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Opened 26 hours ago

Last modified 7 hours ago

#19396 closed defect

ChimeraX bug report submission — at Initial Version

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

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:\Users\TAMU\OneDrive - Texas A&M University\BICH 603\BICH 603
> Project\20251114 region_4_wip.cxs" format session

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 1, values float32  
Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.109, step 1, values float32  
Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
level 0.017, step 1, values float32  
Opened region_1.mrc as #7, grid size 55,88,59, pixel 1.12,1.12,1.12, shown at
level 0.017, step 1, values float32  
Opened volume difference_190_regions.mrc as #8, grid size 215,224,227, pixel
1.12,1.12,1.12, shown at level 0.017, step 1, values float32  
Opened region_2.mrc as #9, grid size 42,26,41, pixel 1.12, shown at level
0.017, step 1, values float32  
Opened region_3.mrc as #11, grid size 69,49,52, pixel 1.12,1.12,1.12, shown at
level 0.017, step 1, values float32  
Opened region_4_2.mrc as #15, grid size 108,100,92, pixel 1.12, shown at level
0.017, step 1, values float32  
Opened vol diff region_3 as #21, grid size 215,224,227, pixel 1.12,1.12,1.12,
shown at level 0.017, step 1, values float32  
Opened region_4_jxn.mrc as #22, grid size 166,122,96, pixel 1.12,1.12,1.12,
shown at level 0.017, step 1, values float32  
Log from Fri Nov 14 16:00:29 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 1, values float32  
Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.109, step 1, values float32  
Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
level 0.017, step 1, values float32  
Opened region_1.mrc as #7, grid size 55,88,59, pixel 1.12,1.12,1.12, shown at
level 0.017, step 1, values float32  
Opened volume difference_190_regions.mrc as #8, grid size 215,224,227, pixel
1.12,1.12,1.12, shown at level 0.017, step 1, values float32  
Opened region_2.mrc as #9, grid size 42,26,41, pixel 1.12, shown at level
0.017, step 1, values float32  
Opened region_3.mrc as #11, grid size 69,49,52, pixel 1.12,1.12,1.12, shown at
level 0.017, step 1, values float32  
Opened region_4_2.mrc as #15, grid size 108,100,92, pixel 1.12, shown at level
0.017, step 1, values float32  
Opened vol diff region_3 as #21, grid size 215,224,227, pixel 1.12,1.12,1.12,
shown at level 0.017, step 1, values float32  
Opened region_4_jxn.mrc as #22, grid size 166,122,96, pixel 1.12,1.12,1.12,
shown at level 0.017, step 1, values float32  
Log from Fri Nov 14 11:51:38 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113 region_3.cxs"

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 1, values float32  
Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.109, step 1, values float32  
Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
level 0.0119, step 1, values float32  
Opened 3UTR_phiCb5_segment.mrc as #7, grid size 55,88,59, pixel
1.12,1.12,1.12, shown at level 0.00565, step 1, values float32  
Opened volume difference_190_regions.mrc as #8, grid size 215,224,227, pixel
1.12,1.12,1.12, shown at level 0.00353, step 1, values float32  
Opened volume difference_region_2.mrc as #9, grid size 42,26,41, pixel 1.12,
shown at level 0.00204, step 1, values float32  
Opened region_3.mrc as #11, grid size 69,49,52, pixel 1.12,1.12,1.12, shown at
level 0.00395, step 1, values float32  
Log from Thu Nov 13 15:31:54 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:\Users\TAMU\OneDrive - Texas A&M University\BICH 603\BICH 603
> Project\20251113 region_4 start.cxs" format session

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 1, values float32  
Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.109, step 1, values float32  
Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
level 0.0119, step 1, values float32  
Opened 3UTR_phiCb5_segment.mrc as #7, grid size 55,88,59, pixel
1.12,1.12,1.12, shown at level 0.00565, step 1, values float32  
Opened volume difference_190_regions.mrc as #8, grid size 215,224,227, pixel
1.12,1.12,1.12, shown at level 0.00353, step 1, values float32  
Opened volume difference_region_2.mrc as #9, grid size 42,26,41, pixel 1.12,
shown at level 0.00204, step 1, values float32  
Opened region_3.mrc as #11, grid size 69,49,52, pixel 1.12,1.12,1.12, shown at
level 0.00395, step 1, values float32  
Opened region_4.mrc as #16, grid size 83,94,52, pixel 1.12,1.12,1.12, shown at
level 0.0157, step 1, values float32  
Log from Thu Nov 13 13:38:11 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251112 JT.cxs"

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 1, values float32  
Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.109, step 1, values float32  
Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
level 0.0119, step 1, values float32  
Opened 3UTR_phiCb5_segment.mrc as #7, grid size 55,88,59, pixel
1.12,1.12,1.12, shown at level 0.00565, step 1, values float32  
Opened volume difference_190_regions.mrc as #8, grid size 215,224,227, pixel
1.12,1.12,1.12, shown at level 0.00353, step 1, values float32  
Opened volume difference_region_3014.mrc as #9, grid size 42,26,41, pixel
1.12, shown at level 0.00204, step 1, values float32  
Opened volume difference_region_3016.mrc as #11, grid size 69,49,52, pixel
1.12,1.12,1.12, shown at level 0.00395, step 1, values float32  
Log from Wed Nov 12 18:34:04 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251110 start.cxs"

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 1, values float32  
Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.109, step 1, values float32  
Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
level 0.0119, step 1, values float32  
Opened 3UTR_phiCb5_segment.mrc as #7, grid size 55,88,59, pixel
1.12,1.12,1.12, shown at level 0.00565, step 1, values float32  
Log from Mon Nov 10 12:39:23 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\TAMU\OneDrive - Texas A&M University\BICH 603\BICH 603
> Project\map.mrc" format mrc

Opened map.mrc as #1, grid size 400,400,400, pixel 1.12, shown at level
0.0263, step 2, values float32  

> volume #1 step 1

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/8uej-assembly1.cif"

8uej-assembly1.cif title:  
ssRNA phage PhiCb5 virion [more info...]  
  
Chain information for 8uej-assembly1.cif #2  
---  
Chain | Description  
AA AB AC AG AH AI AM AN AO AS AT AU AY AZ BA BE BF BG BK BL BM BQ BR BS BW BX BY CC CD CE CI CJ CK CO CP CQ CU CV CW DA DB DC DG DH DI DM DN DO DS DT DU DY DZ EA EE EF EG EK EL EM EQ ER ES EW EX EY FC FD FE FI FJ FK FO FP FQ FU FV FW GA GB GC GG GH GI GM GN GO GS GT GU GY GZ HC HD HE HI HJ HK HO HP HQ HU HV HW IA IB IC IG IH II IM IN IO IS IT IU IY IZ JA JE JF JG JK JL JM JQ JR JS JW JX JY KC KD KE KI KJ KK KO KP KQ KU KV KW LA LB LC LG LH LI LM LN LO LS LT LU LY LZ MA ME MF MG MK ML MM MQ MR MS MW MX NA NB NC NG NH NI NM NN NO | Coat protein  
M | Maturation protein  
  
Non-standard residues in 8uej-assembly1.cif #2  
---  
CA — calcium ion  
  

> fitmap #2 inMap #1

Fit molecule 8uej-assembly1.cif (#2) to map map.mrc (#1) using 172913 atoms  
average map value = 0.02774, steps = 64  
shifted from previous position = 5.32  
rotated from previous position = 0.352 degrees  
atoms outside contour = 78559, contour level = 0.026347  
  
Position of 8uej-assembly1.cif (#2) relative to map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998204 0.00599197 -0.00014922 -1.79149795  
-0.00599176 0.99998112 0.00136605 6.32454468  
0.00015741 -0.00136513 0.99999906 -0.10520794  
Axis -0.22214011 -0.02493963 -0.97469574  
Axis point 1056.05477447 289.44125711 0.00000000  
Rotation angle (degrees) 0.35222353  
Shift along axis 0.34277746  
  

> molmap #2 4

Opened 8uej-assembly1.cif map 4 as #3, grid size 236,251,238, pixel 1.33,
shown at level 0.0961, step 1, values float32  

> vop subtract #1 #3

Opened volume difference as #4, grid size 400,400,400, pixel 1.12, shown at
step 1, values float32  

> hide #2 models

> volume #4 level -0.05544

> volume #4 level 0.04452

> volume #4 level -0.03424

> lighting simple

> lighting soft

> lighting full

> lighting soft

> volume #4 level 0.002113

> volume #4 level 0.0112

> volume #4 level 0.012

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/3UTR_phiCb5.pdb"

Chain information for 3UTR_phiCb5.pdb #5  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #!4 models

> show #!4 models

> transparency #4.1 50

> volume #!4 showOutlineBox true

> volume #!4 showOutlineBox false

> volume #!4 style image

> volume #!4 style surface

> transparency #4.1 0

> transparency #4.1 50

> view

> hide #!4 models

> show #!4 models

> ui mousemode right zoom

[Repeated 1 time(s)]

> view

> volume #4 change image level -1.622,1 level -0.016,0.8 level 0,0 level 0,0
> level 0.016,0.8 level 0.05904,1

> volume #4 level 0.01503

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251110 start.cxs"

> hide #!4 models

> show #!4 models

> view

[Repeated 1 time(s)]

> hide #!4 models

> show #!4 models

> hide #5 models

> show #5 models

> view

> ui tool show "Segment Map"

Segmenting volume difference, density threshold 0.015029  
Showing 194 region surfaces  
2131 watershed regions, grouped to 194 regions  
Showing volume difference.seg - 194 regions, 194 surfaces  

> hide #!4 models

> transparency #6 50

> ui tool show "Segment Map"

> select #6.125

1 model selected  

> select #6.14

1 model selected  

> select add #6

195 models selected  

> select subtract #6

Nothing selected  

> select add #6.125

1 model selected  

> select add #6.165

2 models selected  

> select add #6.14

3 models selected  

> select add #6.26

4 models selected  

> select add #6.35

5 models selected  
Grouped 5 regions  

> transparency sel 0

[Repeated 3 time(s)]

> select add #6

191 models selected  

> select subtract #6

Nothing selected  

> select add #6

191 models selected  

> transparency sel 0

> transparency sel 50

> select subtract #6

Nothing selected  

> select add #6.14

1 model selected  

> ui tool show "Segment Map"

Saving 1 regions to mrc file...  
Opened 3UTR_phiCb5_segment.mrc as #7, grid size 55,88,59, pixel 1.12, shown at
step 1, values float32  
Wrote 3UTR_phiCb5_segment.mrc  

> hide #!7 models

> hide #5 models

> show #5 models

> hide #5 models

> hide #!6 models

> show #!7 models

> show #5 models

> select add #6

191 models selected  

> select subtract #6

Nothing selected  

> volume #4 level 0.01192

> hide #!4 models

> volume #7 level 0.004521

> transparency #7.1 50

> hide #!7 models

> hide #5 models

> show #!6 models

> view

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!6 models

> view

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> view

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251110 start.cxs"

> view

> hide #!6 models

> show #!6 models

> volume #7 level 0.005651

> hide #!6 models

> show #!6 models

> view

> view orient

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> show #5 models

> view

> hide #!7 models

> hide #5 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!7 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #5 models

> show #!6 models

> hide #5 models

> show #5 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> show #!7 models

> hide #5 models

> show #5 models

> vop subtract #6 #4

volume subtract operation requires exactly two volumes  

> molmap #6 4

No atoms specified  

> select add #6

191 models selected  

> select subtract #6

Nothing selected  

> select add #6

191 models selected  

> select subtract #6

Nothing selected  

> hide #!7 models

> show #!7 models

> vop subtract #7 #4

Opened volume difference as #8, grid size 55,88,59, pixel 1.12, shown at step
1, values float32  

> hide #!6 models

> hide #5 models

> hide #!8 models

> show #!8 models

> undo

[Repeated 1 time(s)]

> select add #8

2 models selected  

> close #8

> show #!3 models

> view

> volume #3 level 0.1826

> volume #3 level 0.1493

> volume #3 level 0.1128

> volume #3 level 0.1094

> hide #!3 models

> show #!4 models

> show #!3 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!6 models

> view

> hide #!6 models

> hide #!4 models

> show #5 models

> hide #5 models

> show #!7 models

> view

> show #!4 models

> show #!6 models

> hide #!4 models

> hide #!6 models

> show #!6 models

> select ~sel & ##selected

Nothing selected  

> vop #4 #7

> hide #!6 models

> show #!6 models

> hide #!7 models

> show #!7 models

> vop subtract #4 #7

Opened volume difference as #8, grid size 400,400,400, pixel 1.12, shown at
step 1, values float32  

> hide #!6 models

> show #!6 models

> undo

[Repeated 3 time(s)]

> close #8

> show #!3 models

> volume #3 step 4

> volume #3 step 1

> hide #!3 models

> show #2 models

> hide #2 models

> hide #!7 models

> hide #!6 models

> show #!7 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> select add #6.14

1 model selected  

> hide #6.14 models

> show #6.14 models

> hide #6.14 models

> select add #6

191 models selected  

> select subtract #6

Nothing selected  

> show #5 models

> show #!7 models

> hide #!7 models

> select add #6.55

1 model selected  

> select add #6.41

2 models selected  

> select subtract #6.41

1 model selected  

> select add #6.162

2 models selected  

> select add #6.187

3 models selected  

> select add #6.2

4 models selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251110 start.cxs"

——— End of log from Mon Nov 10 12:39:23 2025 ———

> view name session-start

opened ChimeraX session  
Showing volume difference.seg - 190 regions, 190 surfaces  

> view

> view orient

> hide #5 models

> hide #!6 models

> show #!4 models

Saving 190 regions to mrc file...  
Opened volume difference_190_regions.mrc as #8, grid size 215,224,227, pixel
1.12, shown at step 1, values float32  
Wrote volume difference_190_regions.mrc  

> hide #!4 models

> volume #8 level 0.005139

> volume #8 level 0.003527

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_11_12_43_rna_phicb5_seg_1_1/fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_0.cif"

Chain information for fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_0.cif #9  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_11_12_43_rna_phicb5_seg_1_1/fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_4.cif"

Chain information for fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_4.cif #10  
---  
Chain | Description  
A | .  
  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_11_12_43_rna_phicb5_seg_1_1/fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_1.cif"

Chain information for fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_1.cif #11  
---  
Chain | Description  
A | .  
  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_11_12_43_rna_phicb5_seg_1_1/fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_2.cif"

Chain information for fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_2.cif #12  
---  
Chain | Description  
A | .  
  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_11_12_43_rna_phicb5_seg_1_1/fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_3.cif"

Chain information for fold_2025_11_11_12_43_rna_phicb5_seg_1_1_model_3.cif #13  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
[Repeated 3 time(s)]

> lighting simple

> lighting soft

> lighting simple

> hide #10 models

> hide #11 models

> hide #12 models

> hide #13 models

> select add #9

2792 atoms, 3122 bonds, 131 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,194.44,0,1,0,423.76,0,0,1,0

> select subtract #9

Nothing selected  
Must specify one map, got 0  

> show #!6 models

> hide #!6 models

> hide #!8 models

> show #5 models

> hide #5 models

> show #!7 models

> hide #!7 models

> hide #9 models

> show #9 models

> show #!8 models

Must specify one map, got 0  

> select add #9

2792 atoms, 3122 bonds, 131 residues, 1 model selected  

> view matrix models #9,1,0,0,222.74,0,1,0,235.41,0,0,1,0

> view matrix models #9,1,0,0,213.89,0,1,0,216.49,0,0,1,224.9

Must specify one map, got 0  
Must specify one map, got 0  

> select subtract #9

Nothing selected  

> close #9-13

> view

> show #5 models

> select add #8

2 models selected  

> volume sel style mesh

> transparency sel 50

> transparency sel 0

> select subtract #8

Nothing selected  

> volume #!8 style surface

> transparency #8.1 50

> view orient

> ui tool show "Side View"

> view

> ui tool show "Side View"

[Repeated 2 time(s)]

> view

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!6 models

> hide #5 models

> show #5 models

> select add #6

191 models selected  

> hide #6.25 models

> show #6.25 models

> hide #6.28 models

> show #6.28 models

> hide #6.31 models

> show #6.31 models

> hide #6.190 models

> hide #!8 models

> show #6.190 models

> hide #6.190 models

> show #6.190 models

> hide #6.190 models

> hide #!6 models

> show #!6 models

> select subtract #6

Nothing selected  

> view

> select add #6.159

1 model selected  

> select #6.50

1 model selected  

> select add #6.159

2 models selected  

> select subtract #6.50

1 model selected  

> select add #6.50

2 models selected  

> select subtract #6.50

1 model selected  

> select add #6.50

2 models selected  

> ui tool show "Segment Map"

Ungrouped to 6 regions  

> select subtract #6.194

5 models selected  

> select subtract #6.196

4 models selected  

> select subtract #6.193

3 models selected  

> select subtract #6.191

2 models selected  

> select add #6.191

3 models selected  

> select add #6.193

4 models selected  
Ungrouped to 8 regions  

> select subtract #6.50

7 models selected  

> select subtract #6.159

6 models selected  

> select add #6.50

7 models selected  

> select add #6.195

8 models selected  

> select add #6

200 models selected  

> select subtract #6

Nothing selected  

> select add #6.159

1 model selected  

> select add #6.50

2 models selected  
Ungrouped to 0 regions  

> select add #6.50

1 model selected  

> select add #6.159

2 models selected  
Grouped 2 regions  
Ungrouped to 2 regions  
Ungrouped to 0 regions  

> select add #6.159

1 model selected  
Ungrouped to 0 regions  

> select add #6.159

1 model selected  

> select add #6.198

2 models selected  

> select add #6.197

3 models selected  

> select add #6.201

4 models selected  

> select add #6.199

5 models selected  

> select add #6.195

6 models selected  

> select add #6.200

7 models selected  

> view

Grouped 7 regions  
Saving 1 regions to mrc file...  
Opened volume difference_region_3014.mrc as #9, grid size 42,26,41, pixel
1.12, shown at step 1, values float32  
Wrote volume difference_region_3014.mrc  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1514)))  

> select add #6

194 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> ui tool show "Side View"

[Repeated 1 time(s)]

> color #9 #55aa00ff models

> volume #9 level 0.002042

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!9 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!9 models

> hide #!9 models

> show #!9 models

> color #9 #fbd3c7ff models

> color #9 #eeaca3ff models

> color #9 #eff6efff models

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> color #9 #ffd0c5ff models

> color #9 #ffc7bcff models

> color #9 #ffc3b9ff models

> color #9 #ffcdc2ff models

> hide #!9 models

> hide #5 models

> show #5 models

> hide #!6 models

> show #!9 models

> hide #!7 models

> show #!7 models

> show #!6 models

> hide #!6 models

> hide #!9 models

> show #!6 models

> hide #6.202 models

> show #6.202 models

> show #!9 models

> hide #!9 models

> hide #!6 models

> show #!6 models

> hide #6.28 models

> show #6.28 models

> show #!9 models

> hide #!9 models

> hide #6.187 models

> show #6.187 models

> show #6.190 models

> select add #6.50

1 model selected  

> ui tool show "Segment Map"

> color #9 #ebc3bdff models

> color #9 #efc8c3ff models

> color #9 #050708ff models

> color #9 #e9a89fff models

> show #!9 models

> hide #!9 models

> hide #!7 models

> show #!7 models

> hide #5 models

> show #5 models

> hide #5 models

> select add #6.190

2 models selected  

> ui tool show "Segment Map"

> hide #!7 models

> select subtract #6.190

1 model selected  

> select add #6.190

2 models selected  

> select subtract #6.190

1 model selected  

> select add #6.190

2 models selected  

> select subtract #6.190

1 model selected  

> select add #6.190

2 models selected  

> show #6.190 models

> hide #6.190 models

> color #7 #eff6efff models

> color #7 #d88c86ff models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> color #6.190 #aaaaff80

> color #7 #aaaaffff models

> view

> hide #!6 models

> show #!9 models

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_12_13_33_rna_phicb5_region_3014/fold_2025_11_12_13_33_rna_phicb5_region_3014_model_0.cif"

Chain information for fold_2025_11_12_13_33_rna_phicb5_region_3014_model_0.cif
#10  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select add #10

530 atoms, 590 bonds, 25 residues, 3 models selected  

> view matrix models
> #6.190,1,0,0,294.39,0,1,0,109.12,0,0,1,135.19,#6.50,1,0,0,294.39,0,1,0,109.12,0,0,1,135.19,#10,1,0,0,294.39,0,1,0,109.12,0,0,1,135.19

> view

> view matrix models
> #6.190,1,0,0,271.25,0,1,0,55.282,0,0,1,203.02,#6.50,1,0,0,271.25,0,1,0,55.282,0,0,1,203.02,#10,1,0,0,271.25,0,1,0,55.282,0,0,1,203.02

> view matrix models
> #6.190,1,0,0,231.85,0,1,0,125.52,0,0,1,254.11,#6.50,1,0,0,231.85,0,1,0,125.52,0,0,1,254.11,#10,1,0,0,231.85,0,1,0,125.52,0,0,1,254.11

> ui mousemode right "rotate selected models"

> view matrix models
> #6.190,-0.13797,0.95704,0.25501,236.08,-0.53891,-0.28856,0.79139,121.6,0.83098,-0.02824,0.55558,253.31,#6.50,-0.13797,0.95704,0.25501,236.08,-0.53891,-0.28856,0.79139,121.6,0.83098,-0.02824,0.55558,253.31,#10,-0.13797,0.95704,0.25501,236.08,-0.53891,-0.28856,0.79139,121.6,0.83098,-0.02824,0.55558,253.31

> view matrix models
> #6.190,-0.52277,0.30428,0.79632,234.25,0.1037,-0.9045,0.41368,118.77,0.84615,0.29884,0.44129,254.42,#6.50,-0.52277,0.30428,0.79632,234.25,0.1037,-0.9045,0.41368,118.77,0.84615,0.29884,0.44129,254.42,#10,-0.52277,0.30428,0.79632,234.25,0.1037,-0.9045,0.41368,118.77,0.84615,0.29884,0.44129,254.42

> ui mousemode right "translate selected models"

> view matrix models
> #6.190,-0.52277,0.30428,0.79632,226.62,0.1037,-0.9045,0.41368,130.09,0.84615,0.29884,0.44129,262.13,#6.50,-0.52277,0.30428,0.79632,226.62,0.1037,-0.9045,0.41368,130.09,0.84615,0.29884,0.44129,262.13,#10,-0.52277,0.30428,0.79632,226.62,0.1037,-0.9045,0.41368,130.09,0.84615,0.29884,0.44129,262.13

> ui mousemode right "rotate selected models"

> view matrix models
> #6.190,-0.12874,0.96782,0.21622,228.47,-0.65477,-0.24671,0.71443,133.08,0.74478,-0.049596,0.66547,261.06,#6.50,-0.12874,0.96782,0.21622,228.47,-0.65477,-0.24671,0.71443,133.08,0.74478,-0.049596,0.66547,261.06,#10,-0.12874,0.96782,0.21622,228.47,-0.65477,-0.24671,0.71443,133.08,0.74478,-0.049596,0.66547,261.06

> view matrix models
> #6.190,-0.14631,0.96339,0.22468,228.46,-0.64748,-0.26498,0.71453,133,0.7479,-0.040937,0.66255,261.08,#6.50,-0.14631,0.96339,0.22468,228.46,-0.64748,-0.26498,0.71453,133,0.7479,-0.040937,0.66255,261.08,#10,-0.14631,0.96339,0.22468,228.46,-0.64748,-0.26498,0.71453,133,0.7479,-0.040937,0.66255,261.08

> ui mousemode right "translate selected models"

> view matrix models
> #6.190,-0.14631,0.96339,0.22468,217.63,-0.64748,-0.26498,0.71453,147.05,0.7479,-0.040937,0.66255,268.9,#6.50,-0.14631,0.96339,0.22468,217.63,-0.64748,-0.26498,0.71453,147.05,0.7479,-0.040937,0.66255,268.9,#10,-0.14631,0.96339,0.22468,217.63,-0.64748,-0.26498,0.71453,147.05,0.7479,-0.040937,0.66255,268.9

> transparency #9.1 50

> view matrix models
> #6.190,-0.14631,0.96339,0.22468,217.64,-0.64748,-0.26498,0.71453,148.55,0.7479,-0.040937,0.66255,271.2,#6.50,-0.14631,0.96339,0.22468,217.64,-0.64748,-0.26498,0.71453,148.55,0.7479,-0.040937,0.66255,271.2,#10,-0.14631,0.96339,0.22468,217.64,-0.64748,-0.26498,0.71453,148.55,0.7479,-0.040937,0.66255,271.2

> fitmap #10 inMap #9

Fit molecule fold_2025_11_12_13_33_rna_phicb5_region_3014_model_0.cif (#10) to
map volume difference_region_3014.mrc (#9) using 530 atoms  
average map value = 0.01886, steps = 248  
shifted from previous position = 6.78  
rotated from previous position = 107 degrees  
atoms outside contour = 88, contour level = 0.0020422  
  
Position of fold_2025_11_12_13_33_rna_phicb5_region_3014_model_0.cif (#10)
relative to volume difference_region_3014.mrc (#9) coordinates:  
Matrix rotation and translation  
0.07537840 0.01802738 0.99699203 212.70889336  
0.69500529 -0.71791520 -0.03956526 147.54253448  
0.71504248 0.69589711 -0.06664442 267.89961555  
Axis 0.70812546 0.27146958 0.65181485  
Axis point -0.00000000 27.10853361 45.61703518  
Rotation angle (degrees) 148.71453673  
Shift along axis 365.29884075  
  

> select add #5

2865 atoms, 3193 bonds, 136 residues, 4 models selected  

> select subtract #5

530 atoms, 590 bonds, 25 residues, 3 models selected  

> show #5 models

> select subtract #10

2 models selected  

> select add #10

530 atoms, 590 bonds, 25 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #6.190,0.54945,-0.14304,0.82319,216.52,-0.65168,-0.68995,0.31508,144.68,0.52289,-0.70958,-0.47231,262.36,#6.50,0.54945,-0.14304,0.82319,216.52,-0.65168,-0.68995,0.31508,144.68,0.52289,-0.70958,-0.47231,262.36,#10,0.87339,0.4749,-0.10796,213.23,0.36017,-0.77904,-0.5132,147.13,-0.32782,0.40934,-0.85145,266.77

