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Opened 13 hours ago
#20771 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open D:\HBc_Mature\2025_0520\Fig3_A-form_B-form_DNA\Fig_FC\FC3.cxs format
> session
Opened run_eq3_it025_class006.mrc gaussian as #6, grid size 320,320,320, pixel
1.4, shown at level 0.00233, step 1, values float32
Opened eq6f1-cls3_maxpob.mrc as #7, grid size 320,320,320, pixel 1.4, shown at
level 0.0035, step 2, values float32
Opened eq6f1-cls3_maxpob.mrc copy as #9, grid size 320,320,320, pixel 1.4,
shown at level 0.00237, step 1, values float32
Opened run_eq3_it025_class006.mrc as #1, grid size 320,320,320, pixel 1.4,
shown at level 0.00022, step 2, values float32
Opened run_eq3_it025_class006.mrc copy as #2, grid size 320,320,320, pixel
1.4, shown at level 0.00421, step 1, values float32
Opened run_eq3_it025_class006.mrc copy gaussian as #3, grid size 320,320,320,
pixel 1.4, shown at level 0.00222, step 1, values float32
Opened B_DNA.pdb map 10 as #4, grid size 52,25,30, pixel 3.33, shown at level
0.202, step 1, values float32
Opened A_DNA.pdb map 10 as #5, grid size 52,25,30, pixel 3.33, shown at level
0.0538, step 1, values float32
Opened A_DNA.pdb map 10 as #12, grid size 52,25,30, pixel 3.33, shown at level
0.233, step 1, values float32
Log from Fri Jul 17 22:49:11 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open E:/rcDNA_FC/FC_DNA.cxs
Opened run_eq3_it025_class003.mrc as #1, grid size 320,320,320, pixel 1.4,
shown at level 0.00451, step 1, values float32
Opened run_eq3_it025_class004.mrc as #2, grid size 320,320,320, pixel 1.4,
shown at level 0.000462, step 2, values float32
Opened run_eq3_it025_class006.mrc as #3, grid size 320,320,320, pixel 1.4,
shown at level 0.00022, step 2, values float32
Opened run_eq3_it025_class003.mrc gaussian as #4, grid size 320,320,320, pixel
1.4, shown at level 0.00348, step 1, values float32
Opened run_eq3_it025_class004.mrc gaussian as #5, grid size 320,320,320, pixel
1.4, shown at level 0.0017, step 1, values float32
Opened run_eq3_it025_class006.mrc gaussian as #6, grid size 320,320,320, pixel
1.4, shown at level 0.00155, step 1, values float32
Opened eq6f1-cls3_maxpob.mrc as #7, grid size 320,320,320, pixel 1.4, shown at
level 0.0035, step 2, values float32
Opened eq6f1-cls3_maxpob.mrc copy as #9, grid size 320,320,320, pixel 1.4,
shown at level 0.00237, step 1, values float32
Log from Thu Jul 16 14:08:07 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:\\\Projects\\\HBc_Mature\\\Combined_All\\\2x_FC_on_Cp-from-
> Job121\\\6f_qual\\\run_eq3_it025_class003.mrc
Opened run_eq3_it025_class003.mrc as #1, grid size 320,320,320, pixel 1.4,
shown at level 0.000623, step 2, values float32
> open E:\\\Projects\\\HBc_Mature\\\Combined_All\\\2x_FC_on_Cp-from-
> Job121\\\6f_qual\\\run_eq3_it025_class004.mrc
Opened run_eq3_it025_class004.mrc as #2, grid size 320,320,320, pixel 1.4,
shown at level 0.000462, step 2, values float32
> open E:\\\Projects\\\HBc_Mature\\\Combined_All\\\2x_FC_on_Cp-from-
> Job121\\\6f_qual\\\run_eq3_it025_class006.mrc
Opened run_eq3_it025_class006.mrc as #3, grid size 320,320,320, pixel 1.4,
shown at level 0.00022, step 2, values float32
> hide #!3 models
> volume #1 level 0.00223
> volume #1 step 1
> volume #1 level 0.004513
> select down
Nothing selected
> select ~sel & ##selected
Nothing selected
> volume gaussian #1,2,3 sDev 1.5
Opened run_eq3_it025_class003.mrc gaussian as #4, grid size 320,320,320, pixel
