to 295 regions  
Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces  
Drag select of 4917, 2456 of 27676 triangles, 4914, 4515 of 23484 triangles,
4777, 20659 of 21324 triangles, 4913, 4693, 9326 of 19524 triangles, 4688,
3362 of 20760 triangles, 4953, 9370 of 20004 triangles, 4898, 7845 of 20040
triangles, 4966, 8000 of 19788 triangles, 4947, 4324 of 18268 triangles, 4672,
6676 of 18776 triangles, 4958, 11735 of 19080 triangles, 4965, 7488 of 16572
triangles, 4923, 10655 of 19480 triangles, 4742, 6902 of 18496 triangles,
4969, 7819 of 16128 triangles, 4894, 5986 of 19516 triangles, 4915, 4711 of
16732 triangles, 4897, 6387 of 17880 triangles, 4971, 8820 of 18612 triangles,
4955, 6160 of 17068 triangles, 4960, 3460 of 15704 triangles, 4940, 5627 of
15616 triangles, 4957, 4194 of 15808 triangles, 4868, 7876 of 16436 triangles,
4905, 8875 of 16712 triangles, 4922, 4947 of 15528 triangles, 4674, 6630 of
14628 triangles, 4954, 3366 of 14652 triangles, 4951, 3686 of 14820 triangles,
4771, 705 of 15692 triangles, 4721, 5425 of 14464 triangles, 4941, 5325 of
15676 triangles, 4972, 6301 of 14184 triangles, 4759, 7430 of 13076 triangles,
4946, 8730 of 13764 triangles, 4743, 3311 of 13128 triangles, 4936, 7780 of
13408 triangles, 4798, 1997 of 14384 triangles, 4945, 4944, 5942 of 12836
triangles, 4896, 4904, 7882 of 13164 triangles, 4967, 4216 of 13064 triangles,
4800, 6473 of 13300 triangles, 4683, 5380 of 13212 triangles, 4797, 4958 of
12652 triangles, 4950, 4924, 7745 of 14044 triangles, 4860, 4700, 4131 of
12816 triangles, 4712, 3616 of 12332 triangles, 4714, 4338 of 13132 triangles,
4938, 2263 of 12916 triangles, 4918, 5703 of 11432 triangles, 4773, 8204 of
12228 triangles, 4722, 4122 of 11564 triangles, 4751, 4591 of 11416 triangles,
4772, 1690 of 11660 triangles, 4935, 6125 of 12532 triangles, 4849, 4682, 4995
of 10644 triangles, 4942, 6983 of 10200 triangles, 4943, 4515 of 10976
triangles, 4921, 3815 of 10060 triangles, 4853, 6928 of 10608 triangles, 4699,
710 of 11424 triangles, 4906, 3249 of 10540 triangles, 4902, 8613 of 12076
triangles, 4119, 4690 of 9840 triangles, 4843, 4704, 7216 of 9924 triangles,
4750, 5791 of 8764 triangles, 4710, 2416 of 9272 triangles, 4795, 6634 of 9780
triangles, 4864, 4696, 5466 of 9492 triangles, 4701, 5641 of 9124 triangles,
4307, 4170 of 8288 triangles, 4774, 4815 of 9908 triangles, 4839, 1788 of 8044
triangles, 4709, 3439 of 8564 triangles, 4702, 2046 of 9240 triangles, 4318,
5032 of 9276 triangles, 4724, 4563 of 8056 triangles, 4851, 2899 of 8268
triangles, 4837, 4194, 5032 of 7952 triangles, 4113, 1833 of 6928 triangles,
4767, 2476 of 7772 triangles, 4760, 4779 of 7528 triangles, 4749, 3903 of 7860
triangles, 4207, 1641 of 8160 triangles, 4270, 4484 of 7056 triangles, 4808,
3328 of 7512 triangles, 4414, 540 of 6884 triangles, 4345, 1609 of 6432
triangles, 4167, 854 of 4872 triangles, 4761, 4235 of 6232 triangles, 3403,
343 of 4816 triangles, 4601, 3703 of 4892 triangles, 4098, 1092 of 4880
triangles, 1 PflA-2.1A-230911.mrc  
Grouped 102 regions  

> hide #!1 models

Drag select of 4903, 8878 of 34032 triangles, 4752, 24936 of 31216 triangles,
4685, 4861, 8260 of 15472 triangles, 4757, 7852 of 15336 triangles, 4729, 4922
of 11360 triangles, 4779, 1926 of 11008 triangles, 4708, 4745, 2272 of 6484
triangles, 4620  

> select add #2.107

14 models selected  
Grouped 12 regions  

> select add #2.83

4 models selected  

> select add #2.197

5 models selected  

> select add #2.106

6 models selected  

> select add #2.148

7 models selected  

> select add #2.229

8 models selected  

> select add #2.230

9 models selected  

> select add #2.191

10 models selected  

> select add #2.138

11 models selected  

> select add #2.228

12 models selected  

> select add #2.164

13 models selected  

> select add #2.216

14 models selected  
Grouped 12 regions  

> select add #2.1

4 models selected  

> select add #2.103

5 models selected  

> select add #2.7

6 models selected  

> select add #2.2

7 models selected  

> select add #2.206

8 models selected  

> select add #2.23

9 models selected  

> select add #2.11

10 models selected  

> select add #2.53

11 models selected  

> select add #2.9

12 models selected  

> select add #2.49

13 models selected  

> select subtract #2.49

12 models selected  

> select add #2.49

13 models selected  

> select add #2.20

14 models selected  

> select add #2.116

15 models selected  

> select add #2.212

16 models selected  

> select add #2.179

17 models selected  

> select subtract #2.179

16 models selected  

> select add #2.179

17 models selected  

> select add #2.176

18 models selected  

> select add #2.266

19 models selected  

> select add #2.177

20 models selected  

> select add #2.147

21 models selected  

> select add #2.209

22 models selected  

> select add #2.96

23 models selected  

> select add #2.125

24 models selected  

> select add #2.187

25 models selected  

> select add #2.113

26 models selected  

> select add #2.141

27 models selected  

> select add #2.259

28 models selected  

> select add #2.287

29 models selected  

> select add #2.104

30 models selected  

> select add #2.286

31 models selected  

> select add #2.196

32 models selected  

> select add #2.95

33 models selected  

> select add #2.10

34 models selected  

> select add #2.262

35 models selected  

> select add #2.221

36 models selected  

> select add #2.167

37 models selected  

> select add #2.264

38 models selected  

> select subtract #2.167

37 models selected  

> select subtract #2.221

36 models selected  

> select subtract #2.10

35 models selected  

> select add #2.271

36 models selected  

> select add #2.283

37 models selected  

> select add #2.199

38 models selected  

> select add #2.112

39 models selected  

> select subtract #2.112

38 models selected  

> select add #2.256

39 models selected  

> select add #2.236

40 models selected  

> select add #2.278

41 models selected  

> select add #2.289

42 models selected  

> select add #2.149

43 models selected  

> select add #2.198

44 models selected  

> select add #2.165

45 models selected  

> select add #2.250

46 models selected  

> select add #2.279

47 models selected  

> select add #2.181

48 models selected  

> select add #2.219

49 models selected  

> select add #2.294

50 models selected  
Grouped 48 regions  
Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  
Segmenting PflA-2.1A-230911_imasked, density threshold 0.046682  
Showing 122 region surfaces  
793 watershed regions, grouped to 122 regions  
Showing PflA-2.seg - 122 regions, 122 surfaces  
Showing 122 region surfaces  

> select #2.105

1 model selected  

> select add #2.8

2 models selected  

> select add #2.21

3 models selected  

> select add #2.30

4 models selected  

> select add #2.25

5 models selected  
Grouped 5 regions  

> select add #2.22

2 models selected  
Grouped 2 regions  

> select add #2.61

2 models selected  

> select add #2.44

3 models selected  

> select add #2.75

4 models selected  

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/For-FlgY-model_June2024/Rev-Hp-PflB.mrc

Opened Rev-Hp-PflB.mrc as #1, grid size 220,220,220, pixel 4.3, shown at level
3.57, step 1, values float32  

> volume #1 level 0.4885

> volume #1 level 0.3839

> ui tool show "Segment Map"

Segmenting Rev-Hp-PflB.mrc, density threshold 0.383927  
Showing 764 region surfaces  
5878 watershed regions, grouped to 764 regions  
Showing Rev-Hp-PflB.seg - 764 regions, 764 surfaces  
Drag select of 8536, 57 of 28120 triangles, 8544, 8666 of 26268 triangles,
8653, 35203 of 39008 triangles, 8637, 8615, 8046, 8677, 8734, 6946 of 18500
triangles, 8562, 3040 of 19812 triangles, 8652, 10841 of 18308 triangles,
8740, 3627 of 16592 triangles, 8593, 8627, 8539, 7230 of 16668 triangles,
8655, 8678, 145 of 16336 triangles, 8634, 8669, 8181, 64 of 17716 triangles,
8012, 21724 of 22204 triangles, 8076, 4510 of 15852 triangles, 8712, 8665,
8533, 3272 of 14972 triangles, 8668, 8651, 8578, 8674, 8670, 8324, 8801, 8071,
1110 of 13696 triangles, 8599, 140 of 12148 triangles, 8426, 8565, 8586, 8263,
8644, 8727, 8540, 5474 of 12288 triangles, 8224, 5750 of 11444 triangles,
8774, 8058, 8777, 8115, 8711, 6132 of 11512 triangles, 8623, 8640, 8722, 8555,
3924 of 10388 triangles, 8091, 8528, 235 of 10756 triangles, 8325, 3952 of
11704 triangles, 8597, 8260, 8671, 8738, 8770, 8610, 860 of 12196 triangles,
8664, 8537, 8359, 5226 of 10624 triangles, 8621, 176 of 10412 triangles, 8110,
8735, 796 of 9768 triangles, 8374, 3298 of 9860 triangles, 8203, 29 of 9844
triangles, 8120, 8622, 15682 of 15772 triangles, 8701, 9932 of 10512
triangles, 8366, 8373, 1211 of 10100 triangles, 8721, 8629, 7219, 8541, 8002,
8243, 102 of 8284 triangles, 7452, 8538, 488 of 8584 triangles, 8710, 8370,
147 of 8780 triangles, 8096, 8617, 8694, 8518, 3708 of 8916 triangles, 8059,
8784, 8289, 8001, 545 of 8676 triangles, 8566, 6306 of 9552 triangles, 8093,
8730, 8089, 6124 of 8420 triangles, 8595, 1655 of 9352 triangles, 8084, 8545,
1084 of 8600 triangles, 8087, 397 of 9180 triangles, 8080, 6573 of 8792
triangles, 8164, 9847 of 10612 triangles, 8527, 3922 of 8004 triangles, 8682,
8350, 8500, 8147, 4490 of 7536 triangles, 8725, 8416, 8050, 8090, 8067, 3257
of 7488 triangles, 8590, 3285 of 7856 triangles, 7436, 7302, 3983 of 6620
triangles, 8479, 8709, 5093 of 7868 triangles, 8786, 8556, 1289 of 7084
triangles, 8395, 7624, 6762 of 7068 triangles, 8245, 3401 of 6688 triangles,
8258, 8225, 601 of 6612 triangles, 8762, 7082, 3213 of 6704 triangles, 8608,
8732, 7698, 2847 of 6596 triangles, 7287, 8543, 3440 of 6372 triangles, 7111,
1387 of 7252 triangles, 7167, 5034 of 6684 triangles, 7300, 13 of 7644
triangles, 7130, 3210 of 6448 triangles, 7638, 7281, 4201 of 6464 triangles,
8204, 648 of 6956 triangles, 7101, 8752, 8371, 4196 of 6748 triangles, 8375,
2301 of 7088 triangles, 7092, 8393, 3571 of 6144 triangles, 7151, 4724 of 6004
triangles, 8383, 7038, 2962 of 5624 triangles, 8364, 8016, 4479 of 5636
triangles, 8475, 8335, 402 of 6264 triangles, 8038, 8613, 8020, 8631, 8112,
464 of 5084 triangles, 7217, 7172, 3851 of 5596 triangles, 7678, 901 of 6008
triangles, 8354, 8619, 8448, 8009, 2956 of 5524 triangles, 8720, 7376, 8625,
8358, 7574, 8311, 4143, 6637, 3044 of 5024 triangles, 7129, 3273 of 4648
triangles, 7675, 488 of 5476 triangles, 7380, 8800, 7164, 1731 of 4936
triangles, 7607, 1357 of 5392 triangles, 7112, 2546 of 4920 triangles, 8776,
7294, 3017 of 5008 triangles, 8357, 8072, 2411 of 5240 triangles, 7387, 7591,
8184, 7234, 6746, 693 of 4172 triangles, 5914, 17 of 4436 triangles, 7896,
8508, 8799, 7657, 461 of 3992 triangles, 8739, 6734, 338 of 3520 triangles,
8097, 8620, 4489 of 4496 triangles, 8291, 7542, 8299, 8753, 8626, 3104 of 3140
triangles, 6816, 8294, 8248, 5313, 7960, 5865, 867 of 892 triangles, 7957,
5868, 1 Rev-Hp-PflB.mrc  

> hide #!1 models

> select add #2.134

210 models selected  

> select subtract #2.134

209 models selected  

> select add #2.89

210 models selected  

> select add #2.15

211 models selected  

> select add #2.5

212 models selected  

> select add #2.198

213 models selected  

> select add #2.178

214 models selected  

> select add #2.338

215 models selected  

> select add #2.248

216 models selected  

> select add #2.419

217 models selected  

> select add #2.134

218 models selected  

> select add #2.503

219 models selected  

> select add #2.49

220 models selected  

> select add #2.268

221 models selected  

> select add #2.250

222 models selected  

> select add #2.466

223 models selected  

> select add #2.478

224 models selected  

> select add #2.96

225 models selected  

> select add #2.131

226 models selected  

> select add #2.57

227 models selected  

> select add #2.298

228 models selected  

> select add #2.406

229 models selected  

> select add #2.426

230 models selected  

> select add #2.256

231 models selected  

> select add #2.286

232 models selected  

> select add #2.212

233 models selected  

> select add #2.398

234 models selected  

> select add #2.191

235 models selected  

> select add #2.352

236 models selected  

> select add #2.448

237 models selected  

> select add #2.342

238 models selected  

> select add #2.158

239 models selected  

> select add #2.200

240 models selected  

> select add #2.150

241 models selected  
Drag select of 8658, 62 of 26828 triangles, 8743, 16616 of 20440 triangles,
8624, 55 of 26256 triangles, 8559, 8628, 95 of 20304 triangles, 8769, 12547 of
15180 triangles, 8706, 84 of 17300 triangles, 8515, 15 of 19696 triangles,
8750, 11009 of 13028 triangles, 8729, 9544 of 12292 triangles, 8125, 10602 of
11560 triangles, 8249, 8016 of 11676 triangles, 8787, 8524, 3485 of 10364
triangles, 8273, 9486 of 10444 triangles, 8723, 7844 of 10284 triangles, 8201,
8252, 8332, 7876 of 8376 triangles, 8352, 8657 of 8704 triangles, 7502, 8716,
7547 of 7940 triangles, 8529, 8639, 7878, 8635, 24 of 14008 triangles, 8339,
7437 of 10124 triangles, 8129, 6435 of 7852 triangles, 8583, 154 of 12500
triangles, 8605, 7420, 8612, 8574, 341 of 12536 triangles, 8764, 4049 of 7428
triangles, 8748, 8534, 8761, 1403 of 6948 triangles, 8768, 7741, 7602, 8347,
8523, 3210 of 7180 triangles, 8714, 8296, 7873, 1154 of 6540 triangles, 8233,
8007, 453 of 11036 triangles, 8319, 393 of 6688 triangles, 8765, 847 of 6412
triangles, 8477, 8277, 2540 of 7128 triangles, 8589, 3913 of 6304 triangles,
8428, 5592 of 6196 triangles, 8054, 1518 of 7100 triangles, 8356, 845 of 6604
triangles, 8118, 6114 of 7296 triangles, 8611, 5887 of 8228 triangles, 8679,
8253, 8642, 949 of 9196 triangles, 8318, 4620 of 5372 triangles, 8802, 8409,
8327, 2390 of 6412 triangles, 7178, 2642 of 5336 triangles, 7188, 2590 of 6288
triangles, 7752, 565 of 6664 triangles, 7447, 3881 of 6288 triangles, 6872,
1489 of 5080 triangles, 8334, 8785, 487 of 5752 triangles, 8042, 3057 of 5756
triangles, 8159, 898 of 5388 triangles, 8519, 2773 of 4980 triangles, 8797,
3138 of 5580 triangles, 8471, 1546 of 5312 triangles, 916, 1207 of 4716
triangles, 6864, 2546 of 4384 triangles, 8766, 3991 of 5488 triangles, 8525,
225 of 4368 triangles, 8489, 8737, 8064, 1399 of 4200 triangles, 7842, 2902 of
4644 triangles, 8469, 1189 of 4900 triangles, 8633, 8783, 6079, 906 of 4728
triangles, 8741, 908, 1810 of 3960 triangles, 907, 1695 of 3892 triangles,
6070, 1496 of 3916 triangles, 8713, 7705, 8043, 276 of 3812 triangles, 8452,
8742, 8648, 6212 of 7104 triangles, 7947, 179 of 3880 triangles, 8804, 4471 of
6556 triangles, 7199, 2014 of 3356 triangles, 6144, 25 of 3708 triangles,
8771, 5728 of 5820 triangles, 8381, 378 of 6144 triangles, 8660, 2059 of 7024
triangles, 922, 901 of 3532 triangles, 8521, 2933 of 6164 triangles, 8401,
7196, 2679 of 3556 triangles, 900, 2048 of 3584 triangles, 7849, 1716 of 3524
triangles, 8460, 959, 1645 of 3240 triangles, 448, 7847, 2089 of 3616
triangles, 7841, 2216 of 3624 triangles, 8681, 2801 of 5252 triangles, 7930,
8550, 897 of 5832 triangles, 7843, 1487 of 3536 triangles, 8782, 1132 of 5748
triangles, 7751, 888 of 3332 triangles, 8530, 8229, 8719, 4778 of 5096
triangles, 6064, 1530 of 2796 triangles, 8662, 1262 of 4756 triangles, 8548,
3024 of 3744 triangles, 8546, 223 of 4436 triangles, 8708, 6716, 1431 of 2684
triangles, 8542, 7589, 8328, 8747, 6941, 347 of 2496 triangles, 868, 2238 of
2536 triangles, 8531, 8520, 3436 of 3812 triangles, 6334, 2427 of 2632
triangles, 8788, 8704, 8789, 8636, 8577, 7899, 7257, 8213, 8790, 8705, 8717,
7742, 2008 of 2132 triangles, 8667, 2777 of 2864 triangles, 8297, 140 of 2780
triangles, 8576, 8803, 8155, 2292 of 2376 triangles, 8170, 1837 of 2068
triangles, 7710, 8794, 8609, 8758, 8798, 7865, 864 of 2092 triangles, 7733,
8215, 466, 8231, 6888, 8600, 1978 of 2256 triangles, 6678, 8715, 8603, 8481,
7709, 7718, 8449, 8700, 8269, 8746, 847, 781 of 1456 triangles, 6348, 7894,
54, 8773, 8618, 7713, 227, 6420, 6567, 6703, 82, 1040, 8698, 266, 8459, 8697,
8563, 8560, 8696, 8757, 1514 of 2232 triangles, 8047, 264, 240, 8270, 199,
8772, 1830 of 1960 triangles, 8792, 247, 8433, 621, 677, 8695, 202, 313, 8756,
8434, 289, 6824, 8441, 8440, 263, 417, 8404, 498, 537, 354, 7823, 8793, 18,
579, 737, 968 of 992 triangles, 385, 6099, 338, 326, 8699, 312, 418, 8060, 442
of 1148 triangles, 8554, 782, 698 of 832 triangles, 111, 297, 201, 8573, 314,
59, 8557, 965 of 1104 triangles, 8333, 8791, 419, 119, 200, 6809, 139, 8442,
293, 98, 242, 122, 342, 6846, 379, 554, 238, 239, 594, 176, 228, 53, 756, 437
of 588 triangles, 8755, 1169, 523 of 592 triangles, 77, 106, 378, 27, 146,
7457, 299 of 656 triangles, 7209, 399 of 632 triangles, 8109, 779, 365, 7210,
268, 48, 785, 790, 6817, 30, 473, 279, 580, 8726, 567, 1167, 50, 1101, 128 of
264 triangles, 273, 799, 77 of 216 triangles, 76  

> select add #2.95

544 models selected  

> select add #2.173

545 models selected  

> select add #2.43

546 models selected  

> select add #2.565

547 models selected  

> select add #2.126

548 models selected  

> select add #2.18

549 models selected  

> select add #2.480

550 models selected  

> select add #2.387

551 models selected  

> select add #2.396

552 models selected  

> select add #2.454

553 models selected  

> select add #2.310

554 models selected  

> select add #2.117

555 models selected  

> select add #2.6

556 models selected  

> select add #2.328

557 models selected  

> select add #2.385

558 models selected  

> select add #2.434

559 models selected  

> select add #2.400

560 models selected  

> select add #2.403

561 models selected  

> select add #2.464

562 models selected  

> select add #2.337

563 models selected  

> select add #2.450

564 models selected  

> select add #2.77

565 models selected  

> select add #2.75

566 models selected  

> select add #2.213

567 models selected  

> select add #2.221

568 models selected  

> select add #2.234

569 models selected  

> select subtract #2.18

568 models selected  

> select add #2.18

569 models selected  

> select subtract #2.126

568 models selected  

> select add #2.65

569 models selected  

> select add #2.126

570 models selected  

> select subtract #2.43

569 models selected  

> select add #2.61

570 models selected  

> select subtract #2.95

569 models selected  

> select add #2.95

570 models selected  

> select add #2.161

571 models selected  

> select add #2.38

572 models selected  

> select add #2.22

573 models selected  

> select add #2.339

574 models selected  

> select add #2.349

575 models selected  

> select add #2.545

576 models selected  

> select add #2.535

577 models selected  

> select add #2.344

578 models selected  

> select add #2.361

579 models selected  

> select add #2.23

580 models selected  

> select add #2.382

581 models selected  

> select add #2.86

582 models selected  

> select add #2.39

583 models selected  
Drag select of 8659, 82 of 18068 triangles, 8604, 6 of 12792 triangles, 8474,
69 of 9604 triangles, 7680, 46 of 4496 triangles, 3036, 41 of 3268 triangles  

> select add #2.10

589 models selected  

> select add #2.460

590 models selected  
Drag select of 8512, 189 of 23920 triangles, 8675, 534 of 17068 triangles,
8575, 532 of 13132 triangles, 8522, 6419 of 7876 triangles, 8779, 125 of 10904
triangles, 8396, 197 of 9736 triangles, 8582, 865 of 8368 triangles, 8034, 296
of 10924 triangles, 8535, 380 of 10464 triangles, 8736, 1762 of 10760
triangles, 8572, 229 of 8488 triangles, 8796, 83 of 8092 triangles, 8137, 10
of 7124 triangles, 7103, 927 of 7712 triangles, 8399, 326 of 6276 triangles,
8051, 3524 of 3968 triangles, 7961, 1060 of 3256 triangles, 7255, 2368 of 3080
triangles, 8754, 3639 of 4580 triangles, 989, 1904 of 2440 triangles, 1055,
943 of 2116 triangles, 8646, 7241, 931 of 1628 triangles, 1034, 7909, 8402,
1202 of 1924 triangles, 1092, 706 of 1092 triangles, 938, 8410, 628 of 1284
triangles, 1058, 608 of 1000 triangles, 1062, 697 of 904 triangles, 7280, 318
of 1032 triangles, 1228, 14 of 560 triangles, 836, 7137, 148 of 532 triangles,
807  
Grouped 624 regions  

> select clear

> select #2.225

1 model selected  

> select add #2.275

2 models selected  

> select add #2.422

3 models selected  

> select add #2.232

4 models selected  
Grouped 4 regions  

> select add #2.190

2 models selected  

> select add #2.227

3 models selected  

> select subtract #2.227

2 models selected  

> select add #2.227

3 models selected  

> select add #2.266

4 models selected  

> select add #2.258

5 models selected  

> select add #2.283

6 models selected  

> select add #2.290

7 models selected  

> select add #2.432

8 models selected  

> select add #2.249

9 models selected  

> select add #2.175

10 models selected  

> select add #2.254

11 models selected  

> select add #2.343

12 models selected  

> select add #2.233

13 models selected  

> select add #2.136

14 models selected  

> select add #2.220

15 models selected  

> select add #2.427

16 models selected  

> select add #2.500

17 models selected  

> select add #2.241

18 models selected  
Grouped 18 regions  

> select add #2.531

2 models selected  
Grouped 2 regions  

> select add #2.271

2 models selected  
Grouped 2 regions  

> select clear

> select #2.2

1 model selected  
Opened Rev-Hp-PflB_imasked as #3, grid size 220,220,220, pixel 4.3, shown at
step 1, values float32  
Segmenting Rev-Hp-PflB_imasked, density threshold 0.383927  
Showing 23 region surfaces  
103 watershed regions, grouped to 23 regions  
Showing Rev-Hp-PflB_imasked.seg - 23 regions, 23 surfaces  