> view matrix models
> #6.190,0.92259,-0.18034,-0.34104,213.94,-0.17897,-0.9832,0.035747,144.17,-0.34176,0.028057,-0.93937,261.05,#6.50,0.92259,-0.18034,-0.34104,213.94,-0.17897,-0.9832,0.035747,144.17,-0.34176,0.028057,-0.93937,261.05,#10,-0.24327,0.89061,-0.38422,215.08,0.16054,-0.35368,-0.92149,148.5,-0.95658,-0.28586,-0.05694,265.07

> view matrix models
> #6.190,0.29497,-0.94677,0.1289,208.3,-0.8855,-0.32155,-0.33541,143.47,0.359,-0.0152,-0.93321,264.01,#6.50,0.29497,-0.94677,0.1289,208.3,-0.8855,-0.32155,-0.33541,143.47,0.359,-0.0152,-0.93321,264.01,#10,0.28233,0.11411,-0.95251,211.57,-0.35117,-0.91169,-0.21331,147.19,-0.89273,0.39472,-0.21732,267.43

> hide #5 models

> view matrix models
> #6.190,0.77345,-0.42841,-0.46716,211.38,-0.57081,-0.7912,-0.21949,142.6,-0.27559,0.43642,-0.8565,263.99,#6.50,0.77345,-0.42841,-0.46716,211.38,-0.57081,-0.7912,-0.21949,142.6,-0.27559,0.43642,-0.8565,263.99,#10,-0.34386,0.70566,-0.61952,214.27,-0.14738,-0.69213,-0.70657,147.55,-0.92738,-0.15166,0.34199,265.84

> view matrix models
> #6.190,-0.16868,-0.98037,-0.10211,205.18,-0.75326,0.19503,-0.62814,146.03,0.63572,-0.029039,-0.77137,265.76,#6.50,-0.16868,-0.98037,-0.10211,205.18,-0.75326,0.19503,-0.62814,146.03,0.63572,-0.029039,-0.77137,265.76,#10,0.024794,-0.33647,-0.94137,210.04,-0.70317,-0.67521,0.22281,148.53,-0.71059,0.65642,-0.25333,268.28

> view matrix models
> #6.190,-0.99901,0.044483,0.0027185,207.68,0.0057292,0.18868,-0.98202,148.22,-0.044196,-0.98103,-0.18875,259.2,#6.50,-0.99901,0.044483,0.0027185,207.68,0.0057292,0.18868,-0.98202,148.22,-0.044196,-0.98103,-0.18875,259.2,#10,-0.077255,-0.97385,0.21365,208.57,-0.99568,0.086421,0.033888,151.33,-0.051466,-0.21011,-0.97632,264.27

> view matrix models
> #6.190,-0.34127,-0.93832,-0.055532,204.8,-0.5883,0.16714,0.79118,151.58,-0.7331,0.30268,-0.60905,262,#6.50,-0.34127,-0.93832,-0.055532,204.8,-0.5883,0.16714,0.79118,151.58,-0.7331,0.30268,-0.60905,262,#10,0.052135,-0.50076,-0.86401,209.48,0.7142,-0.58603,0.38274,148.32,-0.698,-0.63703,0.32709,263.94

> view

> view matrix models
> #6.190,-0.34179,-0.9393,-0.029987,204.88,-0.56971,0.18172,0.8015,151.78,-0.7474,0.29103,-0.59724,261.91,#6.50,-0.34179,-0.9393,-0.029987,204.88,-0.56971,0.18172,0.8015,151.78,-0.7474,0.29103,-0.59724,261.91,#10,0.077455,-0.50267,-0.861,209.47,0.72371,-0.56565,0.39534,148.4,-0.68575,-0.65373,0.31997,263.86

> fitmap #10 inMap #9

Fit molecule fold_2025_11_12_13_33_rna_phicb5_region_3014_model_0.cif (#10) to
map volume difference_region_3014.mrc (#9) using 530 atoms  
average map value = 0.01947, steps = 96  
shifted from previous position = 2.97  
rotated from previous position = 22.5 degrees  
atoms outside contour = 73, contour level = 0.0020422  
  
Position of fold_2025_11_12_13_33_rna_phicb5_region_3014_model_0.cif (#10)
relative to volume difference_region_3014.mrc (#9) coordinates:  
Matrix rotation and translation  
-0.00014600 -0.14372550 -0.98961757 212.12072647  
0.75790327 -0.64560970 0.09365227 147.49562255  
-0.65236692 -0.75002073 0.10902429 264.79020287  
Axis -0.65910815 -0.26347252 0.70438532  
Axis point 191.52179676 179.09287847 0.00000000  
Rotation angle (degrees) 140.20735657  
Shift along axis 7.84278847  
  

> show #5 models

> select subtract #10

2 models selected  

> hide #!9 models

> show #!6 models

> transparency #6.1-49,51-158,160-189,191,194,196,202#!6 0

> transparency #6.1-49,51-158,160-189,191,194,196,202#!6 50

> hide #5 models

> show #5 models

> view

[Repeated 1 time(s)]

> hide #5 models

> select add #6.131

3 models selected  

> select add #6.169

4 models selected  

> select add #6.39

5 models selected  

> select add #6.137

6 models selected  

> hide #10 models

> show #10 models

> hide #10 models

> view sel

> show #10 models

> ui tool show "Segment Map"

QWindowsWindow::setGeometry: Unable to set geometry 1920x1109+0+35 (frame:
1942x1165-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 624x739 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1165)))  

Grouped 6 regions  
Ungrouped to 6 regions  

> select subtract #6.137

5 models selected  

> select subtract #6.190

4 models selected  
Grouped 4 regions  
Saving 1 regions to mrc file...  
Opened volume difference_region_3016.mrc as #11, grid size 69,49,52, pixel
1.12, shown at step 1, values float32  
Wrote volume difference_region_3016.mrc  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1559+0+35 (frame:
1942x1615-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 624x1039 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1615)))  

> hide #6.39 models

> color #11 #c5bec7ff models

> select add #11

3 models selected  

> select subtract #11

1 model selected  

> hide #!6 models

> select add #11

3 models selected  

> ui tool show "Volume Viewer"

> volume #11 level 0.003947

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_12_14_20_rna_phicb5_region_3016/fold_2025_11_12_14_20_rna_phicb5_region_3016_model_0.cif"

Chain information for fold_2025_11_12_14_20_rna_phicb5_region_3016_model_0.cif
#12  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> view

> select subtract #11

1 model selected  

> select add #12

1705 atoms, 1906 bonds, 80 residues, 2 models selected  

> view matrix models
> #6.39,0.87374,-0.28989,0.39058,-4.007,0.14235,0.92023,0.36457,-0.17275,-0.46511,-0.26294,0.8453,-4.4943,#12,0.87374,-0.28989,0.39058,-4.007,0.14235,0.92023,0.36457,-0.17275,-0.46511,-0.26294,0.8453,-4.4943

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.87374,-0.28989,0.39058,296.63,0.14235,0.92023,0.36457,102.65,-0.46511,-0.26294,0.8453,178.93,#12,0.87374,-0.28989,0.39058,296.63,0.14235,0.92023,0.36457,102.65,-0.46511,-0.26294,0.8453,178.93

> view sel

> view

> view matrix models
> #6.39,0.87374,-0.28989,0.39058,269.5,0.14235,0.92023,0.36457,104.24,-0.46511,-0.26294,0.8453,194.73,#12,0.87374,-0.28989,0.39058,269.5,0.14235,0.92023,0.36457,104.24,-0.46511,-0.26294,0.8453,194.73

> view matrix models
> #6.39,0.87374,-0.28989,0.39058,301.04,0.14235,0.92023,0.36457,105.98,-0.46511,-0.26294,0.8453,187.05,#12,0.87374,-0.28989,0.39058,301.04,0.14235,0.92023,0.36457,105.98,-0.46511,-0.26294,0.8453,187.05

> view matrix models
> #6.39,0.87374,-0.28989,0.39058,301.69,0.14235,0.92023,0.36457,105.52,-0.46511,-0.26294,0.8453,185.4,#12,0.87374,-0.28989,0.39058,301.69,0.14235,0.92023,0.36457,105.52,-0.46511,-0.26294,0.8453,185.4

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,0.70179,-0.26755,0.66023,300.31,0.036035,0.93894,0.34219,105.11,-0.71147,-0.21636,0.66858,184.75,#12,0.70179,-0.26755,0.66023,300.31,0.036035,0.93894,0.34219,105.11,-0.71147,-0.21636,0.66858,184.75

> view matrix models
> #6.39,0.72253,-0.61543,-0.31496,299.43,0.6913,0.6381,0.33902,105.89,-0.007669,-0.46268,0.88649,186.35,#12,0.72253,-0.61543,-0.31496,299.43,0.6913,0.6381,0.33902,105.89,-0.007669,-0.46268,0.88649,186.35

> view matrix models
> #6.39,0.85889,-0.18021,-0.4794,303.91,0.16388,0.98354,-0.076126,106.66,0.48523,-0.013178,0.87429,192.51,#12,0.85889,-0.18021,-0.4794,303.91,0.16388,0.98354,-0.076126,106.66,0.48523,-0.013178,0.87429,192.51

> view matrix models
> #6.39,0.85088,-0.18485,-0.49177,303.94,0.16709,0.98267,-0.080263,106.7,0.49808,-0.013877,0.86702,192.61,#12,0.85088,-0.18485,-0.49177,303.94,0.16709,0.98267,-0.080263,106.7,0.49808,-0.013877,0.86702,192.61

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.85088,-0.18485,-0.49177,261.14,0.16709,0.98267,-0.080263,111.3,0.49808,-0.013877,0.86702,223.79,#12,0.85088,-0.18485,-0.49177,261.14,0.16709,0.98267,-0.080263,111.3,0.49808,-0.013877,0.86702,223.79

> view

> view matrix models
> #6.39,0.85088,-0.18485,-0.49177,265.8,0.16709,0.98267,-0.080263,106.34,0.49808,-0.013877,0.86702,207.11,#12,0.85088,-0.18485,-0.49177,265.8,0.16709,0.98267,-0.080263,106.34,0.49808,-0.013877,0.86702,207.11

> view matrix models
> #6.39,0.85088,-0.18485,-0.49177,270.3,0.16709,0.98267,-0.080263,103.06,0.49808,-0.013877,0.86702,182.25,#12,0.85088,-0.18485,-0.49177,270.3,0.16709,0.98267,-0.080263,103.06,0.49808,-0.013877,0.86702,182.25

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,0.64975,-0.75299,-0.10405,264.13,0.28319,0.11276,0.95241,94.503,-0.70542,-0.6483,0.28651,171.95,#12,0.64975,-0.75299,-0.10405,264.13,0.28319,0.11276,0.95241,94.503,-0.70542,-0.6483,0.28651,171.95

> view matrix models
> #6.39,0.44247,-0.85325,-0.27602,262.56,0.024583,-0.29614,0.95483,89.885,-0.89645,-0.42927,-0.11006,173.38,#12,0.44247,-0.85325,-0.27602,262.56,0.024583,-0.29614,0.95483,89.885,-0.89645,-0.42927,-0.11006,173.38

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.44247,-0.85325,-0.27602,226.54,0.024583,-0.29614,0.95483,105.61,-0.89645,-0.42927,-0.11006,227.61,#12,0.44247,-0.85325,-0.27602,226.54,0.024583,-0.29614,0.95483,105.61,-0.89645,-0.42927,-0.11006,227.61

> transparency #11.1 50

> view matrix models
> #6.39,0.44247,-0.85325,-0.27602,238.99,0.024583,-0.29614,0.95483,115.07,-0.89645,-0.42927,-0.11006,240.01,#12,0.44247,-0.85325,-0.27602,238.99,0.024583,-0.29614,0.95483,115.07,-0.89645,-0.42927,-0.11006,240.01

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,0.61687,-0.78657,-0.027842,239.94,0.20161,0.12372,0.97162,119.25,-0.7608,-0.60498,0.2349,238.67,#12,0.61687,-0.78657,-0.027842,239.94,0.20161,0.12372,0.97162,119.25,-0.7608,-0.60498,0.2349,238.67

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_12_14_20_rna_phicb5_region_3016/fold_2025_11_12_14_20_rna_phicb5_region_3016_model_1.cif"

Chain information for fold_2025_11_12_14_20_rna_phicb5_region_3016_model_1.cif
#13  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,240.89,0.45904,0.4949,0.7378,124.06,-0.54062,-0.5034,0.67403,239.91,#12,0.70499,-0.70828,0.03647,240.89,0.45904,0.4949,0.7378,124.06,-0.54062,-0.5034,0.67403,239.91

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,267.27,0.45904,0.4949,0.7378,90.552,-0.54062,-0.5034,0.67403,313.55,#12,0.70499,-0.70828,0.03647,267.27,0.45904,0.4949,0.7378,90.552,-0.54062,-0.5034,0.67403,313.55

> select add #13

3410 atoms, 3812 bonds, 160 residues, 3 models selected  

> select add #11

3410 atoms, 3812 bonds, 160 residues, 5 models selected  

> select subtract #12

1705 atoms, 1906 bonds, 80 residues, 4 models selected  

> select subtract #11

1705 atoms, 1906 bonds, 80 residues, 2 models selected  

> view

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,337.45,0.45904,0.4949,0.7378,6.422,-0.54062,-0.5034,0.67403,481.72,#13,1,0,0,70.182,0,1,0,-84.13,0,0,1,168.17

> view

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,347.93,0.45904,0.4949,0.7378,-10.673,-0.54062,-0.5034,0.67403,531.78,#13,1,0,0,80.664,0,1,0,-101.22,0,0,1,218.23

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,455.07,0.45904,0.4949,0.7378,186.2,-0.54062,-0.5034,0.67403,551.35,#13,1,0,0,187.8,0,1,0,95.647,0,0,1,237.79

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,492.8,0.45904,0.4949,0.7378,190.35,-0.54062,-0.5034,0.67403,571.35,#13,1,0,0,225.53,0,1,0,99.799,0,0,1,257.8

> view matrix models
> #6.39,0.70499,-0.70828,0.03647,460.33,0.45904,0.4949,0.7378,186.56,-0.54062,-0.5034,0.67403,582.41,#13,1,0,0,193.06,0,1,0,96.007,0,0,1,268.86

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,0.88317,-0.45042,-0.13091,345.4,0.45104,0.73891,0.50057,45.543,-0.12874,-0.50113,0.85574,656.34,#13,0.93687,0.085917,-0.33895,193.5,-0.18712,0.94206,-0.27842,97.549,0.29539,0.32427,0.89866,266.25

> view matrix models
> #6.39,0.81019,-0.58614,-0.00602,417.57,0.47002,0.64347,0.60418,104.66,-0.35026,-0.49233,0.79683,624.73,#13,0.9861,0.077388,-0.147,193.1,-0.10237,0.97998,-0.17079,96.832,0.13084,0.18346,0.97428,267.66

> view matrix models
> #6.39,0.89928,-0.034943,-0.43597,135.24,0.3431,0.67455,0.65365,102.66,0.27124,-0.7374,0.6186,680.47,#13,0.64283,0.07386,-0.76244,195.81,-0.21205,0.9736,-0.084474,97.662,0.73607,0.21598,0.64152,263.03

> view matrix models
> #6.39,0.16921,-0.92489,-0.3405,387.42,0.95622,0.07036,0.28406,209.91,-0.23877,-0.37366,0.89631,623.97,#13,0.76196,-0.63128,0.14461,195.6,0.63465,0.68335,-0.3609,91.577,0.12901,0.36677,0.92132,267.39

> view matrix models
> #6.39,0.16599,-0.96055,-0.22313,431.58,0.96091,0.10671,0.25547,191.14,-0.22158,-0.25681,0.94072,602.89,#13,0.78922,-0.56381,0.24341,195.38,0.61117,0.68239,-0.40101,91.738,0.059988,0.46525,0.88314,267.82

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.16599,-0.96055,-0.22313,474.23,0.96091,0.10671,0.25547,227.06,-0.22158,-0.25681,0.94072,576.6,#13,0.78922,-0.56381,0.24341,238.03,0.61117,0.68239,-0.40101,127.66,0.059988,0.46525,0.88314,241.53

> view matrix models
> #6.39,0.16599,-0.96055,-0.22313,469.41,0.96091,0.10671,0.25547,227.28,-0.22158,-0.25681,0.94072,560.12,#13,0.78922,-0.56381,0.24341,233.21,0.61117,0.68239,-0.40101,127.88,0.059988,0.46525,0.88314,225.04

> view sel

> view matrix models
> #6.39,0.16599,-0.96055,-0.22313,495.35,0.96091,0.10671,0.25547,211.3,-0.22158,-0.25681,0.94072,540,#13,0.78922,-0.56381,0.24341,259.15,0.61117,0.68239,-0.40101,111.89,0.059988,0.46525,0.88314,204.93

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,0.82399,0.39418,-0.40702,75.852,0.46166,-0.88354,0.078936,427.76,-0.3285,-0.25295,-0.91,2.4496,#13,0.28687,0.27302,-0.91824,262.37,0.95414,-0.1671,0.2484,110,-0.085621,-0.94738,-0.30844,207.83

> view matrix models
> #6.39,-0.071327,0.77366,-0.62957,-149.72,0.66921,-0.43092,-0.60536,108.05,-0.73964,-0.4645,-0.487,164.2,#13,-0.62121,-0.11436,-0.77525,269.75,0.75492,-0.3527,-0.55289,111.59,-0.21021,-0.92872,0.30544,208.71

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-137.2,0.86979,-0.42082,-0.25765,215.76,-0.47487,-0.57203,-0.66879,158.48,#13,-0.42959,-0.10455,-0.89695,268.33,0.90185,0.00091337,-0.43205,110.11,0.045991,-0.99452,0.093898,206.8

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-163.11,0.86979,-0.42082,-0.25765,238.36,-0.47487,-0.57203,-0.66879,184.48,#13,-0.42959,-0.10455,-0.89695,242.42,0.90185,0.00091337,-0.43205,132.71,0.045991,-0.99452,0.093898,232.8

> close #13

> select add #12

1705 atoms, 1906 bonds, 80 residues, 2 models selected  

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-188.9,0.86979,-0.42082,-0.25765,279.86,-0.47487,-0.57203,-0.66879,98.721,#12,0.70499,-0.70828,0.03647,241.47,0.45904,0.4949,0.7378,132.06,-0.54062,-0.5034,0.67403,227.79

> fitmap #12 inMap #11

Fit molecule fold_2025_11_12_14_20_rna_phicb5_region_3016_model_0.cif (#12) to
map volume difference_region_3016.mrc (#11) using 1705 atoms  
average map value = 0.009483, steps = 172  
shifted from previous position = 5.94  
rotated from previous position = 29.6 degrees  
atoms outside contour = 1007, contour level = 0.0039469  
  
Position of fold_2025_11_12_14_20_rna_phicb5_region_3016_model_0.cif (#12)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.51677531 -0.85611747 -0.00250790 236.41297484  
0.23660746 0.14000612 0.96146519 129.16942749  
-0.82277603 -0.49745477 0.27491555 230.64230608  
Axis -0.72988572 0.41037343 0.54668134  
Axis point 0.00000000 281.37027035 120.12038277  
Rotation angle (degrees) 91.95711790  
Shift along axis 6.54109267  
  

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-187.32,0.86979,-0.42082,-0.25765,283.03,-0.47487,-0.57203,-0.66879,94.871,#12,0.51678,-0.85612,-0.0025079,238,0.23661,0.14001,0.96147,132.33,-0.82278,-0.49745,0.27492,226.79

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-185.58,0.86979,-0.42082,-0.25765,279.15,-0.47487,-0.57203,-0.66879,84.68,#12,0.51678,-0.85612,-0.0025079,239.74,0.23661,0.14001,0.96147,128.45,-0.82278,-0.49745,0.27492,216.6

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-193.43,0.86979,-0.42082,-0.25765,298.36,-0.47487,-0.57203,-0.66879,77.602,#12,0.51678,-0.85612,-0.0025079,231.89,0.23661,0.14001,0.96147,147.67,-0.82278,-0.49745,0.27492,209.52

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-194.91,0.86979,-0.42082,-0.25765,302.85,-0.47487,-0.57203,-0.66879,73.365,#12,0.51678,-0.85612,-0.0025079,230.41,0.23661,0.14001,0.96147,152.15,-0.82278,-0.49745,0.27492,205.29

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-197.08,0.86979,-0.42082,-0.25765,302.91,-0.47487,-0.57203,-0.66879,95.384,#12,0.51678,-0.85612,-0.0025079,228.24,0.23661,0.14001,0.96147,152.22,-0.82278,-0.49745,0.27492,227.3

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-188.64,0.86979,-0.42082,-0.25765,291.76,-0.47487,-0.57203,-0.66879,104.04,#12,0.51678,-0.85612,-0.0025079,236.68,0.23661,0.14001,0.96147,141.06,-0.82278,-0.49745,0.27492,235.96

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-189.89,0.86979,-0.42082,-0.25765,292.48,-0.47487,-0.57203,-0.66879,99.522,#12,0.51678,-0.85612,-0.0025079,235.43,0.23661,0.14001,0.96147,141.79,-0.82278,-0.49745,0.27492,231.44

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-192.76,0.86979,-0.42082,-0.25765,287.31,-0.47487,-0.57203,-0.66879,85.174,#12,0.51678,-0.85612,-0.0025079,232.56,0.23661,0.14001,0.96147,136.62,-0.82278,-0.49745,0.27492,217.1

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-187.22,0.86979,-0.42082,-0.25765,286.35,-0.47487,-0.57203,-0.66879,87.789,#12,0.51678,-0.85612,-0.0025079,238.09,0.23661,0.14001,0.96147,135.66,-0.82278,-0.49745,0.27492,219.71

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,-190.47,0.86979,-0.42082,-0.25765,276.31,-0.47487,-0.57203,-0.66879,91.543,#12,0.51678,-0.85612,-0.0025079,234.85,0.23661,0.14001,0.96147,125.61,-0.82278,-0.49745,0.27492,223.46

> view

> view orient

> hide #12 models

> select subtract #12

1 model selected  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/fold_2025_11_12_15_46_rna_phicb5_region_3016/fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif"

Chain information for fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
#13  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> view

> select add #13

1387 atoms, 1551 bonds, 65 residues, 2 models selected  

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,20.213,0.86979,-0.42082,-0.25765,415.12,-0.47487,-0.57203,-0.66879,306.19,#13,1,0,0,210.68,0,1,0,138.81,0,0,1,214.65

> view sel

> lighting shadows false

> lighting shadows true

> lighting shadows false

> view matrix models
> #6.39,0.13406,0.70405,-0.69738,22.445,0.86979,-0.42082,-0.25765,414.81,-0.47487,-0.57203,-0.66879,307.4,#13,1,0,0,212.91,0,1,0,138.5,0,0,1,215.85

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,-0.35688,-0.93246,0.056192,436.4,-0.84935,0.34894,0.39605,-121.37,-0.3889,0.093615,-0.91651,119.07,#13,-0.74353,0.067509,0.66528,215.23,-0.14438,-0.98763,-0.061149,129.62,0.65293,-0.14152,0.74408,214.42

> view matrix models
> #6.39,-0.28814,-0.93696,0.19769,449.85,-0.75668,0.3493,0.55265,-105.21,-0.58687,0.0096495,-0.80963,110.04,#13,-0.83617,0.092736,0.54058,215.48,-0.24092,-0.94753,-0.2101,129.95,0.49273,-0.30591,0.81464,213.83

> view matrix models
> #6.39,0.49248,-0.79356,0.35739,542.9,-0.40899,-0.5735,-0.70981,237.22,0.76824,0.2034,-0.607,288.39,#13,-0.74192,0.67022,-0.018949,218.14,0.036401,0.068483,0.99699,133.97,0.6695,0.739,-0.075206,218.6

> view matrix models
> #6.39,0.5864,-0.77247,0.24377,552.86,0.054953,-0.26231,-0.96342,223.48,0.80816,0.57834,-0.11137,181.05,#13,-0.63525,0.7723,0.00038375,218.44,0.49455,0.40641,0.76828,135.05,0.59319,0.48824,-0.64011,217.73

> view matrix models
> #6.39,0.98137,-0.1507,0.11915,432.22,0.16735,0.36607,-0.91541,51.333,0.094335,0.9183,0.38447,-47.733,#13,-0.057628,0.8863,-0.4595,218.42,0.91856,0.22736,0.32335,133.86,0.39106,-0.40345,-0.82723,213.95

> view matrix models
> #6.39,0.8611,-0.36277,-0.35623,475.77,-0.49863,-0.46567,-0.7311,188.62,0.099331,0.80719,-0.58188,-13.136,#13,0.10846,0.99342,0.036849,218.57,0.11515,-0.049373,0.99212,133.38,0.98741,-0.10336,-0.11975,214.45

> view matrix models
> #6.39,0.62495,-0.53532,-0.56821,487.04,-0.71376,-0.097009,-0.69364,38.333,0.3162,0.83906,-0.44272,15.167,#13,0.10314,0.91525,0.38946,218.15,0.31974,-0.40128,0.85833,131.53,0.94187,0.036001,-0.33403,215.19

> view matrix models
> #6.39,0.99079,0.040835,0.12911,375.35,0.10102,-0.85783,-0.5039,413.56,0.09018,0.5123,-0.85406,75.244,#13,0.071534,0.81132,-0.5802,217.92,-0.23901,0.57869,0.77974,136.76,0.96838,0.082895,0.23531,215.24

> view matrix models
> #6.39,0.95287,0.29134,0.084668,292.18,0.23061,-0.51415,-0.82612,331.19,-0.19715,0.80671,-0.5571,-64.924,#13,0.27381,0.68438,-0.67576,217.1,0.24504,0.62979,0.7371,136.37,0.93004,-0.36742,0.0047416,213.3

> view matrix models
> #6.39,0.98975,0.11983,-0.077629,350.97,-0.0052073,-0.51304,-0.85835,289.52,-0.14268,0.84996,-0.50716,-68.573,#13,0.27119,0.83045,-0.48663,217.71,0.23668,0.43252,0.87,135.44,0.93297,-0.35111,-0.079257,213.4

> view matrix models
> #6.39,0.9914,-0.030287,-0.12734,397.08,-0.12513,-0.50464,-0.85421,265.93,-0.038387,0.8628,-0.50409,-54.214,#13,0.20038,0.90786,-0.3683,218.12,0.22364,0.32361,0.91938,134.95,0.95385,-0.26659,-0.13819,213.77

> ui mousemode right "translate selected models"