1.4, shown at step 1, values float32
Opened run_eq3_it025_class004.mrc gaussian as #5, grid size 320,320,320, pixel
1.4, shown at step 1, values float32
Opened run_eq3_it025_class006.mrc gaussian as #6, grid size 320,320,320, pixel
1.4, shown at step 1, values float32
> volume #4 level 0.00252
> open C:/Users/cwang6/Desktop/rcDNA_FC/eq6f1-cls3_maxpob.mrc
Opened eq6f1-cls3_maxpob.mrc as #7, grid size 320,320,320, pixel 1.4, shown at
level 0.0105, step 2, values float32
> volume #7 level 0.003501
> ui tool show "Side View"
> lighting soft
> ui tool show "Map Eraser"
> volume erase #4 center 218.43,223.84,223.97 radius 125.89 outside true
> show #!5 models
> hide #!4 models
> volume erase #5 center 218.43,223.84,223.97 radius 125.89 outside true
> hide #!5 models
> show #!6 models
> volume erase #6 center 218.43,223.84,223.97 radius 125.89 outside true
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> volume erase #7 center 218.43,223.84,223.97 radius 125.89 outside true
Opened eq6f1-cls3_maxpob.mrc copy as #9, grid size 320,320,320, pixel 1.4,
shown at step 1, values float32
> volume #6 level 0.001551
> volume #5 level 0.00115
> volume #5 level 0.001699
> volume #4 level 0.003478
> volume #9 level 0.002367
> save C:/Users/cwang6/Desktop/rcDNA_FC/FC_DNA.cxs includeMaps true
——— End of log from Thu Jul 16 14:08:07 2026 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!6 models
> volume #6 level 0.002838
> lighting simple
[Repeated 1 time(s)]
> open D:/HBc_Mature/2025_0520/Fig3_A-form_B-form_DNA/B_DNA.pdb
Chain information for B_DNA.pdb #8
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> view
> open D:/HBc_Mature/2025_0520/Fig3_A-form_B-form_DNA/A_DNA.pdb
Chain information for A_DNA.pdb #10
---
Chain | Description
A B | No description available
Computing secondary structure
> select add #8
1312 atoms, 1470 bonds, 64 residues, 1 model selected
> select add #10
3034 atoms, 3400 bonds, 148 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,1,0,0,59.608,0,1,0,274.22,0,0,1,213.74,#10,1,0,0,59.608,0,1,0,274.22,0,0,1,213.74
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.37776,-0.92362,-0.065026,60.437,0.91941,0.36588,0.14429,274.21,-0.10948,-0.11429,0.9874,213.86,#10,0.37776,-0.92362,-0.065026,60.437,0.91941,0.36588,0.14429,274.21,-0.10948,-0.11429,0.9874,213.86
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.37776,-0.92362,-0.065026,109.12,0.91941,0.36588,0.14429,257.8,-0.10948,-0.11429,0.9874,213.33,#10,0.37776,-0.92362,-0.065026,109.12,0.91941,0.36588,0.14429,257.8,-0.10948,-0.11429,0.9874,213.33
> view matrix models
> #8,0.37776,-0.92362,-0.065026,115.42,0.91941,0.36588,0.14429,256.71,-0.10948,-0.11429,0.9874,213.33,#10,0.37776,-0.92362,-0.065026,115.42,0.91941,0.36588,0.14429,256.71,-0.10948,-0.11429,0.9874,213.33
> view matrix models
> #8,0.37776,-0.92362,-0.065026,116.6,0.91941,0.36588,0.14429,256.74,-0.10948,-0.11429,0.9874,224.22,#10,0.37776,-0.92362,-0.065026,116.6,0.91941,0.36588,0.14429,256.74,-0.10948,-0.11429,0.9874,224.22
> view
> volume #6 level 0.0006542
> volume #6 level 0.0008337
> volume #6 color #ffb2b29b
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui tool show "Fit in Map"
> fitmap #8 inMap #6
Fit molecule B_DNA.pdb (#8) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1312 atoms
average map value = 0.003492, steps = 124
shifted from previous position = 3.6
rotated from previous position = 7.05 degrees
