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Opened 20 hours ago
Closed 31 minutes ago
#19396 closed defect (duplicate)
Orthoplanes: 'NoneType' object has no attribute 'image_colors'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: 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
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 31 minutes ago
| Component: | Unassigned → DICOM |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Orthoplanes: 'NoneType' object has no attribute 'image_colors' |
comment:2 by , 31 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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