> view matrix models
> #6.39,0.9914,-0.030287,-0.12734,409.2,-0.12513,-0.50464,-0.85421,273.13,-0.038387,0.8628,-0.50409,-41.975,#13,0.20038,0.90786,-0.3683,230.23,0.22364,0.32361,0.91938,142.15,0.95385,-0.26659,-0.13819,226.01

> view matrix models
> #6.39,0.9914,-0.030287,-0.12734,413.95,-0.12513,-0.50464,-0.85421,272.33,-0.038387,0.8628,-0.50409,-38.994,#13,0.20038,0.90786,-0.3683,234.99,0.22364,0.32361,0.91938,141.35,0.95385,-0.26659,-0.13819,228.99

> view matrix models
> #6.39,0.9914,-0.030287,-0.12734,407.66,-0.12513,-0.50464,-0.85421,260.61,-0.038387,0.8628,-0.50409,-41.902,#13,0.20038,0.90786,-0.3683,228.69,0.22364,0.32361,0.91938,129.62,0.95385,-0.26659,-0.13819,226.08

> fitmap #13 inMap #11

Fit molecule fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13) to
map volume difference_region_3016.mrc (#11) using 1387 atoms  
average map value = 0.008746, steps = 212  
shifted from previous position = 7.58  
rotated from previous position = 43.4 degrees  
atoms outside contour = 854, contour level = 0.0039469  
  
Position of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.26055850 0.59566394 -0.75979848 235.71694989  
0.76779572 0.34927123 0.53712134 129.81569734  
0.58531957 -0.72332155 -0.36634263 229.09550948  
Axis -0.68080466 -0.72654036 0.09297376  
Axis point -58.89076083 0.00000000 158.33098735  
Rotation angle (degrees) 112.22572501  
Shift along axis -233.49367044  
  

> fitmap #13 inMap #11

Fit molecule fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13) to
map volume difference_region_3016.mrc (#11) using 1387 atoms  
average map value = 0.008746, steps = 60  
shifted from previous position = 0.00747  
rotated from previous position = 0.0256 degrees  
atoms outside contour = 855, contour level = 0.0039469  
  
Position of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.26014062 0.59577571 -0.75985404 235.72292699  
0.76793587 0.34938398 0.53684759 129.81071789  
0.58532158 -0.72317503 -0.36662857 229.09671342  
Axis -0.68066649 -0.72666629 0.09300123  
Axis point -58.80506179 0.00000000 158.33854278  
Rotation angle (degrees) 112.24401819  
Shift along axis -233.47149472  
  

> fitmap #13 inMap #11

Fit molecule fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13) to
map volume difference_region_3016.mrc (#11) using 1387 atoms  
average map value = 0.008746, steps = 60  
shifted from previous position = 0.00427  
rotated from previous position = 0.0218 degrees  
atoms outside contour = 855, contour level = 0.0039469  
  
Position of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.26047631 0.59573555 -0.75977052 235.71856612  
0.76777168 0.34932210 0.53712262 129.81199020  
0.58538768 -0.72323801 -0.36639875 229.09750782  
Axis -0.68077336 -0.72657607 0.09292389  
Axis point -58.86666002 0.00000000 158.32528583  
Rotation angle (degrees) 112.22843070  
Shift along axis -233.50057357  
  

> show #!1 models

> show #!4 models

> hide #!1 models

> view

> hide #!4 models

> hide #13 models

> show #13 models

> view matrix models
> #6.39,0.9914,-0.030287,-0.12734,407.99,-0.12513,-0.50464,-0.85421,260.32,-0.038387,0.8628,-0.50409,-42.2,#13,0.26048,0.59574,-0.75977,236.05,0.76777,0.34932,0.53712,129.52,0.58539,-0.72324,-0.3664,228.8

> ui mousemode right "rotate selected models"

> view matrix models
> #6.39,0.70512,-0.11715,-0.69934,384.69,-0.5643,-0.68993,-0.45339,245.91,-0.42939,0.71433,-0.55259,-61.936,#13,0.77386,0.50784,-0.37846,235.05,0.29164,0.2447,0.9247,129.64,0.56221,-0.82597,0.041258,228.24

> view matrix models
> #6.39,0.50517,0.078601,-0.85943,290.18,-0.84796,-0.14,-0.51124,28.464,-0.1605,0.98703,-0.0040731,-98.908,#13,0.92496,0.2343,-0.29927,233.62,0.36929,-0.36778,0.85344,126.77,0.089898,-0.89991,-0.4267,228.58

> view matrix models
> #6.39,0.41178,0.26177,-0.87288,217.96,-0.90883,0.18819,-0.3723,-82.457,0.066811,0.9466,0.3154,-47.112,#13,0.94524,0.030863,-0.32491,232.68,0.26008,-0.67267,0.69273,125.56,-0.19718,-0.7393,-0.64387,229.7

> fitmap #13 inMap #11

Fit molecule fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13) to
map volume difference_region_3016.mrc (#11) using 1387 atoms  
average map value = 0.0139, steps = 196  
shifted from previous position = 11.9  
rotated from previous position = 21.3 degrees  
atoms outside contour = 675, contour level = 0.0039469  
  
Position of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.92913814 -0.28325218 -0.23763528 232.03816450  
0.06661619 -0.50395342 0.86115808 136.46693967  
-0.36368201 -0.81596516 -0.44937316 235.00632136  
Axis -0.97628715 0.07337434 0.20366541  
Axis point 0.00000000 155.31379507 98.40522533  
Rotation angle (degrees) 120.80342594  
Shift along axis -168.66004978  
  

> hide #10 models

> combine #13

> hide #13 models

> show #13 models

> hide #13 models

> hide #14 models

> select subtract #13

1 model selected  

> show #13 models

> select add #13

1387 atoms, 1551 bonds, 65 residues, 2 models selected  
Alignment identifier is 13/A  

> select clear

> hide #!11 models

> select #13/A:22

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #13/A:55

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #13/A:22

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #13/A:22-55

725 atoms, 810 bonds, 34 residues, 1 model selected  

> select ~sel & ##selected

662 atoms, 741 bonds, 31 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!11 models

> fitmap #13 inMap #11

Fit molecule fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13) to
map volume difference_region_3016.mrc (#11) using 725 atoms  
average map value = 0.01881, steps = 84  
shifted from previous position = 1.67  
rotated from previous position = 14 degrees  
atoms outside contour = 125, contour level = 0.0039469  
  
Position of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.95302321 -0.16294148 -0.25533671 230.55205203  
0.07748094 -0.68379390 0.72554987 135.31450169  
-0.29281985 -0.71124959 -0.63904660 230.61019494  
Axis -0.98596100 0.02572169 0.16498275  
Axis point 0.00000000 127.95955263 103.87187803  
Rotation angle (degrees) 133.22842279  
Shift along axis -185.78810946  
  

> fitmap #13 inMap #11

Fit molecule fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13) to
map volume difference_region_3016.mrc (#11) using 725 atoms  
average map value = 0.01881, steps = 44  
shifted from previous position = 0.0164  
rotated from previous position = 0.0356 degrees  
atoms outside contour = 125, contour level = 0.0039469  
  
Position of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#13)
relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.95313495 -0.16237158 -0.25528268 230.55889079  
0.07774349 -0.68400334 0.72532433 135.29739990  
-0.29238626 -0.71117853 -0.63932415 230.59368784  
Axis -0.98599620 0.02546740 0.16481175  
Axis point 0.00000000 127.89169317 103.86906329  
Rotation angle (degrees) 133.24317883  
Shift along axis -185.87996745  
  

> show #14 models

> hide #13 models

> select add #14

1387 atoms, 1551 bonds, 65 residues, 1 model selected  

> hide #!11 models

Alignment identifier is 14/A  

> select clear

> color #14 bynucleotide

> select clear

> select #14/A:55@C4'

1 atom, 1 residue, 1 model selected  

> select add #14/A:22

23 atoms, 24 bonds, 2 residues, 1 model selected  

> select #14/A:22

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #14/A:22-55

725 atoms, 810 bonds, 34 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #13 models

> hide #13 models

> show #!11 models

> show #13 models

> hide #!11 models

> select #14/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #14/A:21

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #14/A:21

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #14/A:3-21

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select ~sel & ##selected

264 atoms, 296 bonds, 1 pseudobond, 12 residues, 2 models selected  

> combine #14

> hide #!15 models

> select #14/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #14/A:3-21

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select ~sel & ##selected

264 atoms, 296 bonds, 1 pseudobond, 12 residues, 2 models selected  

> delete atoms (#!14 & sel)

> delete bonds (#!14 & sel)

> select add #14

398 atoms, 443 bonds, 19 residues, 1 model selected  

> show #!11 models

> view matrix models
> #14,0.57897,-0.40594,0.70711,218.89,-0.81422,-0.24219,0.52763,119.61,-0.042931,-0.88122,-0.47074,242

> view matrix models
> #14,0.63527,-0.15383,0.75682,218.03,-0.75301,-0.341,0.56276,121.18,0.1715,-0.92739,-0.33246,245.5

> view matrix models
> #14,0.6708,0.5424,0.50579,216.14,0.15706,-0.77042,0.61789,141.28,0.72481,-0.33504,-0.60199,254.52

> view matrix models
> #14,-0.0096955,0.8583,0.51306,200.68,0.23548,-0.4967,0.83537,139.53,0.97183,0.12891,-0.19729,253.57

> view matrix models
> #14,-0.043091,0.81466,0.57833,199.81,0.078596,-0.57431,0.81486,137.07,0.99597,0.080568,-0.039281,253.18

> view matrix models
> #14,0.18371,0.80389,0.5657,204.48,0.48828,-0.5741,0.65726,146.38,0.85313,0.15548,-0.49799,253.26

> view matrix models
> #14,0.31116,0.74123,0.59478,207.2,0.61668,-0.63367,0.46708,150.66,0.72311,0.22145,-0.65427,251.38

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.31116,0.74123,0.59478,229.64,0.61668,-0.63367,0.46708,133.88,0.72311,0.22145,-0.65427,234.23

> fitmap #14 inMap #11

Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) to map volume difference_region_3016.mrc (#11) using 398 atoms  
average map value = 0.01366, steps = 164  
shifted from previous position = 9.19  
rotated from previous position = 25.9 degrees  
atoms outside contour = 159, contour level = 0.0039469  
  
Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.44237445 0.83737600 0.32110168 241.23365048  
0.43361643 -0.51311710 0.74073454 131.62595737  
0.78503609 -0.18844707 -0.59008988 240.44462097  
Axis -0.83388001 -0.41635093 -0.36234793  
Axis point 0.00000000 26.78409318 69.85789243  
Rotation angle (degrees) 146.14152143  
Shift along axis -343.08712124  
  

> fitmap #14 inMap #11

Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) to map volume difference_region_3016.mrc (#11) using 398 atoms  
average map value = 0.01366, steps = 84  
shifted from previous position = 0.00107  
rotated from previous position = 0.0113 degrees  
atoms outside contour = 159, contour level = 0.0039469  
  
Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.44228295 0.83745750 0.32101517 241.23186129  
0.43378042 -0.51301909 0.74070641 131.62900073  
0.78499704 -0.18835172 -0.59017226 240.44261670  
Axis -0.83385383 -0.41643580 -0.36231067  
Axis point 0.00000000 26.77227104 69.86521066  
Rotation angle (degrees) 146.14542280  
Shift along axis -343.08206462  
  

> view matrix models
> #14,0.44228,0.83746,0.32102,238.12,0.43378,-0.51302,0.74071,130.3,0.785,-0.18835,-0.59017,241.33

> view matrix models
> #14,0.44228,0.83746,0.32102,235.42,0.43378,-0.51302,0.74071,128.18,0.785,-0.18835,-0.59017,246.76

> view matrix models
> #14,0.44228,0.83746,0.32102,241.38,0.43378,-0.51302,0.74071,132.34,0.785,-0.18835,-0.59017,237.24

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.65001,0.45793,0.60645,245.93,0.50956,-0.85469,0.099228,140.62,0.56377,0.24453,-0.7889,231.48

> view matrix models
> #14,0.82543,0.02422,0.56398,252.52,0.43785,-0.65806,-0.61257,143.14,0.3563,0.75257,-0.55379,222.36

> view matrix models
> #14,0.87475,-0.19216,0.44484,255.8,0.42474,-0.13785,-0.89476,141.48,0.23326,0.97163,-0.038966,214.76

> view matrix models
> #14,0.86023,-0.29738,0.4142,256.41,0.47657,0.18003,-0.86051,140.25,0.18133,0.93763,0.29659,211.43

> view matrix models
> #14,0.6592,-0.73696,0.14952,257.04,0.29733,0.072809,-0.95199,137.97,0.69069,0.67201,0.26711,223.64

> view matrix models
> #14,0.42019,-0.90733,0.013617,254.31,0.16772,0.062905,-0.98383,135.64,0.8918,0.41568,0.17861,230.02

> view matrix models
> #14,0.29225,-0.94377,-0.15453,253.25,0.5821,0.30375,-0.75425,140.71,0.75878,0.13048,0.63814,225.69

> view matrix models
> #14,0.19583,-0.97443,-0.11021,251.22,0.65554,0.21366,-0.7243,142.51,0.72933,0.069595,0.68062,225.18

> view matrix models
> #14,0.2664,-0.96386,-0.0034393,251.75,0.69404,0.1943,-0.69322,143.16,0.66883,0.18229,0.72072,222.97

> fitmap #14 inMap #11

Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) to map volume difference_region_3016.mrc (#11) using 398 atoms  
average map value = 0.01977, steps = 108  
shifted from previous position = 3.79  
rotated from previous position = 24.6 degrees  
atoms outside contour = 51, contour level = 0.0039469  
  
Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.20806683 -0.94482438 0.25301206 245.31730866  
0.49213996 -0.12241887 -0.86186536 140.91802461  
0.84528485 0.30384293 0.43951452 227.20931476  
Axis 0.60000999 -0.30485293 0.73963012  
Axis point -88.33522929 160.77013316 0.00000000  
Rotation angle (degrees) 103.73424325  
Shift along axis 272.28441377  
  

> fitmap #14 inMap #11

Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) to map volume difference_region_3016.mrc (#11) using 398 atoms  
average map value = 0.01977, steps = 48  
shifted from previous position = 0.0218  
rotated from previous position = 0.0598 degrees  
atoms outside contour = 52, contour level = 0.0039469  
  
Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.20889893 -0.94456618 0.25329030 245.35231743  
0.49253493 -0.12213559 -0.86167990 140.92150924  
0.84484945 0.30475832 0.43971784 227.19009581  
Axis 0.60028626 -0.30443518 0.73957800  
Axis point -88.41121626 160.68071724 0.00000000  
Rotation angle (degrees) 103.69535646  
Shift along axis 272.40495819  
  

> fitmap #14 inMap #11

Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) to map volume difference_region_3016.mrc (#11) using 398 atoms  
average map value = 0.01977, steps = 48  
shifted from previous position = 0.00476  
rotated from previous position = 0.00986 degrees  
atoms outside contour = 52, contour level = 0.0039469  
  
Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
(#14) relative to volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
0.20890985 -0.94454457 0.25336187 245.35121844  
0.49267792 -0.12214409 -0.86159694 140.91961113  
0.84476337 0.30482188 0.43983915 227.18531334  
Axis 0.60026697 -0.30434933 0.73962900  
Axis point -88.38914790 160.65954736 0.00000000  
Rotation angle (degrees) 103.69170825  
Shift along axis 272.42028832  
  

> select subtract #14

Nothing selected  

> show #!15 models

> hide #!15 models

> show #12 models

> hide #12 models

> show #12 models

> hide #12 models

> hide #13 models

> show #13 models

> hide #13 models

> show #13 models

> hide #13 models

> hide #!14 models

> show #!14 models

> show #13 models

> show #!15 models

> hide #!15 models

> hide #!14 models

> show #!14 models

> hide #13 models

> show #13 models

> nucleotides #13#!14 atoms

> style nucleic & #13#!14 stick

Changed 1123 atom styles  

> color #13#!14 bynucleotide

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251112 JT.cxs"

——— End of log from Wed Nov 12 18:34:04 2025 ———

> view name session-start

opened ChimeraX session  
Showing volume difference.seg - 190 regions, 190 surfaces  

> hide #!6 models

> select add #13

725 atoms, 810 bonds, 34 residues, 1 model selected  

> select add #14

1123 atoms, 1253 bonds, 53 residues, 2 models selected  

> color sel bynucleotide

> nucleotides sel stubs

> select subtract #13

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select subtract #14

Nothing selected  

> show #!15 models

> select add #15

662 atoms, 739 bonds, 1 pseudobond, 31 residues, 3 models selected  

> nucleotides sel stubs

> select subtract #15

Nothing selected  

> select add #15

662 atoms, 739 bonds, 1 pseudobond, 31 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92914,-0.28325,-0.23764,207.96,0.066616,-0.50395,0.86116,157.33,-0.36368,-0.81597,-0.44937,216.66

> show #!4 models

> hide #!4 models

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.44033,0.86492,0.24087,198.66,-0.53009,-0.46698,0.70777,155,0.72464,0.18397,0.66411,216.96

> view matrix models
> #15,-0.5898,0.76607,-0.25549,202.43,0.75019,0.40267,-0.52447,180.8,-0.2989,-0.501,-0.81219,222.37

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.5898,0.76607,-0.25549,228.3,0.75019,0.40267,-0.52447,106.18,-0.2989,-0.501,-0.81219,190.99

> show #10 models

> hide #10 models

> view matrix models
> #15,-0.5898,0.76607,-0.25549,227.98,0.75019,0.40267,-0.52447,113.3,-0.2989,-0.501,-0.81219,261.42

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.61037,0.75534,-0.23857,227.61,0.67906,0.65402,0.33337,104.89,0.40784,0.041476,-0.91211,269.82

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.61037,0.75534,-0.23857,226.14,0.67906,0.65402,0.33337,104.13,0.40784,0.041476,-0.91211,259.49

> view matrix models
> #15,-0.61037,0.75534,-0.23857,235.37,0.67906,0.65402,0.33337,130.29,0.40784,0.041476,-0.91211,272.29

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.15592,0.94238,-0.29597,239.97,0.88226,0.26761,0.38729,129.37,0.44418,-0.20074,-0.87316,271.02

> view orient

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.15592,0.94238,-0.29597,229.73,0.88226,0.26761,0.38729,128.58,0.44418,-0.20074,-0.87316,248.19

> select subtract #15

Nothing selected  

> select add #15/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

662 atoms, 739 bonds, 31 residues, 1 model selected  

> select down

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #15

662 atoms, 739 bonds, 1 pseudobond, 31 residues, 3 models selected  

> view matrix models
> #15,-0.15592,0.94238,-0.29597,206.87,0.88226,0.26761,0.38729,110.59,0.44418,-0.20074,-0.87316,221.39

> select subtract #15

Nothing selected  
Drag select of 8 residues, 19 shapes  

> select ~sel & ##selected

439 atoms, 488 bonds, 1 pseudobond, 21 residues, 2 models selected  

> delete atoms (#!15 & sel)

> delete bonds (#!15 & sel)

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> view matrix models
> #15,-0.15592,0.94238,-0.29597,230.07,0.88226,0.26761,0.38729,138.82,0.44418,-0.20074,-0.87316,231.95

> view matrix models
> #15,-0.15592,0.94238,-0.29597,226.49,0.88226,0.26761,0.38729,128.37,0.44418,-0.20074,-0.87316,245.68

> select subtract #15

Nothing selected  

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> view matrix models
> #15,-0.15592,0.94238,-0.29597,225.61,0.88226,0.26761,0.38729,128.31,0.44418,-0.20074,-0.87316,246.98

> view matrix models
> #15,-0.15592,0.94238,-0.29597,230.1,0.88226,0.26761,0.38729,129.09,0.44418,-0.20074,-0.87316,250.41

> fitmap #15 inMap #11

Fit molecule copy of copy of
fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) to map volume
difference_region_3016.mrc (#11) using 223 atoms  
average map value = 0.02543, steps = 132  
shifted from previous position = 5.25  
rotated from previous position = 16.9 degrees  
atoms outside contour = 1, contour level = 0.0039469  
  
Position of copy of copy of
fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) relative to
volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.27108821 0.96021231 -0.06710817 231.36559527  
0.92731396 0.27922003 0.24924886 132.89262157  
0.25806976 0.00533809 -0.96611153 253.72195023  
Axis -0.59808743 -0.79736059 -0.08066921  
Axis point 50.82941084 0.00000000 124.85438837  
Rotation angle (degrees) 168.23436216  
Shift along axis -264.80774107  
  

> fitmap #15 inMap #11

Fit molecule copy of copy of
fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) to map volume
difference_region_3016.mrc (#11) using 223 atoms  
average map value = 0.02543, steps = 100  
shifted from previous position = 0.00562  
rotated from previous position = 0.0243 degrees  
atoms outside contour = 1, contour level = 0.0039469  
  
Position of copy of copy of
fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) relative to
volume difference_region_3016.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.27095722 0.96024980 -0.06710071 231.36710944  
0.92745359 0.27909367 0.24887056 132.89784192  
0.25770528 0.00520048 -0.96620957 253.72893157  
Axis -0.59815543 -0.79732594 -0.08050733  
Axis point 50.83325559 0.00000000 124.86559187  
Rotation angle (degrees) 168.24749354  
Shift along axis -264.78342854  
  

> hide #!15 models

> show #!15 models

> select subtract #15

Nothing selected  

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select #14/A

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select #14/A:3-13

227 atoms, 251 bonds, 11 residues, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select #14/A:3-16

289 atoms, 320 bonds, 14 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> color #13#!14-15 bynucleotide

> ui tool show "Show Sequence Viewer"

> sequence chain #13/A #14/A #15/A

Alignment identifier is 1  

> select clear

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> select subtract #13

621 atoms, 694 bonds, 29 residues, 2 models selected  

> select subtract #14

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> hide #13 models

> show #13 models

> vop add #13-15

> vop add #13,14,15

> vop add #13 #14 #15

> show #!6 models

> transparency #6#11.1 0

> transparency #6#11.1 50

> hide #!11 models

> show #!11 models

> hide #!6 models

> hide #!11 models

> select clear

[Repeated 1 time(s)]

> select #14/A

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select clear

> select #14/A

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select #14/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #14/A:3-5

60 atoms, 65 bonds, 3 residues, 1 model selected  

> show #!11 models

> hide #13 models

> show #13 models

> hide #!14 models

> show #!14 models

> hide #!15 models

> hide #13 models

> show #13 models

> hide #13 models

> show #13 models

> show #!15 models

> select add #14

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select add #15

621 atoms, 694 bonds, 29 residues, 2 models selected  

> select subtract #14

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select clear

[Repeated 1 time(s)]

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15.1

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select add #15.1

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15.1

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select #14/A:12-14

60 atoms, 65 bonds, 3 residues, 1 model selected  

> select #14/A:12-18

145 atoms, 160 bonds, 7 residues, 1 model selected  

> select clear

[Repeated 4 time(s)]

> select #14/A:3-5

60 atoms, 65 bonds, 3 residues, 1 model selected  

> select add #14

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select add #15

621 atoms, 694 bonds, 29 residues, 2 models selected  

> hide #13 models

> hide #!14 models

> hide #!15 models

> select subtract #14

223 atoms, 251 bonds, 10 residues, 1 model selected  

> show #!15 models

> hide #!15 models

> select subtract #15

Nothing selected  

> show #!9 models

> hide #!9 models

> show #!7 models

> hide #!7 models

> show #!6 models

> rename #12 region_3016.cif

> hide #!6 models

> show #12 models

> undo

> show #12 models

> color #12 bynucleotide

> ui tool show "Show Sequence Viewer"

> sequence chain #12/A

Alignment identifier is 12/A  

> rename #12 region_3016_80nu.cif

> hide #!11 models

> show #!11 models

> hide #12 models

> show #13 models

> show #!14 models

> show #!15 models

> rename #15 region_3016_65nu_1

> hide #!14 models

> hide #13 models

> show #13 models

> rename #13 region_3016_65nu_2

> rename #14 region_3016_65nu_3

> hide #13 models

> hide #!15 models

> show #12 models

> hide #12 models

> show #13 models

> show #!14 models

> show #!15 models

> ui tool show "Show Sequence Viewer"

> sequence chain #13/A #14/A #15/A

Alignment identifier is 1  

> select clear

[Repeated 1 time(s)]

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> select clear

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> select #15/A:62

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #15/A:62

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> select subtract #13

621 atoms, 694 bonds, 29 residues, 2 models selected  

> select subtract #14

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #13

725 atoms, 810 bonds, 34 residues, 1 model selected  

> select subtract #13

Nothing selected  

> select add #15

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select add #14

621 atoms, 694 bonds, 29 residues, 2 models selected  

> select subtract #15

398 atoms, 443 bonds, 19 residues, 1 model selected  

> select #14/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> select #14/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> select #14/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #13/A #14/A #15/A

1346 atoms, 1504 bonds, 63 residues, 3 models selected  

> show #!9 models

> hide #!9 models

> show #!7 models

> hide #!7 models

> show #!6 models

> select subtract #13

621 atoms, 694 bonds, 29 residues, 2 models selected  

> select subtract #14

223 atoms, 251 bonds, 10 residues, 1 model selected  

> select subtract #15

Nothing selected  

> ui tool show "Side View"

> select add #6.152

1 model selected  

> select add #6.27

2 models selected  

> select add #6.148

3 models selected  

> hide #13#!14-15 surfaces

> surface hidePatches #6.27,148,152

> select add #6

191 models selected  

> select subtract #6

Nothing selected  

> show #5 models

> hide #5 models

> select add #6.188

1 model selected  

> hide #13#!14-15 surfaces

> hide #6.188 models

> hide #6.190 models

> show #6.190 models

> select add #6.189

2 models selected  

> select subtract #6.188

1 model selected  

> select add #6.188

2 models selected  

> hide #6.189 models

> select subtract #6.189

1 model selected  

> select subtract #6.188

Nothing selected  

> select add #6.40

1 model selected  

> select add #6.141

2 models selected  

> hide #6.40 models

> select subtract #6.40

1 model selected  

> hide #6.141 models

> select subtract #6.141

Nothing selected  

> select add #6.46

1 model selected  

> select add #6.179

2 models selected  

> select add #6.138

3 models selected  

> hide #6.138 models

> select subtract #6.138

2 models selected  

> hide #6.46 models

> select subtract #6.46

1 model selected  

> select subtract #6.179

Nothing selected  

> hide #6.179 models

> undo

> select #6.90

1 model selected  

> undo

[Repeated 6 time(s)]