atoms outside contour = 277, contour level = 0.00083367
Position of B_DNA.pdb (#8) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.29116939 -0.95660343 0.01141354 117.46493003
0.94253639 0.28889015 0.16783218 253.27395236
-0.16384610 -0.03810991 0.98574951 223.78505285
Axis -0.10735678 0.09136214 0.99001388
Axis point -85.90204540 212.49162340 0.00000000
Rotation angle (degrees) 73.56636754
Shift along axis 232.07930254
> fitmap #8 inMap #6
Fit molecule B_DNA.pdb (#8) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1312 atoms
average map value = 0.003494, steps = 80
shifted from previous position = 0.137
rotated from previous position = 2.74 degrees
atoms outside contour = 275, contour level = 0.00083367
Position of B_DNA.pdb (#8) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28323146 -0.95736366 0.05687503 117.49665717
0.94468425 0.28872397 0.15559609 253.40500519
-0.16538323 0.00965924 0.98618208 223.74093138
Axis -0.07598732 0.11572683 0.99037025
Axis point -84.24351047 205.00826257 0.00000000
Rotation angle (degrees) 73.79536711
Shift along axis 241.98386300
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002791, steps = 2000
shifted from previous position = 4.73
rotated from previous position = 131 degrees
atoms outside contour = 452, contour level = 0.00083367
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.34603860 0.73297071 -0.58567160 116.43888104
0.91605532 -0.12906551 0.37971666 252.32682278
0.20273118 -0.66790421 -0.71610337 225.10642841
Axis -0.79133741 -0.59553282 0.13829593
Axis point -0.00000000 143.14629844 92.48719290
Rotation angle (degrees) 138.55272294
Shift along axis -211.28004494
> hide #10 models
> ui tool show "Side View"
> volume #6 level 0.001851
> volume #6 color #ffffff9b
> volume #6 color #9d9d9d9b
> hide #8 models
> camera ortho
> ui tool show "Hide Dust"
> surface dust #6 size 8.4
> show #8 models
> hide #8 models
> show #8 models
> view matrix models
> #8,0.28323,-0.95736,0.056875,117.1,0.94468,0.28872,0.1556,255.75,-0.16538,0.0096592,0.98618,207.34,#10,0.34604,0.73297,-0.58567,116.05,0.91606,-0.12907,0.37972,254.67,0.20273,-0.6679,-0.7161,208.71
> show #10 models
> select subtract #10
1312 atoms, 1470 bonds, 64 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #9
2 models selected
> select subtract #9
Nothing selected
> select add #10
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> view matrix models
> #10,0.34604,0.73297,-0.58567,119.66,0.91606,-0.12907,0.37972,259.39,0.20273,-0.6679,-0.7161,239.22
> view matrix models
> #10,0.34604,0.73297,-0.58567,114.49,0.91606,-0.12907,0.37972,253.52,0.20273,-0.6679,-0.7161,191.51
> view matrix models
> #10,0.34604,0.73297,-0.58567,115.01,0.91606,-0.12907,0.37972,253.52,0.20273,-0.6679,-0.7161,165.31
> view matrix models
> #10,0.34604,0.73297,-0.58567,112.22,0.91606,-0.12907,0.37972,261.46,0.20273,-0.6679,-0.7161,188.55
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002912, steps = 124
shifted from previous position = 13.9
rotated from previous position = 4.61 degrees
atoms outside contour = 624, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.41388474 0.72586767 -0.54937741 124.68880392
0.89120067 -0.20001840 0.40712898 261.28904503
0.18563618 -0.65810999 -0.72967832 194.65012542
Axis -0.81644551 -0.56334640 0.12671840
Axis point 0.00000000 138.32510408 76.34020560
Rotation angle (degrees) 139.27994067
Shift along axis -224.33210563
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002913, steps = 48