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/PDB-
> files/Hp_motElikeproteindimer_ed02a_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
Hp_motElikeproteindimer_ed02a_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
#4  
---  
Chain | Description  
A B | No description available  
  

> select add #4

3420 atoms, 3458 bonds, 430 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

3420 atoms, 3458 bonds, 430 residues, 1 model selected  

> view matrix models #4,1,0,0,-18.183,0,1,0,119.32,0,0,1,25.036

> view matrix models #4,1,0,0,-2.2723,0,1,0,128.67,0,0,1,-24.184

> view matrix models #4,1,0,0,1.0942,0,1,0,124.99,0,0,1,-24.281

> view matrix models #4,1,0,0,-16.19,0,1,0,121.95,0,0,1,-57.422

> view matrix models #4,1,0,0,-13.434,0,1,0,120.81,0,0,1,-57.512

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.84172,-0.30814,0.44335,-8.8352,0.031429,0.84772,0.52951,120.21,-0.539,-0.43177,0.72323,-42.743

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.84172,-0.30814,0.44335,-16.152,0.031429,0.84772,0.52951,122.98,-0.539,-0.43177,0.72323,-35.613

> select clear

> select #2.7

1 model selected  

> select add #2.19

2 models selected  

> select add #2.16

3 models selected  

> select add #2.21

4 models selected  

> select add #2.20

5 models selected  

> select add #2.18

6 models selected  

> select add #2.15

7 models selected  

> select add #2.17

8 models selected  
Grouped 8 regions  

> select #2.3

1 model selected  
Ungrouped to 3 regions  
Ungrouped to 5 regions  
Ungrouped to 0 regions  

> select #2.3

1 model selected  

> select add #2.20

2 models selected  

> select add #2.18

3 models selected  
Grouped 3 regions  

> select add #2.7

2 models selected  
Grouped 2 regions  

> select clear

> select #2.8

1 model selected  
Ungrouped to 3 regions  
Ungrouped to 6 regions  
Ungrouped to 0 regions  

> select #2.16

1 model selected  

> select add #2.8

2 models selected  
Grouped 2 regions  

> select add #2.3

2 models selected  
Grouped 2 regions  

> select clear

> select #2.6

1 model selected  
Ungrouped to 4 regions  
Ungrouped to 2 regions  

> select #2.17

1 model selected  

> select add #2.16

2 models selected  

> select add #2.7

3 models selected  
Grouped 3 regions  

> select #2.27

1 model selected  

> hide #!3 models

> select clear

> select #2.7

1 model selected  

> select add #2.3

2 models selected  
Grouped 2 regions  

> select #2.10

1 model selected  
Ungrouped to 3 regions  

> select clear

> select #2.7

1 model selected  

> select add #2.16

2 models selected  

> select add #2.3

3 models selected  
Grouped 3 regions  

> select #2.5

1 model selected  
Ungrouped to 4 regions  

> select clear

> select #2.17

1 model selected  

> select add #2.16

2 models selected  

> select add #2.7

3 models selected  
Grouped 3 regions  

> select add #2.3

2 models selected  
Grouped 2 regions  

> select #2.9

1 model selected  

> select #2.1

1 model selected  
Ungrouped to 3 regions  
[Repeated 1 time(s)]Ungrouped to 5 regions  
Ungrouped to 0 regions  

> select #2.3

1 model selected  

> select add #2.16

2 models selected  

> select add #2.31

3 models selected  

> select add #2.32

4 models selected  

> select add #2.1

5 models selected  
Grouped 5 regions  

> select clear

> select #2.9

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #2.3

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select #2.12

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #2.1

1 model selected  

> select add #2.9

2 models selected  
Grouped 2 regions  

> select #2.4

1 model selected  

> select clear

> select #2.4

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 4 regions  

> select clear

> select #2.31

1 model selected  

> select add #2.32

2 models selected  

> select add #2.4

3 models selected  
Grouped 3 regions  

> select #2.11

1 model selected  
Ungrouped to 2 regions  
[Repeated 1 time(s)]

> select clear

> select #2.1

1 model selected  

> select add #2.31

2 models selected  

> select add #2.11

3 models selected  
Grouped 3 regions  

> select clear

> select #2.9

1 model selected  

> select #2.2

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 4 regions  
Ungrouped to 2 regions  

> select clear

> select #2.2

1 model selected  

> select add #2.33

2 models selected  

> select add #2.1

3 models selected  
Grouped 3 regions  

> select #2.13

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 0 regions  

> select #2.32

1 model selected  

> select add #2.2

2 models selected  

> select add #2.1

3 models selected  
Grouped 3 regions  

> select clear

> select #2.14

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #2.13

1 model selected  

> select add #2.1

2 models selected  

> select clear

> select #2.13

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 3 regions  

> select clear

> select #2.13

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select clear

> select #2.4

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  
Opened Rev-Hp-PflB_imasked_imasked as #5, grid size 220,220,220, pixel 4.3,
shown at step 1, values float32  
Segmenting Rev-Hp-PflB_imasked_imasked, density threshold 0.383927  
Showing 21 region surfaces  
71 watershed regions, grouped to 21 regions  
Showing Rev-Hp-PflB_imasked_imasked.seg - 21 regions, 21 surfaces  

> select #2.2

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 0 regions  

> hide #4 models

> hide #!2 models

> show #!2 models

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/For-FlgY-model_June2024/Segments/FlgY-with-joints.mrc models
> #5

> select #2.18

1 model selected  

> select add #2.13

2 models selected  

> select add #2.8

3 models selected  

> select add #2.9

4 models selected  

> select add #2.11

5 models selected  

> select add #2.12

6 models selected  

> select add #2.6

7 models selected  

> select add #2.17

8 models selected  

> select add #2.15

9 models selected  

> select add #2.23

10 models selected  

> select add #2.22

11 models selected  

> select add #2.16

12 models selected  

> select add #2.10

13 models selected  

> select add #2.5

14 models selected  
Ungrouped to 24 regions  
Ungrouped to 18 regions  
Ungrouped to 0 regions  

> select #2.24

1 model selected  

> select add #2.14

2 models selected  

> select add #2.33

3 models selected  

> select add #2.3

4 models selected  

> select add #2.7

5 models selected  

> select add #2.1

6 models selected  

> select add #2.19

7 models selected  

> select add #2.4

8 models selected  

> select add #2.21

9 models selected  

> select add #2.20

10 models selected  

> hide #!5 models

> select subtract #2.12

34 models selected  

> select subtract #2.45

33 models selected  

> select subtract #2.46

32 models selected  

> select clear

> select add #2.12

1 model selected  

> select add #2.45

2 models selected  

> select add #2.46

3 models selected  

> select add #2.21

4 models selected  

> select add #2.20

5 models selected  

> select add #2.14

6 models selected  

> select add #2.24

7 models selected  

> select add #2.48

8 models selected  

> select add #2.18

9 models selected  
Grouped 9 regions  

> select add #2.52

2 models selected  

> select add #2.8

3 models selected  

> select add #2.33

4 models selected  

> select add #2.3

5 models selected  

> select add #2.30

6 models selected  

> select add #2.7

7 models selected  

> select add #2.1

8 models selected  

> select add #2.19

9 models selected  

> select add #2.4

10 models selected  
Grouped 10 regions  

> select add #2.15

2 models selected  

> select clear

> select #2.26

1 model selected  

> select add #2.11

2 models selected  
Ungrouped to 0 regions  
Ungrouped to 10 regions  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/For-FlgY-
> model_June2024/Segments/Segmentation_FlgY_June2024.cxs includeMaps true

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/PflA-2.1A-230911.mrc

Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 4.29, step 1, values float32  

> volume #1 level 0.04668

> ui tool show "Segment Map"

Segmenting PflA-2.1A-230911.mrc, density threshold 0.046682  
Showing 295 region surfaces  
3353 watershed regions, grouped to 295 regions  
Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces  
Drag select of 4912, 2073 of 27676 triangles, 4895, 1858 of 23484 triangles,
4753, 17818 of 21324 triangles, 4925, 16701 of 20336 triangles, 4688, 13072 of
19524 triangles, 4681, 62 of 20760 triangles, 4893, 3877 of 20004 triangles,
4965, 5486 of 20040 triangles, 4959, 8950 of 19788 triangles, 4921, 11627 of
18268 triangles, 4701, 11608 of 18776 triangles, 4958, 7623 of 19080
triangles, 4944, 12405 of 16572 triangles, 4930, 8286 of 19480 triangles,
4687, 10865 of 18496 triangles, 4927, 9131 of 16128 triangles, 4899, 15393 of
19516 triangles, 4905, 10808 of 16732 triangles, 4938, 9705 of 17880
triangles, 4945, 5453 of 18612 triangles, 4892, 15229 of 17068 triangles,
4937, 12209 of 15616 triangles, 4948, 9712 of 15808 triangles, 4828, 9026 of
16436 triangles, 4917, 7074 of 16712 triangles, 4946, 5740 of 15528 triangles,
4749, 6345 of 14628 triangles, 4953, 7293 of 14652 triangles, 4924, 5379 of
14820 triangles, 4814, 1274 of 15692 triangles, 4672, 7717 of 14464 triangles,
4943, 9823 of 15676 triangles, 4926, 7517 of 14184 triangles, 4790, 5831 of
13076 triangles, 4949, 5754 of 13764 triangles, 4779, 8226 of 13128 triangles,
4955, 1711 of 13408 triangles, 4878, 2869 of 14384 triangles, 4909, 4933, 7556
of 12836 triangles, 4939, 4919, 3987 of 13164 triangles, 4931, 9538 of 13064
triangles, 4787, 5468 of 13300 triangles, 4847, 8107 of 13212 triangles, 4774,
8059 of 12652 triangles, 4900, 4897, 718 of 14044 triangles, 4836, 4969, 196
of 11808 triangles, 4720, 6164 of 12816 triangles, 4706, 1125 of 12332
triangles, 4752, 8297 of 13132 triangles, 4918, 4384 of 12916 triangles, 4960,
3394 of 11432 triangles, 4668, 6980 of 12228 triangles, 4791, 7757 of 11564
triangles, 4879, 5193 of 11416 triangles, 4766, 3336 of 11660 triangles, 4964,
832 of 12532 triangles, 4730, 4865, 5181 of 10644 triangles, 4902, 592 of
10200 triangles, 4914, 6601 of 10976 triangles, 4952, 4941 of 10060 triangles,
4710, 3265 of 11424 triangles, 4932, 5705 of 10540 triangles, 4922, 2699 of
12076 triangles, 4146, 4602 of 9840 triangles, 4775, 4671, 3540 of 9924
triangles, 4729, 3033 of 8764 triangles, 4680, 1509 of 9780 triangles, 4829,
4823, 2999 of 9492 triangles, 4806, 2571 of 9124 triangles, 4409, 3902 of 8288
triangles, 4777, 4386 of 9908 triangles, 4690, 1212 of 8044 triangles, 4860,
7037 of 8564 triangles, 4858, 1787 of 9240 triangles, 4167, 5091 of 9276
triangles, 4744, 1927 of 8056 triangles, 4857, 5105 of 8268 triangles, 4783,
4427, 1470 of 7952 triangles, 4242, 5623 of 6928 triangles, 4793, 1778 of 7528
triangles, 4799, 3560 of 7860 triangles, 4526, 810 of 8160 triangles, 4156,
3036 of 7056 triangles, 4853, 3870 of 7512 triangles, 4393, 447 of 6884
triangles, 4505, 1549 of 6432 triangles, 4822, 3122 of 6232 triangles, 3688,
2024 of 4816 triangles, 4254, 220 of 4892 triangles, 4566, 1624 of 4880
triangles, 1 PflA-2.1A-230911.mrc  

> hide #!1 models

> select add #2.239

101 models selected  

> select add #2.41

102 models selected  

> select add #2.272

103 models selected  

> select add #2.166

104 models selected  

> select add #2.188

105 models selected  
Drag select of 4894, 13014 of 34032 triangles, 4767, 4694, 13173 of 18900
triangles, 4711, 4723, 4712, 4760, 9477 of 11008 triangles, 4841, 4740, 4308  
Drag select of 4903, 5664 of 13508 triangles, 4904, 233 of 12368 triangles,
4896, 10603 of 11052 triangles, 4692, 3757 of 10748 triangles, 4934, 2285 of
10452 triangles, 4722, 8320 of 9168 triangles, 4966, 138 of 8844 triangles,
4446, 1502 of 8072 triangles, 4788, 4826, 4727, 7222 of 7424 triangles  

> select add #2.278

127 models selected  
Grouped 125 regions  
Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  
Segmenting PflA-2.1A-230911_imasked, density threshold 0.046682  
Showing 170 region surfaces  
1322 watershed regions, grouped to 170 regions  
Showing PflA-2.seg - 170 regions, 170 surfaces  

> select subtract #1

Nothing selected  

> hide #!2 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/For-FlgY-model_June2024/Segments/FlgY-with-joints.mrc

Opened FlgY-with-joints.mrc as #4, grid size 220,220,220, pixel 4.3, shown at
level 0.346, step 1, values float32  

> select add #4

2 models selected  

> view matrix models #4,1,0,0,-273.89,0,1,0,-9.814,0,0,1,-18.309

> volume #4 level 0.5615

> view matrix models #4,1,0,0,-248.02,0,1,0,-8.3112,0,0,1,-16.835

> view matrix models #4,1,0,0,-251.4,0,1,0,-10.631,0,0,1,-16.514

> ui mousemode right "rotate selected models"

> view matrix models
> #4,1,0.0014314,0.00027573,-251.39,-0.0014291,0.99996,-0.008294,-10.93,-0.00028759,0.0082936,0.99997,-16.509

> ui mousemode right "translate selected models"

> view orient

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.79655,0.60246,-0.05048,-254.13,-0.60188,0.7981,0.027742,-14.604,0.057002,0.0082847,0.99834,-16.115

> close #4

Segmenting PflA-2.1A-230911_imasked, density threshold 0.046682  
Showing 170 region surfaces  
1322 watershed regions, grouped to 170 regions  
Showing PflA-2.seg - 170 regions, 170 surfaces  

> select #2.140

1 model selected  

> select add #2.15

2 models selected  

> select add #2.30

3 models selected  

> select add #2.61

4 models selected  

> select add #2.34

5 models selected  

> select add #2.58

6 models selected  

> select add #2.79

7 models selected  

> select add #2.102

8 models selected  
Grouped 8 regions  

> select add #2.11

2 models selected  

> select add #2.99

3 models selected  

> select subtract #2.99

2 models selected  

> select #2.11

1 model selected  

> select add #2.99

2 models selected  

> select add #2.109

3 models selected  
Grouped 3 regions  

> select clear

> select #2.15

1 model selected  

> select add #2.74

2 models selected  

> select add #2.11

3 models selected  

> select add #2.111

4 models selected  

> select add #2.101

5 models selected  

> select add #2.167

6 models selected  
Grouped 6 regions  

> select add #2.31

2 models selected  

> select add #2.38

3 models selected  
Grouped 3 regions  

> select #2.11

1 model selected  

> hide #!3 models

Opened PflA-2_imasked as #4, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/1x_Cage-units.mrc models #4

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/Segment-local-PflAB.cxs
> includeMaps true

——— End of log from Tue Jun 11 18:45:39 2024 ———

opened ChimeraX session  
Showing PflA-2.seg - 154 regions, 154 surfaces  

> hide #!2 models

> hide #!4 models

> show #!2 models

> select #2.83

1 model selected  

> select add #2.96

2 models selected  

> select add #2.154

3 models selected  

> select subtract #2.17

150 models selected  

> select clear

> select #2.17

1 model selected  

> select add #2.154

2 models selected  

> select add #2.96

3 models selected  

> select add #2.83

4 models selected  
Grouped 4 regions  
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  
Segmenting PflA-2_imasked, density threshold 0.046682  
Showing 20 region surfaces  
103 watershed regions, grouped to 20 regions  
Showing PflA-2_imasked.seg - 20 regions, 20 surfaces  

> select #2.7

1 model selected  

> hide #!5 models

Opened PflA-2_imasked_imasked as #6, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/MotB_PG.mrc models #6

Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  
Segmenting PflA-2_imasked_imasked, density threshold 0.046682  
Showing 19 region surfaces  
99 watershed regions, grouped to 19 regions  
Showing PflA-2_imasked_imasked.seg - 19 regions, 19 surfaces  

> hide #!6 models

> hide #!7 models

> select #2.17

1 model selected  

> select add #2.2

2 models selected  

> select add #2.4

3 models selected  

> select add #2.10

4 models selected  
Grouped 4 regions  

> select #2.6

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 4 regions  

> select clear

> select #2.17

1 model selected  

> select add #2.2

2 models selected  

> select #2.17

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #2.2

1 model selected  

> select subtract #2.2

Nothing selected  

> select add #2.10

1 model selected  

> select clear

Showing 20 region surfaces  

> select clear

> select #2.2

1 model selected  

> select add #2.10

2 models selected  
Grouped 2 regions  

> select clear

> select #2.2

1 model selected  
Ungrouped to 2 regions  

> select #2.17

1 model selected  

> hide #!2 models

> show #!7 models

> ui tool show "Side View"

> show #!2 models

> select #2.17

1 model selected  

> select clear

> select #2.17

1 model selected  
Opened PflA-2_imasked_imasked_imasked as #8, grid size 240,240,240, pixel 2.1,
shown at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/PflA.mrc models #8

Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at step 1, values float32  
Segmenting PflA-2_imasked_imasked_imasked, density threshold 0.046682  
Showing 15 region surfaces  
71 watershed regions, grouped to 15 regions  
Showing PflA-2_imasked_imasked_imasked.seg - 15 regions, 15 surfaces  

> hide #!7 models

> hide #!8 models

> select #2.9

1 model selected  

> select add #2.12

2 models selected  

> select add #2.7

3 models selected  

> select add #2.13

4 models selected  

> select add #2.15

5 models selected  

> select add #2.10

6 models selected  
Grouped 6 regions  
Opened PflA-2_imasked_imasked_imasked_imasked as #10, grid size 240,240,240,
pixel 2.1, shown at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/Cage.mrc models #10

Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at step 1, values float32  
Segmenting PflA-2_imasked_imasked_imasked_imasked, density threshold 0.046682  
Showing 9 region surfaces  
50 watershed regions, grouped to 9 regions  
Showing PflA-2_imasked_imasked_imasked_imasked.seg - 9 regions, 9 surfaces  

> hide #!9 models

> hide #!10 models

> hide #!11 models

> select #2.4

1 model selected  

> select #2.1

1 model selected  

> select #2.1

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 4 regions  

> select #2.1

1 model selected  

> select #2.1

1 model selected  
Ungrouped to 4 regions  
Ungrouped to 2 regions  
Ungrouped to 0 regions  

> select #2.4

1 model selected  

> select add #2.1

2 models selected  

> select add #2.11

3 models selected  

> select add #2.10

4 models selected  

> select add #2.16

5 models selected  
Grouped 5 regions  

> select #2.6

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select clear

> select #2.1

1 model selected  
Opened PflA-2_imasked_imasked_imasked_imasked_imasked as #12, grid size
240,240,240, pixel 2.1, shown at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/PflB.mrc models #12

Opened PflA-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
240,240,240, pixel 2.1, shown at step 1, values float32  
Segmenting PflA-2_imasked_imasked_imasked_imasked_imasked, density threshold
0.046682  
Showing 7 region surfaces  
34 watershed regions, grouped to 7 regions  
Showing PflA-2_imasked_imasked_imasked_imasked_imasked.seg - 7 regions, 7
surfaces  

> hide #!12 models

> select add #2.7

1 model selected  
Drag select of 51, 7 of 14852 triangles, 13
PflA-2_imasked_imasked_imasked_imasked_imasked  

> select add #2.4

5 models selected  
Opened PflA-2_imasked_imasked_imasked_imasked_imasked_imasked as #14, grid
size 240,240,240, pixel 2.1, shown at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/FliL.mrc models #14

Opened PflA-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 240,240,240, pixel 2.1, shown at step 1, values float32  
Segmenting PflA-2_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.046682  
Showing 4 region surfaces  
18 watershed regions, grouped to 4 regions  
Showing PflA-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 4
regions, 4 surfaces  

> select #2.3

1 model selected  

> select add #2.4

2 models selected  

> select add #2.1

3 models selected  

> select add #2.2

4 models selected  

> hide #!2 models

> select add #2

5 models selected  

> hide #!13 models

> hide #!14 models

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/Other_Cage.mrc models #15

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/Sep11_2023/Segment_june11_2024/Segment2-local-PflAB.cxs
> includeMaps true

——— End of log from Tue Jun 11 23:04:54 2024 ———

opened ChimeraX session  
Showing PflA-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 4
regions, 4 surfaces  

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!10 models

> show #!9 models

> show #!8 models

> show #!6 models

> show #!5 models

> show #!4 models

> show #!3 models

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/PflA-2.1A-230911.mrc

Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 4.29, step 1, values float32  

> volume #1 level 1.73

> volume #1 level 0.1847

> ui tool show "Segment Map"

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  

> select add #2.110

1 model selected  

> select add #2.62

2 models selected  

> select add #2.5

3 models selected  

> select add #2.7

4 models selected  

> select add #2.15

5 models selected  

> select add #2.42

6 models selected  

> select add #2.104

7 models selected  

> select add #2.174

8 models selected  

> select add #2.165

9 models selected  

> select add #2.280

10 models selected  

> select add #2.176

11 models selected  

> select add #2.192

12 models selected  

> select add #2.86

13 models selected  

> select add #2.234

14 models selected  

> select add #2.144

15 models selected  

> select add #2.14

16 models selected  

> select add #2.207

17 models selected  

> select add #2.111

18 models selected  

> select add #2.18

19 models selected  

> select add #2.112

20 models selected  

> select add #2.263

21 models selected  

> select add #2.55

22 models selected  

> select add #2.82

23 models selected  

> select add #2.288

24 models selected  

> select add #2.143

25 models selected  

> select add #2.125

26 models selected  

> select add #2.175

27 models selected  

> select add #2.63

28 models selected  
Drag select of 4753, 6 of 12864 triangles, 4945, 7 of 13180 triangles, 4867,
16 of 9972 triangles, 3781, 12 of 4436 triangles  

> select add #2.30

33 models selected  

> select add #2.24

34 models selected  

> select add #2.70

35 models selected  

> select add #2.35

36 models selected  

> select add #2.236

37 models selected  

> select add #2.33

38 models selected  

> select add #2.40

39 models selected  

> select subtract #2.40

38 models selected  

> select add #2.40

39 models selected  

> select add #2.46

40 models selected  

> select add #2.84

41 models selected  

> select add #2.49

42 models selected  

> select add #2.137

43 models selected  

> select add #2.172

44 models selected  

> select add #2.61

45 models selected  
Drag select of 4929, 12 of 27404 triangles, 4933, 6 of 16236 triangles, 4907,
6 of 14460 triangles, 1 PflA-2.1A-230911.mrc  