> hide #6.46 models

> select subtract #6.46

2 models selected  

> select subtract #6.138

1 model selected  

> hide #6.138 models

> hide #6.179 models

> select subtract #6.179

Nothing selected  

> select add #6.90

1 model selected  

> select add #6.168

2 models selected  

> select subtract #6.90

1 model selected  

> ui tool show "Segment Map"

Ungrouped to 6 regions  

> select subtract #6.195

5 models selected  

> select add #6.195

6 models selected  

> select subtract #6.191

5 models selected  

> select add #6.49

6 models selected  

> select add #6.108

7 models selected  

> select subtract #6.108

6 models selected  

> select subtract #6.49

5 models selected  

> select subtract #6.194

4 models selected  

> select subtract #6.195

3 models selected  

> select subtract #6.196

2 models selected  

> select add #6.108

3 models selected  

> select subtract #6.108

2 models selected  

> select subtract #6.193

1 model selected  

> select subtract #6.192

Nothing selected  

> select add #6.90

1 model selected  

> select add #6.194

2 models selected  

> undo

> select #6.193

1 model selected  

> undo

[Repeated 9 time(s)]

> select subtract #6.108

2 models selected  

> select add #6.108

3 models selected  

> select add #6.194

4 models selected  

> select add #6.195

5 models selected  

> select subtract #6.108

4 models selected  

> select add #6.185

5 models selected  

> select add #6.100

6 models selected  

> select add #6.129

7 models selected  
Grouped 7 regions  
Saving 1 regions to mrc file...  
Opened region_3017.mrc as #16, grid size 83,94,52, pixel 1.12, shown at step
1, values float32  
Wrote region_3017.mrc  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1287+0+35 (frame:
1942x1343-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 624x858 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1343)))  

> hide #!6 models

> volume #16 level 0.0135

> hide #!11 models

> show #!11 models

> rename #11 region_3016.mrc

> hide #!15 models

> show #!15 models

> volume #16 level 0.01566

> show #!6 models

> select add #6

190 models selected  

> select subtract #6

Nothing selected  

> show #!9 models

> show #10 models

> select subtract #9

Nothing selected  

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!4 models

> hide #!9 models

> hide #!4 models

> show #!8 models

> hide #!8 models

> show #!6 models

> rename #5 region_1.pdb

> rename #9 "volume difference_region_2.mrc"

> rename #10 region_2.cif

> rename #11 region_3.mrc

> rename #12 region_3_80nu.cif

> rename #13 region_3_65nu_2

> rename #14 region_3_65nu_3

> rename #15 region_3_65nu_1

> rename #16 region_4.mrc

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113 region_4 start.cxs"

——— End of log from Thu Nov 13 13:38:11 2025 ———

> view name session-start

opened ChimeraX session  
Showing volume difference.seg - 189 regions, 189 surfaces  

> hide #!6 models

> hide #13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113_rna_phicb5_region_3_75nu/fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif"

Chain information for
fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif #17  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #17 region_3_75nu.cif

> select add #17

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #17,1,0,0,151.4,0,1,0,54.629,0,0,1,-7.9536

> view matrix models #17,1,0,0,292.05,0,1,0,135.56,0,0,1,111.02

> view matrix models #17,1,0,0,293.26,0,1,0,101.03,0,0,1,179.18

> view matrix models #17,1,0,0,262.85,0,1,0,133.91,0,0,1,157.56

> ui mousemode right "rotate selected models"

> view matrix models
> #17,-0.315,0.88625,-0.3396,255.28,0.85381,0.10836,-0.50918,138.52,-0.41446,-0.45035,-0.79083,154.43

> view matrix models
> #17,-0.94742,-0.070488,-0.31212,254.27,0.30877,0.054586,-0.94957,135.76,0.083971,-0.99602,-0.029951,158.4

> view matrix models
> #17,-0.87941,-0.11639,-0.46163,254.47,0.47586,-0.18609,-0.85961,137.02,0.014142,-0.97562,0.21903,158.35

> nucleotides sel stubs

> combine #17

[Repeated 1 time(s)]

> rename #18 region_3_75nu.cif

> rename #17 region_3_75nu_stem.cif

> rename #18 region_3_stemloop_1.cif

> rename #17 region_3_stem.cif

> rename #19 region_3_stemloop_2.cif

> select subtract #17

Nothing selected  

> select add #17

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> select add #18

3188 atoms, 3562 bonds, 150 residues, 2 models selected  

> select add #19

4782 atoms, 5343 bonds, 225 residues, 3 models selected  

> nucleotides sel stubs

> select subtract #17

3188 atoms, 3562 bonds, 150 residues, 2 models selected  

> select subtract #18

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> select add #18

3188 atoms, 3562 bonds, 150 residues, 2 models selected  

> select add #17

4782 atoms, 5343 bonds, 225 residues, 3 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #17/A

Alignment identifier is 17/A  

> sequence chain #18/A

Alignment identifier is 18/A  

> sequence chain #19/A

Alignment identifier is 19/A  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1134+0+35 (frame:
1942x1190-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 624x756 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1190)))  

> select subtract #19

3188 atoms, 3562 bonds, 150 residues, 2 models selected  

> select subtract #18

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select #19/A:13

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #19/A:13-32

420 atoms, 468 bonds, 20 residues, 1 model selected  

> select ~sel & ##selected

1174 atoms, 1313 bonds, 55 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #18/A:33

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #18/A:33-59

572 atoms, 638 bonds, 27 residues, 1 model selected  

> select #18/A:33

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #18/A:33-63

660 atoms, 737 bonds, 31 residues, 1 model selected  

> select ~sel & ##selected

934 atoms, 1044 bonds, 44 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #17/A:12-13

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select #17/A:12-63

1100 atoms, 1228 bonds, 52 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #17

494 atoms, 551 bonds, 1 pseudobond, 23 residues, 2 models selected  

> select add #18

1154 atoms, 1288 bonds, 1 pseudobond, 54 residues, 3 models selected  

> select add #19

1574 atoms, 1756 bonds, 1 pseudobond, 74 residues, 4 models selected  

> select subtract #18

914 atoms, 1019 bonds, 1 pseudobond, 43 residues, 3 models selected  

> select subtract #19

494 atoms, 551 bonds, 1 pseudobond, 23 residues, 2 models selected  

> view matrix models
> #17,-0.33746,-0.0025218,-0.94134,251.56,0.92281,-0.19832,-0.33029,126.5,-0.18585,-0.98013,0.069253,162.3

> ui mousemode right "translate selected models"

> view matrix models
> #17,-0.33746,-0.0025218,-0.94134,221.15,0.92281,-0.19832,-0.33029,137.61,-0.18585,-0.98013,0.069253,230.68

> fit#17 inmap #11

Unknown command: fit#17 inmap #11  

> fit#17 inmap #11

Unknown command: fit#17 inmap #11  

> fit#17 inmap #11

Unknown command: fit#17 inmap #11  

> fitmap #17 inMap #11

Fit molecule region_3_stem.cif (#17) to map region_3.mrc (#11) using 494 atoms  
average map value = 0.02034, steps = 152  
shifted from previous position = 15.8  
rotated from previous position = 57.9 degrees  
atoms outside contour = 46, contour level = 0.0039469  
  
Position of region_3_stem.cif (#17) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.13072243 0.68750809 -0.71431383 230.67755924  
0.48701854 -0.58304173 -0.65028860 130.11432530  
-0.86355346 -0.43289139 -0.25861255 248.44280777  
Axis 0.65628298 0.45052750 -0.60524179  
Axis point 0.00000000 -32.19839622 237.14920419  
Rotation angle (degrees) 170.46630204  
Shift along axis 59.64186845  
  

> select subtract #17

Nothing selected  

> select add #18

660 atoms, 737 bonds, 31 residues, 1 model selected  

> view matrix models
> #18,-0.87941,-0.11639,-0.46163,240.73,0.47586,-0.18609,-0.85961,106.49,0.014142,-0.97562,0.21903,227.79

> fitmap #18 inMap #11

Fit molecule region_3_stemloop_1.cif (#18) to map region_3.mrc (#11) using 660
atoms  
average map value = 0.01098, steps = 180  
shifted from previous position = 18  
rotated from previous position = 29.1 degrees  
atoms outside contour = 340, contour level = 0.0039469  
  
Position of region_3_stemloop_1.cif (#18) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.74171820 0.34928190 -0.57258734 233.26637193  
0.51414519 -0.25212314 -0.81981012 120.84020558  
-0.43070736 -0.90246112 0.00742271 213.88373295  
Axis -0.35520974 -0.60975855 0.70853409  
Axis point 165.39454895 161.98845317 0.00000000  
Rotation angle (degrees) 173.31901522  
Shift along axis -4.99792143  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.39586,-0.62219,-0.67541,235.16,0.49734,-0.76354,0.41189,126.2,-0.77198,-0.17286,0.6117,214.24

> view matrix models
> #18,-0.42484,-0.89479,0.13738,238.41,0.18779,0.06135,0.98029,127.01,-0.88558,0.44226,0.14197,211.69

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.42484,-0.89479,0.13738,238.24,0.18779,0.06135,0.98029,134.21,-0.88558,0.44226,0.14197,221.15

> fitmap #18 inMap #11

Fit molecule region_3_stemloop_1.cif (#18) to map region_3.mrc (#11) using 660
atoms  
average map value = 0.02019, steps = 352  
shifted from previous position = 4.74  
rotated from previous position = 46.5 degrees  
atoms outside contour = 92, contour level = 0.0039469  
  
Position of region_3_stemloop_1.cif (#18) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.56096701 -0.77354279 -0.29486870 230.64413736  
0.47714143 -0.59319432 0.64842621 138.54664316  
-0.67649986 0.22305164 0.70185176 227.52913775  
Axis -0.30934926 0.27753732 0.90954718  
Axis point 134.25608165 96.84957985 0.00000000  
Rotation angle (degrees) 136.56499751  
Shift along axis 174.05075680  
  

> select subtract #18

Nothing selected  

> select add #19

420 atoms, 468 bonds, 20 residues, 1 model selected  

> view matrix models
> #19,-0.87941,-0.11639,-0.46163,239.74,0.47586,-0.18609,-0.85961,166.52,0.014142,-0.97562,0.21903,203.3

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.71607,0.10544,0.69002,233.94,-0.38551,0.76435,-0.51686,156.57,-0.58191,-0.63612,-0.50669,202.47

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.71607,0.10544,0.69002,241.84,-0.38551,0.76435,-0.51686,125.89,-0.58191,-0.63612,-0.50669,254.33

> view matrix models
> #19,-0.71607,0.10544,0.69002,242.44,-0.38551,0.76435,-0.51686,113.28,-0.58191,-0.63612,-0.50669,235.85

> fitmap #19 inMap #11

Fit molecule region_3_stemloop_2.cif (#19) to map region_3.mrc (#11) using 420
atoms  
average map value = 0.019, steps = 292  
shifted from previous position = 2.88  
rotated from previous position = 76.3 degrees  
atoms outside contour = 59, contour level = 0.0039469  
  
Position of region_3_stemloop_2.cif (#19) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.09100647 -0.57474089 0.81325932 248.73552558  
-0.99242563 -0.12001126 0.02624228 137.70422521  
0.08251777 -0.80948761 -0.58130940 232.71669253  
Axis -0.70458946 0.61607560 -0.35214280  
Axis point 0.00000000 217.70064286 -2.66111062  
Rotation angle (degrees) 143.62542958  
Shift along axis -172.36972401  
  

> select subtract #19

Nothing selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113 region_3.cxs"

> close #12-16

> hide #!11 models

> hide #10 models

> hide #!17 models

> hide #18 models

> show #18 models

> show #!17 models

> show #10 models

> hide #10 models

> show #5 models

> show #10 models

> nucleotides #5,10,18-19#!17 stubs

> rename #17 id #12

> rename #18 id #13

> rename #19 id #14

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113 region_3.cxs"

——— End of log from Thu Nov 13 15:31:54 2025 ———

> view name session-start

opened ChimeraX session  
Showing volume difference.seg - 189 regions, 189 surfaces  

> show #!11 models

> hide #!11 models

> hide #!6 models

> show #!6 models

> select add #4

3 models selected  

> select subtract #4

Nothing selected  

> select add #6

190 models selected  

> transparency sel 0

> transparency sel 50

> select subtract #6

Nothing selected  

> select add #6.125

1 model selected  

> select add #6.108

2 models selected  

> select add #6.189

3 models selected  
Grouped 3 regions  

> transparency sel 0

[Repeated 1 time(s)]

> select add #6

188 models selected  

> select subtract #6

Nothing selected  

> select add #6.91

1 model selected  

> select add #6.108

2 models selected  
Grouped 2 regions  

> select add #6

187 models selected  

> select subtract #6

Nothing selected  

> hide #5 models

> show #5 models

> hide #6.188 models

> hide #6.185 models

> show #6.185 models

> hide #6.187 models

> select add #6.186

1 model selected  

> hide #6.186 models

> select subtract #6.186

Nothing selected  

> select add #6.121

1 model selected  

> select add #6.50

2 models selected  

> select add #6.141

3 models selected  

> select add #6.40

4 models selected  

> select add #6.87

5 models selected  

> select add #6.83

6 models selected  

> undo

> select #6.87

1 model selected  

> undo

[Repeated 9 time(s)]

> select #6.141

1 model selected  

> undo

> select add #6.50

2 models selected  

> select add #6.43

3 models selected  

> select add #6.95

4 models selected  

> select add #6.172

5 models selected  

> select add #6.173

6 models selected  

> select add #6.61

7 models selected  

> select subtract #6.61

6 models selected  

> select add #6.91

7 models selected  
Grouped 7 regions  

> select add #6

181 models selected  

> select subtract #6

Nothing selected  

> select add #6

181 models selected  

> select subtract #6

Nothing selected  

> select add #6.43

1 model selected  

> select ~sel & ##selected

Nothing selected  

> select add #6.43

1 model selected  

> select ~sel & ##selected

Nothing selected  

> select add #6.43

1 model selected  
Saving 1 regions to mrc file...  
Opened region_4_2.mrc as #15, grid size 108,100,92, pixel 1.12, shown at step
1, values float32  
Wrote region_4_2.mrc  

> hide #5 models

> show #5 models

> hide #!6 models

> volume #15 level 0.017

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113_rna_phicb5_region_4_120nu/fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif"

Chain information for
fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif #16  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #16 region_4_120nu_model_0.cif

> rename #16 region_4_120nu.cif

> view

> select add #16

2557 atoms, 2861 bonds, 120 residues, 2 models selected  

> select add #5

4892 atoms, 5464 bonds, 231 residues, 3 models selected  

> select subtract #5

2557 atoms, 2861 bonds, 120 residues, 2 models selected  

> show #!6 models

> view

> ui mousemode right "translate selected models"

> view matrix models
> #6.43,1,0,0,30.066,0,1,0,5.8403,0,0,1,14.045,#16,1,0,0,30.066,0,1,0,5.8403,0,0,1,14.045

> undo

> select add #6

2557 atoms, 2861 bonds, 120 residues, 182 models selected  

> select subtract #6

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models #16,1,0,0,177.83,0,1,0,-26.18,0,0,1,219.9

> select subtract #16

Nothing selected  

> hide #!6 models

> select add #16

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models #16,1,0,0,249.72,0,1,0,195.7,0,0,1,188.42

> view matrix models #16,1,0,0,220.25,0,1,0,198.26,0,0,1,149.22

> undo

> select subtract #16

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #16

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #16,-0.57831,0.42398,0.69699,242.08,0.41526,0.88837,-0.19585,197.73,-0.70222,0.17617,-0.68982,192.83

> view matrix models
> #16,-0.82518,0.42952,0.36686,242.66,0.49804,0.85966,0.11377,196.96,-0.26651,0.27659,-0.92329,194.2

> select subtract #16

Nothing selected  

> ui mousemode right "translate selected models"

> select add #16

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #16,-0.82518,0.42952,0.36686,186.47,0.49804,0.85966,0.11377,166.94,-0.26651,0.27659,-0.92329,233.94

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.62712,0.76371,-0.1532,186.85,0.66899,0.62883,0.39626,166.67,0.39897,0.14601,-0.90527,236.05

> view matrix models
> #16,-0.36789,0.88151,-0.29597,187.24,0.73741,0.47047,0.48464,167.3,0.56646,-0.039959,-0.82312,237.04

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.36789,0.88151,-0.29597,185.09,0.73741,0.47047,0.48464,181.43,0.56646,-0.039959,-0.82312,241.74

> fitmap #16 inMap #15

Fit molecule region_4_120nu.cif (#16) to map region_4_2.mrc (#15) using 2557
atoms  
average map value = 0.009566, steps = 120  
shifted from previous position = 7.67  
rotated from previous position = 5.26 degrees  
atoms outside contour = 1735, contour level = 0.017  
  
Position of region_4_120nu.cif (#16) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.28475396 0.91689579 -0.27967347 189.69488230  
0.76517002 0.39314944 0.50985129 176.45360329  
0.57743399 -0.06881558 -0.81353205 245.41255409  
Axis -0.55362547 -0.82001673 -0.14515994  
Axis point 0.19311164 -0.00000000 112.54517601  
Rotation angle (degrees) 148.49211885  
Shift along axis -285.33889665  
  

> hide #5 models

> hide #10 models

> hide #!12 models

> hide #13 models

> hide #14 models

> show #!12 models

> select subtract #16

Nothing selected  

> select add #16

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #16,-0.28475,0.9169,-0.27967,188.17,0.76517,0.39315,0.50985,171.38,0.57743,-0.068816,-0.81353,229.14

> select subtract #16

Nothing selected  

> select add #16

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.53508,0.57863,-0.61553,190.83,0.84344,0.32461,-0.42806,175.57,-0.047878,-0.74821,-0.66173,230.98

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.53508,0.57863,-0.61553,174.89,0.84344,0.32461,-0.42806,183.56,-0.047878,-0.74821,-0.66173,233.78

> select subtract #16

Nothing selected  

> fitmap #16 inMap #15

Fit molecule region_4_120nu.cif (#16) to map region_4_2.mrc (#15) using 2557
atoms  
average map value = 0.01117, steps = 168  
shifted from previous position = 11.1  
rotated from previous position = 6.6 degrees  
atoms outside contour = 1531, contour level = 0.017  
  
Position of region_4_120nu.cif (#16) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.61979660 0.50270893 -0.60260757 173.34699647  
0.78430487 0.37058243 -0.49752841 194.64245906  
-0.02679619 -0.78099446 -0.62396281 234.04968581  
Axis -0.40445326 -0.82157557 0.40178495  
Axis point 6.97144648 0.00000000 177.65200697  
Rotation angle (degrees) 159.48631031  
Shift along axis -135.98660569  
  

> hide #16 models

> select add #15

2 models selected  

> ui tool show "Segment Map"

Segmenting volume difference, density threshold 0.011922  
Showing 194 region surfaces  
2209 watershed regions, grouped to 194 regions  
Showing volume difference.seg - 194 regions, 194 surfaces  

> hide #!6 models

> select subtract #15

Nothing selected  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113_rna_phicb5_region_4_stemloop_1/fold_2025_11_13_16_35_rna_phicb5_region_4_stemloop_1_model_0.cif"

Chain information for
fold_2025_11_13_16_35_rna_phicb5_region_4_stemloop_1_model_0.cif #17  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #17 region_4_stemloop_1.cif

> view

> select add #17

767 atoms, 855 bonds, 36 residues, 1 model selected  

> view matrix models #17,1,0,0,60.502,0,1,0,261.29,0,0,1,93.386

> select subtract #17

Nothing selected  

> select add #17

767 atoms, 855 bonds, 36 residues, 1 model selected  

> view matrix models #17,1,0,0,140.1,0,1,0,140.23,0,0,1,193.3

> view matrix models #17,1,0,0,179.86,0,1,0,176.45,0,0,1,205

> select subtract #17

Nothing selected  

> fitmap #17 inMap #15

Fit molecule region_4_stemloop_1.cif (#17) to map region_4_2.mrc (#15) using
767 atoms  
average map value = 0.01573, steps = 196  
shifted from previous position = 16.3  
rotated from previous position = 62 degrees  
atoms outside contour = 352, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#17) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
0.63718988 0.58570337 0.50093973 193.33216599  
-0.16123908 0.73689782 -0.65649339 179.93984192  
-0.75365178 0.33753988 0.56398211 215.41428826  
Axis 0.56275826 0.71026973 -0.42287120  
Axis point 349.66657078 0.00000000 30.77979180  
Rotation angle (degrees) 62.02833176  
Shift along axis 145.51259855  
  

> select add #17

767 atoms, 855 bonds, 36 residues, 1 model selected  

> view matrix models
> #17,0.63719,0.5857,0.50094,179.71,-0.16124,0.7369,-0.65649,134.47,-0.75365,0.33754,0.56398,204.32

> view matrix models
> #17,0.63719,0.5857,0.50094,182.09,-0.16124,0.7369,-0.65649,226.47,-0.75365,0.33754,0.56398,203.71

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.81737,-0.41844,-0.39599,183.75,0.33938,0.90516,-0.25595,224.77,0.46553,0.074822,0.88186,201.01

> select subtract #17

Nothing selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> select add #17

767 atoms, 855 bonds, 36 residues, 1 model selected  

> view matrix models
> #17,0.57938,0.79297,-0.18846,182.94,-0.37806,0.056611,-0.92405,227.84,-0.72208,0.60662,0.33259,203.72

> view matrix models
> #17,-0.88964,-0.12232,0.43997,185.89,-0.2621,-0.65218,-0.71131,227.92,0.37395,-0.74813,0.54814,202.34

> select subtract #17

Nothing selected  

> select add #17

767 atoms, 855 bonds, 36 residues, 1 model selected  

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select subtract #17

Nothing selected  

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> transparency #6#15.1 50

> show #10 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> hide #!6 models

> hide #10 models

> select add #17

767 atoms, 855 bonds, 36 residues, 1 model selected  

> view matrix models
> #17,-0.9658,-0.15764,0.20586,186.38,-0.032602,-0.71383,-0.69956,227.49,0.25723,-0.68235,0.68427,202.34

> ui mousemode right "translate selected models"

> view matrix models
> #17,-0.9658,-0.15764,0.20586,146.38,-0.032602,-0.71383,-0.69956,180.8,0.25723,-0.68235,0.68427,260.34

> fitmap #17 inMap #15

Fit molecule region_4_stemloop_1.cif (#17) to map region_4_2.mrc (#15) using
767 atoms  
average map value = 0.01913, steps = 88  
shifted from previous position = 4.9  
rotated from previous position = 15.8 degrees  
atoms outside contour = 301, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#17) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.86454611 -0.33525618 0.37438389 146.86140773  
-0.06548829 -0.66345498 -0.74534469 183.59063241  
0.49826829 -0.66890261 0.55163210 264.38738669  
Axis 0.24937242 -0.40414064 0.88004758  
Axis point 24.47750757 156.80350177 0.00000000  
Rotation angle (degrees) 171.18358655  
Shift along axis 195.10022874  
  

> color #17 red

> undo

> select subtract #17

Nothing selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114_rna_phicb5_region_4_stemloop_2/fold_2025_11_14_08_10_rna_phicb5_region_4_stemloop_2_model_0.cif"

Chain information for
fold_2025_11_14_08_10_rna_phicb5_region_4_stemloop_2_model_0.cif #18  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #18 region_4_stemloop_2.cif

> view

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models #18,1,0,0,49.192,0,1,0,188.78,0,0,1,201

> view matrix models #18,1,0,0,110.09,0,1,0,184.21,0,0,1,241.09

> select subtract #18

Nothing selected  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models #18,1,0,0,97.509,0,1,0,167.14,0,0,1,280.39

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.052861,-0.98425,0.16871,94.316,-0.57615,-0.10793,-0.81019,166.48,0.81563,-0.14003,-0.56137,283.87

> view matrix models
> #18,0.84482,-0.45859,0.27565,96.502,0.32042,0.021036,-0.94704,169.08,0.4285,0.8884,0.16471,282.01

> view matrix models
> #18,0.82385,-0.032425,0.56588,95.313,0.43211,0.68204,-0.59001,168.74,-0.36682,0.7306,0.57591,279.65

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.82385,-0.032425,0.56588,141.44,0.43211,0.68204,-0.59001,223.97,-0.36682,0.7306,0.57591,241.28

> view matrix models
> #18,0.82385,-0.032425,0.56588,158.67,0.43211,0.68204,-0.59001,229.63,-0.36682,0.7306,0.57591,249.19

> select ~sel & ##selected

Nothing selected  

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01171, steps = 156  
shifted from previous position = 13.7  
rotated from previous position = 18.9 degrees  
atoms outside contour = 808, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
0.65891515 -0.10922066 0.74424569 149.69902909  
0.68455489 0.49717458 -0.53310601 227.06790773  
-0.31179385 0.86074867 0.40236341 259.53256306  
Axis 0.72579569 0.54989158 0.41332779  
Axis point 0.00000000 -52.09164905 123.55093508  
Rotation angle (degrees) 73.78595041  
Shift along axis 340.78566210  
  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,0.65892,-0.10922,0.74425,160.76,0.68455,0.49717,-0.53311,225.24,-0.31179,0.86075,0.40236,254.97

> select subtract #18

Nothing selected  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,0.65892,-0.10922,0.74425,168.78,0.68455,0.49717,-0.53311,220.49,-0.31179,0.86075,0.40236,253.38

> select subtract #18

Nothing selected  

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01678, steps = 504  
shifted from previous position = 8.77  
rotated from previous position = 83.5 degrees  
atoms outside contour = 508, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.20973364 -0.21007278 0.95492472 161.58163537  
-0.00177812 0.97672709 0.21447852 213.89266455  
-0.97775694 0.04328539 -0.20522606 248.71601996  
Axis -0.08772847 0.99040901 0.10674128  
Axis point 181.08562946 0.00000000 39.59869629  
Rotation angle (degrees) 102.65713467  
Shift along axis 224.21417822  
  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,-0.20973,-0.21007,0.95492,155.21,-0.0017781,0.97673,0.21448,221.7,-0.97776,0.043285,-0.20523,251.09