shifted from previous position = 0.0596
rotated from previous position = 0.851 degrees
atoms outside contour = 623, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.41157433 0.73500579 -0.53886275 124.67517134
0.89190643 -0.20327389 0.40395872 261.23281813
0.18737527 -0.64687419 -0.73921870 194.64277361
Axis -0.81651764 -0.56430109 0.12191485
Axis point -0.00000000 137.11339070 76.72264514
Rotation angle (degrees) 139.94785556
Shift along axis -225.48359407
> view matrix models
> #10,0.41157,0.73501,-0.53886,118.23,0.89191,-0.20327,0.40396,258.32,0.18738,-0.64687,-0.73922,224.84
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002809, steps = 316
shifted from previous position = 7.61
rotated from previous position = 15.8 degrees
atoms outside contour = 638, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.29936551 0.88759553 -0.35007780 115.90010327
0.92729183 -0.18422816 0.32586783 251.04448456
0.22474464 -0.42217787 -0.87821164 225.07013004
Axis -0.79222884 -0.60877419 0.04204095
Axis point 0.00000000 118.20017177 98.52782254
Rotation angle (degrees) 151.82834863
Shift along axis -235.18664562
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.00281, steps = 64
shifted from previous position = 0.0916
rotated from previous position = 1.65 degrees
atoms outside contour = 641, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.29432179 0.89868189 -0.32518539 115.86708964
0.92867027 -0.18857144 0.31939369 250.95964266
0.22571265 -0.39599453 -0.89007984 225.05783626
Axis -0.79186643 -0.60979151 0.03319428
Axis point 0.00000000 115.97891021 98.94199897
Rotation angle (degrees) 153.14654107
Shift along axis -237.31368777
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002811, steps = 48
shifted from previous position = 0.0707
rotated from previous position = 1.12 degrees
atoms outside contour = 641, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.29094365 0.90573844 -0.30820394 115.83461079
0.92962736 -0.19148199 0.31484538 250.89628266
0.22615206 -0.37811708 -0.89770971 225.05423156
Axis -0.79160616 -0.61042196 0.02728953
Axis point -0.00000000 114.49694408 99.21178408
Rotation angle (degrees) 154.04316127
Shift along axis -238.70636744
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002811, steps = 44
shifted from previous position = 0.0685
rotated from previous position = 0.812 degrees
atoms outside contour = 640, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28848953 0.91064070 -0.29581633 115.79693033
0.93038515 -0.19362914 0.31127357 250.83852770
0.22617972 -0.36502229 -0.90310656 225.03623237
Axis -0.79141120 -0.61084733 0.02310524
Axis point 0.00000000 113.41850362 99.40248720
Rotation angle (degrees) 154.70543490
Shift along axis -239.66751719
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002811, steps = 28
shifted from previous position = 0.0576
rotated from previous position = 0.536 degrees
atoms outside contour = 643, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28708301 0.91373740 -0.28751924 115.75461887
0.93079352 -0.19518867 0.30907088 250.79917503
0.22628912 -0.35635004 -0.90653620 225.04612889
Axis -0.79134111 -0.61103832 0.02028372
Axis point 0.00000000 112.73230671 99.52490311
Rotation angle (degrees) 155.13770978
Shift along axis -240.28452086
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002811, steps = 40
shifted from previous position = 0.0387
rotated from previous position = 0.332 degrees
