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#16457 assigned defect

Session restore failed: decompression failure

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

Description (last modified by pett)

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

[deleted to fit within ticket size limits]

> 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

Change History (1)

comment:1 by pett, 10 months ago

Cc:	chimera-programmers added
Component:	Unassigned → Sessions
Description:	modified (diff)
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Session restore failed: decompression failure

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