> select subtract #18

Nothing selected  

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01681, steps = 116  
shifted from previous position = 9.59  
rotated from previous position = 10 degrees  
atoms outside contour = 519, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.31825061 -0.28525117 0.90407317 160.86993562  
-0.12129700 0.95807110 0.25958967 214.22093133  
-0.94021464 -0.02704679 -0.33950683 248.95705007  
Axis -0.15298566 0.98434646 0.08750679  
Axis point 178.42765225 0.00000000 47.02600011  
Rotation angle (degrees) 110.47772294  
Shift along axis 208.04225418  
  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,-0.58077,-0.67576,0.45393,160.77,-0.66279,0.71627,0.21831,212.79,-0.47266,-0.17407,-0.86388,250.94

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.58077,-0.67576,0.45393,151.73,-0.66279,0.71627,0.21831,220.69,-0.47266,-0.17407,-0.86388,256.92

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01667, steps = 524  
shifted from previous position = 12.1  
rotated from previous position = 26.3 degrees  
atoms outside contour = 531, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.48377449 -0.45033190 0.75044213 159.41944458  
-0.39242340 0.87804702 0.27392938 214.32135991  
-0.78228262 -0.16197101 -0.60149753 249.82409578  
Axis -0.27336794 0.96122375 0.03631639  
Axis point 173.18356662 0.00000000 67.51007497  
Rotation angle (degrees) 127.12906500  
Shift along axis 171.50332538  
  

> select subtract #18

Nothing selected  

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> volume #15 level 0.015

> volume #15 level 0.02

> volume #15 level 0.017

> volume #15 level 0.015

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01667, steps = 40  
shifted from previous position = 0.104  
rotated from previous position = 1.39 degrees  
atoms outside contour = 475, contour level = 0.015  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.47517140 -0.43900751 0.76255133 159.52208081  
-0.37535668 0.88496373 0.27558402 214.31145790  
-0.79581372 -0.15527909 -0.58529386 249.76369944  
Axis -0.26627981 0.96309275 0.03933716  
Axis point 173.65219894 0.00000000 66.06604205  
Rotation angle (degrees) 125.99755800  
Shift along axis 173.74929821  
  

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01667, steps = 40  
shifted from previous position = 0.0346  
rotated from previous position = 0.505 degrees  
atoms outside contour = 475, contour level = 0.015  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.47191792 -0.43490924 0.76690769 159.55518190  
-0.36917760 0.88740807 0.27607030 214.30110182  
-0.80062560 -0.15284262 -0.57934253 249.75234606  
Axis -0.26370572 0.96375622 0.04041335  
Axis point 173.82598149 0.00000000 65.55170326  
Rotation angle (degrees) 125.58613536  
Shift along axis 174.55173573  
  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,-0.47192,-0.43491,0.76691,150.67,-0.36918,0.88741,0.27607,218.15,-0.80063,-0.15284,-0.57934,252.48

> select subtract #18

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,-0.63756,-0.14493,0.75664,150.29,-0.3077,0.94831,-0.077626,218.85,-0.70628,-0.28231,-0.6492,252.83

> view matrix models
> #18,-0.5574,-0.6642,0.49813,150.78,-0.73589,0.67305,0.073978,217.35,-0.3844,-0.32534,-0.86394,254.06

> view matrix models
> #18,0.20816,-0.96279,-0.17236,153.35,-0.96819,-0.17781,-0.17602,217.28,0.13883,0.20351,-0.96918,255.25

> view matrix models
> #18,0.41964,-0.90726,0.027811,153.6,-0.86658,-0.40957,-0.28511,217.88,0.27006,0.095546,-0.95809,255.62

> view matrix models
> #18,-0.55462,-0.74534,0.36995,150.8,-0.82247,0.55851,-0.10778,217.64,-0.12629,-0.36405,-0.92278,254.77

> view matrix models
> #18,-0.040987,-0.98834,-0.14665,152.55,-0.96567,0.076864,-0.24813,217.56,0.25651,0.13144,-0.95756,255.58

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.040987,-0.98834,-0.14665,152.86,-0.96567,0.076864,-0.24813,224.01,0.25651,0.13144,-0.95756,256.67

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01667, steps = 1080  
shifted from previous position = 13.9  
rotated from previous position = 87.9 degrees  
atoms outside contour = 475, contour level = 0.015  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.48169283 -0.44710906 0.75370120 159.44262379  
-0.38754440 0.88006757 0.27439099 214.32321636  
-0.78599068 -0.15992051 -0.59719685 249.79458485  
Axis -0.27129501 0.96177681 0.03720739  
Axis point 173.27269554 0.00000000 67.11626704  
Rotation angle (degrees) 126.82772950  
Shift along axis 172.16931385  
  

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114_rna_phicb5_region_4_stemloop_2_2/fold_2025_11_14_08_25_rna_phicb5_region_4_stemloop_2_2_model_0.cif"

Chain information for
fold_2025_11_14_08_25_rna_phicb5_region_4_stemloop_2_2_model_0.cif #19  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #19 region_4_stemloop_2_2.cif

> select subtract #18

Nothing selected  

> hide #18 models

> view

> select add #19

1475 atoms, 1648 bonds, 69 residues, 1 model selected  

> view matrix models #19,1,0,0,-37.537,0,1,0,253.28,0,0,1,131.08

> select subtract #19

Nothing selected  

> select add #19

1475 atoms, 1648 bonds, 69 residues, 1 model selected  

> view matrix models #19,1,0,0,200.89,0,1,0,228.69,0,0,1,233.87

> select subtract #19

Nothing selected  

> nucleotides #17,19#!12 stubs

> select add #19

1475 atoms, 1648 bonds, 69 residues, 1 model selected  

> nucleotides sel stubs

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.67503,-0.73307,0.083312,202.62,0.46352,-0.50924,-0.72514,230,0.574,-0.45088,0.68354,233.46

> view matrix models
> #19,-0.70302,-0.70777,-0.069474,202.96,0.41207,-0.32577,-0.85093,230.25,0.57963,-0.62684,0.52067,233.86

> view matrix models
> #19,-0.96675,-0.21485,0.13868,202.69,0.25484,-0.76454,0.59206,227.82,-0.021181,0.60771,0.79387,233.57

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.96675,-0.21485,0.13868,164.99,0.25484,-0.76454,0.59206,224.56,-0.021181,0.60771,0.79387,256.15

> select subtract #19

Nothing selected  

> fitmap #19 inMap #15

Fit molecule region_4_stemloop_2_2.cif (#19) to map region_4_2.mrc (#15) using
1475 atoms  
average map value = 0.01361, steps = 328  
shifted from previous position = 15.4  
rotated from previous position = 30.7 degrees  
atoms outside contour = 732, contour level = 0.015  
  
Position of region_4_stemloop_2_2.cif (#19) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.80630916 -0.39740387 0.43810460 148.86026835  
0.51062823 -0.84149826 0.17646365 223.71740309  
0.29853693 0.36599284 0.88143343 256.30814112  
Axis 0.20204767 0.14878616 0.96800796  
Axis point 24.86292645 103.21513995 0.00000000  
Rotation angle (degrees) 152.02923384  
Shift along axis 311.47124518  
  

> show #18 models

> hide #19 models

> hide #18 models

> show #19 models

> rename #19 region_4_stemloop_1_2.cif

> fitmap #19 inMap #15

Fit molecule region_4_stemloop_1_2.cif (#19) to map region_4_2.mrc (#15) using
1475 atoms  
average map value = 0.0136, steps = 48  
shifted from previous position = 0.0389  
rotated from previous position = 0.599 degrees  
atoms outside contour = 731, contour level = 0.015  
  
Position of region_4_stemloop_1_2.cif (#19) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.80563603 -0.40394439 0.43333528 148.90231522  
0.51271950 -0.84186790 0.16845495 223.71798819  
0.29676464 0.35789284 0.88534932 256.28217507  
Axis 0.20026322 0.14437490 0.96904620  
Axis point 24.76080762 104.01914308 0.00000000  
Rotation angle (degrees) 151.77259501  
Shift along axis 310.46818550  
  

> select add #19

1475 atoms, 1648 bonds, 69 residues, 1 model selected  

> view matrix models
> #19,-0.80564,-0.40394,0.43334,157.73,0.51272,-0.84187,0.16845,219.64,0.29676,0.35789,0.88535,250.57

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.54227,-0.81159,0.2174,157.9,0.78624,-0.5814,-0.20929,220.01,0.29626,0.057435,0.95338,250.47

> view matrix models
> #19,-0.73866,-0.46243,0.49045,157.51,0.62572,-0.74099,0.24373,219.36,0.25071,0.48692,0.83669,250.69

> view matrix models
> #19,-0.40629,-0.90496,0.12637,157.91,0.79755,-0.41871,-0.43427,220.41,0.44591,-0.075653,0.89187,250.46

> view matrix models
> #19,-0.65527,-0.58174,0.48187,157.34,0.60575,-0.78578,-0.12492,220.11,0.45132,0.21004,0.86729,250.42

> view matrix models
> #19,-0.59533,-0.77726,0.20359,157.89,0.53371,-0.57195,-0.62292,221.12,0.60062,-0.26218,0.75533,250.63

> view matrix models
> #19,-0.615,-0.70875,0.34562,157.58,0.55275,-0.70008,-0.45205,220.8,0.56235,-0.086971,0.82231,250.45

> view matrix models
> #19,-0.86921,0.49322,-0.034696,158.1,-0.044614,-0.0083526,0.99897,218.14,0.49242,0.86987,0.029265,251.91

> view matrix models
> #19,-0.73828,0.57146,-0.35829,158.54,0.19235,0.68752,0.70023,218.35,0.64649,0.44805,-0.6175,252.9

> fitmap #19 inMap #15

Fit molecule region_4_stemloop_1_2.cif (#19) to map region_4_2.mrc (#15) using
1475 atoms  
average map value = 0.0145, steps = 408  
shifted from previous position = 8.2  
rotated from previous position = 42.2 degrees  
atoms outside contour = 641, contour level = 0.015  
  
Position of region_4_stemloop_1_2.cif (#19) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.44403872 0.56620002 -0.69444013 162.26647345  
0.56058655 0.78016444 0.27764382 211.87484894  
0.69897946 -0.26600920 -0.66382736 251.23346204  
Axis -0.36347002 -0.93159834 -0.00375300  
Axis point -20.57375469 0.00000000 141.77382209  
Rotation angle (degrees) 131.59422419  
Shift along axis -257.30413352  
  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.31267,-0.112,-0.94324,162.99,0.81877,0.47162,-0.3274,212.93,0.48152,-0.87466,-0.055761,250.56

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.31267,-0.112,-0.94324,159.61,0.81877,0.47162,-0.3274,216.47,0.48152,-0.87466,-0.055761,253.99

> fitmap #19 inMap #15

Fit molecule region_4_stemloop_1_2.cif (#19) to map region_4_2.mrc (#15) using
1475 atoms  
average map value = 0.01413, steps = 400  
shifted from previous position = 2.09  
rotated from previous position = 13.5 degrees  
atoms outside contour = 663, contour level = 0.015  
  
Position of region_4_stemloop_1_2.cif (#19) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.39953735 0.00014085 -0.91671688 160.85509232  
0.71533909 0.62541937 -0.31167375 215.76545376  
0.57328862 -0.78028873 -0.24997917 252.90594132  
Axis -0.27278156 -0.86733469 0.41631809  
Axis point -53.46619538 0.00000000 219.68205002  
Rotation angle (degrees) 120.80038147  
Shift along axis -125.72984834  
  

> select subtract #19

Nothing selected  

> hide #17 models

> show #17 models

> hide #17 models

> show #18 models

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> view matrix models
> #18,-0.48169,-0.44711,0.7537,124.68,-0.38754,0.88007,0.27439,194.18,-0.78599,-0.15992,-0.5972,208.39

> view matrix models
> #18,-0.48169,-0.44711,0.7537,176.65,-0.38754,0.88007,0.27439,177.01,-0.78599,-0.15992,-0.5972,236

> view matrix models
> #18,-0.48169,-0.44711,0.7537,175.44,-0.38754,0.88007,0.27439,167.65,-0.78599,-0.15992,-0.5972,258.91

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.38549,-0.87302,0.29873,175.97,-0.22837,-0.22341,-0.94759,168.81,0.89401,-0.43351,-0.11325,262.34

> view matrix models
> #18,0.32605,-0.94346,-0.059734,178.15,-0.6961,-0.19685,-0.69043,167.17,0.63964,0.26669,-0.72093,262.17

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.32605,-0.94346,-0.059734,162.05,-0.6961,-0.19685,-0.69043,169.54,0.63964,0.26669,-0.72093,263.55

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01176, steps = 272  
shifted from previous position = 14.4  
rotated from previous position = 25 degrees  
atoms outside contour = 799, contour level = 0.015  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
0.65910355 -0.74308173 0.11581037 164.04339614  
-0.53461222 -0.57125533 -0.62278175 182.00238429  
0.52893503 0.34856403 -0.77377700 255.99969199  
Axis 0.90278912 -0.38396672 0.19375593  
Axis point 0.00000000 88.50269799 147.75453533  
Rotation angle (degrees) 147.45448876  
Shift along axis 127.81519395  
  

> select subtract #18

Nothing selected  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.16968,-0.90099,0.39927,161.32,-0.71798,0.39055,0.57618,179.47,-0.67507,-0.1889,-0.71316,252.69

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.16968,-0.90099,0.39927,164.99,-0.71798,0.39055,0.57618,178.8,-0.67507,-0.1889,-0.71316,250.76

> fitmap #18 inMap #15

Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
1377 atoms  
average map value = 0.01248, steps = 248  
shifted from previous position = 4.68  
rotated from previous position = 23.5 degrees  
atoms outside contour = 763, contour level = 0.015  
  
Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.15124652 -0.85928512 0.48862416 168.73822316  
-0.38689683 0.50633479 0.77067237 181.49458118  
-0.90963472 -0.07248563 -0.40903606 248.57523535  
Axis -0.49604447 0.82261994 0.27791422  
Axis point 210.51992295 0.00000000 13.94496782  
Rotation angle (degrees) 121.80122035  
Shift along axis 134.68199153  
  

> select subtract #18

Nothing selected  

> select add #18

1377 atoms, 1538 bonds, 65 residues, 1 model selected  

> nucleotides sel stubs

> select subtract #18

Nothing selected  

> hide #18 models

> hide #19 models

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113_rna_phicb5_region_4_120nu/fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif"

Chain information for
fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif #20  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #20 region_4_120nu.cif

> view

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models #20,1,0,0,147.07,0,1,0,181.24,0,0,1,4.4982

> view matrix models #20,1,0,0,187.8,0,1,0,234.51,0,0,1,225.19

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.97675,-0.13541,-0.16622,189.24,0.099309,0.97287,-0.20896,235.83,0.19,0.18759,0.9637,224.78

> view matrix models
> #20,-0.15807,0.90623,-0.39212,182.32,0.82183,0.34088,0.45651,238.12,0.54737,-0.2501,-0.79865,234.44

> view matrix models
> #20,-0.19588,0.75524,-0.62549,183.79,0.91929,0.36347,0.15098,239.23,0.34138,-0.54543,-0.76548,235.37

> ui mousemode right "translate selected models"

> view matrix models
> #20,-0.19588,0.75524,-0.62549,182.07,0.91929,0.36347,0.15098,183.49,0.34138,-0.54543,-0.76548,242.57

> fitmap #20 inMap #15

Fit molecule region_4_120nu.cif (#20) to map region_4_2.mrc (#15) using 2557
atoms  
average map value = 0.00965, steps = 344  
shifted from previous position = 10.6  
rotated from previous position = 7.82 degrees  
atoms outside contour = 1685, contour level = 0.015  
  
Position of region_4_120nu.cif (#20) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.09007301 0.72102720 -0.68702741 191.56672213  
0.91137050 0.33784720 0.23508107 179.93787550  
0.40161012 -0.60496205 -0.68755382 245.73283063  
Axis -0.60514132 -0.78422113 0.13711749  
Axis point -44.74841808 0.00000000 153.11243538  
Rotation angle (degrees) 136.04538342  
Shift along axis -223.34175502  
  

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.89361,-0.22926,0.38589,190.65,0.38581,-0.83168,0.39933,184.36,0.22938,0.50572,0.83164,233.95

> ui mousemode right "translate selected models"

> view matrix models
> #20,-0.89361,-0.22926,0.38589,172.21,0.38581,-0.83168,0.39933,179.76,0.22938,0.50572,0.83164,227.61

> select subtract #20

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,-0.69753,0.50123,-0.51208,172.2,0.64421,0.75158,-0.14185,174.37,0.31377,-0.42883,-0.84714,238.66

> select subtract #20

Nothing selected  

> fitmap #20 inMap #15

Fit molecule region_4_120nu.cif (#20) to map region_4_2.mrc (#15) using 2557
atoms  
average map value = 0.009375, steps = 108  
shifted from previous position = 5.09  
rotated from previous position = 15.9 degrees  
atoms outside contour = 1687, contour level = 0.015  
  
Position of region_4_120nu.cif (#20) relative to region_4_2.mrc (#15)
coordinates:  
Matrix rotation and translation  
-0.83371377 0.26403476 -0.48498145 174.66873272  
0.42572847 0.86668944 -0.26000902 177.13275157  
0.35167689 -0.42324351 -0.83497803 235.10372112  
Axis -0.18813765 -0.96429949 0.18636181  
Axis point 38.71073478 0.00000000 151.77758101  
Rotation angle (degrees) 154.28998074  
Shift along axis -159.85643138  
  

> hide #20 models

> combine #6

No structures specified  

> show #!6 models

> hide #!6 models

> hide #!15 models

> show #!6 models

> show #10 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #!7 models

> hide #!7 models

> show #13 models

> show #14 models

> show #!15 models

> hide #!15 models

> hide #!6 models

> show #!15 models

> show #!9 models

> hide #!9 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!9 models

> show #!11 models

> show #!7 models

> hide #!7 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select add #6.190

1 model selected  

> select add #6.67

2 models selected  

> select add #6

195 models selected  

> select subtract #6

Nothing selected  

> select add #6.190

1 model selected  

> select add #6.2

2 models selected  

> ui tool show "Segment Map"

Grouped 2 regions  

> select add #6

194 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> show #!6 models

> show #5 models

> hide #5 models

> hide #!6 models

> show #!6 models

> select add #6.147

1 model selected  

> select add #6.66

2 models selected  

> select add #6.187

3 models selected  

> ui tool show "Segment Map"

> select add #6

194 models selected  

> select subtract #6

Nothing selected  

> select add #6.20

1 model selected  

> select add #6.46

2 models selected  

> select add #6.36

3 models selected  

> select add #6.136

4 models selected  

> select add #6.173

5 models selected  

> select add #6.60

6 models selected  

> select subtract #6.60

5 models selected  

> select subtract #6.136

4 models selected  

> select add #6

194 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> show #!6 models

Showing 193 region surfaces  

> select add #6.2

1 model selected  
Region has 9 adjacent regions  

> hide #!6 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #!6 models

> volume #15 level 0.02025

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select add #6.83

1 model selected  

> select add #6.2

2 models selected  

> select add #6.156

3 models selected  

> select add #6.57

4 models selected  

> select add #6.146

5 models selected  

> select add #6.184

6 models selected  

> select add #6.170

7 models selected  

> select subtract #6.170

6 models selected  

> select add #6.48

7 models selected  

> select subtract #6.48

6 models selected  

> select add #6

194 models selected  

> select subtract #6

Nothing selected  

> select add #6.46

1 model selected  

> select add #6.20

2 models selected  

> select add #6.173

3 models selected  

> select add #6.136

4 models selected  

> select add #6.60

5 models selected  

> select add #6.36

6 models selected  

> select add #6.179

7 models selected  

> select subtract #6.179

6 models selected  

> select add #6

194 models selected  

> hide #!6 models

> select subtract #6

Nothing selected  

> show #!7 models

> hide #!7 models

> show #!8 models

> select add #8

2 models selected  

> select subtract #8

Nothing selected  

> hide #!9 models

> select add #7

2 models selected  

> select subtract #7

Nothing selected  

> select add #8

2 models selected  
Segmenting volume difference, density threshold 0.011922  
Showing 194 region surfaces  
2209 watershed regions, grouped to 194 regions  
Showing volume difference.seg - 194 regions, 194 surfaces  

> hide #!6 models

> show #!6 models

> hide #!6 models

> select subtract #8

Nothing selected  

> select add #8

2 models selected  

> select subtract #8

Nothing selected  

> volume #8 level 0.0017

> volume #8 level 0.017

> select subtract #8

Nothing selected  

> show #!9 models

> volume #4 level 0.017

> volume #7 level 0.017

> volume #9 level 0.017

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> volume #11 level 0.017

> volume #15 level 0.017

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> vop subtract #8 #9

Opened volume difference as #21, grid size 215,224,227, pixel 1.12,1.12,1.12,
shown at step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1166+0+34 (frame: 1942x1222-11-11) margins: 11, 45,
11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1514)))  

> hide #!21 models

> show #!6 models

> show #!8 models

> hide #!6 models

> show #!9 models

> hide #!9 models

> hide #!8 models

> show #!21 models

> transparency #11.1#15.1#21.1 0

> select add #21

2 models selected  

> transparency sel 50

> select subtract #21

Nothing selected  

> vop subtract #21 #7

Opened volume difference as #22, grid size 215,224,227, pixel 1.12,1.12,1.12,
shown at step 1, values float32  

> vop subtract #22 #11

Opened volume difference as #23, grid size 215,224,227, pixel 1.12,1.12,1.12,
shown at step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1166+0+34 (frame: 1942x1222-11-11) margins: 11, 45,
11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1514)))  

> close #21-22

> rename #23 "vol diff region_3"

> rename #23 id #21

> select add #21

2 models selected  

> transparency sel 50

> show #5 models

> select subtract #21

Nothing selected  
Segmenting vol diff region_3, density threshold 0.017000  
Showing 199 region surfaces  
1931 watershed regions, grouped to 199 regions  
Showing vol diff region_3.seg - 199 regions, 199 surfaces  

> select add #21

2 models selected  

> transparency sel 0

> select subtract #21

Nothing selected  

> select add #21

2 models selected  

> transparency sel 50

> select subtract #21

Nothing selected  

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!9 models

> hide #!9 models

> rename #9 region_2.mrc

> rename #7 region_1.mrc

> select add #6

200 models selected  

> transparency sel 50

> select subtract #6

Nothing selected  

> hide #!15 models

> select add #6.2

1 model selected  

> select add #6.68

2 models selected  

> select add #6.11

3 models selected  

> select add #6.32

4 models selected  

> select add #6.42

5 models selected  

> select add #6.58

6 models selected  

> ui mousemode right translate

> select add #6.66

7 models selected  

> select subtract #6.66

6 models selected  

> select add #6.66

7 models selected  

> select subtract #6.66

6 models selected  

> select add #6.39

7 models selected  

> select add #6.34

8 models selected  

> select add #6.145

9 models selected  

> select add #6.81

10 models selected  

> select add #6.61

11 models selected  

> select add #6.88

12 models selected  

> select add #6.7

13 models selected  

> select add #6.120

14 models selected  

> select add #6.148

15 models selected  

> select add #6.165

16 models selected  

> select add #6.96

17 models selected  

> select add #6.159

18 models selected  

> select add #6.18

19 models selected  

> select add #6.184

20 models selected  

> select add #6.25

21 models selected  

> select add #6.117

22 models selected  
Saving 22 regions to mrc file...  
Opened region_4_jxn.mrc as #22, grid size 166,122,96, pixel 1.12,1.12,1.12,
shown at step 1, values float32  
Wrote region_4_jxn.mrc  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1166+0+34 (frame: 1942x1222-11-11) margins: 11, 45,
11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1514)))  

> hide #!6 models

> select add #6

200 models selected  

> select subtract #6

Nothing selected  

> select add #22

2 models selected  

> volume #22 level 0.017

> select subtract #22

Nothing selected  

> volume #22 level 0.02478

> volume #22 level 0.02235

> volume #22 level 0.02429

> volume #22 level 0.017

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114_rna_phicb5_region_4_3/fold_2025_11_14_11_03_rna_phicb5_region_4_3_model_0.cif"

Chain information for fold_2025_11_14_11_03_rna_phicb5_region_4_3_model_0.cif
#23  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #23 region_4_3.cif

> view

> ui mousemode right "translate selected models"

> select add #23

2096 atoms, 2348 bonds, 98 residues, 1 model selected  

> view matrix models #23,1,0,0,-4.7303,0,1,0,-51.188,0,0,1,147.86

> view matrix models #23,1,0,0,152.16,0,1,0,129.27,0,0,1,289.71

> view matrix models #23,1,0,0,159.25,0,1,0,162.08,0,0,1,241.61

> select subtract #23

Nothing selected  

> fitmap #23 inMap #22

Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
atoms  
average map value = 0.009486, steps = 140  
shifted from previous position = 13.6  
rotated from previous position = 14.9 degrees  
atoms outside contour = 1443, contour level = 0.017  
  
Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.97814527 0.20472685 -0.03631444 152.26881265  
-0.20787309 0.96669438 -0.14930092 173.70692628  
0.00453906 0.15358678 0.98812474 242.02271617  
Axis 0.58988702 -0.07956398 -0.80355639  
Axis point 947.94058164 -983.94836323 0.00000000  
Rotation angle (degrees) 14.87633671  
Shift along axis -118.47831866  
  

> select add #23

2096 atoms, 2348 bonds, 98 residues, 1 model selected  

> view matrix models
> #23,0.97815,0.20473,-0.036314,114.29,-0.20787,0.96669,-0.1493,143.91,0.0045391,0.15359,0.98812,257.11

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #23,0.71198,0.69496,-0.10061,114.76,0.23992,-0.3754,-0.89527,146.42,-0.65995,0.61328,-0.43401,263.04

> view matrix models
> #23,0.17276,-0.9119,-0.37227,111.43,-0.57716,-0.39999,0.71196,136.14,-0.79815,0.091866,-0.59542,262.3

> view matrix models
> #23,-0.69946,-0.7123,0.058216,107.21,-0.64537,0.66453,0.3767,139.76,-0.30701,0.22591,-0.92451,265.61

> view matrix models
> #23,-0.95467,0.25968,0.14552,107.89,-0.11801,0.11865,-0.9859,147.08,-0.27328,-0.95838,-0.082624,259.32

> view matrix models
> #23,0.10008,-0.54744,-0.83084,114.23,0.99495,0.061255,0.079483,145.05,0.0073802,-0.8346,0.55081,256.86

> view matrix models
> #23,0.20676,-0.23089,0.95076,106.07,-0.95707,-0.24948,0.14755,138.63,0.20313,-0.94045,-0.27257,261.24