atoms outside contour = 643, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28562243 0.91574846 -0.28253244 115.76613130
0.93121293 -0.19555086 0.30757494 250.76413114
0.22641181 -0.35094816 -0.90861052 225.04810534
Axis -0.79109874 -0.61140628 0.01857781
Axis point 0.00000000 112.26974010 99.61136718
Rotation angle (degrees) 155.40459300
Shift along axis -240.72030444
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002811, steps = 40
shifted from previous position = 0.0386
rotated from previous position = 0.39 degrees
atoms outside contour = 642, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28412693 0.91804118 -0.27653623 115.74972850
0.93160470 -0.19614902 0.30600367 250.72882689
0.22668166 -0.34456634 -0.91098269 225.04734667
Axis -0.79088048 -0.61174847 0.01648881
Axis point -0.00000000 111.75246152 99.69665483
Rotation angle (degrees) 155.71380375
Shift along axis -241.21641406
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.002811, steps = 28
shifted from previous position = 0.0354
rotated from previous position = 0.28 degrees
atoms outside contour = 638, contour level = 0.0018506
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28362108 0.91948767 -0.27221591 115.71345246
0.93182666 -0.19724348 0.30462120 250.71992448
0.22640263 -0.34005504 -0.91274554 225.04208710
Axis -0.79092143 -0.61173044 0.01513810
Axis point 0.00000000 111.40907314 99.75844334
Rotation angle (degrees) 155.94912902
Shift along axis -241.48655057
> view matrix models
> #10,0.28362,0.91949,-0.27222,102.52,0.93183,-0.19724,0.30462,191.65,0.2264,-0.34006,-0.91275,251.4
> volume #6 level 0.002329
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 step 1
> volume #3 level 0.003888
> show #!9 models
> view
> ui tool show "Map Eraser"
> show #!7 models
> hide #!3 models
> hide #!6 models
> hide #!7 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #10 models
> hide #!9 models
> show #!7 models
> view orient
> view
> ui tool show "Map Eraser"
> close #1
> close #2
> close #4
> close #5
> show #!3 models
> hide #!7 models
> volume erase #3 center 223.84,223.84,223.97 radius 130.14
> undo
> hide #!7 models
> open E:/Projects/HBc_Mature/Combined_All/2x_FC_on_Cp-from-
> Job121/6f_qual/run_eq3_it025_class006.mrc
Opened run_eq3_it025_class006.mrc as #1, grid size 320,320,320, pixel 1.4,
shown at level 0.00022, step 2, values float32
> close #3
> volume erase #1 center 223.84,223.84,223.97 radius 130.14 outside true
Opened run_eq3_it025_class006.mrc copy as #2, grid size 320,320,320, pixel
1.4, shown at step 1, values float32
> volume #2 level 0.004206
> hide #!2 models
> show #!6 models
> show #8 models
> show #!2 models
> volume gaussian #2 sDev 1.5
Opened run_eq3_it025_class006.mrc copy gaussian as #3, grid size 320,320,320,
pixel 1.4, shown at step 1, values float32
> volume #3 level 0.002382
> close #3
> volume gaussian #2 sDev 2
Opened run_eq3_it025_class006.mrc copy gaussian as #3, grid size 320,320,320,
pixel 1.4, shown at step 1, values float32
> volume #3 level 0.002168
> close #3
> volume gaussian #2 sDev 1.2
Opened run_eq3_it025_class006.mrc copy gaussian as #3, grid size 320,320,320,
pixel 1.4, shown at step 1, values float32
> volume #3 level 0.002341
> close #3
> volume gaussian #2 sDev 1.5
Opened run_eq3_it025_class006.mrc copy gaussian as #3, grid size 320,320,320,
pixel 1.4, shown at step 1, values float32
> volume #3 level 0.002222
> select add #8