> select subtract #2.60

49 models selected  

> select add #2.136

50 models selected  
Grouped 48 regions  

> select add #2.60

4 models selected  

> select clear

> select #2.23

1 model selected  

> select add #2.89

2 models selected  

> select add #2.228

3 models selected  

> select add #2.34

4 models selected  

> select add #2.109

5 models selected  

> select add #2.221

6 models selected  

> select add #2.28

7 models selected  

> select add #2.96

8 models selected  

> select add #2.13

9 models selected  

> select add #2.157

10 models selected  

> select add #2.44

11 models selected  

> select add #2.32

12 models selected  

> select add #2.227

13 models selected  

> select add #2.134

14 models selected  

> select add #2.216

15 models selected  

> select add #2.212

16 models selected  
Grouped 16 regions  

> select add #2.99

2 models selected  

> select add #2.83

3 models selected  

> select add #2.19

4 models selected  

> select add #2.249

5 models selected  

> select subtract #2.249

4 models selected  

> select add #2.249

5 models selected  

> select add #2.171

6 models selected  

> select add #2.87

7 models selected  

> select add #2.51

8 models selected  

> select add #2.200

9 models selected  

> select add #2.76

10 models selected  

> select add #2.37

11 models selected  

> select add #2.211

12 models selected  

> select add #2.225

13 models selected  

> select add #2.79

14 models selected  

> select add #2.237

15 models selected  

> select add #2.181

16 models selected  

> select add #2.184

17 models selected  

> select add #2.26

18 models selected  

> select add #2.251

19 models selected  

> select add #2.271

20 models selected  
Grouped 20 regions  

> select add #2.77

2 models selected  

> select add #2.29

3 models selected  

> select add #2.154

4 models selected  

> select add #2.72

5 models selected  

> select add #2.60

6 models selected  

> select add #2.223

7 models selected  

> select add #2.258

8 models selected  

> select add #2.246

9 models selected  

> select add #2.108

10 models selected  

> select add #2.187

11 models selected  

> select add #2.239

12 models selected  
Grouped 12 regions  

> select add #2.214

2 models selected  

> select add #2.240

3 models selected  

> select add #2.5

4 models selected  
Grouped 4 regions  

> select add #2.56

2 models selected  

> select add #2.159

3 models selected  
Grouped 3 regions  

> select add #2.122

2 models selected  
Grouped 2 regions  

> hide #!1 models

Ungrouped to 2 regions  
Ungrouped to 5 regions  
Ungrouped to 21 regions  
Ungrouped to 95 regions  

> select clear

Drag select of 2080, 1729 of 1900 triangles, 1908, 2947, 576 of 2072
triangles, 2865, 741 of 1336 triangles, 2719, 750 of 1448 triangles, 2779,
1077 of 2408 triangles, 1906, 2629, 1477 of 2104 triangles, 2784, 686 of 1524
triangles, 3769, 4739 of 5428 triangles, 2933, 1034 of 2308 triangles, 2066,
3151 of 3180 triangles, 4339, 4000 of 5896 triangles, 2938, 1082 of 2372
triangles, 2220, 3497, 3675, 3222 of 3340 triangles, 2216, 2057, 2880 of 2948
triangles, 3793, 3805 of 4752 triangles, 4442, 3379 of 3756 triangles, 4564,
2849 of 4116 triangles, 1964, 3592, 2076 of 2164 triangles, 4828, 1957 of 9008
triangles, 4922, 12932 of 19224 triangles, 4907, 9492 of 14460 triangles,
4737, 8287 of 12092 triangles, 4356, 5870 of 7912 triangles, 4969, 127818 of
215268 triangles, 4880, 5733 of 8936 triangles, 4474, 5217 of 6700 triangles,
4691, 11119 of 12868 triangles, 4958, 10083 of 14060 triangles, 4761, 8523 of
10476 triangles, 2698, 1601 of 2268 triangles, 3422, 3523 of 4204 triangles,
3007, 810 of 1864 triangles, 3785, 3399 of 4136 triangles, 2927, 1037 of 1388
triangles, 2687, 1760 of 2584 triangles, 2186, 2835, 891 of 1416 triangles,
3129, 457 of 864 triangles, 2699, 2140 of 2492 triangles, 1939, 4203, 5095 of
6192 triangles, 3571, 1958 of 1996 triangles, 3671, 2079, 2949, 444 of 1212
triangles, 2403, 1794 of 2060 triangles, 4966, 7398 of 10228 triangles, 4941,
8976 of 12716 triangles, 4753, 8772 of 12864 triangles, 4944, 10068 of 15236
triangles, 4932, 5328 of 14104 triangles, 4705, 10933 of 17972 triangles,
4956, 9840 of 15096 triangles, 4096, 4933 of 6712 triangles, 4904, 4964 of
27220 triangles, 4584, 3198 of 4632 triangles, 4685, 4916 of 11200 triangles,
4965, 6846 of 12440 triangles, 4940, 12763 of 18084 triangles, 4939, 3067 of
12096 triangles, 4799, 2637 of 15236 triangles, 4898, 788 of 13532 triangles,
4301, 2382 of 4648 triangles, 4902, 6167 of 23188 triangles, 4485, 5113 of
6248 triangles, 4919, 12179 of 19796 triangles, 4870, 449 of 10328 triangles,
4906, 13362 of 19236 triangles, 4843, 8271 of 11168 triangles, 4943, 11254 of
15304 triangles, 4910, 10584 of 15396 triangles, 4953, 11774 of 16520
triangles, 4927, 7564 of 13064 triangles, 4758, 4696 of 20372 triangles, 4896,
6893 of 11756 triangles, 4783, 8099 of 11256 triangles, 4935, 2929 of 9736
triangles, 4908, 13910 of 19788 triangles, 4281, 4328 of 7764 triangles, 4946,
10147 of 16072 triangles, 4831, 9103 of 14224 triangles, 4862, 5320 of 9596
triangles, 4804, 10005 of 14140 triangles, 4794, 883 of 10880 triangles  
Grouped 90 regions  

> select add #2.105

2 models selected  

> select add #2.211

3 models selected  

> select add #2.299

4 models selected  
Grouped 4 regions  
Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Segment_July_26/Disk.mrc models #3

Opened PflA-2.1A-230911_imasked as #4, 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 204 region surfaces  
1746 watershed regions, grouped to 204 regions  
Showing PflA-2.seg - 204 regions, 204 surfaces  

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!4 models

Drag select of 2455, 14642 of 20620 triangles, 2589, 9697 of 19436 triangles,
2598, 2618, 2522, 11189 of 11436 triangles, 2606, 7432 of 11344 triangles,
2508, 2519, 2521, 2507, 2125, 3803 of 4348 triangles  
Grouped 11 regions  

> select clear

> select add #2.165

1 model selected  

> select add #2.22

2 models selected  

> select add #2.24

3 models selected  

> select add #2.78

4 models selected  

> select add #2.11

5 models selected  

> select add #2.90

6 models selected  

> select add #2.170

7 models selected  

> select add #2.4

8 models selected  

> select add #2.86

9 models selected  

> select add #2.3

10 models selected  
Grouped 10 regions  

> select add #2.7

2 models selected  

> select subtract #2.7

1 model selected  

> select add #2.7

2 models selected  

> select add #2.187

3 models selected  
Grouped 3 regions  

> select add #2.115

2 models selected  

> select add #2.149

3 models selected  

> select clear

> select #2.3

1 model selected  
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  
Segmenting PflA-2_imasked, density threshold 0.184695  
Showing 182 region surfaces  
1409 watershed regions, grouped to 182 regions  
Showing PflA-2_imasked.seg - 182 regions, 182 surfaces  

> select add #2.151

1 model selected  

> select add #2.15

2 models selected  

> select add #2.16

3 models selected  

> select add #2.161

4 models selected  

> select add #2.13

5 models selected  

> select add #2.30

6 models selected  

> select add #2.38

7 models selected  

> select add #2.33

8 models selected  

> select add #2.29

9 models selected  

> select add #2.40

10 models selected  

> select add #2.39

11 models selected  

> select add #2.31

12 models selected  

> select subtract #2.29

11 models selected  

> select add #2.29

12 models selected  

> select add #2.106

13 models selected  

> select add #2.93

14 models selected  

> select add #2.92

15 models selected  

> select add #2.77

16 models selected  

> select add #2.53

17 models selected  

> select add #2.91

18 models selected  

> select add #2.66

19 models selected  

> select add #2.101

20 models selected  

> select add #2.59

21 models selected  

> select add #2.42

22 models selected  

> select add #2.128

23 models selected  

> select add #2.124

24 models selected  

> select add #2.109

25 models selected  

> select add #2.112

26 models selected  

> select add #2.10

27 models selected  

> hide #!5 models

> select add #2.88

28 models selected  

> show #!5 models

> select add #2.72

29 models selected  

> select add #2.9

30 models selected  

> select add #2.27

31 models selected  
Grouped 31 regions  

> select add #2.32

2 models selected  

> select add #2.102

3 models selected  

> select add #2.62

4 models selected  

> select add #2.83

5 models selected  

> select add #2.110

6 models selected  

> select add #2.105

7 models selected  

> select add #2.34

8 models selected  

> select add #2.64

9 models selected  

> select subtract #2.32

8 models selected  
Grouped 8 regions  

> select add #2.46

2 models selected  

> select add #2.26

3 models selected  

> select add #2.121

4 models selected  

> select add #2.57

5 models selected  

> select add #2.24

6 models selected  
Grouped 6 regions  

> select add #2.171

2 models selected  
Grouped 2 regions  

> select add #2.32

2 models selected  
Grouped 2 regions  

> select add #2.107

2 models selected  
Grouped 2 regions  

> select add #2.63

2 models selected  

> select add #2.170

3 models selected  

> select add #2.117

4 models selected  

> select add #2.139

5 models selected  

> select add #2.179

6 models selected  

> select add #2.61

7 models selected  

> select subtract #2.139

6 models selected  

> select add #2.139

7 models selected  
Grouped 7 regions  

> select clear

> select #2.9

1 model selected  

> hide #!5 models

> show #!1 models

> hide #!1 models

> select clear

[Repeated 1 time(s)]

> select #2.9

1 model selected  
Opened PflA-2_imasked_imasked as #6, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Segment_July_26/3Xunits.mrc models #6

Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  
Segmenting PflA-2_imasked_imasked, density threshold 0.184695  
Showing 130 region surfaces  
1128 watershed regions, grouped to 130 regions  
Showing PflA-2_imasked_imasked.seg - 130 regions, 130 surfaces  

> hide #!6 models

> hide #!7 models

> select #2.50

1 model selected  

> select add #2.16

2 models selected  

> select add #2.85

3 models selected  

> select add #2.103

4 models selected  

> select add #2.24

5 models selected  

> select add #2.15

6 models selected  

> select add #2.12

7 models selected  

> select add #2.88

8 models selected  

> select add #2.67

9 models selected  

> show #!6 models

> close #6-7

Segmenting PflA-2_imasked, density threshold 0.184695  
Showing 182 region surfaces  
1409 watershed regions, grouped to 182 regions  
Showing PflA-2_imasked.seg - 182 regions, 182 surfaces  

> select add #2.16

1 model selected  

> select add #2.161

2 models selected  

> select add #2.15

3 models selected  

> select add #2.151

4 models selected  

> select add #2.57

5 models selected  

> select add #2.121

6 models selected  

> select add #2.171

7 models selected  

> select add #2.24

8 models selected  

> select add #2.26

9 models selected  

> select add #2.30

10 models selected  

> select add #2.13

11 models selected  
Grouped 11 regions  

> select add #2.32

2 models selected  

> select add #2.102

3 models selected  

> select add #2.28

4 models selected  

> select add #2.106

5 models selected  

> select add #2.77

6 models selected  

> select add #2.53

7 models selected  

> select add #2.33

8 models selected  

> select add #2.38

9 models selected  

> select subtract #2.102

8 models selected  

> select add #2.102

9 models selected  

> select add #2.62

10 models selected  

> select add #2.83

11 models selected  

> select add #2.34

12 models selected  
Grouped 12 regions  

> select add #2.46

2 models selected  

> select add #2.64

3 models selected  

> select add #2.70

4 models selected  

> select add #2.110

5 models selected  

> select add #2.105

6 models selected  

> select add #2.112

7 models selected  

> select add #2.163

8 models selected  

> select add #2.101

9 models selected  

> select add #2.109

10 models selected  

> select add #2.66

11 models selected  

> select add #2.124

12 models selected  

> select add #2.91

13 models selected  

> select add #2.128

14 models selected  
Grouped 14 regions  

> select add #2.39

2 models selected  

> select add #2.42

3 models selected  

> select add #2.92

4 models selected  

> select add #2.93

5 models selected  

> select add #2.31

6 models selected  

> select add #2.40

7 models selected  
Grouped 7 regions  

> select add #2.9

2 models selected  

> select add #2.72

3 models selected  

> select add #2.59

4 models selected  

> select add #2.10

5 models selected  

> select add #2.88

6 models selected  

> select add #2.27

7 models selected  
Grouped 7 regions  

> select #2.18

1 model selected  
Ungrouped to 5 regions  

> select clear

> select #2.10

1 model selected  

> select add #2.13

2 models selected  

> select add #2.24

3 models selected  

> select subtract #2.24

2 models selected  
Grouped 2 regions  

> select add #2.9

2 models selected  
Grouped 2 regions  

> select clear

> select #2.9

1 model selected  

> select add #2.107

2 models selected  
Grouped 2 regions  
Ungrouped to 2 regions  

> select clear

> select #2.10

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 9 regions  
Ungrouped to 21 regions  
Ungrouped to 63 regions  

> select subtract #2.105

62 models selected  

> select add #2.117

63 models selected  

> select add #2.170

64 models selected  

> select add #2.179

65 models selected  

> select add #2.139

66 models selected  
Grouped 66 regions  

> select add #2.38

2 models selected  
Grouped 2 regions  

> select add #2.13

2 models selected  
Grouped 2 regions  

> select add #2.33

2 models selected  

> select add #2.34

3 models selected  

> select add #2.46

4 models selected  

> select add #2.40

5 models selected  
Grouped 5 regions  
Opened PflA-2_imasked_imasked as #6, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Segment_July_26/3Xunits.mrc models #6

Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  
Segmenting PflA-2_imasked_imasked, density threshold 0.184695  
Showing 130 region surfaces  
1144 watershed regions, grouped to 130 regions  
Showing PflA-2_imasked_imasked.seg - 130 regions, 130 surfaces  

> hide #!6 models

> select #2.68

1 model selected  

> select add #2.89

2 models selected  

> select add #2.12

3 models selected  

> select add #2.24

4 models selected  

> select add #2.14

5 models selected  

> select add #2.103

6 models selected  

> select add #2.51

7 models selected  

> select add #2.15

8 models selected  

> select add #2.86

9 models selected  
Grouped 9 regions  
Opened PflA-2_imasked_imasked_imasked as #8, grid size 240,240,240, pixel 2.1,
shown at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Segment_July_26/3XfliL.mrc models #8

Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at step 1, values float32  
Segmenting PflA-2_imasked_imasked_imasked, density threshold 0.184695  
Showing 121 region surfaces  
1088 watershed regions, grouped to 121 regions  
Showing PflA-2_imasked_imasked_imasked.seg - 121 regions, 121 surfaces  

> hide #!7 models

> hide #!8 models

> select #2.8

1 model selected  

> select add #2.71

2 models selected  

> select add #2.44

3 models selected  

> select add #2.27

4 models selected  

> select add #2.76

5 models selected  

> select add #2.63

6 models selected  

> select add #2.92

7 models selected  

> select add #2.17

8 models selected  

> select add #2.110

9 models selected  

> select add #2.90

10 models selected  

> select add #2.117

11 models selected  

> select add #2.56

12 models selected  

> select add #2.4

13 models selected  

> select add #2.14

14 models selected  

> select add #2.55

15 models selected  

> select add #2.98

16 models selected  

> select add #2.6

17 models selected  

> select add #2.49

18 models selected  

> select add #2.79

19 models selected  

> select add #2.105

20 models selected  

> select add #2.99

21 models selected  

> select add #2.78

22 models selected  

> select add #2.41

23 models selected  

> select add #2.72

24 models selected  

> select add #2.58

25 models selected  

> select add #2.5

26 models selected  

> select add #2.33

27 models selected  

> select subtract #2.33

26 models selected  

> select add #2.33

27 models selected  

> select add #2.112

28 models selected  

> select add #2.73

29 models selected  

> select add #2.57

30 models selected  

> select add #2.10

31 models selected  

> select subtract #2.5

30 models selected  

> select add #2.5

31 models selected  
Grouped 31 regions  

> select add #2.106

2 models selected  
Grouped 2 regions  

> hide #!9 models

> select add #2.1

2 models selected  

> select add #2.3

3 models selected  

> select add #2.2

4 models selected  

> select add #2.114

5 models selected  

> select add #2.115

6 models selected  

> select add #2.65

7 models selected  

> select add #2.28

8 models selected  

> select add #2.88

9 models selected  

> select add #2.68

10 models selected  

> select add #2.22

11 models selected  

> select add #2.43

12 models selected  

> select add #2.94

13 models selected  

> select add #2.29

14 models selected  

> select add #2.38

15 models selected  

> select add #2.64

16 models selected  

> select add #2.39

17 models selected  

> select add #2.100

18 models selected  

> select add #2.59

19 models selected  

> select add #2.12

20 models selected  

> select add #2.66

21 models selected  

> select add #2.34

22 models selected  
Grouped 22 regions  

> select add #2.93

2 models selected  

> select add #2.107

3 models selected  
Grouped 3 regions  

> select clear

> select #2.1

1 model selected  
Opened PflA-2_imasked_imasked_imasked_imasked as #10, grid size 240,240,240,
pixel 2.1, shown at step 1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Segment_July_26/IM.mrc models #10

Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
pixel 2.1, shown at step 1, values float32  
Segmenting 3Xunits.mrc, density threshold 0.184695  
Showing 52 region surfaces  
265 watershed regions, grouped to 52 regions  
Showing 3Xunits.seg - 52 regions, 52 surfaces  

> hide #!10 models

> hide #!2 models

> hide #!11 models

> show #!6 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflA.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/New_PflA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77  
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12  
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3  
679 messages similar to the above omitted  
  
Chain information for New_PflA.pdb  
---  
Chain | Description  
12.1/A0 12.2/A2 12.3/A4 12.4/A6 12.5/A8 12.6/At 12.7/Av 12.8/Ax 12.9/Az 12.10/BB 12.11/BD 12.12/BF 12.13/BH 12.14/BJ 12.15/BL 12.16/BN 12.17/BP 12.18/BR | No description available  
12.19/CK 12.20/CM 12.21/CO 12.22/CQ 12.23/CS 12.24/CU 12.25/CW 12.26/CY 12.27/Ca 12.28/Cc 12.29/Ce 12.30/Cg 12.31/Ci 12.32/Ck 12.33/Cm 12.34/Co 12.35/Cq 12.36/Cs | No description available  
  

> select add #12

109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected  

> ui mousemode right "translate selected models"

> view matrix models #12,1,0,0,-691.77,0,1,0,-586.46,0,0,1,-473.7

> view matrix models #12,1,0,0,-747.48,0,1,0,-578.05,0,0,1,-528.69

> view matrix models #12,1,0,0,-765.74,0,1,0,-634.57,0,0,1,-507.8

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.93968,-0.34172,0.015266,-557.95,0.3415,0.93976,0.015284,-792.76,-0.019569,-0.0091485,0.99977,-492.31

> hide #!6 models

> show #!6 models

> view matrix models
> #12,0.93938,-0.34184,-0.02662,-536.73,0.34264,0.93876,0.036376,-803.4,0.012555,-0.043292,0.99898,-490.81

> view matrix models
> #12,0.93488,-0.35397,-0.026433,-527.92,0.35476,0.93425,0.036495,-807.52,0.011777,-0.043496,0.99898,-490.28

> hide #!6 models

> show #!6 models

> hide #!6 models

> select clear

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

Drag select of 2113 residues  

> select add #12.20

17231 atoms, 1136 bonds, 2113 residues, 6 models selected  

> select add #12.19

17231 atoms, 2272 bonds, 2113 residues, 6 models selected  

> select add #12.18

17231 atoms, 7359 bonds, 4 pseudobonds, 2113 residues, 7 models selected  

> select add #12.6

17231 atoms, 12446 bonds, 8 pseudobonds, 2113 residues, 8 models selected  

> select add #12.4

22198 atoms, 17533 bonds, 12 pseudobonds, 2722 residues, 9 models selected  

> select subtract #12.4

17203 atoms, 12446 bonds, 8 pseudobonds, 2110 residues, 7 models selected  

> select add #12.3

17203 atoms, 17533 bonds, 12 pseudobonds, 2110 residues, 8 models selected  
Drag select of 137 residues  

> select add #12.21

18312 atoms, 18669 bonds, 12 pseudobonds, 2247 residues, 9 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/3XPflA_For_Figure.pdb selectedOnly true

> select add #12

109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected  

> select subtract #12

Nothing selected  

> hide #!12 models

> show #!6 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflB.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/New_PflB.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77  
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12  
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3  
337 messages similar to the above omitted  
  
Chain information for New_PflB.pdb  
---  
Chain | Description  
13.1/CJ 13.2/CL 13.3/CN 13.4/CP 13.5/CR 13.6/CT 13.7/CV 13.8/CX 13.9/CZ 13.10/Cb 13.11/Cd 13.12/Cf 13.13/Ch 13.14/Cj 13.15/Cl 13.16/Cn 13.17/Cp 13.18/Cr | No description available  
  

> select add #13

122922 atoms, 125496 bonds, 15174 residues, 19 models selected  

> ui mousemode right "translate selected models"

> view matrix models #13,1,0,0,-890.52,0,1,0,-614.02,0,0,1,-0.53894

> view matrix models #13,1,0,0,-828.91,0,1,0,-519.77,0,0,1,-541.34

> color #6 #b2b2b27d models

> view matrix models #13,1,0,0,-799.1,0,1,0,-520.23,0,0,1,-537.82

> view matrix models #13,1,0,0,-798.64,0,1,0,-493.13,0,0,1,-531.94

> view matrix models #13,1,0,0,-797.26,0,1,0,-484.01,0,0,1,-531.99

> view matrix models #13,1,0,0,-803.83,0,1,0,-489.12,0,0,1,-536.9

> view matrix models #13,1,0,0,-804.61,0,1,0,-487.3,0,0,1,-536.07

> view matrix models #13,1,0,0,-805.15,0,1,0,-486.78,0,0,1,-536.22

> view matrix models #13,1,0,0,-806.6,0,1,0,-486.23,0,0,1,-536.41

> view matrix models #13,1,0,0,-806.63,0,1,0,-485.73,0,0,1,-536.5

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/3XPflA_For_Figure.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/3XPflA_For_Figure.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  
247 messages similar to the above omitted  
  
Chain information for 3XPflA_For_Figure.pdb  
---  
Chain | Description  
14.1/A4 14.2/At 14.3/BR | No description available  
14.4/CK 14.5/CM 14.6/CO | No description available  
  

> select subtract #13

Nothing selected  

> select add #13.1

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select add #13.2

13658 atoms, 13944 bonds, 1686 residues, 2 models selected  

> select add #13.18

20487 atoms, 20916 bonds, 2529 residues, 3 models selected  

> hide #!14 models

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/3XPflB_For_Figure.pdb selectedOnly true

> select add #13

122922 atoms, 125496 bonds, 15174 residues, 19 models selected  

> select subtract #13

Nothing selected  

> hide #!13 models

> show #!12 models

> select add #12

109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.93917,-0.3423,-0.027997,-535.69,0.34313,0.93867,0.033954,-802.39,0.014657,-0.041495,0.99903,-492.92

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.93917,-0.3423,-0.027997,-544.48,0.34313,0.93867,0.033954,-796.05,0.014657,-0.041495,0.99903,-495.99

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.94942,-0.31252,-0.030531,-564.67,0.31337,0.9492,0.028622,-783.09,0.020035,-0.036742,0.99912,-501.47

> view matrix models
> #12,0.9534,-0.30006,-0.031633,-572.93,0.3009,0.95329,0.026431,-777.51,0.022225,-0.034717,0.99915,-503.74

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.9534,-0.30006,-0.031633,-591.15,0.3009,0.95329,0.026431,-773.38,0.022225,-0.034717,0.99915,-507.83

> view matrix models
> #12,0.9534,-0.30006,-0.031633,-589.15,0.3009,0.95329,0.026431,-773.36,0.022225,-0.034717,0.99915,-523.8

> show #!1 models

> hide #!1 models

> show #!13 models

> view matrix models
> #12,0.9534,-0.30006,-0.031633,-571.9,0.3009,0.95329,0.026431,-763.51,0.022225,-0.034717,0.99915,-523.95

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.9534,-0.30006,-0.031633,-578.46,0.3009,0.95329,0.026431,-764.81,0.022225,-0.034717,0.99915,-524.27

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.97201,-0.22901,-0.052453,-616.07,0.23037,0.97287,0.021462,-735.11,0.046115,-0.032945,0.99839,-537.61

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.97201,-0.22901,-0.052453,-615.62,0.23037,0.97287,0.021462,-720.56,0.046115,-0.032945,0.99839,-542.07

> view matrix models
> #12,0.97201,-0.22901,-0.052453,-634.23,0.23037,0.97287,0.021462,-725.26,0.046115,-0.032945,0.99839,-543.66

> close #12-14

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflA.pdb
> /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflB.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/New_PflA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77  
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12  
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3  
679 messages similar to the above omitted  
  
Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/New_PflB.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77  
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12  
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3  
337 messages similar to the above omitted  
  