> select subtract #23

Nothing selected  

> select add #23

2096 atoms, 2348 bonds, 98 residues, 1 model selected  

> nucleotides sel stubs

> select subtract #23

Nothing selected  

> select add #23

2096 atoms, 2348 bonds, 98 residues, 1 model selected  

> view matrix models
> #23,-0.32679,0.51815,0.79039,106.87,-0.80197,-0.59452,0.058165,138.86,0.50004,-0.61487,0.60983,258.1

> ui mousemode right "translate selected models"

> view matrix models
> #23,-0.32679,0.51815,0.79039,173.31,-0.80197,-0.59452,0.058165,133.69,0.50004,-0.61487,0.60983,236.07

> select subtract #23

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #23

2096 atoms, 2348 bonds, 98 residues, 1 model selected  

> view matrix models
> #23,0.018989,-0.98168,0.18958,174.29,0.78374,-0.10312,-0.61247,141.92,0.6208,0.16021,0.76742,237.07

> view matrix models
> #23,-0.47548,-0.64194,-0.60152,177.71,0.58916,-0.74014,0.32416,135.59,-0.6533,-0.20026,0.73013,233.16

> ui mousemode right "translate selected models"

> view matrix models
> #23,-0.47548,-0.64194,-0.60152,222.45,0.58916,-0.74014,0.32416,188.56,-0.6533,-0.20026,0.73013,221.96

> ui mousemode right "rotate selected models"

> view matrix models
> #23,-0.0052927,-0.21665,-0.97624,226.33,0.96149,0.26718,-0.064505,193.35,0.2748,-0.93898,0.20689,225.63

> view matrix models
> #23,0.52191,-0.56916,-0.63535,225.44,0.72683,0.68658,-0.017993,193.24,0.44646,-0.4524,0.77202,224.27

> select subtract #23

Nothing selected  

> fitmap #23 inMap #22

Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
atoms  
average map value = 0.00904, steps = 288  
shifted from previous position = 21  
rotated from previous position = 31.7 degrees  
atoms outside contour = 1443, contour level = 0.017  
  
Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.25376302 -0.42617964 -0.86831747 221.15007688  
0.93475318 0.33884393 0.10687037 174.37429887  
0.24867811 -0.83878227 0.48435881 232.59258539  
Axis -0.47317683 -0.55891180 0.68097084  
Axis point 76.96850905 335.60681404 0.00000000  
Rotation angle (degrees) 87.79454879  
Shift along axis -43.71417685  
  

> hide #23 models

> show #20 models

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,0.70362,-0.71048,0.011774,180.93,0.19932,0.21325,0.95645,175.46,-0.68205,-0.67063,0.29166,230.04

> ui mousemode right "translate selected models"

> select subtract #20

Nothing selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,0.70362,-0.71048,0.011774,219.95,0.19932,0.21325,0.95645,146.66,-0.68205,-0.67063,0.29166,224.09

> view matrix models
> #20,0.70362,-0.71048,0.011774,304.94,0.19932,0.21325,0.95645,175.08,-0.68205,-0.67063,0.29166,220.99

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.94663,0.3122,-0.080152,300.46,0.28675,-0.70214,0.65174,181.08,0.14719,-0.63994,-0.75419,226.35

> view matrix models
> #20,0.97694,0.20816,0.047473,300.48,-0.15108,0.51688,0.84262,172.81,0.15086,-0.83036,0.53641,222.4

> view matrix models
> #20,0.97094,0.2032,0.12645,300.17,-0.16208,0.16949,0.97211,174.01,0.1761,-0.96435,0.1975,224.52

> view matrix models
> #20,0.97995,0.16549,0.11093,300.43,-0.17688,0.46641,0.8667,172.95,0.091696,-0.86895,0.48634,222.75

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.97995,0.16549,0.11093,247.65,-0.17688,0.46641,0.8667,138.87,0.091696,-0.86895,0.48634,234.14

> select add #19

4032 atoms, 4509 bonds, 189 residues, 2 models selected  

> select subtract #19

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #20

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,0.50696,-0.35054,0.78747,246.55,-0.85954,-0.13702,0.49237,141.85,-0.064698,-0.92647,-0.37076,237.46

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.50696,-0.35054,0.78747,251.08,-0.85954,-0.13702,0.49237,157.1,-0.064698,-0.92647,-0.37076,243.22

> fitmap #23 inMap #22

Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
atoms  
average map value = 0.00904, steps = 80  
shifted from previous position = 0.00622  
rotated from previous position = 0.00572 degrees  
atoms outside contour = 1444, contour level = 0.017  
  
Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.25377019 -0.42608945 -0.86835964 221.14600498  
0.93474480 0.33885811 0.10689869 174.37359049  
0.24870228 -0.83882236 0.48427696 232.59719779  
Axis -0.47321051 -0.55894435 0.68092072  
Axis point 76.98468596 335.61635547 0.00000000  
Rotation angle (degrees) 87.79628314  
Shift along axis -43.73349350  
  

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.50696,-0.35054,0.78747,240.78,-0.85954,-0.13702,0.49237,167.31,-0.064698,-0.92647,-0.37076,226.7

> select subtract #20

Nothing selected  

> fitmap #23 inMap #22

Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
atoms  
average map value = 0.00904, steps = 240  
shifted from previous position = 0.00241  
rotated from previous position = 0.00998 degrees  
atoms outside contour = 1444, contour level = 0.017  
  
Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.25377471 -0.42622353 -0.86829251 221.14362591  
0.93477545 0.33876936 0.10691201 174.37387948  
0.24858246 -0.83879009 0.48439437 232.59784460  
Axis -0.47320132 -0.55885116 0.68100358  
Axis point 76.96439817 335.58572140 0.00000000  
Rotation angle (degrees) 87.79533221  
Shift along axis -43.69453628  
  

> hide #20 models

> hide #!22 models

> show #!22 models

> show #20 models

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,0.50696,-0.35054,0.78747,185.24,-0.85954,-0.13702,0.49237,205.85,-0.064698,-0.92647,-0.37076,271.45

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.78942,0.6136,0.017528,181.03,0.52874,0.66519,0.52721,204.15,0.31184,0.42546,-0.84955,267.25

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,-0.70492,-0.49301,0.50993,184.81,0.13073,-0.79692,-0.58977,215.72,0.69714,-0.34908,0.62621,265.74

> ui mousemode right "translate selected models"

> view matrix models
> #20,-0.70492,-0.49301,0.50993,183.36,0.13073,-0.79692,-0.58977,170.06,0.69714,-0.34908,0.62621,283.89

> view matrix models
> #20,-0.70492,-0.49301,0.50993,169.04,0.13073,-0.79692,-0.58977,165.99,0.69714,-0.34908,0.62621,255.97

> fitmap #20 inMap #22

Fit molecule region_4_120nu.cif (#20) to map region_4_jxn.mrc (#22) using 2557
atoms  
average map value = 0.008799, steps = 324  
shifted from previous position = 3.4  
rotated from previous position = 16.2 degrees  
atoms outside contour = 1887, contour level = 0.017  
  
Position of region_4_120nu.cif (#20) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.87056475 -0.34586323 0.34999370 169.35578872  
0.06101407 -0.78167901 -0.62068926 169.43294108  
0.48825634 -0.51899567 0.70160473 256.11260362  
Axis 0.23028633 -0.31309737 0.92137845  
Axis point 38.17956596 135.40457455 0.00000000  
Rotation angle (degrees) 167.24408354  
Shift along axis 221.92794682  
  

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,-0.87056,-0.34586,0.34999,165.45,0.061014,-0.78168,-0.62069,180.41,0.48826,-0.519,0.7016,236.99

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,-0.87056,-0.34586,0.34999,171.97,0.061014,-0.78168,-0.62069,153.98,0.48826,-0.519,0.7016,253.5

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,-0.87056,-0.34586,0.34999,203.54,0.061014,-0.78168,-0.62069,159.16,0.48826,-0.519,0.7016,172.2

> view matrix models
> #20,-0.87056,-0.34586,0.34999,219.53,0.061014,-0.78168,-0.62069,153.58,0.48826,-0.519,0.7016,176.59

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.97107,-0.07579,0.22646,221.99,0.2165,0.6796,-0.7009,147.08,-0.10078,0.72965,0.67635,169.06

> view matrix models
> #20,0.83288,0.054804,0.55073,219.79,-0.43356,0.6831,0.58771,140.72,-0.344,-0.72826,0.5927,176.28

> view matrix models
> #20,0.69204,-0.13499,0.70913,219.77,-0.72186,-0.1306,0.6796,143.66,0.00087434,-0.9822,-0.18782,181.26

> ui mousemode right "translate selected models"

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,0.69204,-0.13499,0.70913,257.11,-0.72186,-0.1306,0.6796,159.78,0.00087434,-0.9822,-0.18782,228.69

> view matrix models
> #20,0.69204,-0.13499,0.70913,247,-0.72186,-0.1306,0.6796,154.61,0.00087434,-0.9822,-0.18782,241.57

> fitmap #20 inMap #22

Fit molecule region_4_120nu.cif (#20) to map region_4_jxn.mrc (#22) using 2557
atoms  
average map value = 0.01196, steps = 144  
shifted from previous position = 15  
rotated from previous position = 31.3 degrees  
atoms outside contour = 1450, contour level = 0.017  
  
Position of region_4_120nu.cif (#20) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.40381856 -0.17730696 0.89749249 239.22167029  
-0.83503508 -0.47217257 0.28243488 161.59415747  
0.37369368 -0.86349019 -0.33872958 230.73733341  
Axis -0.80624696 0.36853300 -0.46276263  
Axis point 0.00000000 166.41989331 -17.98113275  
Rotation angle (degrees) 134.71185810  
Shift along axis -240.09558153  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.60599,-0.74258,-0.28522,247.26,-0.75472,-0.42343,-0.5011,164.49,0.25133,0.51893,-0.81704,224.75

> select subtract #20

Nothing selected  

> select add #20

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> view matrix models
> #20,0.89255,0.13974,0.42875,240.55,-0.44253,0.45425,0.77319,155.57,-0.086711,-0.87984,0.46728,227.17

> fitmap #20 inMap #22

Fit molecule region_4_120nu.cif (#20) to map region_4_jxn.mrc (#22) using 2557
atoms  
average map value = 0.01196, steps = 312  
shifted from previous position = 6.44  
rotated from previous position = 70.7 degrees  
atoms outside contour = 1454, contour level = 0.017  
  
Position of region_4_120nu.cif (#20) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.40343918 -0.17723559 0.89767719 239.23864776  
-0.83512837 -0.47221021 0.28209590 161.59484487  
0.37389492 -0.86348426 -0.33852257 230.72581851  
Axis -0.80612223 0.36857529 -0.46294622  
Axis point 0.00000000 166.42117224 -18.03030287  
Rotation angle (degrees) 134.72032483  
Shift along axis -240.10937070  
  

> view matrix models
> #20,0.3608,-0.31595,0.8775,239.98,-0.86109,-0.47427,0.18329,161.88,0.35826,-0.82173,-0.44318,230.82

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.3608,-0.31595,0.8775,279.66,-0.86109,-0.47427,0.18329,154.95,0.35826,-0.82173,-0.44318,205.96

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.56431,0.070729,0.82253,278.13,-0.79465,-0.22355,0.56441,152.35,0.22379,-0.97212,-0.069944,205.19

> select subtract #20

Nothing selected  

> mcopy #20

Missing required "to_atoms" argument  

> combine #20

> combine #24

> combine #25

> combine #26

> hide #20 models

> rename #24 region_4_stemloop_1nu.cif

> rename #24 region_4_stemloop_1.cif

> rename #25 region_4_stemloop_2.cif

> rename #26 region_4_stemloop_3.cif

> rename #27 region_4_end.cif

> select add #25

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select add #24

5114 atoms, 5722 bonds, 240 residues, 2 models selected  

> select add #26

7671 atoms, 8583 bonds, 360 residues, 3 models selected  

> select add #27

10228 atoms, 11444 bonds, 480 residues, 4 models selected  

> nucleotides sel stubs

> select subtract #24

7671 atoms, 8583 bonds, 360 residues, 3 models selected  

> select subtract #25

5114 atoms, 5722 bonds, 240 residues, 2 models selected  

> select subtract #26

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #27

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #27/A

Alignment identifier is 27/A  

> sequence chain #24/A

Alignment identifier is 24/A  

> sequence chain #25/A

Alignment identifier is 25/A  

> sequence chain #26/A

Alignment identifier is 26/A  

> select add #24

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #24

Nothing selected  

> select add #24

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #24

Nothing selected  

> select #24/A:15

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #24/A:15-76

1320 atoms, 1477 bonds, 62 residues, 1 model selected  

> select add #24

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #24

Nothing selected  

> select #24/A:15

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #24/A:15-108

2004 atoms, 2244 bonds, 94 residues, 1 model selected  

> select add #24

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #24

Nothing selected  

> select subtract #24/A:109

20 atoms, 1 residue, 1 model selected  

> select add #24

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #24

Nothing selected  

> select add #24/A:107

43 atoms, 21 bonds, 2 residues, 1 model selected  

> select #24/A:70

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #24/A:70-107

810 atoms, 906 bonds, 38 residues, 1 model selected  

> select ~sel & ##selected

1747 atoms, 1955 bonds, 82 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #24/A:70

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #24/A

810 atoms, 906 bonds, 38 residues, 1 model selected  

> select subtract #24

Nothing selected  

> select add #25

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #25

Nothing selected  

> select add #25/A:69

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #25/A:53

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select #25/A:53

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #25/A:53-69

364 atoms, 407 bonds, 17 residues, 1 model selected  

> select ~sel & ##selected

2193 atoms, 2454 bonds, 103 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain #26/A

Destroying pre-existing alignment with identifier 26/A  
Alignment identifier is 26/A  

> select add #25

364 atoms, 407 bonds, 17 residues, 1 model selected  

> select subtract #25

Nothing selected  

> select add #26

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #26

Nothing selected  

> select add #25

364 atoms, 407 bonds, 17 residues, 1 model selected  

> select subtract #25

Nothing selected  

> select add #26

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select subtract #26

Nothing selected  

> select add #26/A:52

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #26/A:16

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select #26/A:16

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #26/A:16-52

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select ~sel & ##selected

1770 atoms, 1980 bonds, 83 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #26/A:16

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #26/A:16-17

42 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #26

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #26

Nothing selected  

> select add #26

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #26

Nothing selected  

> select add #27

2557 atoms, 2861 bonds, 120 residues, 1 model selected  

> select clear

> select #26/A:16-17

42 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #26

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #26

Nothing selected  

> select add #26

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #26

Nothing selected  

> select #27/A:16

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #27/A:16-107

1961 atoms, 2196 bonds, 92 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> rename #27 region_4_stem.cif

> select add #24

810 atoms, 906 bonds, 38 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.56431,0.070729,0.82253,238.68,-0.79465,-0.22355,0.56441,151.88,0.22379,-0.97212,-0.069944,241.45

> view matrix models
> #24,0.56431,0.070729,0.82253,245.91,-0.79465,-0.22355,0.56441,167.94,0.22379,-0.97212,-0.069944,241.64

> fitmap #24 inMap #22

Fit molecule region_4_stemloop_1.cif (#24) to map region_4_jxn.mrc (#22) using
810 atoms  
average map value = 0.01566, steps = 204  
shifted from previous position = 7.99  
rotated from previous position = 33 degrees  
atoms outside contour = 342, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#24) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.47123954 -0.08935096 0.87746776 246.88743327  
-0.66257951 -0.69251904 0.28531695 155.89515151  
0.58216980 -0.71584481 -0.38554447 241.39349735  
Axis -0.84071397 0.24797304 -0.48136202  
Axis point 0.00000000 134.81009863 5.52368848  
Rotation angle (degrees) 143.45716939  
Shift along axis -285.10158049  
  

> select subtract #24

Nothing selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select add #24

810 atoms, 906 bonds, 38 residues, 1 model selected  

> view matrix models
> #24,0.47124,-0.089351,0.87747,249.48,-0.66258,-0.69252,0.28532,155.36,0.58217,-0.71584,-0.38554,242.94

> select subtract #24

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> fitmap #24 inMap #22

Fit molecule region_4_stemloop_1.cif (#24) to map region_4_jxn.mrc (#22) using
810 atoms  
average map value = 0.01566, steps = 60  
shifted from previous position = 3.06  
rotated from previous position = 0.0469 degrees  
atoms outside contour = 341, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#24) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.47149621 -0.08957195 0.87730734 246.88840698  
-0.66297302 -0.69200386 0.28565261 155.89647266  
0.58151362 -0.71631524 -0.38566098 241.39562421  
Axis -0.84076694 0.24820515 -0.48114983  
Axis point 0.00000000 134.87948807 5.51206275  
Rotation angle (degrees) 143.42565114  
Shift along axis -285.02876562  
  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

——— End of log from Fri Nov 14 11:51:38 2025 ———

> view name session-start

opened ChimeraX session  
Showing vol diff region_3.seg - 199 regions, 199 surfaces  

> hide #5 models

> hide #!6 models

> hide #!27 models

> hide #26 models

> hide #25 models

> hide #24 models

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114_region_4_3_21/fold_2025_11_14_15_36_region_4_3_21_model_0.cif"

Chain information for fold_2025_11_14_15_36_region_4_3_21_model_0.cif #28  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> rename #28 region_4_3_21.cif

> view

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!22 models

> hide #!21 models

> show #!22 models

> ui mousemode right "translate selected models"

> view matrix models #28,1,0,0,28.55,0,1,0,160.57,0,0,1,291.63

> view matrix models #28,1,0,0,273.37,0,1,0,231.32,0,0,1,263.01

> view matrix models #28,1,0,0,237.63,0,1,0,157.4,0,0,1,253.66

> select subtract #28

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #28,-0.70736,0.51396,-0.48527,247.22,0.31821,0.84456,0.43065,153.92,0.63118,0.15021,-0.76095,256.69

> select add #27

3176 atoms, 3549 bonds, 1 pseudobond, 149 residues, 3 models selected  

> select subtract #27

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select subtract #28

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> view matrix models
> #28,-0.8442,0.41085,-0.34427,247.78,0.095152,0.74693,0.65806,154.51,0.52751,0.52278,-0.66965,255.98

> ui mousemode right "translate selected models"

> view matrix models
> #28,-0.8442,0.41085,-0.34427,286.95,0.095152,0.74693,0.65806,141.41,0.52751,0.52278,-0.66965,188.35

> select subtract #28

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> view matrix models
> #28,-0.8442,0.41085,-0.34427,248.01,0.095152,0.74693,0.65806,133.17,0.52751,0.52278,-0.66965,230.96

> view matrix models
> #28,-0.8442,0.41085,-0.34427,251.51,0.095152,0.74693,0.65806,152.01,0.52751,0.52278,-0.66965,233.12

> hide #14 models

> hide #13 models

> hide #!12 models

> hide #10 models

> fitmap #28 inMap #22

Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
atoms  
average map value = 0.00902, steps = 212  
shifted from previous position = 14.1  
rotated from previous position = 26.1 degrees  
atoms outside contour = 1728, contour level = 0.017  
  
Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.56696987 0.76211348 -0.31261502 246.06883011  
0.36457387 0.57247410 0.73441079 164.65241079  
0.73866840 0.30241754 -0.60242225 235.21080724  
Axis -0.35876909 -0.87308769 -0.33015545  
Axis point 63.71455261 0.00000000 112.34714572  
Rotation angle (degrees) 142.98320067  
Shift along axis -309.69401300  
  

> view matrix models
> #28,-0.56697,0.76211,-0.31262,252.48,0.36457,0.57247,0.73441,155.72,0.73867,0.30242,-0.60242,253.66

> fitmap #28 inMap #22

Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
atoms  
average map value = 0.00972, steps = 484  
shifted from previous position = 13  
rotated from previous position = 44.1 degrees  
atoms outside contour = 1689, contour level = 0.017  
  
Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.77259137 0.39520601 -0.49690514 245.21759893  
0.42143324 0.90458405 0.06420011 151.75737818  
0.47486475 -0.15981188 -0.86542681 242.82459807  
Axis -0.22455089 -0.97410765 0.02629032  
Axis point 71.10413697 0.00000000 151.04087509  
Rotation angle (degrees) 150.07935587  
Shift along axis -196.50791772  
  

> fitmap #28 inMap #22

Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
atoms  
average map value = 0.009721, steps = 44  
shifted from previous position = 0.025  
rotated from previous position = 0.0776 degrees  
atoms outside contour = 1695, contour level = 0.017  
  
Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.77180971 0.39582846 -0.49762390 245.21078502  
0.42235445 0.90415899 0.06413395 151.73491890  
0.47531718 -0.16067446 -0.86501863 242.81558009  
Axis -0.22504970 -0.97398537 0.02655447  
Axis point 70.99979291 0.00000000 151.08781870  
Rotation angle (degrees) 150.03546065  
Shift along axis -196.52436630  
  

> undo

> view matrix models
> #28,-0.56697,0.76211,-0.31262,295.07,0.36457,0.57247,0.73441,125.94,0.73867,0.30242,-0.60242,183.56

> select add #21

2580 atoms, 2886 bonds, 121 residues, 3 models selected  

> select subtract #21

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> show #!21 models

> select subtract #28

Nothing selected  

> hide #!22 models

> hide #!21 models

> show #!22 models

> combine #28

[Repeated 3 time(s)]

> rename #29 region_4_stemloop_1.cif

> rename #30 region_4_stemloop_2.cif

> rename #31 region_4_stemloop_3.cif

> rename #32 region_4_stem.cif

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

——— End of log from Fri Nov 14 16:00:29 2025 ———

> view name session-start

opened ChimeraX session  
Showing vol diff region_3.seg - 199 regions, 199 surfaces  

> hide #32 models

> hide #31 models

> hide #30 models

> hide #29 models

> hide #28 models

> hide #!22 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!6 models

> open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113_rna_phicb5_region_3_75nt_final/fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif"

Chain information for
fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif #33  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> rename #33 region_3_FL.cif

> combine #33

[Repeated 3 time(s)]

> close #37

> select add #33

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> select add #34

3188 atoms, 3562 bonds, 150 residues, 2 models selected  

> select add #35

4782 atoms, 5343 bonds, 225 residues, 3 models selected  

> select add #36

6376 atoms, 7124 bonds, 300 residues, 4 models selected  

> view

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #33,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58,#34,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58,#35,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58,#36,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58

> view matrix models
> #33,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99,#34,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99,#35,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99,#36,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99

> nucleotides sel stubs

> ui mousemode right "rotate selected models"

> view matrix models
> #33,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76,#34,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76,#35,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76,#36,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76

> view matrix models
> #33,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57,#34,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57,#35,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57,#36,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57

> ui mousemode right "translate selected models"

> view matrix models
> #33,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77,#34,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77,#35,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77,#36,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77

> select subtract #33

4782 atoms, 5343 bonds, 225 residues, 3 models selected  

> select subtract #34

3188 atoms, 3562 bonds, 150 residues, 2 models selected  

> select subtract #35

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> select subtract #36

Nothing selected  

> show #10 models

> hide #10 models

> show #10 models

> hide #33 models

> rename #34 region_3_stem.cif

> rename #35 region_3_stemloop_1.cif

> rename #36 region_3_stemloop_2.cif

> hide #34 models

> hide #36 models

> select add #35

1594 atoms, 1781 bonds, 75 residues, 1 model selected  

> select subtract #35

Nothing selected  

> show #34 models

> show #36 models

> ui tool show "Show Sequence Viewer"

> sequence chain #34/A

Alignment identifier is 34/A  

> sequence chain #35/A

Alignment identifier is 35/A  

> sequence chain #36/A

Alignment identifier is 36/A  

> select #35/A:32-33

42 atoms, 46 bonds, 2 residues, 1 model selected  

> select #35/A:33-44

252 atoms, 280 bonds, 12 residues, 1 model selected  

> select #35/A:33-44

252 atoms, 280 bonds, 12 residues, 1 model selected  

> select #35/A:33-44

252 atoms, 280 bonds, 12 residues, 1 model selected  

> select #35/A:33

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #35/A:33-63

660 atoms, 737 bonds, 31 residues, 1 model selected  

> select ~sel & ##selected

934 atoms, 1044 bonds, 44 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #36/A:21

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #36/A:21-32

253 atoms, 282 bonds, 12 residues, 1 model selected  

> select #36/A:13

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #36/A:13-32

420 atoms, 468 bonds, 20 residues, 1 model selected  

> select ~sel & ##selected

1174 atoms, 1313 bonds, 55 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #34/A:13

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #34/A:13-63

1080 atoms, 1206 bonds, 51 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> undo

Undo failed, probably because structures have been modified.  