3034 atoms, 3400 bonds, 148 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.28323,-0.95736,0.056875,115.06,0.94468,0.28872,0.1556,245.66,-0.16538,0.0096592,0.98618,223.03,#10,0.28362,0.91949,-0.27222,100.48,0.93183,-0.19724,0.30462,181.56,0.2264,-0.34006,-0.91275,267.09
> fitmap #10 inMap #6
Fit molecule A_DNA.pdb (#10) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1722 atoms
average map value = 0.001634, steps = 224
shifted from previous position = 25.6
rotated from previous position = 23.7 degrees
atoms outside contour = 1191, contour level = 0.0023291
Position of A_DNA.pdb (#10) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
-0.06574309 0.88393896 -0.46295763 117.24528902
0.94992491 0.19748259 0.24216375 191.42983512
0.30548404 -0.42385439 -0.85265875 250.25237332
Axis -0.65357586 -0.75408595 0.06475323
Axis point -72.18558851 0.00000000 130.33209878
Rotation angle (degrees) 149.36822895
Shift along axis -204.77858844
> fitmap #8 inMap #6
Fit molecule B_DNA.pdb (#8) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1312 atoms
average map value = 0.003495, steps = 76
shifted from previous position = 8.18
rotated from previous position = 0.651 degrees
atoms outside contour = 469, contour level = 0.0023291
Position of B_DNA.pdb (#8) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.28167455 -0.95711939 0.06768986 117.47744025
0.94512055 0.28893083 0.15253237 253.43931464
-0.16554938 0.02101059 0.98597767 223.72692243
Axis -0.06846551 0.12141596 0.99023767
Axis point -83.90612921 203.18625366 0.00000000
Rotation angle (degrees) 73.84173601
Shift along axis 244.27125003
> view matrix models
> #8,0.28167,-0.95712,0.06769,113.96,0.94512,0.28893,0.15253,251.46,-0.16555,0.021011,0.98598,222.07,#10,-0.065743,0.88394,-0.46296,113.73,0.94992,0.19748,0.24216,189.45,0.30548,-0.42385,-0.85266,248.6
> fitmap #8 inMap #6
Fit molecule B_DNA.pdb (#8) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1312 atoms
average map value = 0.003496, steps = 76
shifted from previous position = 4.42
rotated from previous position = 1.06 degrees
atoms outside contour = 469, contour level = 0.0023291
Position of B_DNA.pdb (#8) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.27839450 -0.95667025 0.08531431 117.51929061
0.94599865 0.28847653 0.14787783 253.48741038
-0.16608149 0.03953885 0.98531904 223.71292730
Axis -0.05636019 0.13078133 0.98980795
Axis point -83.13239582 200.15591036 0.00000000
Rotation angle (degrees) 73.97271835
Shift along axis 247.96084346
> view matrix models
> #8,0.27839,-0.95667,0.085314,115.85,0.946,0.28848,0.14788,246.5,-0.16608,0.039539,0.98532,223.28,#10,-0.065743,0.88394,-0.46296,112.06,0.94992,0.19748,0.24216,182.46,0.30548,-0.42385,-0.85266,248.16
> view matrix models
> #8,0.27839,-0.95667,0.085314,116.22,0.946,0.28848,0.14788,248.1,-0.16608,0.039539,0.98532,222.45,#10,-0.065743,0.88394,-0.46296,112.43,0.94992,0.19748,0.24216,184.06,0.30548,-0.42385,-0.85266,247.33
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.26075,-0.49316,0.82994,115.97,0.90701,0.4196,-0.035633,248.07,-0.33067,0.76206,0.55671,222.24,#10,0.40594,0.26865,-0.87352,117.89,0.88336,0.12969,0.4504,182.07,0.23429,-0.95447,-0.18467,241.62
> view matrix models
> #8,0.25933,-0.56721,0.78168,116.01,0.96251,0.21839,-0.16086,248.14,-0.07947,0.79409,0.60258,222.13,#10,0.35788,0.34269,-0.86861,118.33,0.8046,0.35889,0.4731,179.44,0.47386,-0.8682,-0.14729,225.22
> fitmap #8 inMap #6
Fit molecule B_DNA.pdb (#8) to map run_eq3_it025_class006.mrc gaussian (#6)