Chain information for New_PflA.pdb  
---  
Chain | Description  
12.1/A0 12.2/A2 12.3/A4 12.4/A6 12.5/A8 12.6/At 12.7/Av 12.8/Ax 12.9/Az 12.10/BB 12.11/BD 12.12/BF 12.13/BH 12.14/BJ 12.15/BL 12.16/BN 12.17/BP 12.18/BR | No description available  
12.19/CK 12.20/CM 12.21/CO 12.22/CQ 12.23/CS 12.24/CU 12.25/CW 12.26/CY 12.27/Ca 12.28/Cc 12.29/Ce 12.30/Cg 12.31/Ci 12.32/Ck 12.33/Cm 12.34/Co 12.35/Cq 12.36/Cs | No description available  
  
Chain information for New_PflB.pdb  
---  
Chain | Description  
13.1/CJ 13.2/CL 13.3/CN 13.4/CP 13.5/CR 13.6/CT 13.7/CV 13.8/CX 13.9/CZ 13.10/Cb 13.11/Cd 13.12/Cf 13.13/Ch 13.14/Cj 13.15/Cl 13.16/Cn 13.17/Cp 13.18/Cr | No description available  
  

> select add #12

109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected  

> select add #13

232794 atoms, 237510 bonds, 72 pseudobonds, 28656 residues, 74 models selected  

> view matrix models
> #12,1,0,0,-521.29,0,1,0,-757.15,0,0,1,-99.846,#13,1,0,0,-521.29,0,1,0,-757.15,0,0,1,-99.846

> view matrix models
> #12,1,0,0,-674.3,0,1,0,-816.73,0,0,1,-503,#13,1,0,0,-674.3,0,1,0,-816.73,0,0,1,-503

> view matrix models
> #12,1,0,0,-818.6,0,1,0,-541.33,0,0,1,-541.51,#13,1,0,0,-818.6,0,1,0,-541.33,0,0,1,-541.51

> view matrix models
> #12,1,0,0,-801.6,0,1,0,-547.01,0,0,1,-538.38,#13,1,0,0,-801.6,0,1,0,-547.01,0,0,1,-538.38

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #12,0.99943,-0.0024951,0.03356,-816,0.0025771,0.99999,-0.0023996,-547.24,-0.033554,0.0024847,0.99943,-521.47,#13,0.99943,-0.0024951,0.03356,-816,0.0025771,0.99999,-0.0023996,-547.24,-0.033554,0.0024847,0.99943,-521.47

> view matrix models
> #12,0.99918,-0.029188,0.028162,-798.99,0.030798,0.99781,-0.058541,-534.38,-0.026392,0.05936,0.99789,-555.03,#13,0.99918,-0.029188,0.028162,-798.99,0.030798,0.99781,-0.058541,-534.38,-0.026392,0.05936,0.99789,-555.03

> ui mousemode right "translate selected models"

> view orient

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.78826,0.61515,-0.015745,-1010.3,-0.61478,0.78618,-0.063026,-72.53,-0.026392,0.05936,0.99789,-555.03,#13,0.78826,0.61515,-0.015745,-1010.3,-0.61478,0.78618,-0.063026,-72.53,-0.026392,0.05936,0.99789,-555.03

> view matrix models
> #12,-0.91285,-0.35663,-0.19881,509.75,0.30121,-0.91692,0.26179,196,-0.27565,0.17909,0.94443,-460.28,#13,-0.91285,-0.35663,-0.19881,509.75,0.30121,-0.91692,0.26179,196,-0.27565,0.17909,0.94443,-460.28

> view matrix models
> #12,-0.91231,-0.35669,-0.20115,510.6,0.30125,-0.91733,0.26031,196.89,-0.27737,0.17689,0.94434,-458.14,#13,-0.91231,-0.35669,-0.20115,510.6,0.30125,-0.91733,0.26031,196.89,-0.27737,0.17689,0.94434,-458.14

> view matrix models
> #12,-0.91786,-0.31644,-0.23958,510.27,0.36303,-0.91334,-0.18444,372.99,-0.16046,-0.25626,0.9532,-292.95,#13,-0.91786,-0.31644,-0.23958,510.27,0.36303,-0.91334,-0.18444,372.99,-0.16046,-0.25626,0.9532,-292.95

> undo

> view matrix models
> #12,-0.49013,-0.868,-0.079649,501.01,0.81728,-0.4894,0.3042,-329.87,-0.30303,0.084001,0.94927,-396.92,#13,-0.49013,-0.868,-0.079649,501.01,0.81728,-0.4894,0.3042,-329.87,-0.30303,0.084001,0.94927,-396.92

> view matrix models
> #12,-0.49535,-0.86438,-0.086411,505.08,0.82329,-0.49887,0.27077,-312.12,-0.27716,0.062985,0.95876,-404.01,#13,-0.49535,-0.86438,-0.086411,505.08,0.82329,-0.49887,0.27077,-312.12,-0.27716,0.062985,0.95876,-404.01

> view orient

[Repeated 1 time(s)]

> view matrix models
> #12,-0.18563,-0.98256,0.010887,356.46,0.94272,-0.17496,0.28402,-555.89,-0.27716,0.062985,0.95876,-404.01,#13,-0.18563,-0.98256,0.010887,356.46,0.94272,-0.17496,0.28402,-555.89,-0.27716,0.062985,0.95876,-404.01

> view matrix models
> #12,-0.18351,-0.98301,0.0031045,359.27,0.94593,-0.17572,0.27265,-551.79,-0.26748,0.052971,0.96211,-405.41,#13,-0.18351,-0.98301,0.0031045,359.27,0.94593,-0.17572,0.27265,-551.79,-0.26748,0.052971,0.96211,-405.41

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.18351,-0.98301,0.0031045,359.43,0.94593,-0.17572,0.27265,-548.64,-0.26748,0.052971,0.96211,-395.12,#13,-0.18351,-0.98301,0.0031045,359.43,0.94593,-0.17572,0.27265,-548.64,-0.26748,0.052971,0.96211,-395.12

> view matrix models
> #12,-0.18351,-0.98301,0.0031045,358.91,0.94593,-0.17572,0.27265,-549.61,-0.26748,0.052971,0.96211,-394.94,#13,-0.18351,-0.98301,0.0031045,358.91,0.94593,-0.17572,0.27265,-549.61,-0.26748,0.052971,0.96211,-394.94

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.12979,-0.99153,0.0042033,334.22,0.95586,-0.12399,0.26639,-579.66,-0.26361,0.038591,0.96386,-390.13,#13,-0.12979,-0.99153,0.0042033,334.22,0.95586,-0.12399,0.26639,-579.66,-0.26361,0.038591,0.96386,-390.13

> view matrix models
> #12,-0.19228,-0.98134,0.0028902,362.81,0.94402,-0.18417,0.27368,-544.56,-0.26804,0.055352,0.96182,-395.77,#13,-0.19228,-0.98134,0.0028902,362.81,0.94402,-0.18417,0.27368,-544.56,-0.26804,0.055352,0.96182,-395.77

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.19228,-0.98134,0.0028902,365.42,0.94402,-0.18417,0.27368,-554.48,-0.26804,0.055352,0.96182,-392.9,#13,-0.19228,-0.98134,0.0028902,365.42,0.94402,-0.18417,0.27368,-554.48,-0.26804,0.055352,0.96182,-392.9

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.19228,-0.98134,0.0028902,365.05,0.94402,-0.18417,0.27368,-553.94,-0.26804,0.055352,0.96182,-393.08,#13,-0.19228,-0.98134,0.0028902,365.05,0.94402,-0.18417,0.27368,-553.94,-0.26804,0.055352,0.96182,-393.08

> view matrix models
> #12,-0.19228,-0.98134,0.0028902,362.37,0.94402,-0.18417,0.27368,-553.57,-0.26804,0.055352,0.96182,-393.5,#13,-0.19228,-0.98134,0.0028902,362.37,0.94402,-0.18417,0.27368,-553.57,-0.26804,0.055352,0.96182,-393.5

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.30432,-0.95257,-6.2098e-06,82.602,0.93025,0.29719,0.21522,-776.17,-0.20501,-0.065503,0.97656,-369.52,#13,0.30432,-0.95257,-6.2098e-06,82.602,0.93025,0.29719,0.21522,-776.17,-0.20501,-0.065503,0.97656,-369.52

> view matrix models
> #12,-0.50993,-0.86013,-0.012205,474.59,0.81576,-0.48803,0.31041,-339.58,-0.27295,0.14833,0.95052,-435.32,#13,-0.50993,-0.86013,-0.012205,474.59,0.81576,-0.48803,0.31041,-339.58,-0.27295,0.14833,0.95052,-435.32

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.50993,-0.86013,-0.012205,474.98,0.81576,-0.48803,0.31041,-333.86,-0.27295,0.14833,0.95052,-421.7,#13,-0.50993,-0.86013,-0.012205,474.98,0.81576,-0.48803,0.31041,-333.86,-0.27295,0.14833,0.95052,-421.7

> view matrix models
> #12,-0.50993,-0.86013,-0.012205,481.34,0.81576,-0.48803,0.31041,-331.89,-0.27295,0.14833,0.95052,-421.33,#13,-0.50993,-0.86013,-0.012205,481.34,0.81576,-0.48803,0.31041,-331.89,-0.27295,0.14833,0.95052,-421.33

> select clear

> select add #13.1

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select subtract #13.1

Nothing selected  

> select add #13.4

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select subtract #13.4

Nothing selected  

> select add #13.9

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select subtract #13.9

Nothing selected  

> select add #13.13

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select add #13.14

13658 atoms, 13944 bonds, 1686 residues, 2 models selected  

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> select add #13.12

20487 atoms, 20916 bonds, 2529 residues, 3 models selected  

> select subtract #13.12

13658 atoms, 13944 bonds, 1686 residues, 2 models selected  

> select add #13.15

20487 atoms, 20916 bonds, 2529 residues, 3 models selected  

> select add #12.28

21596 atoms, 22052 bonds, 2666 residues, 4 models selected  

> select subtract #12.28

20487 atoms, 20916 bonds, 2529 residues, 3 models selected  

> select add #12.19

21596 atoms, 22052 bonds, 2666 residues, 4 models selected  

> select subtract #12.19

20487 atoms, 20916 bonds, 2529 residues, 3 models selected  

> select subtract #13.13

13658 atoms, 13944 bonds, 1686 residues, 2 models selected  

> select subtract #13.14

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select subtract #13.15

Nothing selected  

> hide #!13 models

> hide #!6 models

> undo

> show #!13 models

> hide #!13 models

> undo

[Repeated 7 time(s)]

> select add #13

122922 atoms, 125496 bonds, 15174 residues, 19 models selected  

> select subtract #13

Nothing selected  

> hide #!13 models

> hide #!6 models

Drag select of 1603 residues  
Drag select of 128 residues  

> select add #12.33

14230 atoms, 1136 bonds, 1740 residues, 6 models selected  

> select add #12.32

14418 atoms, 2272 bonds, 1765 residues, 6 models selected  

> select add #12.31

14502 atoms, 3408 bonds, 1776 residues, 6 models selected  

> select add #12.15

16773 atoms, 8495 bonds, 4 pseudobonds, 2056 residues, 7 models selected  

> select add #12.14

16773 atoms, 13582 bonds, 8 pseudobonds, 2056 residues, 8 models selected  

> select add #12.9

18312 atoms, 18669 bonds, 12 pseudobonds, 2247 residues, 9 models selected  

> hide #12.36 models

> show #12.36 models

> show #!13 models

> select add #13.13

25141 atoms, 25641 bonds, 12 pseudobonds, 3090 residues, 10 models selected  

> select add #13.14

31970 atoms, 32613 bonds, 12 pseudobonds, 3933 residues, 11 models selected  

> select add #13.15

38799 atoms, 39585 bonds, 12 pseudobonds, 4776 residues, 12 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3XPflA-
> PflB_For_Figure.pdb selectedOnly true

> select add #13

141234 atoms, 144165 bonds, 12 pseudobonds, 17421 residues, 28 models selected  

> select add #12

232794 atoms, 237510 bonds, 72 pseudobonds, 28656 residues, 74 models selected  

> select subtract #12

122922 atoms, 125496 bonds, 15174 residues, 19 models selected  

> select subtract #13

Nothing selected  

> hide #!13 models

> hide #!12 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3XPflA-
> PflB_For_Figure.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/3XPflA-PflB_For_Figure.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  
373 messages similar to the above omitted  
  
Chain information for 3XPflA-PflB_For_Figure.pdb  
---  
Chain | Description  
14.1/Az 14.2/BJ 14.3/BL | No description available  
14.7/Ch 14.8/Cj 14.9/Cl | No description available  
14.4/Ci 14.5/Ck 14.6/Cm | No description available  
  

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!6 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> combine #14 modelId #15 name 3XPflAB

> hide #!14 models

> ui tool show "Fit in Map"

> fitmap #15 inMap #6

Fit molecule 3XPflAB (#15) to map 3Xunits.mrc (#6) using 38799 atoms  
average map value = 2.154, steps = 168  
shifted from previous position = 9.31  
rotated from previous position = 16.8 degrees  
atoms outside contour = 17471, contour level = 0.1847  
  
Position of 3XPflAB (#15) relative to 3Xunits.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99462895 0.03678980 0.09674590 -6.40729211  
-0.00917946 0.96236927 -0.27158998 -9.52019787  
-0.10309702 0.26924318 0.95753805 -12.34964828  
Axis 0.93504439 0.34550766 -0.07947608  
Axis point 0.00000000 43.50384781 -30.52375104  
Rotation angle (degrees) 16.81017889  
Shift along axis -8.29890223  
  

> fitmap #15 inMap #6

Fit molecule 3XPflAB (#15) to map 3Xunits.mrc (#6) using 38799 atoms  
average map value = 2.154, steps = 28  
shifted from previous position = 0.0497  
rotated from previous position = 0.0178 degrees  
atoms outside contour = 17462, contour level = 0.1847  
  
Position of 3XPflAB (#15) relative to 3Xunits.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99464111 0.03692161 0.09657053 -6.40475417  
-0.00937546 0.96242184 -0.27139696 -9.49328505  
-0.10296200 0.26903717 0.95761048 -12.38014369  
Axis 0.93508874 0.34524211 -0.08010574  
Axis point 0.00000000 43.67465586 -30.50033372  
Rotation angle (degrees) 16.79658762  
Shift along axis -8.27477473  
  

> fitmap #15 inMap #6

Fit molecule 3XPflAB (#15) to map 3Xunits.mrc (#6) using 38799 atoms  
average map value = 2.154, steps = 28  
shifted from previous position = 0.05  
rotated from previous position = 0.0179 degrees  
atoms outside contour = 17470, contour level = 0.1847  
  
Position of 3XPflAB (#15) relative to 3Xunits.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99462364 0.03681644 0.09679029 -6.40747251  
-0.00919551 0.96237529 -0.27156812 -9.52193056  
-0.10314675 0.26921804 0.95753976 -12.34665377  
Axis 0.93497610 0.34567518 -0.07955098  
Axis point 0.00000000 43.49956479 -30.52433596  
Rotation angle (degrees) 16.80993871  
Shift along axis -8.30014028  
  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true

[Repeated 1 time(s)]

——— End of log from Fri Jul 26 15:41:13 2024 ———

opened ChimeraX session  
Showing 3Xunits.seg - 52 regions, 52 surfaces  

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/38xcage.pdb

Chain information for 38xcage.pdb  
---  
Chain | Description  
16.1/A 16.2/A 16.3/A 16.4/A 16.5/A 16.6/A 16.7/A 16.8/A 16.9/A 16.10/A 16.11/A 16.12/A 16.13/A 16.14/A 16.15/A 16.16/A 16.17/A 16.18/A 16.19/A 16.20/A 16.21/A 16.22/A 16.23/A 16.24/A 16.25/A 16.26/A 16.27/A 16.28/A 16.29/A 16.30/A 16.31/A 16.32/A 16.33/A 16.34/A 16.35/A 16.36/A | No description available  
16.1/B 16.2/B 16.3/B 16.4/B 16.5/B 16.6/B 16.7/B 16.8/B 16.9/B 16.10/B 16.11/B 16.12/B 16.13/B 16.14/B 16.15/B 16.16/B 16.17/B 16.18/B 16.19/B 16.20/B 16.21/B 16.22/B 16.23/B 16.24/B 16.25/B 16.26/B 16.27/B 16.28/B 16.29/B 16.30/B 16.31/B 16.32/B 16.33/B 16.34/B 16.35/B 16.36/B | No description available  
  

> select add #16

99648 atoms, 101772 bonds, 12096 residues, 37 models selected  

> view matrix models #16,1,0,0,-827.48,0,1,0,-569.5,0,0,1,-43.802

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.99267,0.1207,-0.0060172,-885.78,-0.12075,0.99263,-0.0097829,-496.35,0.0047921,0.010438,0.99993,-51.959

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.99267,0.1207,-0.0060172,-851.95,-0.12075,0.99263,-0.0097829,-530.26,0.0047921,0.010438,0.99993,-505.69

> hide #!6 models

> hide #!2 models

> show #!6 models

> view matrix models
> #16,0.99267,0.1207,-0.0060172,-843.71,-0.12075,0.99263,-0.0097829,-517.73,0.0047921,0.010438,0.99993,-505.14

> view matrix models
> #16,0.99267,0.1207,-0.0060172,-833.32,-0.12075,0.99263,-0.0097829,-552.99,0.0047921,0.010438,0.99993,-547.81

> view matrix models
> #16,0.99267,0.1207,-0.0060172,-832.55,-0.12075,0.99263,-0.0097829,-552.33,0.0047921,0.010438,0.99993,-547.97

> view matrix models
> #16,0.99267,0.1207,-0.0060172,-830.52,-0.12075,0.99263,-0.0097829,-546.96,0.0047921,0.010438,0.99993,-548.4

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.98673,0.16225,-0.0065777,-849.42,-0.16226,0.98675,-0.001445,-525.19,0.0062561,0.0024931,0.99998,-544.93

> view matrix models
> #16,0.98655,0.16312,-0.010639,-848,-0.16318,0.98658,-0.0052162,-522.94,0.0096456,0.0068822,0.99993,-549.09

> view matrix models
> #16,0.98493,0.16616,0.047895,-874.67,-0.16542,0.98604,-0.019171,-515.27,-0.050411,0.01096,0.99867,-518.47

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.98493,0.16616,0.047895,-885.95,-0.16542,0.98604,-0.019171,-505.9,-0.050411,0.01096,0.99867,-516.38

> view matrix models
> #16,0.98493,0.16616,0.047895,-900.24,-0.16542,0.98604,-0.019171,-500.14,-0.050411,0.01096,0.99867,-513.67

> select subtract #16

Nothing selected  

> select add #16.6

2768 atoms, 2827 bonds, 336 residues, 1 model selected  

> select subtract #16.6

Nothing selected  

> select add #16.27

2768 atoms, 2827 bonds, 336 residues, 1 model selected  

> select add #16.28

5536 atoms, 5654 bonds, 672 residues, 2 models selected  

> select add #16.29

8304 atoms, 8481 bonds, 1008 residues, 3 models selected  

> select add #16.9

11072 atoms, 11308 bonds, 1344 residues, 4 models selected  

> select add #16.10

13840 atoms, 14135 bonds, 1680 residues, 5 models selected  

> select add #16.11

16608 atoms, 16962 bonds, 2016 residues, 6 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Cage-
> for-3units.pdb selectedOnly true

> select add #16

99648 atoms, 101772 bonds, 12096 residues, 37 models selected  

> select subtract #16

Nothing selected  

> hide #!16 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Cage-
> for-3units.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Cage-
for-3units.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  
247 messages similar to the above omitted  
  
Chain information for Cage-for-3units.pdb  
---  
Chain | Description  
17.1/A 17.2/A 17.3/A 17.4/A 17.5/A 17.6/A | No description available  
17.1/B 17.2/B 17.3/B 17.4/B 17.5/B 17.6/B | No description available  
  

> select add #17

16608 atoms, 16962 bonds, 2016 residues, 7 models selected  

> select subtract #17

Nothing selected  

> select add #17.1

2768 atoms, 2827 bonds, 336 residues, 1 model selected  

> combine #17 modelId #18 name Cage

Remapping chain ID 'A' in Cage-for-3units.pdb #17.2 to 'C'  
Remapping chain ID 'B' in Cage-for-3units.pdb #17.2 to 'D'  
Remapping chain ID 'A' in Cage-for-3units.pdb #17.3 to 'E'  
Remapping chain ID 'B' in Cage-for-3units.pdb #17.3 to 'F'  
Remapping chain ID 'A' in Cage-for-3units.pdb #17.4 to 'G'  
Remapping chain ID 'B' in Cage-for-3units.pdb #17.4 to 'H'  
Remapping chain ID 'A' in Cage-for-3units.pdb #17.5 to 'I'  
Remapping chain ID 'B' in Cage-for-3units.pdb #17.5 to 'J'  
Remapping chain ID 'A' in Cage-for-3units.pdb #17.6 to 'K'  
Remapping chain ID 'B' in Cage-for-3units.pdb #17.6 to 'L'  

> ui tool show "Fit in Map"

> fitmap #18 inMap #6

Fit molecule Cage (#18) to map 3Xunits.mrc (#6) using 16608 atoms  
average map value = 2.444, steps = 152  
shifted from previous position = 22.7  
rotated from previous position = 11.5 degrees  
atoms outside contour = 8239, contour level = 0.1847  
  
Position of Cage (#18) relative to 3Xunits.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98420114 0.17466936 0.02896094 15.18429004  
-0.17661022 0.98008584 0.09077766 20.68378027  
-0.01252813 -0.09445827 0.99544999 19.05066641  
Axis -0.46391541 0.10390761 -0.87976457  
Axis point 131.82850583 -17.49249647 0.00000000  
Rotation angle (degrees) 11.51614665  
Shift along axis -21.65512535  
  

> select add #17

16608 atoms, 16962 bonds, 2016 residues, 7 models selected  

> hide #!17 models

> select subtract #17

Nothing selected  

> close #17

> split #18

Split Cage (#18) into 12 models  
Chain information for Cage A #18.1  
---  
Chain | Description  
A | No description available  
  
Chain information for Cage B #18.2  
---  
Chain | Description  
B | No description available  
  
Chain information for Cage C #18.3  
---  
Chain | Description  
C | No description available  
  
Chain information for Cage D #18.4  
---  
Chain | Description  
D | No description available  
  
Chain information for Cage E #18.5  
---  
Chain | Description  
E | No description available  
  
Chain information for Cage F #18.6  
---  
Chain | Description  
F | No description available  
  
Chain information for Cage G #18.7  
---  
Chain | Description  
G | No description available  
  
Chain information for Cage H #18.8  
---  
Chain | Description  
H | No description available  
  
Chain information for Cage I #18.9  
---  
Chain | Description  
I | No description available  
  
Chain information for Cage J #18.10  
---  
Chain | Description  
J | No description available  
  
Chain information for Cage K #18.11  
---  
Chain | Description  
K | No description available  
  
Chain information for Cage L #18.12  
---  
Chain | Description  
L | No description available  
  

> split #15]

Expected a structures specifier or a keyword  

> split #15

Split 3XPflAB (#15) into 9 models  
Chain information for 3XPflAB Az #15.1  
---  
Chain | Description  
Az | No description available  
  
Chain information for 3XPflAB BJ #15.2  
---  
Chain | Description  
BJ | No description available  
  
Chain information for 3XPflAB BL #15.3  
---  
Chain | Description  
BL | No description available  
  
Chain information for 3XPflAB Ch #15.4  
---  
Chain | Description  
Ch | No description available  
  
Chain information for 3XPflAB Ci #15.5  
---  
Chain | Description  
Ci | No description available  
  
Chain information for 3XPflAB Cj #15.6  
---  
Chain | Description  
Cj | No description available  
  
Chain information for 3XPflAB Ck #15.7  
---  
Chain | Description  
Ck | No description available  
  
Chain information for 3XPflAB Cl #15.8  
---  
Chain | Description  
Cl | No description available  
  
Chain information for 3XPflAB Cm #15.9  
---  
Chain | Description  
Cm | No description available  
  