> close #34

> combine #33

> rename #34 region_3_stem.cif

> nucleotides #10,34-36 stubs

> ui tool show "Show Sequence Viewer"

> sequence chain #34/A

Alignment identifier is 34/A  

> select #34/A:13

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #34/A:13-63

1080 atoms, 1206 bonds, 51 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #!34 models

> show #!34 models

> hide #35 models

> show #35 models

> hide #36 models

> show #36 models

> ui tool show "Show Sequence Viewer"

> sequence chain #34/A

Alignment identifier is 34/A  

> sequence chain #35/A

Alignment identifier is 35/A  

> sequence chain #36/A

Alignment identifier is 36/A  

> select clear

> select add #34

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected  

> select subtract #34

Nothing selected  

> select add #34

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected  

> select subtract #34

Nothing selected  

> select add #35

660 atoms, 737 bonds, 31 residues, 1 model selected  

> select subtract #35

Nothing selected  

> select add #36

420 atoms, 468 bonds, 20 residues, 1 model selected  

> select subtract #36

Nothing selected  

> select add #34

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected  

> select add #35

1174 atoms, 1310 bonds, 1 pseudobond, 55 residues, 3 models selected  

> select add #36

1594 atoms, 1778 bonds, 1 pseudobond, 75 residues, 4 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #34/A

Alignment identifier is 34/A  

> sequence chain #35/A

Alignment identifier is 35/A  

> sequence chain #36/A

Alignment identifier is 36/A  

> select subtract #34

1080 atoms, 1205 bonds, 51 residues, 2 models selected  

> select subtract #35

420 atoms, 468 bonds, 20 residues, 1 model selected  

> select subtract #36

Nothing selected  

> close #12-14

> rename #34 id #12

> rename #35 id #13

> rename #36 id #14

> hide #!12 models

> show #!12 models

> select add #12

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected  

> select add #13

1174 atoms, 1310 bonds, 1 pseudobond, 55 residues, 3 models selected  

> select add #14

1594 atoms, 1778 bonds, 1 pseudobond, 75 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.28393,0.95753,0.050275,150.24,-0.63519,0.14855,0.75794,140.25,0.71828,-0.24714,0.65039,185.37,#13,0.28393,0.95753,0.050275,150.24,-0.63519,0.14855,0.75794,140.25,0.71828,-0.24714,0.65039,185.37,#14,0.28393,0.95753,0.050275,150.24,-0.63519,0.14855,0.75794,140.25,0.71828,-0.24714,0.65039,185.37

> view matrix models
> #12,-0.22185,0.96905,0.10827,148.24,-0.76762,-0.24204,0.59345,140.95,0.60128,0.04855,0.79756,184.03,#13,-0.22185,0.96905,0.10827,148.24,-0.76762,-0.24204,0.59345,140.95,0.60128,0.04855,0.79756,184.03,#14,-0.22185,0.96905,0.10827,148.24,-0.76762,-0.24204,0.59345,140.95,0.60128,0.04855,0.79756,184.03

> select subtract #12

1080 atoms, 1205 bonds, 51 residues, 2 models selected  

> select subtract #13

420 atoms, 468 bonds, 20 residues, 1 model selected  

> select subtract #14

Nothing selected  

> select add #12

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.22185,0.96905,0.10827,208.19,-0.76762,-0.24204,0.59345,106.42,0.60128,0.04855,0.79756,209.44

> view matrix models
> #12,-0.22185,0.96905,0.10827,212.73,-0.76762,-0.24204,0.59345,145.2,0.60128,0.04855,0.79756,208.63

> view matrix models
> #12,-0.22185,0.96905,0.10827,224.03,-0.76762,-0.24204,0.59345,143.99,0.60128,0.04855,0.79756,226.46

> fitmap #12 inMap #11

Fit molecule region_3_stem.cif (#12) to map region_3.mrc (#11) using 514 atoms  
average map value = 0.01856, steps = 332  
shifted from previous position = 4.24  
rotated from previous position = 92.1 degrees  
atoms outside contour = 165, contour level = 0.017  
  
Position of region_3_stem.cif (#12) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.67024334 0.57228792 -0.47250439 232.01849271  
-0.31171341 -0.79487891 -0.52057878 143.13229758  
-0.67350472 -0.20162850 0.71115212 240.73699862  
Axis 0.33188197 0.20914980 -0.91984277  
Axis point 182.68893013 61.35992766 0.00000000  
Rotation angle (degrees) 151.28078526  
Shift along axis -114.50134148  
  

> select add #11

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 4 models selected  

> transparency sel 50

> select subtract #11

514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected  

> show #!7 models

> hide #!7 models

> show #!6 models

> select subtract #12

Nothing selected  

> hide #!6 models

> select add #13

660 atoms, 737 bonds, 31 residues, 1 model selected  

> select subtract #13

Nothing selected  

> select add #13

660 atoms, 737 bonds, 31 residues, 1 model selected  

> select subtract #13

Nothing selected  

> select add #14

420 atoms, 468 bonds, 20 residues, 1 model selected  

> select subtract #14

Nothing selected  

> select add #13

660 atoms, 737 bonds, 31 residues, 1 model selected  

> view matrix models
> #13,-0.22185,0.96905,0.10827,252.13,-0.76762,-0.24204,0.59345,117.19,0.60128,0.04855,0.79756,253.51

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.23797,-0.95608,-0.17115,243.27,0.74968,-0.29284,0.59349,143.26,-0.61754,0.012927,0.78644,232.24

> fitmap #13 inMap #11

Fit molecule region_3_stemloop_1.cif (#13) to map region_3.mrc (#11) using 660
atoms  
average map value = 0.0207, steps = 96  
shifted from previous position = 6.17  
rotated from previous position = 22.7 degrees  
atoms outside contour = 174, contour level = 0.017  
  
Position of region_3_stemloop_1.cif (#13) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.47098154 -0.78844909 -0.39563167 232.97818477  
0.70742252 -0.60551307 0.36456453 139.47240894  
-0.52700072 -0.10817559 0.84295212 230.51979068  
Axis -0.30028880 0.08344681 0.95019117  
Axis point 120.61892566 131.66491710 0.00000000  
Rotation angle (degrees) 128.08073496  
Shift along axis 160.71565780  
  

> select subtract #13

Nothing selected  

> select add #14

420 atoms, 468 bonds, 20 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.22185,0.96905,0.10827,201.68,-0.76762,-0.24204,0.59345,130.17,0.60128,0.04855,0.79756,226.4

> select subtract #14

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #14

420 atoms, 468 bonds, 20 residues, 1 model selected  

> view matrix models
> #14,0.84509,-0.51135,-0.15605,221.02,-0.17224,-0.53671,0.826,129.76,-0.50613,-0.67116,-0.54164,254.01

> view matrix models
> #14,0.79924,-0.5273,-0.2884,221.81,-0.22377,-0.70643,0.67148,133.87,-0.5578,-0.47214,-0.6826,250.29

> select subtract #14

Nothing selected  

> ui mousemode right "translate selected models"

> select add #14

420 atoms, 468 bonds, 20 residues, 1 model selected  

> view matrix models
> #14,0.79924,-0.5273,-0.2884,231.33,-0.22377,-0.70643,0.67148,151.74,-0.5578,-0.47214,-0.6826,238.69

> select subtract #14

Nothing selected  

> fitmap #14 inMap #11

Fit molecule region_3_stemloop_2.cif (#14) to map region_3.mrc (#11) using 420
atoms  
average map value = 0.01729, steps = 120  
shifted from previous position = 8.45  
rotated from previous position = 51.2 degrees  
atoms outside contour = 157, contour level = 0.017  
  
Position of region_3_stemloop_2.cif (#14) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.38535596 -0.92153920 0.04760545 251.94606474  
-0.13162435 -0.00383197 0.99129226 131.01134564  
-0.91333226 -0.38826641 -0.12277367 243.37850942  
Axis -0.74267035 0.51731032 0.42524204  
Axis point 0.00000000 267.35951271 130.31083100  
Rotation angle (degrees) 111.75415824  
Shift along axis -15.84457702  
  

> select add #14

420 atoms, 468 bonds, 20 residues, 1 model selected  

> view matrix models
> #14,0.38536,-0.92154,0.047605,248.34,-0.13162,-0.003832,0.99129,117.85,-0.91333,-0.38827,-0.12277,239.61

> select subtract #14

Nothing selected  

> select add #14

420 atoms, 468 bonds, 20 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.95819,-0.28542,-0.020102,227.89,-0.012417,-0.11167,0.99367,118.73,-0.28586,-0.95187,-0.11054,244.45

> view matrix models
> #14,0.91501,-0.23497,0.32793,227.5,-0.2214,0.38705,0.89508,110.46,-0.33724,-0.89162,0.30213,243.98

> view matrix models
> #14,0.068816,-0.55322,0.83019,244.42,-0.1128,0.82251,0.55745,99.562,-0.99123,-0.13201,-0.0058028,234.75

> view matrix models
> #14,0.96827,0.0098179,0.24972,221.67,-0.22252,-0.421,0.87934,127.97,0.11377,-0.90701,-0.40546,238.69

> view matrix models
> #14,0.73434,0.10252,0.67099,222.54,-0.67776,0.056552,0.73311,122.82,0.03721,-0.99312,0.11101,241.63

> select subtract #14

Nothing selected  

> fitmap #14 inMap #11

Fit molecule region_3_stemloop_2.cif (#14) to map region_3.mrc (#11) using 420
atoms  
average map value = 0.019, steps = 152  
shifted from previous position = 9.9  
rotated from previous position = 60.6 degrees  
atoms outside contour = 135, contour level = 0.017  
  
Position of region_3_stemloop_2.cif (#14) relative to region_3.mrc (#11)
coordinates:  
Matrix rotation and translation  
0.09053332 -0.57439805 0.81355429 248.73407833  
-0.99249506 -0.11946733 0.02609792 137.69637743  
0.08220257 -0.80981135 -0.58090301 232.72316657  
Axis -0.70435616 0.61625359 -0.35229805  
Axis point 0.00000000 217.80260526 -2.76245318  
Rotation angle (degrees) 143.60238616  
Shift along axis -172.32940869  
  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251113 region_3.cxs"

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> hide #!11 models

> show #!22 models

> show #29 models

> show #30 models

> show #31 models

> show #32 models

> select add #32

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select add #31

5160 atoms, 5772 bonds, 242 residues, 2 models selected  

> select add #30

7740 atoms, 8658 bonds, 363 residues, 3 models selected  

> select add #29

10320 atoms, 11544 bonds, 484 residues, 4 models selected  

> nucleotides sel stubs

> select subtract #29

7740 atoms, 8658 bonds, 363 residues, 3 models selected  

> select subtract #30

5160 atoms, 5772 bonds, 242 residues, 2 models selected  

> select subtract #31

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select subtract #32

Nothing selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> hide #29 models

> hide #30 models

> hide #31 models

> hide #32 models

> show #29 models

> show #30 models

> show #31 models

> select add #29

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select add #30

5160 atoms, 5772 bonds, 242 residues, 2 models selected  

> select add #31

7740 atoms, 8658 bonds, 363 residues, 3 models selected  

> show #32 models

> select add #32

10320 atoms, 11544 bonds, 484 residues, 4 models selected  

> ui tool show "Show Sequence Viewer"

> select subtract #29

7740 atoms, 8658 bonds, 363 residues, 3 models selected  

> select subtract #30

5160 atoms, 5772 bonds, 242 residues, 2 models selected  

> select subtract #31

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select subtract #32

Nothing selected  

> ui tool show "Show Sequence Viewer"

[Repeated 1 time(s)]

> sequence chain #29/A

Alignment identifier is 29/A  

> sequence chain #30/A

Alignment identifier is 30/A  

> sequence chain #31/A

Alignment identifier is 31/A  

> sequence chain #32/A

Alignment identifier is 32/A  

> select #31/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #31/A:14-50

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select #31/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #31/A:14-47

723 atoms, 809 bonds, 34 residues, 1 model selected  

> select add #31

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select subtract #31

Nothing selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> hide #29 models

> hide #30 models

> hide #31 models

> hide #32 models

> show #28 models

> select add #22

2 models selected  

> transparency sel 50

> select subtract #22

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #28,-0.56697,0.76211,-0.31262,265.75,0.36457,0.57247,0.73441,172.72,0.73867,0.30242,-0.60242,241.18

> select subtract #28

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> select subtract #28

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> view matrix models
> #28,-0.56697,0.76211,-0.31262,253.23,0.36457,0.57247,0.73441,155.29,0.73867,0.30242,-0.60242,254.21

> select subtract #28

Nothing selected  

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> view matrix models
> #28,-0.56697,0.76211,-0.31262,259.51,0.36457,0.57247,0.73441,150.54,0.73867,0.30242,-0.60242,248.11

> select subtract #28

Nothing selected  

> fitmap #28 inMap #22

Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
atoms  
average map value = 0.005419, steps = 128  
shifted from previous position = 8.73  
rotated from previous position = 14.1 degrees  
atoms outside contour = 2088, contour level = 0.017  
  
Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.69253716 0.58630432 -0.42028497 255.21353005  
0.25319026 0.74309928 0.61943367 156.05085047  
0.67549013 0.32256879 -0.66307044 253.54901589  
Axis -0.25091303 -0.92615958 -0.28155119  
Axis point 75.57428244 0.00000000 135.75975715  
Rotation angle (degrees) 143.73155176  
Shift along axis -279.95141943  
  

> hide #28 models

> show #29 models

> show #30 models

> hide #30 models

> hide #29 models

> show #29 models

> show #30 models

> show #31 models

> show #32 models

> ui tool show "Show Sequence Viewer"

> sequence chain #29/A

Alignment identifier is 29/A  

> sequence chain #29/B

Alignment identifier is 29/B  

> sequence chain #30/A

Alignment identifier is 30/A  

> sequence chain #30/B

Alignment identifier is 30/B  

> sequence chain #31/A

Alignment identifier is 31/A  

> sequence chain #31/B

Alignment identifier is 31/B  

> sequence chain #32/A

Alignment identifier is 32/A  

> sequence chain #32/B

Alignment identifier is 32/B  

> select #31/B:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select #31/B

1458 atoms, 1633 bonds, 68 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #30/B:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select #30/B:1-9

193 atoms, 215 bonds, 9 residues, 1 model selected  

> select #30/B:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select #30/B:1-14

303 atoms, 339 bonds, 14 residues, 1 model selected  

> select ~sel & ##selected

2277 atoms, 2547 bonds, 107 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #29/B:15

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #29/B:15-52

810 atoms, 906 bonds, 38 residues, 1 model selected  

> select ~sel

200707 atoms, 207188 bonds, 2 pseudobonds, 23630 residues, 245 models selected  

> select subtract #32

198127 atoms, 204302 bonds, 2 pseudobonds, 23509 residues, 244 models selected  

> select add #32

200707 atoms, 207188 bonds, 2 pseudobonds, 23630 residues, 245 models selected  

> select subtract #33

199113 atoms, 205407 bonds, 2 pseudobonds, 23555 residues, 244 models selected  

> select subtract #32

196533 atoms, 202521 bonds, 2 pseudobonds, 23434 residues, 243 models selected  

> select subtract #31

195411 atoms, 201268 bonds, 2 pseudobonds, 23381 residues, 242 models selected  

> select subtract #30

195108 atoms, 200929 bonds, 2 pseudobonds, 23367 residues, 241 models selected  

> select add #29

195918 atoms, 201837 bonds, 2 pseudobonds, 23405 residues, 241 models selected  

> select subtract #28

193338 atoms, 198951 bonds, 2 pseudobonds, 23284 residues, 240 models selected  

> select subtract #29

190758 atoms, 196065 bonds, 2 pseudobonds, 23163 residues, 239 models selected  

> select subtract #27

190162 atoms, 195402 bonds, 1 pseudobond, 23135 residues, 237 models selected  

> select subtract #26

189375 atoms, 194521 bonds, 1 pseudobond, 23098 residues, 236 models selected  

> select subtract #25

189011 atoms, 194114 bonds, 1 pseudobond, 23081 residues, 235 models selected  

> select subtract #24

188201 atoms, 193208 bonds, 1 pseudobond, 23043 residues, 234 models selected  

> select subtract #1

188201 atoms, 193208 bonds, 1 pseudobond, 23043 residues, 232 models selected  

> select subtract #2

15288 atoms, 17082 bonds, 1 pseudobond, 719 residues, 231 models selected  

> select subtract #3

15288 atoms, 17082 bonds, 1 pseudobond, 719 residues, 229 models selected  

> select subtract #4

15288 atoms, 17082 bonds, 1 pseudobond, 719 residues, 226 models selected  

> select subtract #5

12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 225 models selected  

> select subtract #6

12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 25 models selected  

> select subtract #7

12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 23 models selected  

> select subtract #8

12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 21 models selected  

> select subtract #9

12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 19 models selected  

> select subtract #10

12423 atoms, 13889 bonds, 1 pseudobond, 583 residues, 18 models selected  

> select subtract #11

12423 atoms, 13889 bonds, 1 pseudobond, 583 residues, 16 models selected  

> select subtract #12

11909 atoms, 13316 bonds, 559 residues, 14 models selected  

> select subtract #13

11249 atoms, 12579 bonds, 528 residues, 13 models selected  

> select subtract #14

10829 atoms, 12111 bonds, 508 residues, 12 models selected  

> select subtract #15

10829 atoms, 12111 bonds, 508 residues, 10 models selected  

> select subtract #16

8272 atoms, 9250 bonds, 388 residues, 9 models selected  

> select subtract #17

7505 atoms, 8395 bonds, 352 residues, 8 models selected  

> select subtract #18

6128 atoms, 6857 bonds, 287 residues, 7 models selected  

> select subtract #19

4653 atoms, 5209 bonds, 218 residues, 6 models selected  

> select subtract #20

2096 atoms, 2348 bonds, 98 residues, 5 models selected  

> select subtract #21

2096 atoms, 2348 bonds, 98 residues, 3 models selected  

> select subtract #22

2096 atoms, 2348 bonds, 98 residues, 1 model selected  

> select subtract #23

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #32/B

Alignment identifier is 32/B  

> select #29/B:15

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #29/B:15-52

810 atoms, 906 bonds, 38 residues, 1 model selected  

> select ~sel & ##selected

1770 atoms, 1980 bonds, 83 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #32/B:53

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #32/B:53-68

345 atoms, 386 bonds, 16 residues, 1 model selected  

> select ~sel & ##selected

2235 atoms, 2500 bonds, 105 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> ui tool show "Show Sequence Viewer"

> sequence chain #31/A

Alignment identifier is 31/A  

> hide #29 models

> hide #30 models

> hide #31 models

> show #31 models

> select #31/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #31/A:14-53

849 atoms, 950 bonds, 40 residues, 1 model selected  

> select #31/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #31/A:14-50

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select ~sel & ##selected

335 atoms, 372 bonds, 16 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #31 models

> show #31 models

> hide #32 models

> show #32 models

> combine #28

> nucleotides #10,13-14,31-32,34#!12 stubs

> select add #34

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> view matrix models
> #34,-0.69254,0.5863,-0.42028,319.7,0.25319,0.7431,0.61943,157.07,0.67549,0.32257,-0.66307,160.03

> close #32

> rename #34 id #32

> select subtract #32

Nothing selected  

> rename #32 region_4_stem.cif

> select add #32

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #32/A

Alignment identifier is 32/A  

> sequence chain #32/B

Alignment identifier is 32/B  

> select subtract #32

Nothing selected  

> select #32/A:10

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #32/A:10-53

935 atoms, 1046 bonds, 44 residues, 1 model selected  

> select #32/B:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select #32/B:1-62

1328 atoms, 1487 bonds, 62 residues, 1 model selected  

> select #32/B:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select #32/B:1-52

1113 atoms, 1246 bonds, 52 residues, 1 model selected  

> select #32/A:10-53

935 atoms, 1046 bonds, 44 residues, 1 model selected  

> select #32/B:1-52

1113 atoms, 1246 bonds, 52 residues, 1 model selected  

> select #32/A:10

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #32/A:10-53

935 atoms, 1046 bonds, 44 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #31 models

> show #31 models

> hide #32 models

> show #32 models

> select #32/B:1-2

41 atoms, 44 bonds, 2 residues, 1 model selected  

> select #32/B:1-52

1113 atoms, 1246 bonds, 52 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #32 models

> hide #31 models

> show #29 models

> select add #29

810 atoms, 906 bonds, 38 residues, 1 model selected  

> view matrix models
> #29,-0.56697,0.76211,-0.31262,250.78,0.36457,0.57247,0.73441,125.34,0.73867,0.30242,-0.60242,206

> select subtract #29

Nothing selected  

> select add #29

810 atoms, 906 bonds, 38 residues, 1 model selected  

> view matrix models
> #29,-0.56697,0.76211,-0.31262,257.63,0.36457,0.57247,0.73441,161.86,0.73867,0.30242,-0.60242,235.08

> ui mousemode right "rotate selected models"

> view matrix models
> #29,-0.63643,0.64018,-0.43026,256.1,0.15177,0.65084,0.74389,160.45,0.75626,0.40813,-0.51137,236.02

> select subtract #29

Nothing selected  

> ui mousemode right "translate selected models"

> select add #29

810 atoms, 906 bonds, 38 residues, 1 model selected  

> view matrix models
> #29,-0.63643,0.64018,-0.43026,252.87,0.15177,0.65084,0.74389,156.85,0.75626,0.40813,-0.51137,239.38

> select subtract #29

Nothing selected  

> fitmap #29 inMap #22

Fit molecule region_4_stemloop_1.cif (#29) to map region_4_jxn.mrc (#22) using
810 atoms  
average map value = 0.01816, steps = 88  
shifted from previous position = 5.93  
rotated from previous position = 16.6 degrees  
atoms outside contour = 288, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#29) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.68199888 0.63380522 -0.36492245 247.90306600  
-0.02540658 0.47813566 0.87791839 160.06788290  
0.73091173 0.60801082 -0.30998519 240.60501449  
Axis -0.20650840 -0.83843132 -0.50436811  
Axis point 85.18732791 -0.00000000 113.09498303  
Rotation angle (degrees) 139.19378912  
Shift along axis -306.75349048  
  

> hide #29 models

> show #30 models

> select add #30

303 atoms, 339 bonds, 14 residues, 1 model selected  

> view matrix models
> #30,-0.56697,0.76211,-0.31262,248.74,0.36457,0.57247,0.73441,141.48,0.73867,0.30242,-0.60242,243.5

> select subtract #30

Nothing selected  

> select add #30

303 atoms, 339 bonds, 14 residues, 1 model selected  

> view matrix models
> #30,-0.56697,0.76211,-0.31262,255.04,0.36457,0.57247,0.73441,151.88,0.73867,0.30242,-0.60242,254.4

> select subtract #30

Nothing selected  

> select add #30

303 atoms, 339 bonds, 14 residues, 1 model selected  

> view matrix models
> #30,-0.56697,0.76211,-0.31262,262.99,0.36457,0.57247,0.73441,152.52,0.73867,0.30242,-0.60242,249.56

> select subtract #30

Nothing selected  

> fitmap #30 inMap #22

Fit molecule region_4_stemloop_2.cif (#30) to map region_4_jxn.mrc (#22) using
303 atoms  
average map value = 0.01962, steps = 212  
shifted from previous position = 7.58  
rotated from previous position = 35.1 degrees  
atoms outside contour = 83, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#30) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.53707071 0.48728711 -0.68855375 271.64553529  
-0.21318196 0.71136454 0.66971178 145.72331222  
0.81615467 0.50646983 -0.27817226 251.29000150  
Axis -0.09788045 -0.90222851 -0.42000374  
Axis point 86.05913368 0.00000000 164.93201980  
Rotation angle (degrees) 123.50015394  
Shift along axis -263.60725321  
  

> select add #30

303 atoms, 339 bonds, 14 residues, 1 model selected  

> view matrix models
> #30,-0.53707,0.48729,-0.68855,264.35,-0.21318,0.71136,0.66971,152.09,0.81615,0.50647,-0.27817,244.54

> ui mousemode right "rotate selected models"

> view matrix models
> #30,-0.50486,0.24864,-0.82662,264.28,-0.12808,0.92544,0.35659,161.22,0.85365,0.2859,-0.43537,245.09

> view matrix models
> #30,-0.51162,0.32306,-0.79617,264.62,-0.15457,0.8769,0.45514,158.52,0.8452,0.35592,-0.3987,245.23

> view matrix models
> #30,-0.50008,0.16546,-0.85003,264.01,-0.098524,0.96433,0.24567,164.4,0.86036,0.2066,-0.46594,245.04

> select subtract #30

Nothing selected  

> select add #30

303 atoms, 339 bonds, 14 residues, 1 model selected  

> view matrix models
> #30,0.26476,0.61284,-0.74453,276.29,0.61252,0.48946,0.62069,159.55,0.7448,-0.62037,-0.24579,229.33

> view matrix models
> #30,-0.24286,0.77473,-0.5838,269.78,0.39394,0.62872,0.67046,157.99,0.88647,-0.067151,-0.45789,241.73

> view matrix models
> #30,0.54886,0.67514,-0.49289,275.85,0.76936,-0.17744,0.61368,153.3,0.32686,-0.71603,-0.61681,230.34

> view matrix models
> #30,0.16435,0.89395,-0.41695,272.82,0.74616,0.1638,0.6453,156.67,0.64516,-0.41717,-0.6401,238.05

> view matrix models
> #30,0.018524,0.99241,-0.12154,267.05,0.7684,0.063645,0.6368,155.84,0.63971,-0.10519,-0.76139,244.16

> view matrix models
> #30,0.36365,0.88244,-0.29843,272.88,0.8484,-0.18145,0.49728,156.29,0.38467,-0.43402,-0.81465,238.18

> view matrix models
> #30,-0.16359,0.98573,0.039594,261.95,0.72565,0.093041,0.68175,154.85,0.66834,0.14026,-0.73051,246.96

> fitmap #30 inMap #22

Fit molecule region_4_stemloop_2.cif (#30) to map region_4_jxn.mrc (#22) using
303 atoms  
average map value = 0.01923, steps = 80  
shifted from previous position = 8  
rotated from previous position = 25.6 degrees  
atoms outside contour = 91, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#30) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.06067038 0.93967256 -0.33665184 274.38137931  
0.68803802 0.20497358 0.69612453 152.11390626  
0.72313390 -0.27386343 -0.63409466 246.97978374  
Axis -0.66503981 -0.72660666 -0.17252481  
Axis point 11.24022883 0.00000000 120.68250058  
Rotation angle (degrees) 133.17471791  
Shift along axis -335.61165809  
  

> ui mousemode right "translate selected models"

> view matrix models
> #30,0.06067,0.93967,-0.33665,267.15,0.68804,0.20497,0.69612,156.48,0.72313,-0.27386,-0.63409,240.43

> fitmap #30 inMap #22

Fit molecule region_4_stemloop_2.cif (#30) to map region_4_jxn.mrc (#22) using
303 atoms  
average map value = 0.01923, steps = 132  
shifted from previous position = 10.7  
rotated from previous position = 0.0541 degrees  
atoms outside contour = 91, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#30) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.06067287 0.93948475 -0.33717516 274.37889887  
0.68750978 0.20555984 0.69647347 152.10779560  
0.72363592 -0.27406828 -0.63343309 246.98315683  
Axis -0.66488520 -0.72672566 -0.17261949  
Axis point 11.22052976 0.00000000 120.70939886  
Rotation angle (degrees) 133.12562133  
Shift along axis -335.60521406  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #30,0.70967,0.21295,-0.67158,278.97,0.5009,-0.82284,0.2684,145.14,-0.49545,-0.52687,-0.69061,230.95

> ui mousemode right "translate selected models"

> view matrix models
> #30,0.70967,0.21295,-0.67158,270.8,0.5009,-0.82284,0.2684,150.09,-0.49545,-0.52687,-0.69061,227.43

> select subtract #30

Nothing selected  

> select add #30

303 atoms, 339 bonds, 14 residues, 1 model selected  

> view matrix models
> #30,0.70967,0.21295,-0.67158,271.35,0.5009,-0.82284,0.2684,147.9,-0.49545,-0.52687,-0.69061,224.45