using 1312 atoms
average map value = 0.003513, steps = 92
shifted from previous position = 9.9
rotated from previous position = 6.08 degrees
atoms outside contour = 451, contour level = 0.0023291
Position of B_DNA.pdb (#8) relative to run_eq3_it025_class006.mrc gaussian
(#6) coordinates:
Matrix rotation and translation
0.16835064 -0.60383771 0.77912649 117.96358265
0.97908338 0.19404756 -0.06116604 257.70716229
-0.11425324 0.77312713 0.62387549 223.52455888
Axis 0.41715641 0.44670038 0.79147918
Axis point -65.97335805 50.47534600 0.00000000
Rotation angle (degrees) 90.39323267
Shift along axis 341.24218798
Opened B_DNA.pdb map 10 as #4, grid size 52,25,30, pixel 3.33, shown at level
0.0414, step 1, values float32
Opened B_DNA.pdb map 10 as #5, grid size 52,25,30, pixel 3.33, shown at level
0.0414, step 1, values float32
> fitmap #8 inMap #6 resolution 10
Fit map B_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 1153
points
correlation = 0.6978, correlation about mean = 0.4397, overlap = 0.7583
steps = 84, shift = 0.296, angle = 2.32 degrees
Position of B_DNA.pdb map 10 (#5) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.16886060 -0.57411087 0.80117589 118.09951811
0.98008955 0.18394523 -0.07475707 257.94950558
-0.10445363 0.79784764 0.59374117 223.61362170
Axis 0.43645827 0.45297657 0.77737790
Axis point -68.18140754 44.24540203 0.00000000
Rotation angle (degrees) 91.53149813
Shift along axis 342.22288262
Average map value = 0.00351 for 1312 atoms, 447 outside contour
> close #5
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.2022
> select add #4
3034 atoms, 3400 bonds, 148 residues, 4 models selected
> view matrix models
> #8,0.080271,0.79584,0.60017,117.69,0.98092,-0.17002,0.094249,258.05,0.17704,0.58115,-0.7943,224.04,#10,0.62417,-0.77585,-0.092086,105.13,0.77763,0.60551,0.16928,185.36,-0.07558,-0.17727,0.98126,197.1,#4,0.08802,0.78972,0.60712,117.69,0.98059,-0.17589,0.086625,258.05,0.1752,0.58771,-0.78988,224.04
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.080271,0.79584,0.60017,113.73,0.98092,-0.17002,0.094249,260.98,0.17704,0.58115,-0.7943,175.28,#10,0.62417,-0.77585,-0.092086,101.17,0.77763,0.60551,0.16928,188.29,-0.07558,-0.17727,0.98126,148.34,#4,0.080271,0.79584,0.60017,113.74,0.98092,-0.17002,0.094249,260.97,0.17704,0.58115,-0.7943,175.43
> view matrix models
> #8,0.080271,0.79584,0.60017,113.75,0.98092,-0.17002,0.094249,260.95,0.17704,0.58115,-0.7943,175.57,#10,0.62417,-0.77585,-0.092086,101.19,0.77763,0.60551,0.16928,188.27,-0.07558,-0.17727,0.98126,148.64,#4,0.080271,0.79584,0.60017,113.69,0.98092,-0.17002,0.094249,260.67,0.17704,0.58115,-0.7943,175.55
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.32035,0.62556,0.71137,113.85,-0.90851,-0.41557,-0.043686,261.49,0.2683,-0.66028,0.70146,175.36,#10,0.30575,-0.86584,-0.39602,135.21,-0.88179,-0.10063,-0.46078,336.73,0.35911,0.49009,-0.79426,168.37,#4,-0.32157,0.62644,0.71004,113.85,-0.9105,-0.41046,-0.050217,261.49,0.25998,-0.66264,0.70236,175.36
> view matrix models
> #8,-0.37756,0.10639,0.91985,114.04,-0.86427,-0.39709,-0.30882,261.56,0.33241,-0.91159,0.24187,175.61,#10,0.19946,-0.5228,-0.82879,148.17,-0.97516,-0.022729,-0.22035,331.29,0.096359,0.85216,-0.51434,163.8,#4,-0.37031,0.11053,0.92231,114.03,-0.86772,-0.39555,-0.30099,261.56,0.33155,-0.91177,0.24239,175.61
> view matrix models