> select add #18.12

1486 atoms, 1517 bonds, 179 residues, 1 model selected  

> select subtract #18.12

Nothing selected  

> hide #18.1 models

> show #18.1 models

> hide #18.1 models

> hide #18.2 models

> hide #!6 models

> hide #!18 models

Drag select of 564 residues  
Drag select of 129 residues  

> select clear

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!15 models

Drag select of 515 residues  

> select add #15.1

8499 atoms, 5088 bonds, 1047 residues, 3 models selected  

> select subtract #15.1

3504 atoms, 435 residues, 2 models selected  

> hide #15.1 models

> hide #15.4 models

> hide #15.5 models

> select add #15.9

4613 atoms, 1136 bonds, 572 residues, 3 models selected  

> select subtract #15.9

3504 atoms, 435 residues, 2 models selected  

> select add #15.8

10333 atoms, 6972 bonds, 1278 residues, 3 models selected  

> select subtract #15.8

3504 atoms, 435 residues, 2 models selected  

> select add #15.7

4613 atoms, 1136 bonds, 572 residues, 3 models selected  

> select subtract #15.7

3504 atoms, 435 residues, 2 models selected  

> select add #15.6

10333 atoms, 6972 bonds, 1278 residues, 3 models selected  

> select subtract #15.6

3504 atoms, 435 residues, 2 models selected  

> select add #15.3

8499 atoms, 5088 bonds, 1047 residues, 3 models selected  

> select subtract #15.3

3504 atoms, 435 residues, 2 models selected  

> select add #15.2

8499 atoms, 5088 bonds, 1047 residues, 3 models selected  

> select subtract #15.2

3504 atoms, 435 residues, 2 models selected  

> show #!2 models

> hide #!2 models

> show #!18 models

> show #!6 models

> show #15.5 models

> hide #15.5 models

> show #15.4 models

> select add #15.4

7938 atoms, 6972 bonds, 980 residues, 2 models selected  

> select subtract #15.4

1109 atoms, 137 residues, 1 model selected  

> hide #15.2 models

> show #15.2 models

> hide #15.9 models

> show #15.9 models

> hide #15.8 models

> hide #15.2 models

> show #15.2 models

> hide #15.3 models

> hide #15.4 models

> show #15.4 models

> hide #15.6 models

> show #15.6 models

> hide #15.7 models

> show #15.7 models

> select add #15.5

1109 atoms, 1136 bonds, 137 residues, 1 model selected  
Drag select of 15 residues  

> hide #15.9 models

> select add #15.9

2218 atoms, 2272 bonds, 274 residues, 2 models selected  

> select subtract #15.9

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> set bgColor white

> set bgColor #ffffff00

> color #6 #72727233 models

> hide #15.2 models

> show #15.2 models

> color #15.2 #9850ffff models

> color #15.2 #d310c9ff

> color #15.2 #ec701aff

> color #15.2 #ca676980

> color #15.2 #ca6769ff

> color #15.2 #ca5254ff

> color #15.2 #ca515eff

> color #15.2 #ca4949ff

> select subtract #15.5

Nothing selected  

> hide #15.6 models

> show #15.6 models

> hide #15.7 models

> show #15.7 models

> color #15.7 #9850ffff models

> color #15.7 #ca4949ff

> hide #15.4 models

> show #15.4 models

> hide #15.4 models

> show #15.4 models

> hide #15.6 models

> show #15.6 models

> color #15.6 #0067b6ff models

> show #15.5 models

> hide #15.5 models

> show #15.4 models

> color #15.4 magenta models

> color #15.6 magenta models

> color #15.6 #93329aff

> color #15.4 magenta models

[Repeated 1 time(s)]

> color #15.6 magenta models

> color #15.4 #b53ebdff

> color #15.4 #8c3092ff

> color #18 #52cdd6ff models

> select add #6

2 models selected  

> select add #15

38799 atoms, 39588 bonds, 4776 residues, 12 models selected  

> select add #18

55407 atoms, 56550 bonds, 6792 residues, 25 models selected  

> show sel & #15.2,4,6-7#18.3-12 surfaces

> hide sel & #!15.2,4,6-7#!18.3-12 atoms

> hide sel & #!15.2,4,6-7#!18.3-12 cartoons

> lighting soft

> view orient

> select subtract #15

16608 atoms, 16962 bonds, 2016 residues, 29 models selected  

> select clear

> select add #15.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #15.2

1 model selected  

> select add #15.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #15.2

1 model selected  

> hide #!15.2 models

> show #!15.2 models

> select add #15.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #15.2

1 model selected  

> select add #15.4

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select add #15.6

13658 atoms, 13944 bonds, 1686 residues, 3 models selected  

> select subtract #15.6

6829 atoms, 6972 bonds, 843 residues, 3 models selected  

> select add #15.6

13658 atoms, 13944 bonds, 1686 residues, 3 models selected  

> select subtract #15.6

6829 atoms, 6972 bonds, 843 residues, 3 models selected  

> select add #15.7

7938 atoms, 8108 bonds, 980 residues, 3 models selected  

> select subtract #15.7

6829 atoms, 6972 bonds, 843 residues, 3 models selected  

> select add #15.6

13658 atoms, 13944 bonds, 1686 residues, 3 models selected  
Alignment identifier is 1  

> select #15.4/Ch:1 #15.6/Cj:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #15.4/Ch:1-142 #15.6/Cj:1-142

2204 atoms, 2218 bonds, 282 residues, 2 models selected  
1 [ID: 1] region chains Ch,Cj [1-141] RMSD: 127.125  
  

> hide sel surfaces

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true

> view

[Repeated 1 time(s)]

> view name Top1

> save /Users/shoichi/Desktop/PflAB_local.png supersample 2
> transparentBackground true

> turn x 35

> turn x -35

[Repeated 2 time(s)]

> view Top1

> turn x 90

[Repeated 2 time(s)]

> turn x 10

[Repeated 5 time(s)]

> view Top1

> turn x -35

> select up

13658 atoms, 13944 bonds, 1686 residues, 4 models selected  

> select up

13658 atoms, 13944 bonds, 1686 residues, 4 models selected  

> view Top1

> select add #15

38799 atoms, 39588 bonds, 4776 residues, 12 models selected  

> select subtract #15

4 models selected  

> save /Users/shoichi/Desktop/PflAB_local.png supersample 2
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> hide #!15 models

> hide #!18 models

> ui tool show "Map Eraser"

> volume erase #6 center 28.224,-131.56,-185.36 radius 57.668

> show #!18 models

> close #17

> show #!16 models

> hide #!16 models

> show #!15 models

> view Top1

> turn x 90

[Repeated 2 time(s)]

> view Top1

> turn x -40

[Repeated 1 time(s)]

> view Top1

> turn x -70

> view Top1

> turn x -50

> save /Users/shoichi/Desktop/PflAB_local-tilt50.png supersample 2
> transparentBackground true

> hide #!18 models

> hide #!15 models

> ui tool show "Segment Map"

Segmenting 3Xunits.mrc, density threshold 0.184695  
Showing 51 region surfaces  
262 watershed regions, grouped to 51 regions  
Showing 3Xunits.seg - 51 regions, 51 surfaces  

> show #!16 models

> hide #!16 models

> show #!18 models

> hide #!18 models

> select add #2.49

1 model selected  

> select add #2.5

2 models selected  

> select add #2.3

3 models selected  

> select add #2.11

4 models selected  

> select add #2.8

5 models selected  

> select add #2.33

6 models selected  

> select add #2.32

7 models selected  

> select add #2.18

8 models selected  

> select add #2.16

9 models selected  

> select add #2.17

10 models selected  

> select add #2.31

11 models selected  

> select add #2.45

12 models selected  

> select add #2.30

13 models selected  

> select add #2.25

14 models selected  

> select add #2.44

15 models selected  

> select add #2.2

16 models selected  

> select subtract #2.2

15 models selected  

> show #!16 models

> hide #!16 models

> show #!18 models

> hide #!18 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> select add #2.21

16 models selected  

> select subtract #2.21

15 models selected  

> select add #2.43

16 models selected  

> select add #2.6

17 models selected  

> select add #2.7

18 models selected  

> select add #2.12

19 models selected  

> select add #2.19

20 models selected  

> select add #2.14

21 models selected  

> select add #2.35

22 models selected  

> select add #2.23

23 models selected  

> select add #2.24

24 models selected  

> select add #2.29

25 models selected  

> select add #2.40

26 models selected  

> select add #2.36

27 models selected  

> select add #2.26

28 models selected  

> select add #2.46

29 models selected  

> select add #2.38

30 models selected  

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> select subtract #2.30

29 models selected  

> show #!15 models

> select add #2.37

30 models selected  

> select add #2.9

31 models selected  

> select add #2.28

32 models selected  

> select add #2.20

33 models selected  

> select add #2.13

34 models selected  

> select add #2.15

35 models selected  

> select add #2.50

36 models selected  

> show #!18 models

> hide #!18 models

Opened 3Xunits_imasked as #17, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1Xunit-no-
> topcage.mrc models #17

> select add #2

52 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> hide #!6 models

> show #!18 models

> hide #!18.3 models

> show #!18.3 models

> hide #!18.3 models

> show #!18.3 models

> hide #!18.3 models

> show #!18.3 models

> hide #!18.4 models

> show #!18.4 models

> hide #!18.5 models

> show #!18.5 models

> hide #!18.6 models

> show #!18.6 models

> hide #!18.7 models

> show #!18.7 models

> hide #!18.7 models

> hide #!18.8 models

> show #!18.8 models

> show #!18.7 models

> hide #!18.9 models

> show #!18.9 models

> hide #!18.10 models

> show #!18.10 models

> hide #!18.11 models

> hide #!18.12 models

> view Top1

> turn x -50

> view name Tilt50

> turn y 10

[Repeated 3 time(s)]

> view Tilt50

> view Top1

> save /Users/shoichi/Desktop/PflAB_local-mono.png supersample 2
> transparentBackground true

> view Tilt50

> save /Users/shoichi/Desktop/PflAB_local-mono-tilt50.png supersample 2
> transparentBackground true

> turn x -40

> save /Users/shoichi/Desktop/PflAB_local-mono-tilt90.png supersample 2
> transparentBackground true

> turn y 90

> turn y -90

[Repeated 1 time(s)]

> show #!6 models

> view Top1

> turn y -90

[Repeated 3 time(s)]

> view Top1

[Repeated 1 time(s)]

> turn z -90

[Repeated 4 time(s)]

> turn x -50

> hide #!6 models

> save /Users/shoichi/Desktop/PflAB_local-mono-fromcage.png supersample 2
> transparentBackground true

> save /Users/shoichi/Desktop/PflAB_local-mono-fromcage-zoom.png supersample 2
> transparentBackground true

> save /Users/shoichi/Desktop/PflAB_local-mono-fromcage.png supersample 2
> transparentBackground true

> show #!1 models

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true

——— End of log from Fri Jul 26 17:21:33 2024 ———

opened ChimeraX session  
Showing 3Xunits.seg - 51 regions, 51 surfaces  

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> hide #!18 models

> show #!18 models

> color #18 #48a9c0ff models

> color #18 #4a9ed2ff models

> view Top1

> save /Users/shoichi/Desktop/Fig4D-1_08222024.png supersample 2
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> save /Users/shoichi/Desktop/Fig4D-2_08222024.png supersample 2
> transparentBackground true

> turn -Y 90

> turn -x 1

> turn -x -1

> turn -z -1

> turn -z 1

[Repeated 9 time(s)]

> turn -z -0.5

> view name Fig4E

> turn -Y -90

> view name Fig4D2

> turn -x -90

> view name Fig4D1

> save /Users/shoichi/Desktop/Fig4D-1_08222024.png supersample 2
> transparentBackground true

> view Fig4D2

> save /Users/shoichi/Desktop/Fig4D-2_08222024.png supersample 2
> transparentBackground true

> view Fig4E

> save /Users/shoichi/Desktop/Fig4E-1_08222024.png supersample 2
> transparentBackground true

> turn x 1

> turn x -1

> turn x 40

> save /Users/shoichi/Desktop/Fig4E-2_08222024.png supersample 2
> transparentBackground true

> view name Fig4E2

> view Fig4D1

> hide #!15 models

> show #!15 models

> show #!4 models

> hide #!4 models

> show #!6 models

> hide #!17 models

> save /Users/shoichi/Desktop/Fig4C1.png supersample 2 transparentBackground
> true

> turn x 50

> turn x -50

[Repeated 1 time(s)]

> save /Users/shoichi/Desktop/Fig4C2.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/For_Figure4_PflAB.cxs includeMaps true

——— End of log from Thu Aug 22 11:39:22 2024 ———

opened ChimeraX session  
Showing 3Xunits.seg - 51 regions, 51 surfaces  

> hide #!2 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!15 models

> show #!15 models

> show #!17 models

> hide #!18 models

> show #!18 models

> hide #17.1 models

> show #17.1 models

> hide #!15 models

> show #!15 models

> hide #!18 models

> show #!2 models

> hide #!15 models

> hide #!17 models

> hide #17.1 models

> show #!15 models

> hide #!15 models

> select #2.6

1 model selected  

> select add #2.47

2 models selected  

> select add #2.37

3 models selected  

> select clear

> select #2.30

1 model selected  

> select add #2.45

2 models selected  

> select add #2.12

3 models selected  

> select add #2.33

4 models selected  

> select add #2.50

5 models selected  

> select add #2.21

6 models selected  

> select add #2.16

7 models selected  

> select add #2.15

8 models selected  

> select add #2.24

9 models selected  

> select add #2.26

10 models selected  

> select add #2.18

11 models selected  

> select add #2.19

12 models selected  

> select add #2.9

13 models selected  

> select add #2.40

14 models selected  

> select add #2.10

15 models selected  

> select add #2.8

16 models selected  

> select add #2.14

17 models selected  

> select add #2.41

18 models selected  

> select add #2.46

19 models selected  

> select add #2.3

20 models selected  

> select add #2.7

21 models selected  

> select add #2.51

22 models selected  

> select add #2.48

23 models selected  

> select add #2.20

24 models selected  

> select add #2.47

25 models selected  

> select subtract #2.47

24 models selected  

> select add #2.25

25 models selected  

> select add #2.13

26 models selected  

> select add #2.42

27 models selected  

> select add #2.38

28 models selected  

> select add #2.35

29 models selected  

> select add #2.34

30 models selected  

> select add #2.17

31 models selected  

> select add #2.29

32 models selected  

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

Grouped 32 regions  

> select add #2.22

2 models selected  

> show #!15 models

> hide #!15 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Opened 3Xunits_imasked as #19, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  

> hide #!19 models

> show #!19 models

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New-1xPflAB.cxs
> includeMaps true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Segmenting 3Xunits_imasked, density threshold 0.184695  
Showing 18 region surfaces  
89 watershed regions, grouped to 18 regions  
Showing 3Xunits_imasked.seg - 18 regions, 18 surfaces  

> select #2.14

1 model selected  

> select add #2.18

2 models selected  

> select add #2.16

3 models selected  
Grouped 3 regions  

> select clear

> select #2.11

1 model selected  
Ungrouped to 2 regions  
[Repeated 1 time(s)]Ungrouped to 0 regions  

> select #2.19

1 model selected  

> select add #2.14

2 models selected  

> select clear

> select #2.14

1 model selected  
Opened 3Xunits_imasked_imasked as #20, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  

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/1xPflAB-New.mrc
> models #19

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/1xPflAB-New-no-
> cyt-cage.mrc models #20

> hide #!19 models

> hide #!2 models

> select add #2

19 models selected  

> select subtract #2

Nothing selected  

> show #!15 models

> color #20 #72727240 models

> view orient

[Repeated 1 time(s)]

> view name Fig4C

> ls

Unknown command: ls  

> save /Users/shoichitachiyama/Desktop/Fig4Ca_09042024.png supersample 2
> transparentBackground true

[Repeated 1 time(s)]

> view name Fig4C

> turn x 50

> turn x -50

[Repeated 1 time(s)]

> save /Users/shoichitachiyama/Desktop/Fig4Cb_09042024.png supersample 2
> transparentBackground true

> show #!8 models

> hide #!8 models

> show #!17 models

> hide #!17 models

> show #17.1 models

> hide #17.1 models

> save /Users/shoichitachiyama/Desktop/Fig4Cb_09042024.png supersample 2
> transparentBackground true

> hide #!20 models

> show #!20 models

> show #!8 models

> hide #!8 models

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/For_Figure4_PflAB_Sep2024.cxs includeMaps true

——— End of log from Wed Sep 4 18:57:11 2024 ———

opened ChimeraX session  
Showing 3Xunits_imasked.seg - 18 regions, 18 surfaces  

> hide #!2 models

> show #!8 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Segmenting 3XfliL.mrc, density threshold 0.184695  
Showing 9 region surfaces  
56 watershed regions, grouped to 9 regions  
Showing 3XfliL.seg - 9 regions, 9 surfaces  

> select #2.1

1 model selected  

> select add #2.8

2 models selected  

> select add #2.6

3 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Opened 3XfliL_imasked as #21, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  

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/2xFliL.mrc models
> #21

> close #2

> hide #!8 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Stator-
> complexb.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/Stator-complexb.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  
919 messages similar to the above omitted  
  
Chain information for Stator-complexb.pdb  
---  
Chain | Description  
2.1/? | No description available  
2.2/C 2.3/D 2.4/E 2.5/F 2.6/G 2.7/H 2.8/I 2.9/J 2.10/K 2.11/L | No description available  
2.22/K | No description available  
2.22/L | No description available  
2.12/M 2.13/N 2.14/O 2.15/P 2.16/Q 2.17/R 2.18/S 2.19/T 2.20/U 2.21/V | No description available  
  

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Stator-
> complexb.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/Stator-complexb.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  
919 messages similar to the above omitted  
  
Chain information for Stator-complexb.pdb  
---  
Chain | Description  
22.1/? | No description available  
22.2/C 22.3/D 22.4/E 22.5/F 22.6/G 22.7/H 22.8/I 22.9/J 22.10/K 22.11/L | No description available  
22.22/K | No description available  
22.22/L | No description available  
22.12/M 22.13/N 22.14/O 22.15/P 22.16/Q 22.17/R 22.18/S 22.19/T 22.20/U 22.21/V | No description available  
  

> select add #21

2 models selected  

> show #!6 models

> view orient

> view matrix models #21,1,0,0,-0.48533,0,1,0,4.9028,0,0,1,0

> undo

> select subtract #21

Nothing selected  

> select add #22

23554 atoms, 23886 bonds, 2988 residues, 23 models selected  

> select add #2

47108 atoms, 47772 bonds, 5976 residues, 46 models selected  

> select subtract #2

23554 atoms, 23886 bonds, 2988 residues, 23 models selected  

> view matrix models #22,1,0,0,-14.173,0,1,0,103.19,0,0,1,0

> view matrix models #22,1,0,0,-15.419,0,1,0,106.11,0,0,1,-1.9686

> select add #2

47108 atoms, 47772 bonds, 5976 residues, 46 models selected  

> select subtract #2

23554 atoms, 23886 bonds, 2988 residues, 23 models selected  

> hide #2.11 models

> show #2.11 models

> hide #2.12 models

> show #2.12 models

> hide #2.21 models

> show #2.21 models

> hide #2.21 models

> hide #2.20 models

> hide #2.19 models

> hide #2.18 models

> hide #2.17 models

> hide #2.16 models

> hide #2.15 models

> hide #2.14 models

> hide #2.13 models

> hide #2.12 models

> close #2.12-21

> hide #22.12 models

> hide #22.13 models

> hide #22.14 models

> hide #22.15 models

> hide #22.16 models

> hide #22.17 models

> hide #22.18 models

> hide #22.19 models

> hide #22.20 models

> hide #22.21 models

> close #22.12-21

> select subtract #22

Nothing selected  

> select add #22

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> select subtract #22

Nothing selected  

> select add #2

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99996,-0.0049032,-0.0077954,-0.63495,0.0050391,0.99983,0.017514,1.0297,0.0077082,-0.017552,0.99982,-0.63371

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99996,-0.0049032,-0.0077954,-0.92663,0.0050391,0.99983,0.017514,1.3841,0.0077082,-0.017552,0.99982,-1.1098

> select subtract #2

Nothing selected  

> hide #!6 models

> color #2 #b7a359ff models

> color #22 #b7a359ff models

> select add #22.22

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> select subtract #22.22

Nothing selected  

> hide #22.22 models

> show #22.22 models

> color #22.22 #905d12ff models

> color #2.22 #905d12ff models

> color #2.1 #a69b32ff models

> color #22.1 #a69b32ff models

> select add #22

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> select add #2

43388 atoms, 44012 bonds, 5496 residues, 26 models selected  

> hide sel cartoons

> show sel surfaces

> select clear

> color #21 #72727240 models

Cell requested for row 0 is out of bounds for table with 34 rows! Resizing
table model.  

> show #!16 models

> hide #!16 models

> show #!18 models

> view orient

> view Fig4C1

Expected an objects specifier or a view name or a keyword  

> view Fig4Ca

Expected an objects specifier or a view name or a keyword  

> view Fig4C

> save /Users/shoichitachiyama/Desktop/Fig4CD_09042024.png supersample 2
> transparentBackground true

> save /Users/shoichitachiyama/Desktop/Fig4D_09042024.png supersample 2
> transparentBackground true

> view Fig5Cb

Expected an objects specifier or a view name or a keyword  

> view Fig5C2

Expected an objects specifier or a view name or a keyword  

> turn x 90

[Repeated 3 time(s)]

> turn x 45

> turn x -45

[Repeated 1 time(s)]

> view Fig5D

Expected an objects specifier or a view name or a keyword  

> view Fig4C

> turn x -90

> view Fig4C

> turn x -90

> save /Users/shoichitachiyama/Desktop/Fig4Db_09042024.png supersample 2
> transparentBackground true

> view Fig4C

> turn x -90

> turn y -90

> save /Users/shoichitachiyama/Desktop/Fig4Dc_09042024.png supersample 2
> transparentBackground true

> turn x -40

> turn x 40

[Repeated 1 time(s)]

> save /Users/shoichitachiyama/Desktop/Fig4Dd_09042024.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/For_Figure4_PflAB_Sep2024.cxs includeMaps true

——— End of log from Wed Sep 4 20:03:04 2024 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> hide #!18 models

> show #!18 models

> hide #!20 models

> hide #!21 models

> hide #!22 models

> show #!22 models

> view orient

> save /Users/shoichi/Desktop/HP-Fig4D_09172024.png supersample 2
> transparentBackground true

> turn x -90

> save /Users/shoichi/Desktop/HP-Fig4D2_09172024.png supersample 2
> transparentBackground true

> view orient

> hide #!18 models

> hide #!22 models

> hide #!2 models

> show #!20 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> show #!19 models

> hide #!19 models

> hide #!20 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!14 models

> hide #!14 models

> hide #!15 models

> show #!15 models

> show #!6 models

> volume #6 level 0.03792

> hide #!6 models

> show #!19 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> color #1 #b2b2b283 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> hide #!1 models

> show #!20 models

> select add #15

38799 atoms, 39588 bonds, 4776 residues, 10 models selected  

> hide sel & #!15.2,4,6-7 surfaces

> show sel & #!15.2,4,6-7 cartoons

> show sel & #!15.2,4,6-7 surfaces

> ui mousemode right "translate selected models"

> select subtract #15

4 models selected  

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!12 models

> hide #!12 models

> show #!13 models

> hide #!13 models

> show #!6 models

> hide #!6 models

> select add #20

2 models selected  

> select subtract #20

Nothing selected  

> select add #20

2 models selected  

> select subtract #20

Nothing selected  

> show #!6 models

> hide #!15 models

> ui tool show "Segment Map"