> select subtract #30

Nothing selected  

> fitmap #30 inMap #22

Fit molecule region_4_stemloop_2.cif (#30) to map region_4_jxn.mrc (#22) using
303 atoms  
average map value = 0.01936, steps = 96  
shifted from previous position = 5.48  
rotated from previous position = 27 degrees  
atoms outside contour = 89, contour level = 0.017  
  
Position of region_4_stemloop_2.cif (#30) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.63469002 0.57632017 -0.51480432 275.80465168  
0.76120519 -0.58106772 0.28797021 153.32780289  
-0.13317313 -0.57464356 -0.80749584 233.84022293  
Axis -0.89742358 -0.39703149 0.19234584  
Axis point 0.00000000 56.24274284 139.52273445  
Rotation angle (degrees) 151.27503015  
Shift along axis -263.41136795  
  

> show #29 models

> hide #29 models

> show #29 models

> hide #30 models

> select add #29

810 atoms, 906 bonds, 38 residues, 1 model selected  

> view matrix models
> #29,-0.682,0.63381,-0.36492,250.31,-0.025407,0.47814,0.87792,157.42,0.73091,0.60801,-0.30999,243.23

> ui mousemode right "rotate selected models"

> view matrix models
> #29,-0.67646,0.56929,-0.46724,249.07,-0.18121,0.48626,0.85482,156.18,0.71384,0.66292,-0.22577,244.2

> fitmap #29 inMap #22

Fit molecule region_4_stemloop_1.cif (#29) to map region_4_jxn.mrc (#22) using
810 atoms  
average map value = 0.01816, steps = 88  
shifted from previous position = 3.97  
rotated from previous position = 9.03 degrees  
atoms outside contour = 287, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#29) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.68214736 0.63346310 -0.36523885 247.89850402  
-0.02600772 0.47816098 0.87788700 160.06125921  
0.73075201 0.60834735 -0.30970135 240.60896443  
Axis -0.20619754 -0.83843182 -0.50449446  
Axis point 85.21397840 0.00000000 113.11707714  
Rotation angle (degrees) 139.18674535  
Shift along axis -306.70240351  
  

> view matrix models
> #29,-0.82249,0.4047,-0.39965,248.14,-0.26327,0.35196,0.89823,160.01,0.50417,0.844,-0.18294,239.92

> ui mousemode right "translate selected models"

> view matrix models
> #29,-0.82249,0.4047,-0.39965,250.4,-0.26327,0.35196,0.89823,157.63,0.50417,0.844,-0.18294,239.7

> fitmap #29 inMap #22

Fit molecule region_4_stemloop_1.cif (#29) to map region_4_jxn.mrc (#22) using
810 atoms  
average map value = 0.01816, steps = 188  
shifted from previous position = 3.69  
rotated from previous position = 21.1 degrees  
atoms outside contour = 289, contour level = 0.017  
  
Position of region_4_stemloop_1.cif (#29) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.68215255 0.63381433 -0.36461928 247.90715068  
-0.02553552 0.47769861 0.87815254 160.08934105  
0.73076381 0.60834476 -0.30967857 240.60697071  
Axis -0.20648404 -0.83829730 -0.50460081  
Axis point 85.20999801 0.00000000 113.05286491  
Rotation angle (degrees) 139.20624509  
Shift along axis -306.80180554  
  

> select subtract #29

Nothing selected  

> hide #29 models

> show #24 models

> hide #24 models

> show #29 models

> hide #29 models

> show #29 models

> hide #29 models

> show #30 models

> hide #30 models

> show #31 models

> hide #31 models

> show #30 models

> hide #30 models

> show #31 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.56697,0.76211,-0.31262,238.51,0.36457,0.57247,0.73441,124.18,0.73867,0.30242,-0.60242,238.99

> select subtract #31

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.56697,0.76211,-0.31262,253.93,0.36457,0.57247,0.73441,169.53,0.73867,0.30242,-0.60242,250.29

> select subtract #31

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.7243,0.65046,-0.22867,254.07,0.30326,0.59839,0.7416,169.52,0.61921,0.46779,-0.63067,250.18

> view matrix models
> #31,-0.42692,0.84704,-0.31663,254.73,0.50472,0.51373,0.69379,169.2,0.75033,0.13638,-0.64684,248.99

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01266, steps = 260  
shifted from previous position = 13.5  
rotated from previous position = 55.1 degrees  
atoms outside contour = 427, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.85603160 0.42976147 -0.28725411 253.04516875  
0.47934489 0.86795699 -0.12991944 146.00269090  
0.19348985 -0.24890893 -0.94900261 240.53669686  
Axis -0.23906596 -0.96587958 0.09961978  
Axis point 91.55492192 0.00000000 141.57983155  
Rotation angle (degrees) 165.58974146  
Shift along axis -177.55329122  
  

> select subtract #31

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #31/A

Alignment identifier is 31/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #32/A

Alignment identifier is 32/A  

> select clear

[Repeated 4 time(s)]

> show #32 models

> hide #32 models

> show #32 models

> select #32/A:1

24 atoms, 26 bonds, 1 residue, 1 model selected  

> select #32/A

187 atoms, 206 bonds, 9 residues, 1 model selected  

> select #31/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #31/A

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.88195,0.37602,-0.28422,252.77,0.4374,0.8776,-0.19622,144.96,0.17565,-0.29737,-0.93847,240.41

> view matrix models
> #31,-0.84845,0.44625,-0.28459,253.18,0.49449,0.86006,-0.1256,146.08,0.18872,-0.24729,-0.95039,240.51

> ui mousemode right "rotate selected models"

> select subtract #31

Nothing selected  

> hide #!22 models

> show #!22 models

> hide #32 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.78343,-0.15347,-0.60223,246.37,0.075564,0.93832,-0.33741,141.96,0.61687,-0.30985,-0.72351,244.94

> ui mousemode right "translate selected models"

> view matrix models
> #31,-0.78343,-0.15347,-0.60223,239.41,0.075564,0.93832,-0.33741,145.68,0.61687,-0.30985,-0.72351,241.33

> select subtract #31

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.78343,-0.15347,-0.60223,237.09,0.075564,0.93832,-0.33741,141.34,0.61687,-0.30985,-0.72351,242.69

> select subtract #31

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #31,-0.81518,-0.47971,-0.3246,239.48,-0.46895,0.87554,-0.11624,142.25,0.33996,0.057467,-0.93868,240.26

> select subtract #31

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #31,-0.81518,-0.47971,-0.3246,242.83,-0.46895,0.87554,-0.11624,146.17,0.33996,0.057467,-0.93868,244.36

> select subtract #31

Nothing selected  

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01496, steps = 116  
shifted from previous position = 2.76  
rotated from previous position = 26.2 degrees  
atoms outside contour = 365, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.93041109 -0.04663486 -0.36353862 245.91604768  
-0.04613802 0.99888442 -0.01005539 150.50432210  
0.36360202 0.00741731 -0.93152482 244.29485486  
Axis 0.02402240 -0.99971119 0.00068309  
Axis point 101.75194744 0.00000000 145.68318740  
Rotation angle (degrees) 158.67391522  
Shift along axis -144.38648672  
  

> select subtract #22

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select subtract #31

Nothing selected  

> hide #!22 models

> show #!22 models

> ui mousemode right "translate selected atoms"

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> hide #!22 models

> show #!22 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> hide #!22 models

> select subtract #31

Nothing selected  

> show #!22 models

> hide #!22 models

> select subtract #22

84 atoms, 4 residues, 1 model selected  

> select subtract #31/A:47

64 atoms, 3 residues, 1 model selected  

> show #!22 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> hide #!22 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> show #!22 models

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01659, steps = 252  
shifted from previous position = 6.08  
rotated from previous position = 77.4 degrees  
atoms outside contour = 297, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.10155596 0.45124731 -0.88660148 234.58619507  
0.85524557 0.49484513 0.15389355 151.06658608  
0.50817451 -0.74263320 -0.43618175 244.02833194  
Axis -0.52533897 -0.81729873 0.23673140  
Axis point -30.33091760 0.00000000 190.32527444  
Rotation angle (degrees) 121.42931646  
Shift along axis -188.93463079  
  

> select subtract #31

Nothing selected  

> hide #10 models

> hide #!12 models

> hide #13 models

> hide #14 models

> show #!12 models

> hide #!12 models

> select add #31/A:45

44 atoms, 24 bonds, 2 residues, 1 model selected  

> select subtract #31/A:45

22 atoms, 1 residue, 1 model selected  

> select subtract #31/A:44

Nothing selected  

> select subtract #31/A:45

Nothing selected  

> select add #31/A:46

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select subtract #31/A:46

Nothing selected  

> select subtract #31/A:45

2 models selected  

> select add #31/A:45

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select subtract #31/A:46

Nothing selected  

> select add #31/A:47

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 3 models selected  

> select subtract #22

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select subtract #22

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> hide #!22 models

> select add #31/A:48

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #22

22 atoms, 24 bonds, 1 residue, 3 models selected  

> select subtract #22

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show #!22 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select add #22

2 models selected  

> select subtract #22

Nothing selected  

> hide #!22 models

> select add #31/A:47

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show #!22 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select add #31/A:48

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01794, steps = 44  
shifted from previous position = 0.488  
rotated from previous position = 1.87 degrees  
atoms outside contour = 257, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.10242603 0.47594005 -0.87349294 235.26825722  
0.84798760 0.50083058 0.17345226 151.68884897  
0.52002488 -0.72294517 -0.45488935 244.00374819  
Axis -0.52785550 -0.82059142 0.21908513  
Axis point -28.23608988 0.00000000 187.01539040  
Rotation angle (degrees) 121.88677869  
Shift along axis -195.20461885  
  

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01794, steps = 64  
shifted from previous position = 0.00658  
rotated from previous position = 0.055 degrees  
atoms outside contour = 257, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.10316225 0.47605748 -0.87334229 235.27882330  
0.84762805 0.50150969 0.17324733 151.68725890  
0.52046533 -0.72239686 -0.45525655 244.00071655  
Axis -0.52749396 -0.82088972 0.21883828  
Axis point -28.09987769 0.00000000 186.97698888  
Rotation angle (degrees) 121.90109588  
Shift along axis -195.22997284  
  

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01794, steps = 60  
shifted from previous position = 0.000873  
rotated from previous position = 0.0169 degrees  
atoms outside contour = 257, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.10291841 0.47598133 -0.87341257 235.27646793  
0.84771170 0.50134151 0.17332480 151.68756155  
0.52037737 -0.72256375 -0.45509222 244.00169133  
Axis -0.52759147 -0.82080709 0.21891313  
Axis point -28.14558882 0.00000000 186.99280609  
Rotation angle (degrees) 121.89299751  
Shift along axis -195.22090861  
  

> ui mousemode right "translate selected models"

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> view matrix models
> #31,-0.10292,0.47598,-0.87341,214.05,0.84771,0.50134,0.17332,130.6,0.52038,-0.72256,-0.45509,254.85

> view matrix models
> #31,-0.10292,0.47598,-0.87341,231.82,0.84771,0.50134,0.17332,152.35,0.52038,-0.72256,-0.45509,241.84

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01794, steps = 100  
shifted from previous position = 4.12  
rotated from previous position = 0.211 degrees  
atoms outside contour = 258, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.09986601 0.47571972 -0.87390930 235.24929653  
0.84898869 0.49876949 0.17449106 151.69814107  
0.51888816 -0.72451340 -0.45369079 244.00773778  
Axis -0.52906204 -0.81965808 0.21966792  
Axis point -28.68044913 0.00000000 187.11357018  
Rotation angle (degrees) 121.82952413  
Shift along axis -195.20140641  
  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4_wip.cxs"

> hide #31 models

> select subtract #31

Nothing selected  

> show #28 models

> hide #28 models

> show #32 models

> select add #32

532 atoms, 592 bonds, 25 residues, 1 model selected  

> view matrix models
> #32,-0.69254,0.5863,-0.42028,257.26,0.25319,0.7431,0.61943,160.24,0.67549,0.32257,-0.66307,239.97

> select subtract #32

Nothing selected  

> select add #32

532 atoms, 592 bonds, 25 residues, 1 model selected  

> view matrix models
> #32,-0.69254,0.5863,-0.42028,241.66,0.25319,0.7431,0.61943,144.22,0.67549,0.32257,-0.66307,234.96

> select subtract #32

Nothing selected  

> fitmap #32 inMap #22

Fit molecule region_4_stem.cif (#32) to map region_4_jxn.mrc (#22) using 532
atoms  
average map value = 0.02357, steps = 144  
shifted from previous position = 4.31  
rotated from previous position = 33.7 degrees  
atoms outside contour = 100, contour level = 0.017  
  
Position of region_4_stem.cif (#32) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.76967722 0.63355334 -0.07878498 236.33318723  
0.59492722 0.75652018 0.27154878 144.18849450  
0.23164307 0.16213360 -0.95919452 249.78826019  
Axis -0.33015555 -0.93670315 -0.11655264  
Axis point 82.88923207 0.00000000 122.88707700  
Rotation angle (degrees) 170.46195516  
Shift along axis -242.20201290  
  

> ui mousemode right "rotate selected models"

> select add #32

532 atoms, 592 bonds, 25 residues, 1 model selected  

> view matrix models
> #32,-0.043278,0.022874,-0.9988,245.72,0.67204,-0.73908,-0.046046,154.08,-0.73925,-0.67323,0.016614,247.51

> ui mousemode right "translate selected models"

> view matrix models
> #32,-0.043278,0.022874,-0.9988,235.92,0.67204,-0.73908,-0.046046,159.7,-0.73925,-0.67323,0.016614,243.62

> select subtract #32

Nothing selected  

> fitmap #32 inMap #22

Fit molecule region_4_stem.cif (#32) to map region_4_jxn.mrc (#22) using 532
atoms  
average map value = 0.02208, steps = 68  
shifted from previous position = 1.84  
rotated from previous position = 5.1 degrees  
atoms outside contour = 122, contour level = 0.017  
  
Position of region_4_stem.cif (#32) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.01857841 0.08636443 -0.99609034 235.60216425  
0.66667317 -0.74353174 -0.05203238 158.96646870  
-0.74511855 -0.66310004 -0.07139048 245.34281446  
Axis -0.69495673 -0.28542589 0.65997515  
Axis point 0.00000000 77.17440076 210.29703709  
Rotation angle (degrees) 153.91880532  
Shift along axis -47.18629608  
  

> show #31 models

> hide #!22 models

> ui mousemode right pivot

> select add #31/A:48

22 atoms, 24 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #31,-0.035288,0.44741,-0.89363,234.79,0.8578,0.47237,0.20263,152.01,0.51278,-0.7594,-0.40046,244.68

> ui mousemode right "translate selected atoms"

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> ui mousemode right "translate selected models"

> select add #31/A:50

22 atoms, 24 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> select add #31/A:49

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> hide #31 models

> show #31 models

> combine #28

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #31

Nothing selected  

> select add #34

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> nucleotides sel stubs

> ui tool show "Show Sequence Viewer"

> sequence chain #34/A

Alignment identifier is 34/A  

> sequence chain #31/A

Alignment identifier is 31/A  

> select #34/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #34/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #34/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #34/A:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #34/A:14-50

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select ~sel & ##selected

1793 atoms, 2005 bonds, 84 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> close #31

> rename #34 id #31

> rename #31 region_4_stemloop_3.cif

> show #!22 models

> select add #31

787 atoms, 881 bonds, 37 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #31,-0.679,0.34719,-0.64685,251.05,0.26748,0.93754,0.22244,151.36,0.68368,-0.021984,-0.72946,251.17

> view matrix models
> #31,-0.67417,0.3756,-0.63594,251.34,0.27559,0.92678,0.25522,151.81,0.68524,-0.0031997,-0.72831,251.27

> ui mousemode right "translate selected models"

> view matrix models
> #31,-0.67417,0.3756,-0.63594,245.76,0.27559,0.92678,0.25522,156.44,0.68524,-0.0031997,-0.72831,248.3

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01496, steps = 168  
shifted from previous position = 3.45  
rotated from previous position = 32.9 degrees  
atoms outside contour = 365, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
-0.93046474 -0.04619119 -0.36345793 245.90337480  
-0.04592815 0.99890076 -0.00937080 150.49708634  
0.36349127 0.00797376 -0.93156345 244.30354879  
Axis 0.02385260 -0.99971542 0.00036173  
Axis point 101.74298785 0.00000000 145.65325466  
Rotation angle (degrees) 158.67989883  
Shift along axis -144.50045152  
  

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!6 models

> select subtract #31

Nothing selected  

> select add #6.76

1 model selected  

> select add #6.23

2 models selected  

> select add #6.5

3 models selected  

> select add #6.161

4 models selected  

> select add #6.125

5 models selected  

> ui tool show Segmentations

Created segmentation sphere cursor with ID #34  
Created segmentation sphere cursor with ID #35  
Created segmentation sphere cursor with ID #36  

> ui view fourup

Exception ignored in: <function Texture.__del__ at 0x0000024C3BE7D300>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3165, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1542+0+35 (frame:
1942x1598-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 734x1028 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1123,
y=1598)))  

> ui tool show Segmentations

> ui tool show "Segment Map"

> ui tool show Segmentations

Created segmentation sphere cursor with ID #34  
Created segmentation sphere cursor with ID #35  
Created segmentation sphere cursor with ID #36  

> ui view fourup

No segmentations to remove.  

> ui tool show Segmentations

Created segmentation sphere cursor with ID #34  
Created segmentation sphere cursor with ID #35  
Created segmentation sphere cursor with ID #36  

> ui view fourup

> ui view overunder

> ui view sidebyside

> ui view default

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 1087, in
_on_view_changed  
self._create_3d_segmentation_sphere()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 920, in
_create_3d_segmentation_sphere  
origin=current_reference_model.bounds().center()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'center'  
  
AttributeError: 'NoneType' object has no attribute 'center'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 920, in
_create_3d_segmentation_sphere  
origin=current_reference_model.bounds().center()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Segment Map"

[Repeated 1 time(s)]Saving 5 regions to mrc file...  
Opened region_3_R.mrc as #34, grid size 64,72,73, pixel 1.12,1.12,1.12, shown
at step 1, values float32  
Wrote region_3_R.mrc  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1287+0+35 (frame:
1942x1343-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 624x858 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
y=1343)))  

> volume #34 level 0.017

> hide #!6 models

> select add #6

200 models selected  

> select subtract #6

Nothing selected  

> transparency #34.1 50

> fitmap #31 inMap #34

Fit molecule region_4_stemloop_3.cif (#31) to map region_3_R.mrc (#34) using
787 atoms  
average map value = 0.01578, steps = 372  
shifted from previous position = 7.36  
rotated from previous position = 89.1 degrees  
atoms outside contour = 330, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_3_R.mrc (#34)
coordinates:  
Matrix rotation and translation  
0.03612755 0.37232970 -0.92739708 232.76600134  
0.92142062 0.34685291 0.17514860 150.02117406  
0.38688342 -0.86085050 -0.33054131 245.57806711  
Axis -0.58820608 -0.74620507 0.31175569  
Axis point -62.57812951 0.00000000 206.74540672  
Rotation angle (degrees) 118.27997416  
Shift along axis -172.30057613  
  

> fitmap #31 inMap #34

Fit molecule region_4_stemloop_3.cif (#31) to map region_3_R.mrc (#34) using
787 atoms  
average map value = 0.01578, steps = 40  
shifted from previous position = 0.0248  
rotated from previous position = 0.13 degrees  
atoms outside contour = 329, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_3_R.mrc (#34)
coordinates:  
Matrix rotation and translation  
0.03753886 0.37104119 -0.92785732 232.73098076  
0.92182744 0.34559464 0.17549487 150.00888031  
0.38577836 -0.86191224 -0.32906273 245.60185504  
Axis -0.58871241 -0.74546784 0.31256263  
Axis point -62.98162070 0.00000000 206.97918526  
Rotation angle (degrees) 118.22690942  
Shift along axis -172.07244936  
  

> show #28 models

> select add #28

2580 atoms, 2886 bonds, 121 residues, 1 model selected  

> view matrix models
> #28,-0.69254,0.5863,-0.42028,224.25,0.25319,0.7431,0.61943,172.95,0.67549,0.32257,-0.66307,292.01

> select subtract #28

Nothing selected  

> hide #28 models

> fitmap #31 inMap #34

Fit molecule region_4_stemloop_3.cif (#31) to map region_3_R.mrc (#34) using
787 atoms  
average map value = 0.01578, steps = 44  
shifted from previous position = 0.00319  
rotated from previous position = 0.116 degrees  
atoms outside contour = 328, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_3_R.mrc (#34)
coordinates:  
Matrix rotation and translation  
0.03599607 0.37178828 -0.92761937 232.74084552  
0.92146770 0.34690547 0.17479648 150.00824335  
0.38678354 -0.86106329 -0.33010366 245.59172523  
Axis -0.58806255 -0.74619282 0.31205563  
Axis point -62.61080588 0.00000000 206.82546883  
Rotation angle (degrees) 118.26830503  
Shift along axis -172.16296716  
  

> show #!22 models

> show #!12 models

> hide #!34 models

> fitmap #31 inMap #22

Fit molecule region_4_stemloop_3.cif (#31) to map region_4_jxn.mrc (#22) using
787 atoms  
average map value = 0.01578, steps = 40  
shifted from previous position = 0.00759  
rotated from previous position = 0.0287 degrees  
atoms outside contour = 328, contour level = 0.017  
  
Position of region_4_stemloop_3.cif (#31) relative to region_4_jxn.mrc (#22)
coordinates:  
Matrix rotation and translation  
0.03559107 0.37198569 -0.92755586 232.74800555  
0.92139691 0.34719556 0.17459356 150.00228508  
0.38698959 -0.86086109 -0.33038940 245.58522881  
Axis -0.58790448 -0.74636505 0.31194154  
Axis point -62.50863487 0.00000000 206.78584365  
Rotation angle (degrees) 118.28133789  
Shift along axis -172.18182422  
  

> show #30 models

> show #29 models

> hide #29 models

> hide #31 models

> hide #32 models

> hide #30 models

> show #24 models

> show #25 models

> show #26 models

> show #!27 models

> close #23-27

> rename #34 id #23

> close #15-20

> rename #14 id #15

> rename #13 id #14

> rename #12 id #13

> rename #33 id #12

> rename #21 id #16

> rename #22 id #17

> rename #23 id #18

> rename #28 id #19

> rename #32 id #20

> rename #29 id #21

> rename #30 id #22

> rename #31 id #23

> show #20 models

> hide #20 models

> ui tool show "Show Sequence Viewer"

> sequence chain #20/B

Alignment identifier is 20/B  

> sequence chain #21/B

Alignment identifier is 21/B  

> sequence chain #22/B

Alignment identifier is 22/B  

> sequence chain #23/A

Alignment identifier is 23/A  

> select add #20

532 atoms, 592 bonds, 25 residues, 1 model selected  

> select add #21

1342 atoms, 1498 bonds, 63 residues, 2 models selected  

> select add #22

1645 atoms, 1837 bonds, 77 residues, 3 models selected  

> select add #23

2432 atoms, 2718 bonds, 114 residues, 4 models selected  

> show #23 models

> show #22 models

> show #21 models

> show #20 models

> ui tool show "Show Sequence Viewer"

> sequence chain #20/B

Alignment identifier is 20/B  

> sequence chain #21/B

Alignment identifier is 21/B  

> sequence chain #22/B

Alignment identifier is 22/B  

> sequence chain #23/A

Alignment identifier is 23/A  

> select subtract #20

1900 atoms, 2126 bonds, 89 residues, 3 models selected  

> select subtract #21

1090 atoms, 1220 bonds, 51 residues, 2 models selected  

> select subtract #22

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select subtract #23

Nothing selected  

> hide #23 models

> hide #22 models

> hide #21 models

> show #21 models

> show #23 models

> show #22 models

> select add #23

787 atoms, 881 bonds, 37 residues, 1 model selected  

> select add #22

1090 atoms, 1220 bonds, 51 residues, 2 models selected  

> select add #21

1900 atoms, 2126 bonds, 89 residues, 3 models selected  

> select add #20

2432 atoms, 2718 bonds, 114 residues, 4 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #20/A

Alignment identifier is 20/A  

> sequence chain #20/B

Alignment identifier is 20/B  

> sequence chain #21/B

Alignment identifier is 21/B  

> sequence chain #22/B

Alignment identifier is 22/B  

> sequence chain #23/A

Alignment identifier is 23/A  

> select #21/B:15

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #21/B

810 atoms, 906 bonds, 38 residues, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select #22/B:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select #22/B

303 atoms, 339 bonds, 14 residues, 1 model selected  

> select #20/A:1

24 atoms, 26 bonds, 1 residue, 1 model selected  

> select #20/A

187 atoms, 206 bonds, 9 residues, 1 model selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251114 region_4.cxs"

> hide #!13 models

> show #!13 models

> select add #20

532 atoms, 592 bonds, 25 residues, 1 model selected  

> select subtract #20

Nothing selected  

> hide #!17 models

> show #!6 models

> hide #!6 models

> show #!17 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!17 models

> ui tool show "Side View"

> select add #6.182

1 model selected  

> select add #6.79

2 models selected  

> select add #6.178

3 models selected  

> select add #6.192

4 models selected  

> select add #6.91

5 models selected  

> select add #6.110

6 models selected  

> select add #6.127

7 models selected  

> select add #6.7

8 models selected  

> ui tool show "Segment Map"

Saving 8 regions to mrc file...  
Opened region_5_jxn.mrc as #24, grid size 85,86,81, pixel 1.12,1.12,1.12,
shown at step 1, values float32  
Wrote region_5_jxn.mrc  

> select add #6

200 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> transparency #24.1 50

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!6 models

> select add #24

3 models selected  

> save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
> Project/20251119 region_5_wip.cxs"

> ui tool show "Side View"

> hide #!6 models

> show #!6 models

> hide #!6 models

> select subtract #24

Nothing selected  

> select add #24

3 models selected  

> show #!6 models

> hide #!6 models

> select subtract #24

Nothing selected  

> volume #18 level 0.01768

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2185, in mouseReleaseEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2185, in mouseReleaseEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2185, in mouseReleaseEvent  
self._drag(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2182, in _drag  
cb(event)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\histogram.py", line 416, in move_marker_cb  
cb(m)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1931, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 754, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.6881
OpenGL renderer: Intel(R) Arc(TM) Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Dell 14 Plus 2-in-1 DB04250
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,749,641,728
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) Ultra 7 256V
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

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