> hide #!20 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Segmenting 3Xunits.mrc, density threshold 0.037925  
Showing 318 region surfaces  
26453 watershed regions, grouped to 318 regions  
Showing 3Xunits.seg - 318 regions, 318 surfaces  
Drag select of 31808, 15646 of 51436 triangles, 31845, 10703 of 26232
triangles, 31801, 11883 of 25260 triangles, 31805, 31816, 31757, 31835, 7743
of 20008 triangles, 31665, 1005 of 18676 triangles, 31826, 11641 of 19392
triangles, 31711, 3506 of 17600 triangles, 31789, 8007 of 16980 triangles,
31833, 9323 of 17928 triangles, 31672, 31815, 10093 of 17432 triangles, 31753,
31736, 5704 of 17348 triangles, 31828, 11195 of 17232 triangles, 31842, 8537
of 16596 triangles, 31851, 9605 of 16580 triangles, 31836, 9456 of 15488
triangles, 31745, 31661, 31817, 31790, 6439 of 13600 triangles, 31853, 288 of
12348 triangles, 31803, 4501 of 14200 triangles, 31775, 8083 of 13516
triangles, 31673, 6794 of 12616 triangles, 31806, 31618, 8406 of 10620
triangles, 31579, 7487 of 11588 triangles, 31748, 7457 of 11728 triangles,
31717, 31776, 7683 of 11900 triangles, 31715, 7583 of 11552 triangles, 31841,
6433 of 11336 triangles, 30874, 5372 of 10376 triangles, 31691, 4405 of 10484
triangles, 31694, 6562 of 9188 triangles, 31864, 6686 of 10620 triangles,
31802, 4554 of 9644 triangles, 31659, 4942 of 10672 triangles, 31539, 30901,
4075 of 8316 triangles, 31832, 4954 of 9116 triangles, 31601, 30837, 7063 of
9164 triangles, 31859, 5346 of 9508 triangles, 30843, 2361 of 7456 triangles,
31865, 5101 of 8924 triangles, 31779, 6356 of 9084 triangles, 31738, 5023 of
9760 triangles, 31587, 5689 of 8816 triangles, 31855, 5432 of 8876 triangles,
31741, 5792 of 8972 triangles, 31708, 4173 of 8704 triangles, 31696, 5317 of
8284 triangles, 31631, 4074 of 9032 triangles, 31628, 5031 of 7848 triangles,
31308, 1501 of 7300 triangles, 31720, 4394 of 7736 triangles, 31699, 5754 of
7664 triangles, 31718, 3292 of 7676 triangles, 31723, 3342 of 7700 triangles,
31866, 4720 of 7680 triangles, 31848, 4086 of 7816 triangles, 31645, 3792 of
7496 triangles, 31643, 3950 of 7200 triangles, 31862, 4364 of 6784 triangles,
31584, 4153 of 6740 triangles, 30847, 5304 of 6668 triangles, 31728, 4636 of
7048 triangles, 31846, 4388 of 7240 triangles, 31710, 4258 of 6136 triangles,
31630, 3402 of 6072 triangles, 31627, 2921 of 5568 triangles, 31821, 3963 of
6220 triangles, 31780, 3080 of 6032 triangles, 31849, 2208 of 5944 triangles,
31684, 3293 of 5500 triangles, 31649, 3028 of 6004 triangles, 31121, 3008 of
5176 triangles, 30850, 2505 of 5224 triangles, 31207, 3581 of 4728 triangles,
30939, 3720 of 5092 triangles, 31614, 3094 of 5448 triangles, 30948, 3503 of
5120 triangles, 31582, 2748 of 5156 triangles, 31639, 2544 of 4796 triangles,
31732, 3367 of 4856 triangles, 31730, 2908 of 4520 triangles, 31770, 2124 of
3700 triangles, 31844, 3162 of 3856 triangles, 31856, 1664 of 3760 triangles,
31784, 2600 of 3976 triangles, 31622, 841 of 3336 triangles, 30917, 660 of
2900 triangles, 31774, 2220 of 3028 triangles, 31424, 1624 of 2188 triangles,
31266, 308 of 2052 triangles, 30868, 1098 of 1280 triangles, 31210, 352 of
1100 triangles, 31020, 48 of 964 triangles, 30839, 851 of 888 triangles,
31011, 28692, 310 of 380 triangles, 6 3Xunits.mrc  

> select clear

> select #23.71

1 model selected  

> select add #23.310

2 models selected  

> select add #23.263

3 models selected  

> select add #23.53

4 models selected  

> hide #!6 models

Drag select of 31815, 3679 of 17432 triangles, 31851, 4783 of 16580 triangles,
31775, 1474 of 13516 triangles, 31579, 1842 of 11588 triangles, 31748, 2215 of
11728 triangles, 31694, 1423 of 9188 triangles, 31864, 1344 of 10620
triangles, 31659, 141 of 10672 triangles, 30901, 3021 of 8316 triangles,
30837, 1419 of 9164 triangles, 31859, 1937 of 9508 triangles, 31738, 2701 of
9760 triangles, 31631, 3152 of 9032 triangles, 31699, 2345 of 7664 triangles,
31723, 570 of 7700 triangles, 31848, 1248 of 7816 triangles, 31645, 2741 of
7496 triangles, 31862, 81 of 6784 triangles, 31584, 958 of 6740 triangles,
31728, 140 of 7048 triangles, 31630, 622 of 6072 triangles, 31780, 107 of 6032
triangles, 31849, 125 of 5944 triangles, 31649, 1114 of 6004 triangles, 31207,
765 of 4728 triangles, 30939, 911 of 5092 triangles, 31614, 1806 of 5448
triangles, 31770, 465 of 3700 triangles, 31856, 741 of 3760 triangles, 31784,
1398 of 3976 triangles, 31774, 916 of 3028 triangles, 31210, 318 of 1100
triangles, 30839, 71 of 888 triangles  
Drag select of 31808, 81 of 51436 triangles, 31801, 553 of 25260 triangles,
31826, 1444 of 19392 triangles, 31828, 2305 of 17232 triangles, 31842, 2279 of
16596 triangles, 31836, 25 of 15488 triangles, 31790, 795 of 13600 triangles,
31673, 70 of 12616 triangles, 31776, 1479 of 11900 triangles, 31715, 768 of
11552 triangles, 31841, 1142 of 11336 triangles, 31691, 185 of 10484
triangles, 31802, 34 of 9644 triangles, 31779, 801 of 9084 triangles, 31587,
209 of 8816 triangles, 31855, 718 of 8876 triangles, 31741, 1429 of 8972
triangles, 31708, 1140 of 8704 triangles, 31696, 1323 of 8284 triangles,
31720, 107 of 7736 triangles, 31718, 535 of 7676 triangles, 31643, 267 of 7200
triangles, 30847, 380 of 6668 triangles, 31846, 884 of 7240 triangles, 31710,
109 of 6136 triangles, 31627, 13 of 5568 triangles, 31821, 529 of 6220
triangles, 31684, 328 of 5500 triangles, 31121, 731 of 5176 triangles, 30850,
349 of 5224 triangles, 31732, 225 of 4856 triangles, 31730, 640 of 4520
triangles, 31844, 847 of 3856 triangles, 31266, 59 of 2052 triangles, 31011,
54 of 620 triangles  
Drag select of 31845, 7035 of 26232 triangles, 31805, 31816, 31757, 20325 of
21016 triangles, 31835, 4532 of 20008 triangles, 31665, 68 of 18676 triangles,
31711, 1002 of 17600 triangles, 31789, 6633 of 16980 triangles, 31833, 7775 of
17928 triangles, 31753, 14962 of 14964 triangles, 31736, 3588 of 17348
triangles, 31745, 10624 of 13572 triangles, 31661, 31817, 31803, 2607 of 14200
triangles, 31806, 31618, 6795 of 10620 triangles, 31717, 30874, 3861 of 10376
triangles, 31539, 31832, 3444 of 9116 triangles, 31601, 9680 of 9764
triangles, 30843, 523 of 7456 triangles, 31865, 3029 of 8924 triangles, 31628,
4586 of 7848 triangles, 31308, 142 of 7300 triangles, 31866, 4612 of 7680
triangles, 30948, 3160 of 5120 triangles, 31639, 2358 of 4796 triangles,
31622, 192 of 3336 triangles, 31424, 1566 of 2188 triangles, 31020, 44 of 964
triangles, 28692, 206 of 380 triangles  

> select add #23.101

106 models selected  

> select add #23.74

107 models selected  

> select add #23.201

108 models selected  

> select add #23.96

109 models selected  

> select add #23.88

110 models selected  

> select add #23.115

111 models selected  

> select add #23.57

112 models selected  

> select add #23.58

113 models selected  

> select add #23.77

114 models selected  

> select add #23.130

115 models selected  

> select add #23.138

116 models selected  

> select subtract #23.138

115 models selected  

> select add #23.138

116 models selected  

> select add #23.122

117 models selected  

> select add #23.205

118 models selected  

> select add #23.64

119 models selected  
Drag select of 30917, 939 of 2900 triangles  

> select add #23.170

121 models selected  

> select add #23.145

122 models selected  

> select add #23.105

123 models selected  

> select add #23.79

124 models selected  

> select add #23.183

125 models selected  

> select add #23.118

126 models selected  

> select subtract #23.118

125 models selected  

> select add #23.139

126 models selected  

> select add #23.118

127 models selected  

> select add #23.200

128 models selected  

> select add #23.104

129 models selected  

> select subtract #23.104

128 models selected  

> select add #23.110

129 models selected  

> select add #23.269

130 models selected  

> select add #23.104

131 models selected  

> select add #23.192

132 models selected  

> select add #23.135

133 models selected  

> select add #23.127

134 models selected  

> select add #23.169

135 models selected  

> select add #23.153

136 models selected  

> select add #23.266

137 models selected  

> select add #23.95

138 models selected  

> select add #23.124

139 models selected  

> select add #23.176

140 models selected  

> select add #23.91

141 models selected  

> select add #23.83

142 models selected  

> select add #23.154

143 models selected  

> select add #23.166

144 models selected  

> select add #23.186

145 models selected  

> select add #23.222

146 models selected  

> select add #23.188

147 models selected  

> select add #23.117

148 models selected  

> select add #23.34

149 models selected  

> select add #23.66

150 models selected  

> select add #23.235

151 models selected  

> select add #23.81

152 models selected  

> select add #23.234

153 models selected  

> select add #23.46

154 models selected  

> select add #23.76

155 models selected  

> select add #23.99

156 models selected  

> select add #23.82

157 models selected  

> select subtract #23.117

156 models selected  

> select add #23.132

157 models selected  

> select add #23.117

158 models selected  
Drag select of 31813, 7756 of 36304 triangles, 31703, 13 of 14596 triangles,
31768, 31793, 1968 of 12160 triangles, 31704, 6782 of 10356 triangles, 31662,
749 of 8176 triangles, 31829, 4006 of 7124 triangles  
Drag select of 1769, 31771, 31840, 7329 of 16068 triangles, 31818, 6770 of
16040 triangles, 31762, 31800, 2967 of 11620 triangles, 31838, 3746 of 10984
triangles, 31794, 5854 of 10336 triangles, 31706, 5479 of 9924 triangles,
31823, 5043 of 9616 triangles, 31132, 31824, 4295 of 7836 triangles, 31687,
3465 of 8048 triangles, 30861, 3431 of 7340 triangles, 31820, 3503 of 7556
triangles, 30909, 2558 of 5784 triangles, 30954, 2789 of 5640 triangles,
31577, 2918 of 4476 triangles, 31097, 31573, 1840 of 4408 triangles, 30869,
1248 of 2960 triangles, 31139, 558 of 2520 triangles, 31152, 523 of 2232
triangles  

> select add #23.246

189 models selected  

> select add #23.298

190 models selected  

> select add #23.219

191 models selected  

> select add #23.216

192 models selected  

> select add #23.252

193 models selected  

> select add #23.126

194 models selected  

> select add #23.202

195 models selected  

> select add #23.241

196 models selected  

> select add #23.111

197 models selected  

> select add #23.155

198 models selected  

> select add #23.173

199 models selected  

> select add #23.260

200 models selected  

> select add #23.302

201 models selected  

> select add #23.167

202 models selected  

> select add #23.10

203 models selected  

> select subtract #23.10

202 models selected  

> select add #23.295

203 models selected  

> select add #23.276

204 models selected  

> select add #23.210

205 models selected  

> select add #23.265

206 models selected  

> select add #23.134

207 models selected  

> select add #23.119

208 models selected  

> select add #23.75

209 models selected  

> select add #23.211

210 models selected  

> select add #23.113

211 models selected  

> select add #23.177

212 models selected  

> select add #23.128

213 models selected  

> select add #23.226

214 models selected  

> select add #23.259

215 models selected  

> select add #23.236

216 models selected  

> select add #23.247

217 models selected  

> select add #23.294

218 models selected  

> select add #23.315

219 models selected  

> select add #23.291

220 models selected  

> select add #23.233

221 models selected  

> select add #23.254

222 models selected  

> select add #23.151

223 models selected  

> select add #23.237

224 models selected  

> select add #23.171

225 models selected  

> select add #23.225

226 models selected  

> select subtract #23.225

225 models selected  

> select add #23.8

226 models selected  

> select add #23.17

227 models selected  

> select subtract #23.8

226 models selected  

> select subtract #23.17

225 models selected  

> select add #23.225

226 models selected  

> select add #23.42

227 models selected  

> select subtract #23.42

226 models selected  
Drag select of 31607, 1565 of 6884 triangles, 31680, 1071 of 5808 triangles  

> select add #23.273

229 models selected  

> select add #23.284

230 models selected  

> select add #23.288

231 models selected  

> select add #23.308

232 models selected  

> select add #23.313

233 models selected  

> select add #23.244

234 models selected  

> select add #23.108

235 models selected  

> select add #23.114

236 models selected  

> select add #23.274

237 models selected  
Drag select of 30947, 31289, 1390 of 3768 triangles, 31321, 2312 of 2832
triangles, 31328, 27021, 148 of 352 triangles  
Drag select of 31867, 2101 of 19448 triangles, 31588, 1801 of 9000 triangles,
31273, 3306 of 9504 triangles, 31481, 1474 of 8272 triangles, 31275, 1366 of
4792 triangles, 31482, 3114 of 7212 triangles, 30973, 2628 of 6800 triangles,
30977, 4416 of 6628 triangles, 31571, 3425 of 7012 triangles, 31000, 3303 of
6396 triangles, 31791, 1098 of 5672 triangles, 31619, 6 of 4736 triangles  
Drag select of 31295, 4490 of 8232 triangles, 31758, 4678 of 6880 triangles,
31381, 657 of 4136 triangles, 31620, 1376 of 4012 triangles  

> select add #23.261

259 models selected  

> select add #23.214

260 models selected  

> select add #23.290

261 models selected  

> select add #23.27

262 models selected  

> select subtract #23.27

261 models selected  

> select add #23.301

262 models selected  

> select add #23.272

263 models selected  

> select add #23.204

264 models selected  

> select add #23.293

265 models selected  

> select add #23.7

266 models selected  

> select subtract #23.7

265 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Opened 3Xunits_imasked as #24, grid size 240,240,240, pixel 2.1, shown at step
1, values float32  
Segmenting 3Xunits_imasked, density threshold 0.037925  
Showing 53 region surfaces  
1349 watershed regions, grouped to 53 regions  
Showing 3Xunits_imasked.seg - 53 regions, 53 surfaces  

> select add #23.40

1 model selected  

> select add #23.31

2 models selected  

> select add #23.33

3 models selected  

> select add #23.28

4 models selected  

> select add #23.36

5 models selected  

> select add #23.23

6 models selected  

> select add #23

54 models selected  

> select subtract #23

Nothing selected  

> hide #!23 models

> show #!23 models

> hide #!24 models

> select add #23.9

1 model selected  

> select add #23.11

2 models selected  

> select add #23.12

3 models selected  

> show #!15 models

> select add #23.18

4 models selected  

> select add #23.16

5 models selected  

> select add #23.17

6 models selected  

> select subtract #23.16

5 models selected  

> select subtract #23.17

4 models selected  

> select add #23.17

5 models selected  

> select add #23.32

6 models selected  

> select add #23.41

7 models selected  

> select add #23.8

8 models selected  

> select subtract #23.8

7 models selected  

> select add #23.15

8 models selected  

> select add #23.19

9 models selected  
Grouped 9 regions  

> select clear

> select #23.9

1 model selected  

> select clear

> select #23.13

1 model selected  

> select add #23.14

2 models selected  

> select add #23.16

3 models selected  
Ungrouped to 8 regions  
Ungrouped to 15 regions  
Ungrouped to 6 regions  
Ungrouped to 0 regions  

> select #23.32

1 model selected  

> select add #23.41

2 models selected  

> select add #23.11

3 models selected  

> select add #23.54

4 models selected  

> select add #23.19

5 models selected  

> select add #23.18

6 models selected  

> select add #23.20

7 models selected  

> select subtract #23.20

6 models selected  
Grouped 6 regions  

> select add #23.59

2 models selected  

> select add #23.58

3 models selected  

> select add #23.63

4 models selected  

> select add #23.62

5 models selected  
Grouped 5 regions  

> select #23.17

1 model selected  

> select add #23.15

2 models selected  

> select add #23.13

3 models selected  

> select add #23.57

4 models selected  

> select add #23.56

5 models selected  
Grouped 5 regions  

> select add #23.11

2 models selected  
Grouped 2 regions  
Showing 48 region surfaces  

> select add #23.9

2 models selected  
Grouped 2 regions  

> select add #23.23

2 models selected  

> select add #23.36

3 models selected  

> select add #23.28

4 models selected  

> select add #23.40

5 models selected  

> select add #23.33

6 models selected  

> select add #23.31

7 models selected  
Grouped 7 regions  

> select add #23.20

2 models selected  

> select clear

> select #23.20

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 5 regions  
Ungrouped to 0 regions  

> select #23.9

1 model selected  

> select add #23.15

2 models selected  

> select add #23.18

3 models selected  

> select add #23.19

4 models selected  

> select add #23.20

5 models selected  

> select add #23.29

6 models selected  
Grouped 6 regions  

> select #23.1

1 model selected  
Grouped 1 regions  
Showing 40 region surfaces  

> select clear

> select #23.9

1 model selected  

> select add #23.22

2 models selected  

> select add #23.39

3 models selected  

> select add #23.38

4 models selected  

> select add #23.37

5 models selected  

> select add #23.25

6 models selected  

> select add #23.43

7 models selected  

> select add #23.49

8 models selected  

> select add #23.42

9 models selected  

> select add #23.34

10 models selected  

> select add #23.24

11 models selected  

> select add #23.35

12 models selected  
Grouped 12 regions  

> select clear

> select #23.9

1 model selected  
Opened 3Xunits_imasked_imasked as #25, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32  
Segmenting 3Xunits_imasked_imasked, density threshold 0.037925  
Showing 22 region surfaces  
491 watershed regions, grouped to 22 regions  
Showing 3Xunits_imasked_imasked.seg - 22 regions, 22 surfaces  

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 #25

> select #23.8

1 model selected  

> select add #23.3

2 models selected  

> select add #23.5

3 models selected  

> select add #23.17

4 models selected  

> select clear

> select #23.3

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #23.24

1 model selected  

> select add #23.8

2 models selected  

> select add #23.23

3 models selected  

> select add #23.5

4 models selected  

> select add #23.17

5 models selected  

> select add #23.18

6 models selected  

> select add #23.14

7 models selected  

> select add #23.6

8 models selected  

> select add #23.7

9 models selected  

> hide #!25 models

> select add #23.13

10 models selected  

> select add #23.12

11 models selected  

> select add #23.15

12 models selected  
Grouped 12 regions  

> select clear

> select #23.3

1 model selected  

> select clear

> select #23.2

1 model selected  

> select clear

> select #23.2

1 model selected  
Ungrouped to 3 regions  
Ungrouped to 8 regions  
Ungrouped to 3 regions  
Ungrouped to 0 regions  

> select #23.8

1 model selected  

> select add #23.2

2 models selected  

> select add #23.5

3 models selected  
Grouped 3 regions  
Showing 19 region surfaces  

> select clear

> select #23.2

1 model selected  

> select clear

> select #23.2

1 model selected  
Opened 3xOnly-PflAB_imasked as #26, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32  

> hide #!23 models

> select add #23

20 models selected  

> select subtract #23

Nothing selected  

> hide #!26 models

> show #!26 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 #26

Segmenting 3xOnly-PflAB.mrc, density threshold 0.037925  
Showing 22 region surfaces  
488 watershed regions, grouped to 22 regions  
Showing 3xOnly-PflAB.seg - 22 regions, 22 surfaces  

> select #23.8

1 model selected  

> select add #23.2

2 models selected  

> select add #23.4

3 models selected  

> select add #23.17

4 models selected  

> select add #23.18

5 models selected  

> select add #23.14

6 models selected  

> select add #23.6

7 models selected  

> select add #23.13

8 models selected  

> select add #23.7

9 models selected  

> select add #23.15

10 models selected  

> select add #23.12

11 models selected  

> hide #!26 models

Grouped 11 regions  

> select clear

> select #23.20

1 model selected  

> select add #23.2

2 models selected  
Grouped 2 regions  

> select clear

> select add #23.21

1 model selected  

> select add #23.22

2 models selected  

> select add #15.2/BJ:459@CD

1 atom, 1 residue, 3 models selected  

> select clear

> select #23.21

1 model selected  

> select add #23.22

2 models selected  

> select add #23.2

3 models selected  

> hide #!15 models

Grouped 3 regions  

> select clear

> select #23.11

1 model selected  

> select add #23.10

2 models selected  
Ungrouped to 4 regions  
Ungrouped to 11 regions  
Ungrouped to 68 regions  
Ungrouped to 29 regions  

> select clear

[Repeated 1 time(s)]Drag select of 608, 23 of 125476 triangles, 211, 15 of 56
triangles, 79, 140 of 148 triangles, 77, 104, 72, 58 of 80 triangles, 163, 69
of 132 triangles, 80, 13 of 56 triangles, 78, 105, 81, 26 of 56 triangles,
103, 191, 147, 10 of 56 triangles, 227, 48 of 56 triangles, 128, 179, 138 of
156 triangles, 193, 212, 28 of 56 triangles, 226, 18 of 120 triangles  

> select add #23.103

21 models selected  

> select clear

> select add #23.92

1 model selected  

> select add #23.93

2 models selected  

> select add #23.42

3 models selected  

> select add #23.44

4 models selected  

> select add #23.88

5 models selected  

> select add #23.40

6 models selected  

> select add #23.21

7 models selected  

> select add #23.91

8 models selected  

> select add #23.22

9 models selected  

> select add #23.87

10 models selected  

> select add #23.100

11 models selected  

> select add #23.9

12 models selected  

> select subtract #23.9

11 models selected  

> select add #23.101

12 models selected  

> select add #23.54

13 models selected  

> select add #23.62

14 models selected  

> select add #23.68

15 models selected  

> select add #23.96

16 models selected  

> select add #23.107

17 models selected  

> select add #23.67

18 models selected  

> select add #23.66

19 models selected  

> select add #23.108

20 models selected  

> select add #23.99

21 models selected  

> select add #23.104

22 models selected  

> select add #23.97

23 models selected  

> select add #23.60

24 models selected  

> select add #23.78

25 models selected  

> select add #23.49

26 models selected  

> select add #23.79

27 models selected  

> select add #23.105

28 models selected  

> select add #23.109

29 models selected  

> select add #23.89

30 models selected  

> select add #23.20

31 models selected  

> select add #23.58

32 models selected  

> select add #23.102

33 models selected  

> select add #23.51

34 models selected  

> select subtract #23.42

33 models selected  

> select add #23.19

34 models selected  
Grouped 34 regions  

> select add #23.2

2 models selected  
Grouped 2 regions  
Drag select of 244, 44 of 56 triangles, 84, 131 of 160 triangles, 195, 108,
243, 17 of 56 triangles, 192, 148, 228, 11 of 56 triangles, 229, 194, 19 of 56
triangles, 129, 164, 22 of 56 triangles, 151, 88 of 112 triangles, 211, 32 of
56 triangles, 106, 130, 196, 150, 133, 162, 41 of 56 triangles, 181, 107, 109
of 172 triangles, 80, 54 of 56 triangles, 103, 147  
Grouped 26 regions  
Drag select of 201, 134, 156, 37 of 56 triangles, 169  

> select add #23.1

6 models selected  

> select subtract #23.1

5 models selected  

> select add #23.59

6 models selected  

> select add #23.61

7 models selected  

> select add #23.63

8 models selected  

> select add #23.64

9 models selected  

> select add #23.106

10 models selected  

> select add #23.95

11 models selected  

> select add #23.32

12 models selected  

> select add #23.39

13 models selected  

> select add #23.33

14 models selected  

> select add #23.27

15 models selected  

> select add #23.31

16 models selected  
Grouped 16 regions  

> select add #23.82

2 models selected  

> select add #23.29

3 models selected  

> select add #23.30

4 models selected  

> select add #23.34

5 models selected  

> select add #23.23

6 models selected  

> select add #23.8

7 models selected  

> select add #23.28

8 models selected  

> select add #23.7

9 models selected  

> select add #23.4

10 models selected  

> select add #23.35

11 models selected  

> select add #23.81

12 models selected  
Grouped 12 regions  

> select add #23.25

2 models selected  
Grouped 2 regions  
Opened 3xOnly-PflAB_imasked as #27, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32  

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/1xOnly-PflAB.mrc
> models #27

> close #23

> show #!26 models

> hide #!27 models

> hide #!26 models

> show #!27 models

> show #!17 models

> hide #!17 models

> show #!15 models

> select add #15

38799 atoms, 39588 bonds, 4776 residues, 10 models selected  
Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  

> select #15.4/Ch:1-2 #15.6/Cj:1-2 #15.8/Cl:1-2

48 atoms, 45 bonds, 6 residues, 3 models selected  

> select #15.4/Ch:1-107 #15.6/Cj:1-107 #15.8/Cl:1-107

2523 atoms, 2544 bonds, 321 residues, 3 models selected  
2 [ID: 2] region chains Ch,Cj,Cl [1-107] RMSD: 183.500  
  

> select #15.4/Ch:121-122 #15.6/Cj:121-122 #15.8/Cl:121-122

51 atoms, 48 bonds, 6 residues, 3 models selected  

> select #15.4/Ch:1-122 #15.6/Cj:1-122 #15.8/Cl:1-122

2859 atoms, 2880 bonds, 366 residues, 3 models selected  
2 [ID: 2] region chains Ch,Cj,Cl [1-122] RMSD: 179.940  
  

> select #15.4/Ch:135 #15.6/Cj:135 #15.8/Cl:135

24 atoms, 21 bonds, 3 residues, 3 models selected  

> select #15.4/Ch:1-135 #15.6/Cj:1-135 #15.8/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 & #!15.4,6 surfaces

> hide sel & #!15.4,6 cartoons

> view orient

> save /Users/shoichi/Desktop/HP-Fig4C2_09172024.png supersample 2
> transparentBackground true

> show #15.1 models

> show #15.3 models

> show #15.5 models

> show #15.8 models

> show #15.9 models

> show #!26 models

> combine #15 modelId #28 name 3xPflAB

> select add #15

38799 atoms, 39588 bonds, 4776 residues, 12 models selected  

> select subtract #15

4 models selected  

> hide #!15 models

> ui tool show "Fit in Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> fitmap #28 inMap #26

Fit molecule 3xPflAB (#28) to map 3xOnly-PflAB.mrc (#26) using 38799 atoms  
average map value = 1.878, steps = 48  
shifted from previous position = 1.88  
rotated from previous position = 1.35 degrees  
atoms outside contour = 18849, contour level = 0.037925  
  
Position of 3xPflAB (#28) relative to 3xOnly-PflAB.mrc (#26) coordinates:  
Matrix rotation and translation  
0.99197492 0.04194380 0.11927478 -7.25388896  
-0.00861248 0.96359505 -0.26722724 -10.03562167  
-0.12614112 0.26405547 0.95622337 -12.21729786  
Axis 0.90445517 0.41779579 -0.08606696  
Axis point 0.00000000 44.70924253 -28.47666633  
Rotation angle (degrees) 17.07979035  
Shift along axis -9.70215212  
  

> fitmap #28 inMap #26

Fit molecule 3xPflAB (#28) to map 3xOnly-PflAB.mrc (#26) using 38799 atoms  
average map value = 1.878, steps = 60  
shifted from previous position = 0.0218  
rotated from previous position = 0.00175 degrees  
atoms outside contour = 18848, contour level = 0.037925  
  
Position of 3xPflAB (#28) relative to 3xOnly-PflAB.mrc (#26) coordinates:  
Matrix rotation and translation  
0.99197770 0.04194422 0.11925151 -7.27068129  
-0.00862150 0.96359995 -0.26720930 -10.02121140  
-0.12611863 0.26403754 0.95623129 -12.21052200  
Axis 0.90447225 0.41775398 -0.08609046  
Axis point 0.00000000 44.70236205 -28.41007722  
Rotation angle (degrees) 17.07826916  
Shift along axis -9.71132087  
  

> fitmap #28 inMap #26

Fit molecule 3xPflAB (#28) to map 3xOnly-PflAB.mrc (#26) using 38799 atoms  
average map value = 1.878, steps = 40  
shifted from previous position = 0.00987  
rotated from previous position = 0.00587 degrees  
atoms outside contour = 18849, contour level = 0.037925  
  
Position of 3xPflAB (#28) relative to 3xOnly-PflAB.mrc (#26) coordinates:  
Matrix rotation and translation  
0.99196661 0.04194146 0.11934472 -7.27163799  
-0.00858908 0.96359028 -0.26724522 -10.02508686  
-0.12620806 0.26407327 0.95620962 -12.20228003  
Axis 0.90438160 0.41796667 -0.08601034  
Axis point 0.00000000 44.66325190 -28.40049253  
Rotation angle (degrees) 17.08240812  
Shift along axis -9.71696549  
  

> split #28

Split 3xPflAB (#28) into 9 models  
Chain information for 3xPflAB Az #28.1  
---  
Chain | Description  
Az | No description available  
  
Chain information for 3xPflAB BJ #28.2  
---  
Chain | Description  
BJ | No description available  
  
Chain information for 3xPflAB BL #28.3  
---  
Chain | Description  
BL | No description available  
  
Chain information for 3xPflAB Ch #28.4  
---  
Chain | Description  
Ch | No description available  
  
Chain information for 3xPflAB Ci #28.5  
---  
Chain | Description  
Ci | No description available  
  
Chain information for 3xPflAB Cj #28.6  
---  
Chain | Description  
Cj | No description available  
  
Chain information for 3xPflAB Ck #28.7  
---  
Chain | Description  
Ck | No description available  
  
Chain information for 3xPflAB Cl #28.8  
---  
Chain | Description  
Cl | No description available  
  
Chain information for 3xPflAB Cm #28.9  
---  
Chain | Description  
Cm | No description available  
  

> hide #28.1 models

> hide #28.2 models

> show #28.2 models

> hide #28.3 models

> hide #28.5 models

> hide #28.8 models

> hide #28.9 models

> select add #28

38799 atoms, 39588 bonds, 4776 residues, 10 models selected  

> select subtract #28

Nothing selected  

> select add #28.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select add #28.4

11824 atoms, 12060 bonds, 1455 residues, 2 models selected  

> select add #28.6

18653 atoms, 19032 bonds, 2298 residues, 3 models selected  

> select add #28.7

19762 atoms, 20168 bonds, 2435 residues, 4 models selected  

> hide sel cartoons

> show sel surfaces

> select add #27

19762 atoms, 20168 bonds, 2435 residues, 10 models selected  

> select add #28

38799 atoms, 39588 bonds, 4776 residues, 16 models selected  

> select subtract #27

38799 atoms, 39588 bonds, 4776 residues, 14 models selected  
Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  

> select #28.4/Ch:1-2 #28.6/Cj:1-2 #28.8/Cl:1-2

48 atoms, 45 bonds, 6 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 #!26 models

> view orient

> save /Users/shoichi/Desktop/HP-Fig4C2_09172024.png supersample 2
> transparentBackground true

> select add #28.4

8931 atoms, 9090 bonds, 1113 residues, 5 models selected  

> select add #28.6

14709 atoms, 15003 bonds, 1821 residues, 5 models selected  

> select add #28.8

20487 atoms, 20916 bonds, 2529 residues, 5 models selected  

> select subtract #28.8

13658 atoms, 13944 bonds, 1686 residues, 4 models selected  

> select add #28.7

14767 atoms, 15080 bonds, 1823 residues, 5 models selected  

> select add #28.2

19762 atoms, 20168 bonds, 2435 residues, 7 models selected  

> hide sel surfaces

> show sel cartoons

> select add #28

38799 atoms, 39588 bonds, 4776 residues, 14 models selected  

> select subtract #28

4 models selected  

> 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  

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/1X_PflAB-
> Sep18-2024.pdb selectedOnly true

> select add #28

38799 atoms, 39588 bonds, 4776 residues, 14 models selected  

> select subtract #28

4 models selected  

> hide #!28 models

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1X_PflAB-
> Sep18-2024.pdb

Chain information for 1X_PflAB-Sep18-2024.pdb  
---  
Chain | Description  
23.1/BJ | No description available  
23.2/Ch 23.3/Cj | No description available  
23.4/Ck | No description available  
  

> combine #23 modelId #29 name 1xPflAB-Sep18-2024

> show #!28 models

> hide #!28 models

> show #!26 models

> view orient

> sym #29 C18 copies true center #29

Made 18 copies for 1xPflAB-Sep18-2024 symmetry C18  

> close #30

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> ui tool show "Segment Map"

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  

> hide #!1 models

> select #30.16

1 model selected  

> select add #30.145

2 models selected  

> select add #30.256

3 models selected  
Grouped 3 regions  
Opened PflA-2.1A-230911_imasked as #31, grid size 240,240,240, pixel 2.1,
shown at step 1, values float32  

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/Rod.mrc models
> #31

> close #30

> view orient

> sym #29 C18 copies true center #31

Made 18 copies for 1xPflAB-Sep18-2024 symmetry C18  

> show #29 models

> hide #!30 models

> show #!30 models

> hide #30.2 models

> show #30.2 models

> hide #30.1 models

> hide #30.3 models

> hide #30.4 models

> hide #30.5 models

> hide #30.6 models

> hide #30.7 models

> hide #30.8 models

> hide #30.9 models

> hide #30.10 models

> hide #30.11 models

> hide #30.12 models

> hide #30.13 models

> hide #30.14 models

> hide #30.15 models

> hide #30.16 models

> hide #30.17 models

> select add #30.2

19762 atoms, 20168 bonds, 2435 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #30.2,0.90121,-0.43338,0,-9.7896,0.43338,0.90121,0,76.344,0,0,1,0

> ui mousemode right "translate selected models"

> view matrix models
> #30.2,0.90121,-0.43338,0,-8.5295,0.43338,0.90121,0,88.133,0,0,1,0

> select subtract #30.2

Nothing selected  

> hide #30.2 models

> show #30.2 models

> hide #30.2 models

> show #30.2 models

> select add #30.2

19762 atoms, 20168 bonds, 2435 residues, 1 model selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P2.pdb
> selectedOnly true

> hide #!31 models

> select subtract #30.2

Nothing selected  

> hide #30.2 models

> select add #30.18

19762 atoms, 20168 bonds, 2435 residues, 1 model selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P3.pdb
> selectedOnly true

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P2.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/1xPflAB-P2.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  
37 messages similar to the above omitted  
  
Chain information for 1xPflAB-P2.pdb #32  
---  
Chain | Description  
BJ | No description available  
Ch Cj | No description available  
Ck | No description available  
  

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P3.pdb

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-
version_model/Flo_PflA_Local/1xPflAB-P3.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  
37 messages similar to the above omitted  
  
Chain information for 1xPflAB-P3.pdb #33  
---  
Chain | Description  
BJ | No description available  
Ch Cj | No description available  
Ck | No description available  
  

> select add #30

355716 atoms, 363024 bonds, 43830 residues, 19 models selected  

> select subtract #30

Nothing selected  

> hide #!30 models

> hide #!23 models

> hide #!27 models

> fitmap #32 inMap #26

Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 1.609, steps = 76  
shifted from previous position = 4.75  
rotated from previous position = 5.97 degrees  
atoms outside contour = 10293, contour level = 0.037925  
  
Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99473557 0.10193329 0.01052391 -18.34266851  
-0.10172536 0.99463679 -0.01869760 -0.21008206  
-0.01237338 0.01752862 0.99976980 -2.55026439  
Axis 0.17406499 0.11002022 -0.97856882  
Axis point -10.67948235 178.16616913 0.00000000  
Rotation angle (degrees) 5.97297980  
Shift along axis -0.72032053  
  

> fitmap #32 inMap #26

Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 1.609, steps = 48  
shifted from previous position = 0.0247  
rotated from previous position = 0.0292 degrees  
atoms outside contour = 10296, contour level = 0.037925  
  
Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99470505 0.10225763 0.01025897 -18.39976411  
-0.10205776 0.99460805 -0.01841292 -0.16726036  
-0.01208652 0.01726842 0.99977783 -2.53376431  
Axis 0.17104502 0.10711715 -0.97942305  
Axis point -10.33923583 178.25674648 0.00000000  
Rotation angle (degrees) 5.98706579  
Shift along axis -0.68347725  
  

> fitmap #32 inMap #26

Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 1.609, steps = 44  
shifted from previous position = 0.0147  
rotated from previous position = 0.0133 degrees  
atoms outside contour = 10294, contour level = 0.037925  
  
Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99471763 0.10212357 0.01037345 -18.37068452  
-0.10191993 0.99461944 -0.01856086 -0.19105890  
-0.01221314 0.01740555 0.99977392 -2.54759165  
Axis 0.17256978 0.10837229 -0.97901742  
Axis point -10.53934899 178.16422167 0.00000000  
Rotation angle (degrees) 5.98155561  
Shift along axis -0.69679389  
  

> select add #32

19762 atoms, 20168 bonds, 2435 residues, 1 model selected  

> view matrix models
> #32,0.99472,0.10212,0.010373,-17.328,-0.10192,0.99462,-0.018561,-1.3395,-0.012213,0.017406,0.99977,-2.5476

> fitmap #32 inMap #26

Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 1.609, steps = 72  
shifted from previous position = 1.53  
rotated from previous position = 0.00799 degrees  
atoms outside contour = 10291, contour level = 0.037925  
  
Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99472682 0.10202677 0.01044519 -18.35075180  
-0.10182104 0.99462828 -0.01862955 -0.21776303  
-0.01228980 0.01746777 0.99977189 -2.52370286  
Axis 0.17332496 0.10916437 -0.97879599  
Axis point -10.74529701 178.05945517 0.00000000  
Rotation angle (degrees) 5.97715484  
Shift along axis -0.73422497  
  

> view matrix models
> #32,0.99473,0.10203,0.010445,-15.954,-0.10182,0.99463,-0.01863,0.054505,-0.01229,0.017468,0.99977,-2.5237

> fitmap #32 inMap #26

Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 1.609, steps = 52  
shifted from previous position = 2.43  
rotated from previous position = 0.016 degrees  
atoms outside contour = 10292, contour level = 0.037925  
  
Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99473661 0.10191776 0.01057617 -18.35162729  
-0.10170703 0.99463581 -0.01884877 -0.20848970  
-0.01244046 0.01767389 0.99976641 -2.57228974  
Axis 0.17546256 0.11057672 -0.97825645  
Axis point -10.66158881 178.26136266 0.00000000  
Rotation angle (degrees) 5.97389706  
Shift along axis -0.72671868  
  

> view matrix models
> #32,0.99474,0.10192,0.010576,-16.201,-0.10171,0.99464,-0.018849,-2.3657,-0.01244,0.017674,0.99977,-2.5723

> select subtract #32

Nothing selected  

> fitmap #33 inMap #26

Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 2.097, steps = 64  
shifted from previous position = 9.88  
rotated from previous position = 1.13 degrees  
atoms outside contour = 9345, contour level = 0.037925  
  
Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99984804 -0.01417461 0.01014753 -3.52645977  
0.01408196 0.99985903 0.00914379 -9.84630785  
-0.01027571 -0.00899950 0.99990670 0.34137374  
Axis -0.46162681 0.51963656 0.71894265  
Axis point 575.92914554 -360.58206793 0.00000000  
Rotation angle (degrees) 1.12601899  
Shift along axis -3.24316504  
  

> fitmap #33 inMap #26

Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 2.097, steps = 24  
shifted from previous position = 0.00676  
rotated from previous position = 0.00417 degrees  
atoms outside contour = 9345, contour level = 0.037925  
  
Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99984849 -0.01418178 0.01009336 -3.52415361  
0.01409012 0.99985936 0.00909589 -9.84776388  
-0.01022093 -0.00895230 0.99990769 0.33633104  
Axis -0.46025304 0.51804168 0.72097154  
Axis point 576.30743341 -359.71068987 0.00000000  
Rotation angle (degrees) 1.12345930  
Shift along axis -3.23706458  
  

> fitmap #33 inMap #26

Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 2.097, steps = 28  
shifted from previous position = 0.00519  
rotated from previous position = 0.00508 degrees  
atoms outside contour = 9343, contour level = 0.037925  
  
Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99984932 -0.01418343 0.01000828 -3.52396480  
0.01409227 0.99985910 0.00912103 -9.84536330  
-0.01013624 -0.00897861 0.99990832 0.32653865  
Axis -0.46228627 0.51451490 0.72219514  
Axis point 578.18872638 -358.91993357 0.00000000  
Rotation angle (degrees) 1.12170651  
Shift along axis -3.20068097  
  

> select add #33

19762 atoms, 20168 bonds, 2435 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #33,0.99973,0.020993,0.010323,-1.3467,-0.021084,0.99974,0.0087634,-9.5356,-0.010136,-0.0089786,0.99991,0.32654

> ui mousemode right "translate selected models"

> view matrix models
> #33,0.99973,0.020993,0.010323,0.99315,-0.021084,0.99974,0.0087634,-13.601,-0.010136,-0.0089786,0.99991,0.32654

> view matrix models
> #33,0.99973,0.020993,0.010323,4.8889,-0.021084,0.99974,0.0087634,-14.985,-0.010136,-0.0089786,0.99991,0.32394

> fitmap #33 inMap #26

Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
atoms  
average map value = 2.097, steps = 72  
shifted from previous position = 9.49  
rotated from previous position = 2.01 degrees  
atoms outside contour = 9338, contour level = 0.037925  
  
Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
coordinates:  
Matrix rotation and translation  
0.99984739 -0.01410746 0.01030409 -3.54810052  
0.01401132 0.99985818 0.00934308 -9.84531491  
-0.01043444 -0.00919728 0.99990326 0.37354334  
Axis -0.46873867 0.52431284 0.71090091  
Axis point 577.97851061 -365.18963893 0.00000000  
Rotation angle (degrees) 1.13320465  
Shift along axis -3.23334081  
  

> select add #32

39524 atoms, 40336 bonds, 4870 residues, 2 models selected  

> split #32

Split 1xPflAB-P2.pdb (#32) into 4 models  
Chain information for 1xPflAB-P2.pdb BJ #32.1  
---  
Chain | Description  
BJ | No description available  
  
Chain information for 1xPflAB-P2.pdb Ch #32.2  
---  
Chain | Description  
Ch | No description available  
  
Chain information for 1xPflAB-P2.pdb Cj #32.3  
---  
Chain | Description  
Cj | No description available  
  
Chain information for 1xPflAB-P2.pdb Ck #32.4  
---  
Chain | Description  
Ck | No description available  
  

> split #33

Split 1xPflAB-P3.pdb (#33) into 4 models  
Chain information for 1xPflAB-P3.pdb BJ #33.1  
---  
Chain | Description  
BJ | No description available  
  
Chain information for 1xPflAB-P3.pdb Ch #33.2  
---  
Chain | Description  
Ch | No description available  
  
Chain information for 1xPflAB-P3.pdb Cj #33.3  
---  
Chain | Description  
Cj | No description available  
  
Chain information for 1xPflAB-P3.pdb Ck #33.4  
---  
Chain | Description  
Ck | No description available  
  

> hide #32.1 models

> show #32.1 models

> hide #32.2 models

> show #32.2 models

> hide #32.2 models

> hide #32.3 models

> show #32.3 models

> hide #32.3 models

> show #32.3 models

> hide #33.1 models

> show #33.1 models

> hide #33.2 models

> show #33.2 models

> hide #33.3 models

> select add #33.4

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> select subtract #33.4

Nothing selected  

> select add #33.2

6829 atoms, 6972 bonds, 843 residues, 1 model selected  
Alignment identifier is 33.2/Ch  

> select #33.2/Ch:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #33.2/Ch:1-135

1051 atoms, 1059 bonds, 135 residues, 1 model selected  

> hide sel cartoons

Drag select of 26 3xOnly-PflAB.mrc , 191 residues  

> hide sel cartoons

> hide sel surfaces

> select #33.2/Ch:315

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #33.2/Ch:315-841

4318 atoms, 4420 bonds, 527 residues, 1 model selected  

> show sel surfaces

> select #33.2/Ch:841-842

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #33.2/Ch:838-842

42 atoms, 42 bonds, 5 residues, 1 model selected  

> hide sel surfaces

> select add #33.2

6829 atoms, 6972 bonds, 843 residues, 2 models selected  

> show sel surfaces

> select #33.2/Ch:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #33.2/Ch:1-135

1051 atoms, 1059 bonds, 135 residues, 1 model selected  

> hide sel surfaces

> select add #33.2

6829 atoms, 6972 bonds, 843 residues, 2 models selected  

> select add #33

19762 atoms, 20168 bonds, 2435 residues, 6 models selected  

> select subtract #33

1 model selected  

> select add #33

19762 atoms, 20168 bonds, 2435 residues, 5 models selected  

> select subtract #33

1 model selected  

> close #30

> close #29

> select add #28.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #28.2

1 model selected  

> show #!28 models

> hide #32.3 models

> show #32.3 models

> hide #32.1 models

> show #32.1 models

> color #32.1 #ca4949ff

> color #33.1 #ca4949ff

> hide #!28.4 models

> show #!28.4 models

> hide #32.4 models

> show #32.4 models

> hide #32.3 models

> show #32.3 models

> color #32.3 #8c3092ff

> hide #33.4 models

> show #33.4 models

> hide #!33.2 models

> show #!33.2 models

> color #33.2 magenta

> show #!1 models

> hide #!1 models

> hide #32.4 models

> show #32.4 models

> color #32.4 #ca4949ff

> color #33.4 #ca4949ff

> hide #!28 models

> hide #!32 models

> hide #!33 models

> ui tool show "Segment Map"

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  

> select add #29.3

1 model selected  

> select add #29.256

2 models selected  

> select add #29.4

3 models selected  

> select add #29.145

4 models selected  

> select add #29.16

5 models selected  

> select add #29.250

6 models selected  
Drag select of 4700, 489 of 20620 triangles, 4887, 3576 of 19436 triangles,
4964, 26 of 13104 triangles, 4763, 4895, 4696, 550 of 9412 triangles, 4866  
Drag select of 4899, 615 of 27220 triangles, 4902, 5446 of 23188 triangles,
4949, 15956 of 19796 triangles, 4692, 3867 of 20372 triangles, 4932, 13845 of
19788 triangles, 4915, 16250 of 18084 triangles, 4897, 751 of 19224 triangles,
4704, 8950 of 17972 triangles, 4922, 44 of 17548 triangles, 4886, 3440 of
16072 triangles, 4943, 14122 of 15236 triangles, 4708, 639 of 14432 triangles,
4909, 12696 of 14460 triangles, 4691, 8890 of 14140 triangles, 4918, 10905 of
15304 triangles, 4675, 5509 of 12864 triangles, 4850, 7532 of 14224 triangles,
4910, 3199 of 13064 triangles, 4952, 3122 of 13532 triangles, 4756, 9030 of
12092 triangles, 4959, 2165 of 11244 triangles, 4916, 1297 of 12440 triangles,
4742, 2132 of 11168 triangles, 4721, 609 of 11256 triangles, 4728, 277 of
11200 triangles, 4926, 5930 of 12096 triangles, 4942, 2162 of 9944 triangles,
4904, 6909 of 9736 triangles, 4913, 4703, 2359 of 10328 triangles, 4712, 3174
of 9008 triangles, 4805, 3653 of 9596 triangles, 4758, 7801 of 7876 triangles,
4762, 7903 of 8936 triangles, 4294, 6972 of 7764 triangles, 4282, 1463 of 6712
triangles, 4321, 4605, 6426 of 6700 triangles, 4573, 5123 of 6248 triangles,
4342, 2525 of 4648 triangles, 4340, 1758 of 4632 triangles  
Drag select of 4668, 14222 of 14912 triangles, 4896, 2950 of 15160 triangles,
4663, 12051 of 14720 triangles, 4761, 3120 of 15236 triangles, 4891, 971 of
14104 triangles, 4888, 6670 of 11360 triangles, 4726, 9406 of 10748 triangles,
4713, 3094 of 10880 triangles, 4380, 1387 of 4444 triangles, 3860, 866 of 4348
triangles  

> select add #29.239

65 models selected  
Drag select of 4689, 1369 of 19220 triangles, 4889, 7346 of 19404 triangles,
4738, 8412 of 18596 triangles, 4885, 6608 of 18508 triangles, 4954, 3180 of
16240 triangles, 4938, 10669 of 19236 triangles, 4951, 9496 of 18276
triangles, 4914, 8181 of 16520 triangles, 4735, 3535 of 16136 triangles, 4934,
5144 of 15096 triangles, 4944, 7567 of 15396 triangles, 4940, 10304 of 16352
triangles, 4900, 9260 of 14060 triangles, 4892, 11398 of 13456 triangles,
4857, 4266 of 12868 triangles, 4923, 10595 of 13012 triangles, 4946, 7135 of
12704 triangles, 4905, 4951 of 12716 triangles, 4734, 6050 of 13180 triangles,
4719, 7639 of 13024 triangles, 4903, 4366 of 12188 triangles, 4694, 4063 of
12536 triangles, 4784, 4118 of 12580 triangles, 4746, 4022 of 12820 triangles,
4671, 360 of 11748 triangles, 4676, 7112 of 10476 triangles, 4941, 3032 of
10760 triangles, 4269, 5558 of 9676 triangles, 4890, 11050 of 11756 triangles,
4782, 6972 of 9776 triangles, 4879, 2916 of 8508 triangles, 4698, 2987 of 9220
triangles, 4877, 6702 of 9200 triangles, 4724, 6962 of 8944 triangles, 4091,
1619 of 8108 triangles, 4774, 2105 of 8116 triangles, 4711, 7128 of 7880
triangles, 4800, 5186 of 8140 triangles, 4715, 1608 of 6440 triangles, 4874,
5216 of 7408 triangles, 4853, 5165 of 7556 triangles, 4741, 3827 of 7216
triangles  
Drag select of 4927, 13477 of 15704 triangles, 4878, 9453 of 9600 triangles,
4309, 7829 of 8912 triangles, 4534, 6567 of 6700 triangles, 4670, 5829 of 6004
triangles  
Drag select of 4750, 6730 of 11416 triangles, 4906, 12393 of 12516 triangles,
4930, 4834, 7953 of 10404 triangles, 4865, 4183 of 10016 triangles, 4815,
4928, 4577, 8835 of 9196 triangles, 4172, 4688, 4804, 4965, 8439 of 8488
triangles, 4795, 3745 of 8332 triangles, 4214, 2221 of 7504 triangles, 4788,
4880, 4789, 3398, 2931 of 5904 triangles, 4359, 4420, 5129 of 5492 triangles,
3375, 4992 of 5048 triangles, 3388, 4562, 59 of 4036 triangles, 160, 895 of
2876 triangles  

> select add #29.179

137 models selected  

> select add #29.224

138 models selected  

> select add #29.213

139 models selected  

> show #!33 models

> hide #!33 models

> select add #33

19762 atoms, 20168 bonds, 2435 residues, 144 models selected  

> select add #32

39524 atoms, 40336 bonds, 4870 residues, 150 models selected  

> show #!32 models

> show #!33 models

> select add #29

39524 atoms, 40336 bonds, 4870 residues, 307 models selected  

> select subtract #29

39524 atoms, 40336 bonds, 4870 residues, 11 models selected  

> hide sel & #32.1,3-4#33.1,4#!33.2 cartoons

> show sel & #32.1,3-4#33.1,4#!33.2 surfaces

> select subtract #32

19762 atoms, 20168 bonds, 2435 residues, 11 models selected  

> select subtract #33

3 models selected  

> hide #!32 models

> show #!32 models

> hide #!33 models

> hide #!32 models

> select clear

Drag select of 4911, 4939, 4937, 4947, 4901, 4933, 4812, 4908, 4864, 4907,
4779, 4935, 4953, 4958, 13741 of 14800 triangles, 4966, 4948, 4936, 4217,
4917, 4793, 4748, 4919, 4894, 4845, 4772, 4669, 4679, 4855, 4818, 4823, 4539,
4781, 4957, 4797, 4119, 4072, 4174, 4524, 4452, 4611, 4754, 4570, 4962, 4559,
4961, 4912, 4209, 4553, 4955, 4727, 4771, 4821, 4808, 4137, 4893, 4876, 4664,
4262, 3475, 4783, 4235, 4929, 4852, 4199, 4707, 4505, 4861, 4920, 4817, 4830,
4921, 4405, 4856, 4162, 4950, 4460, 4595, 3405, 4149, 4747, 4567, 1073, 4422,
4446, 4841, 4931, 4835, 4963, 4682, 4787, 4924, 4148, 3917, 8386 of 8404
triangles, 4413, 4945, 4110, 4538, 4208, 4956, 4336, 3440, 4868, 4138, 4454,
4838, 4725, 4705, 4858, 4833, 4813, 855, 4960, 4204, 4544, 3450, 4461, 4171,
4839, 4099, 4677, 4201, 4822, 3446, 4547, 4898, 4502, 3410, 4518, 4860, 4200,
4731, 3411, 3453, 4872, 4732, 4831, 4825, 4525, 4477, 4632, 4437, 4847, 4596,
4205, 4187, 4491, 4807, 4770, 4472, 712, 4001, 3470, 3517, 858, 696, 4470,
4656, 4315, 1461, 26 3xOnly-PflAB.mrc  
Grouped 159 regions  
Showing 137 region surfaces  

> select #29.1

1 model selected  
Opened PflA-2.1A-230911_imasked as #30, 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 159 region surfaces  
1246 watershed regions, grouped to 159 regions  
Showing PflA-2.seg - 159 regions, 159 surfaces  

> select add #29.7

1 model selected  

> select add #29.81

2 models selected  

> select add #29.134

3 models selected  

> select add #29.60

4 models selected  

> select add #29.106

5 models selected  

> select add #29.16

6 models selected  

> select add #29.13

7 models selected  

> select add #29.31

8 models selected  

> select add #29.84

9 models selected  

> select add #29.39

10 models selected  

> select add #29.40

11 models selected  

> select add #29.28

12 models selected  

> select add #29.97

13 models selected  

> select add #29.72

14 models selected  

> select add #29.51

15 models selected  

> select add #29.33

16 models selected  

> select add #29.56

17 models selected  

> select add #29.93

18 models selected  

> select add #29.32

19 models selected  

> select add #29.38

20 models selected  

> select add #29.30

21 models selected  
Grouped 21 regions  

> select add #29.15

2 models selected  

> select add #29.133

3 models selected  

> select add #29.141

4 models selected  

> select add #29.54

5 models selected  

> select add #29.109

6 models selected  

> select add #29.149

7 models selected  

> select add #29.26

8 models selected  

> select add #29.44

9 models selected  

> select add #29.34

10 models selected  

> select add #29.59

11 models selected  

> select add #29.14

12 models selected  

> select add #29.78

13 models selected  

> select add #29.53

14 models selected  

> select add #29.36

15 models selected  

> select add #29.11

16 models selected  

> select add #29.37

17 models selected  

> select add #29.24

18 models selected  

> select add #29.120

19 models selected  

> select add #29.90

20 models selected  

> select add #29.94

21 models selected  
Grouped 21 regions  

> 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.  

> show #!2 models

> select add #2

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> hide sel surfaces

> show sel cartoons

> view orient

> select subtract #2

13 models selected  

> select add #2.1

9605 atoms, 9765 bonds, 1250 residues, 1 model selected  

> select subtract #2.1

1 model selected  

> select add #2.2

799 atoms, 807 bonds, 98 residues, 1 model selected  

> select add #2.3

1598 atoms, 1614 bonds, 196 residues, 3 models selected  

> select add #2.4

2397 atoms, 2421 bonds, 294 residues, 5 models selected  

> select add #2.5

3196 atoms, 3228 bonds, 392 residues, 7 models selected  

> select add #2.6

3995 atoms, 4035 bonds, 490 residues, 9 models selected  

> select add #2.7

4794 atoms, 4842 bonds, 588 residues, 11 models selected  

> select add #2.8

5593 atoms, 5649 bonds, 686 residues, 13 models selected  

> select add #2.9

6392 atoms, 6456 bonds, 784 residues, 15 models selected  

> select add #2.10

7191 atoms, 7263 bonds, 882 residues, 17 models selected  

> select add #2.11

7990 atoms, 8070 bonds, 980 residues, 19 models selected  

> view matrix models
> #2.2,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.3,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.4,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.5,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.6,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.7,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.8,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.9,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.10,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721,#2.11,0.9687,0.24821,0.0045987,5.7466,-0.24821,0.9687,0.0013642,10.34,-0.0041162,-0.002463,0.99999,0.13721

> select add #2.1

17595 atoms, 17835 bonds, 2230 residues, 21 models selected  

> view matrix models
> #2.1,0.99999,-0.00018683,0.004346,0.46474,0.00014025,0.99994,0.010716,1.145,-0.0043478,-0.010715,0.99993,0.014005,#2.2,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.3,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.4,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.5,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.6,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.7,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.8,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.9,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.10,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432,#2.11,0.96872,0.24801,0.0089444,6.2099,-0.24811,0.96866,0.012081,11.486,-0.0056679,-0.013922,0.99989,0.015432

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #2.1,1,2.8921e-17,-3.4694e-18,1.1462,1.5206e-17,1,-1.3878e-17,1.3962,-4.3368e-18,-1.0408e-17,1,0.015675,#2.2,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.3,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.4,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.5,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.6,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.7,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.8,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.9,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.10,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289,#2.11,0.9687,0.24821,0.0045987,6.8928,-0.24821,0.9687,0.0013642,11.736,-0.0041162,-0.002463,0.99999,0.15289

> ui mousemode right "rotate selected models"

> view matrix models
> #2.1,0.99301,0.11803,0.0021259,3.5303,-0.11803,0.99301,0.00078724,6.4996,-0.0020181,-0.0010327,1,0.086885,#2.2,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.3,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.4,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.5,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.6,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.7,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.8,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.9,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.10,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182,#2.11,0.93262,0.3608,0.0068534,10.457,-0.36082,0.93264,0.0015991,16.089,-0.0058148,-0.0039642,0.99998,0.20182

> view orient

> select clear

> turn x 90

[Repeated 2 time(s)]

> select add #2.22

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> view matrix models
> #2.22,1,-0.0019189,-0.0001748,-0.028518,0.0019129,0.99956,-0.0296,-1.8224,0.00023153,0.029599,0.99956,0.24735

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #2.22,1,5.0226e-17,-3.4694e-18,0.081614,2.8379e-17,1,-2.0817e-17,0.081843,-1.5613e-17,-1.7347e-17,1,-4.6958

> select clear

> select add #2

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> show sel surfaces

> select clear

Cell requested for row 39 is out of bounds for table with 61 rows! Resizing
table model.  

> select add #28

38799 atoms, 39588 bonds, 4776 residues, 10 models selected  

> select subtract #28

4 models selected  

> select add #2

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> select clear

Drag select of 83 residues  

> select add #22

21694 atoms, 22006 bonds, 2748 residues, 14 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_review2.cxs includeMaps true

> view orient

> show #!29 models

> hide #!29 models

> show #!25 models

> hide #!25 models

> show #!30 models

> hide #!30 models

> show #!32 models

> hide #!32 models

> show #!33 models

> hide #!33.2 models

> hide #!33.4 models

> show #!33.4 models

> show #33.3 models

> hide #33.3 models

> hide #!33.1 models

> select add #33.4

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select add #28.2

6104 atoms, 6224 bonds, 749 residues, 3 models selected  

> select subtract #28.2

1109 atoms, 1136 bonds, 137 residues, 3 models selected  

> select add #28.7

2218 atoms, 2272 bonds, 274 residues, 3 models selected  

> hide sel surfaces

> select add #28

39908 atoms, 40724 bonds, 4913 residues, 13 models selected  

> select subtract #28

1109 atoms, 1136 bonds, 137 residues, 6 models selected  

> view matrix models
> #33.4,0.99985,-0.014107,0.010304,-3.0078,0.014011,0.99986,0.0093431,-20.467,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "rotate selected models"

> view matrix models
> #33.4,0.8596,-0.51096,0.0042704,0.66961,0.51087,0.85956,0.013237,-76.555,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "translate selected models"

> view matrix models
> #33.4,0.8596,-0.51096,0.0042704,-2.9484,0.51087,0.85956,0.013237,-75.491,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "rotate selected models"

> view matrix models
> #33.4,0.96516,-0.26154,0.0076663,-8.5386,0.26144,0.96515,0.011606,-46.538,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "translate selected models"

> view matrix models
> #33.4,0.96516,-0.26154,0.0076663,-6.9534,0.26144,0.96515,0.011606,-46.9,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "rotate selected models"

> view matrix models
> #33.4,0.94565,-0.32511,0.0068779,-6.316,0.32502,0.94563,0.01209,-54.112,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "translate selected models"

> view matrix models
> #33.4,0.94565,-0.32511,0.0068779,-6.3134,0.32502,0.94563,0.01209,-53.361,-0.010434,-0.0091973,0.9999,0.37354

> select add #28.2

6104 atoms, 6224 bonds, 749 residues, 3 models selected  

> select subtract #28.2

1109 atoms, 1136 bonds, 137 residues, 3 models selected  

> select add #28.7

2218 atoms, 2272 bonds, 274 residues, 3 models selected  

> show sel surfaces

> select clear

> save /Users/shoichitachiyama/Desktop/Fig4E.png supersample 2
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> save /Users/shoichitachiyama/Desktop/Fig4H.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/Fig4_After_review2.cxs includeMaps true

——— End of log from Wed Dec 4 21:50:17 2024 ———

opened ChimeraX session  
Showing PflA-2.seg - 27 regions, 27 surfaces  

> hide #!11 models

> show #!10 models

> color #10 #5e5e5eff models

> color #10 #5e5e5e20 models

> color #10 #5e5e5e14 models

> hide #!22 models

> show #!22 models

> hide #!2 models

> show #!2 models

> select add #2.1

9605 atoms, 9765 bonds, 1250 residues, 1 model selected  

> select subtract #2.1

1 model selected  

> select add #2.2

799 atoms, 807 bonds, 98 residues, 1 model selected  

> select subtract #2.2

1 model selected  

> select add #2.1

9605 atoms, 9765 bonds, 1250 residues, 1 model selected  

> color #2.1 #a69b3288

> color #2.1 #a69b3287

> color #2.1 #a69b32ff

> mlp sel

Map values for surface "Stator-complexb.pdb_ SES surface": minimum -26.45,
mean -1.388, maximum 31.36  
To also show corresponding color key, enter the above mlp command and add key
true  

> view orient

> turn x 90

[Repeated 2 time(s)]

> select clear

> turn y 90

[Repeated 1 time(s)]

> select add #22.1

9605 atoms, 9765 bonds, 1250 residues, 1 model selected  

> mlp sel

Map values for surface "Stator-complexb.pdb_ SES surface": minimum -26.56,
mean -1.389, maximum 31.15  
To also show corresponding color key, enter the above mlp command and add key
true  

> view matrix models #22.1,1,0,0,2.8145,0,1,0,0.97304,0,0,1,-4.2926

> select clear

> select add #22.1

9605 atoms, 9765 bonds, 1250 residues, 1 model selected  

> view matrix models #22.1,1,0,0,3.0222,0,1,0,0.97304,0,0,1,-6.1273

> select clear

> color #2.1 #a69b32ff

> color #22.1 #a69b32ff

> select clear

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review2.cxs includeMaps true

> view orient

> hide #!10 models

> save /Users/shoichitachiyama/Desktop/Fig4E.png supersample 2
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> save /Users/shoichitachiyama/Desktop/Fig4H.png supersample 2
> transparentBackground true

> select add #22

21694 atoms, 22006 bonds, 2748 residues, 13 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Stator.pdb
> selectedOnly true

> select add #36

32774 atoms, 33322 bonds, 4092 residues, 31 models selected  

> select subtract #36

21694 atoms, 22006 bonds, 2748 residues, 34 models selected  

> turn x 90

> select add #36.1

24464 atoms, 24835 bonds, 3084 residues, 27 models selected  

> select subtract #36.1

21694 atoms, 22006 bonds, 2748 residues, 28 models selected  

> select add #36

32774 atoms, 33322 bonds, 4092 residues, 31 models selected  

> select subtract #36

21694 atoms, 22006 bonds, 2748 residues, 34 models selected  

> select clear

> select add #36.1

2770 atoms, 2829 bonds, 336 residues, 1 model selected  

> select add #36.2

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> select subtract #36.2

2770 atoms, 2829 bonds, 336 residues, 5 models selected  

> select add #36.2

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> select subtract #36.2

2770 atoms, 2829 bonds, 336 residues, 5 models selected  

> select add #36.4

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> select subtract #36.4

2770 atoms, 2829 bonds, 336 residues, 5 models selected  

> select add #36.3

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> select subtract #36.1

2770 atoms, 2829 bonds, 336 residues, 5 models selected  

> select add #36.2

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/2xCage_Dec112024.pdb selectedOnly true

> select add #36

11080 atoms, 11316 bonds, 1344 residues, 9 models selected  

> select subtract #36

8 models selected  

> select add #33.4

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> select subtract #33.4

1 model selected  

> select add #28.7

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> select add #28.6

7938 atoms, 8108 bonds, 980 residues, 3 models selected  

> select add #28.4

14767 atoms, 15080 bonds, 1823 residues, 5 models selected  

> select add #28.2

19762 atoms, 20168 bonds, 2435 residues, 7 models selected  

> select subtract #28.2

14767 atoms, 15080 bonds, 1823 residues, 7 models selected  

> select add #28.2

19762 atoms, 20168 bonds, 2435 residues, 7 models selected  

> select subtract #28.2

14767 atoms, 15080 bonds, 1823 residues, 7 models selected  

> hide #!28.2 models

> show #!28.2 models

> select add #28.2

19762 atoms, 20168 bonds, 2435 residues, 7 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/2xPflB-1PflA_Dec112024.pdb selectedOnly true

> select subtract #28.7

18653 atoms, 19032 bonds, 2298 residues, 7 models selected  

> select add #28.7

19762 atoms, 20168 bonds, 2435 residues, 7 models selected  

> select subtract #28.7

18653 atoms, 19032 bonds, 2298 residues, 7 models selected  

> select add #28.7

19762 atoms, 20168 bonds, 2435 residues, 7 models selected  

> select subtract #28.7

18653 atoms, 19032 bonds, 2298 residues, 7 models selected  

> select subtract #28.2

13658 atoms, 13944 bonds, 1686 residues, 5 models selected  

> hide #!28.2 models

> select add #28.7

14767 atoms, 15080 bonds, 1823 residues, 5 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/2xPflB-1PflAn_Dec112024.pdb selectedOnly true

> color #28.7 #ca4949ff

[Repeated 1 time(s)]

> show #!28.2 models

> color #28.2 #ca4949ff

> select clear

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review2.cxs includeMaps true

——— End of log from Wed Dec 11 17:05:13 2024 ———

opened ChimeraX session  
Showing PflA-2.seg - 27 regions, 27 surfaces  

> hide #!11 models

> view orient

> select add #36.1

2770 atoms, 2829 bonds, 336 residues, 1 model selected  

> select subtract #36.1

2 models selected  

> select add #36.1

2770 atoms, 2829 bonds, 336 residues, 1 model selected  

> select add #36.4

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> select subtract #36.4

2770 atoms, 2829 bonds, 336 residues, 5 models selected  

> select add #36.4

5540 atoms, 5658 bonds, 672 residues, 4 models selected  

> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/2xCage_Dec112024.pdb selectedOnly true

> hide sel surfaces

> hide #!36 models

> select add #36

11080 atoms, 11316 bonds, 1344 residues, 9 models selected  

> view orient

> select subtract #36

8 models selected  

> hide #!2 models

> hide #!37 models

> show #!37 models

> hide #!37 models

> hide #!19 models

> show #!19 models

> hide #!22 models

> hide #!21 models

> view orient

> hide #!33 models

> show #!33 models

> hide #!28 models

> show #!28 models

> hide #!19 models

> show #!19 models

> hide #!33 models

> show #!33 models

Drag select of 19 1xPflAB-New.mrc  

> select subtract #19

Nothing selected  

> hide #!19 models

> show #!17 models

> hide #!17 models

> show #!1 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!7 models

> hide #!7 models

> show #!9 models

> hide #!9 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 #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> show #!21 models

> hide #!21 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!24 models

> hide #!24 models

> show #!25 models

> hide #!25 models

> show #!26 models

> hide #!26 models

> show #!27 models

> hide #!27 models

> show #!27 models

> save /Users/shoichitachiyama/Desktop/Fig4D.png supersample 2
> transparentBackground true

> show #!26 models

> show #!32 models

> select add #28.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #28.2

1 model selected  

> select add #33

19762 atoms, 20168 bonds, 2435 residues, 5 models selected  

> select subtract #33

3 models selected  

> hide #!28 models

> show #!28 models

> hide #!27 models

> show #!27 models

> hide #!27 models

> show #!27 models

> hide #!27 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!34 models

> show #!35 models

> hide #!35 models

> show #33.3 models

> hide #33.3 models

> show #33.3 models

> hide #33.3 models

> show #!33.2 models

> select add #34

2 models selected  

> select subtract #34

Nothing selected  

> select add #33

19762 atoms, 20168 bonds, 2435 residues, 5 models selected  

> select subtract #33

3 models selected  

> show #33.3 models

> hide #33.3 models

> show #!33.1 models

> select add #33.2

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select subtract #33.2

1 model selected  

> hide #!33.2 models

> select add #33.1

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #33.1,0.99261,-0.0076172,-0.12107,-8.5821,0.013757,0.99866,0.04996,-8.3055,0.12053,-0.051257,0.99139,0.9193

> ui mousemode right "translate selected models"

> view matrix models
> #33.1,0.99261,-0.0076172,-0.12107,-8.9542,0.013757,0.99866,0.04996,-8.2219,0.12053,-0.051257,0.99139,2.5548

> select clear

> view orient

> select add #33.4

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> select subtract #33.4

1 model selected  

> select add #34

2 models selected  

> select subtract #34

Nothing selected  

> select add #33.1

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> view matrix models
> #33.1,0.99261,-0.0076172,-0.12107,-5.1,0.013757,0.99866,0.04996,-9.907,0.12053,-0.051257,0.99139,2.5548

> select clear

> select add #33.4

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> view matrix models
> #33.4,0.94565,-0.32511,0.0068779,-5.52,0.32502,0.94563,0.01209,-60.361,-0.010434,-0.0091973,0.9999,0.37354

> ui mousemode right "rotate selected models"

> view matrix models
> #33.4,0.84871,-0.52884,0.0039923,0.25843,0.52876,0.84867,0.013324,-84.365,-0.010434,-0.0091973,0.9999,0.37354

> undo

> view matrix models
> #33.4,0.93228,-0.36169,0.0064018,-4.9141,0.3616,0.93225,0.012348,-64.58,-0.010434,-0.0091973,0.9999,0.37354

> select clear

> select add #28.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #28.2

1 model selected  

> select add #28.4

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> select subtract #28.4

1 model selected  

> select add #28.2

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #28.2

1 model selected  

> select add #32.1

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> select subtract #32.1

1 model selected  

> select add #32.3

6829 atoms, 6972 bonds, 843 residues, 1 model selected  

> hide #!32.3 models

> show #!32.3 models

> select subtract #32.3

1 model selected  

> select add #32.4

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> view matrix models
> #32.4,0.98272,-0.18443,0.015489,45.187,0.18466,0.98269,-0.015074,-10.427,-0.01244,0.017674,0.99977,-2.5723

> ui mousemode right "translate selected models"

> view matrix models
> #32.4,0.98272,-0.18443,0.015489,47.925,0.18466,0.98269,-0.015074,-17.66,-0.01244,0.017674,0.99977,-2.5723

> ui mousemode right "rotate selected models"

> view matrix models
> #32.4,0.95508,-0.29584,0.017114,72.661,0.29608,0.95507,-0.0132,-15.909,-0.01244,0.017674,0.99977,-2.5723

> ui mousemode right "translate selected models"

> view matrix models
> #32.4,0.95508,-0.29584,0.017114,72.919,0.29608,0.95507,-0.0132,-15.756,-0.01244,0.017674,0.99977,-2.5723

> ui mousemode right "rotate selected models"

> view matrix models
> #32.4,0.96681,-0.25496,0.016538,63.784,0.2552,0.96679,-0.013915,-16.736,-0.01244,0.017674,0.99977,-2.5723

> select clear

> select add #28.7

1109 atoms, 1136 bonds, 137 residues, 1 model selected  

> select subtract #28.7

1 model selected  

> select add #32.1

4995 atoms, 5088 bonds, 612 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #32.1,0.99474,0.10192,0.010576,-16.339,-0.10171,0.99464,-0.018849,-1.8429,-0.01244,0.017674,0.99977,1.6917

> view orient

> view matrix models
> #32.1,0.99474,0.10192,0.010576,-15.847,-0.10171,0.99464,-0.018849,-1.1616,-0.01244,0.017674,0.99977,1.6917

> view orient

> show #32.2 models

> select subtract #32.1

1 model selected  

> hide #32.2 models

> show #!33.2 models

> save /Users/shoichitachiyama/Desktop/Fig4C.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/Fig4_After_review2.cxs includeMaps true

——— End of log from Wed Dec 11 17:58:52 2024 ———

opened ChimeraX session  
Showing PflA-2.seg - 27 regions, 27 surfaces  

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/For_Fig4FG_After-cleaned.cxs

Unable to restore session, resetting.  
  
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/core/session.py", line 731, in restore  
data = fdeserialize(stream)  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 81, in msgpack_deserialize  
return next(stream)  
^^^^^^^^^^^^  
File "msgpack/_unpacker.pyx", line 540, in msgpack._cmsgpack.Unpacker.__next__  
File "msgpack/_unpacker.pyx", line 474, in msgpack._cmsgpack.Unpacker._unpack  
File "msgpack/_unpacker.pyx", line 448, in
msgpack._cmsgpack.Unpacker.read_from_file  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 668, in read  
return self._buffer.read(size)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_compression.py",
line 68, in readinto  
data = self.read(len(byte_view))  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_compression.py",
line 103, in read  
data = self._decompressor.decompress(rawblock, size)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 414, in decompress  
decompressed, bytes_read, eoframe = decompress_chunk(  
^^^^^^^^^^^^^^^^^  
RuntimeError: LZ4F_decompress failed with code: ERROR_decompressionFailed  
  
opened ChimeraX session  

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: 38 days, 22 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

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