> #8,-0.42535,0.18804,0.88528,114.03,-0.90043,0.010608,-0.43488,261.45,-0.091166,-0.9821,0.16481,175.77,#10,0.16987,-0.60468,-0.77814,150.52,-0.93739,-0.34277,0.061719,327.66,-0.30404,0.71894,-0.62505,197,#4,-0.42589,0.18986,0.88463,114.03,-0.89928,0.018796,-0.43698,261.45,-0.099591,-0.98163,0.16273,175.77
> view matrix models
> #8,-0.42711,0.19417,0.88311,114.03,-0.89628,0.038064,-0.44185,261.44,-0.11941,-0.98023,0.15777,175.78,#10,0.16932,-0.61002,-0.77408,150.55,-0.92881,-0.36143,0.081663,326.92,-0.3296,0.70515,-0.62779,199.12,#4,-0.42807,0.19784,0.88182,114.03,-0.89342,0.054387,-0.44591,261.44,-0.13618,-0.97872,0.15348,175.78
> view matrix models
> #8,-0.4268,0.19304,0.8835,114.03,-0.8971,0.033049,-0.44059,261.45,-0.11425,-0.98063,0.15907,175.78,#10,0.16941,-0.60905,-0.77483,150.55,-0.93044,-0.35805,0.078011,327.06,-0.32494,0.70772,-0.62734,198.73,#4,-0.4273,0.19487,0.88286,114.03,-0.89575,0.041219,-0.44264,261.44,-0.12265,-0.97996,0.15695,175.78
> view matrix models
> #8,0.39821,-0.35626,-0.84528,114.39,0.91663,0.1897,0.35187,260.76,0.034991,-0.91493,0.4021,175.65,#10,-0.22519,0.71891,0.65762,82.509,0.9724,0.20817,0.10541,190.05,-0.061113,0.6632,-0.74594,187.93,#4,0.39022,-0.35719,-0.84861,114.39,0.92002,0.1872,0.34426,260.76,0.035894,-0.91508,0.40167,175.65
> view matrix models
> #8,0.39887,-0.35443,-0.84574,114.39,0.91597,0.19775,0.34912,260.75,0.043507,-0.91393,0.40352,175.65,#10,-0.2243,0.71785,0.65907,82.43,0.97306,0.20194,0.11121,189.97,-0.053265,0.66626,-0.74381,187.27,#4,0.39952,-0.35259,-0.84621,114.39,0.91525,0.20579,0.34637,260.75,0.052017,-0.91287,0.40492,175.64
> view matrix models
> #8,0.46894,-0.34407,-0.81345,114.35,0.87997,0.26107,0.39686,260.72,0.075825,-0.90192,0.4252,175.63,#10,-0.14856,0.73573,0.66078,77.08,0.98882,0.119,0.089805,192.2,-0.012564,0.66674,-0.74519,184.75,#4,0.46903,-0.35188,-0.81006,114.35,0.88012,0.26257,0.39554,260.72,0.073512,-0.89847,0.43285,175.63
> view matrix models
> #8,0.46459,-0.35705,-0.81035,114.35,0.88536,0.20519,0.41718,260.73,0.017323,-0.91127,0.41145,175.65,#10,-0.15462,0.74342,0.65071,77.615,0.98554,0.16227,0.048794,192.69,-0.069318,0.64885,-0.75776,189.31,#4,0.46391,-0.35889,-0.80993,114.36,0.88584,0.19716,0.42002,260.73,0.0089474,-0.91232,0.40939,175.65
> view matrix models
> #8,0.42611,-0.35419,-0.83245,114.37,0.90435,0.19134,0.3815,260.75,0.024153,-0.91539,0.40184,175.65,#10,-0.1957,0.72773,0.65736,80.404,0.97816,0.19274,0.077832,191.17,-0.070057,0.65823,-0.74955,188.78,#4,0.41824,-0.35513,-0.83604,114.37,0.90799,0.18886,0.37401,260.75,0.02507,-0.91554,0.40144,175.65
> show #10 models
> select subtract #8
1722 atoms, 1930 bonds, 84 residues, 3 models selected
> select add #4
1722 atoms, 1930 bonds, 84 residues, 5 models selected
> select subtract #4
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> view matrix models
> #10,-0.17248,0.68394,0.70886,80.425,0.96132,-0.040021,0.27252,191.36,0.21476,0.72844,-0.65058,188.57
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.17248,0.68394,0.70886,100.51,0.96132,-0.040021,0.27252,268.48,0.21476,0.72844,-0.65058,224.4
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.096039,0.64119,0.76135,100.38,0.96444,-0.24917,0.088183,268.59,0.24624,0.72581,-0.64232,224.38
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.096039,0.64119,0.76135,110.77,0.96444,-0.24917,0.088183,260.98,0.24624,0.72581,-0.64232,225.69
> fitmap #8 inMap #6 resolution 10
Fit map B_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 535
points
correlation = 0.09428, correlation about mean = -0.01346, overlap = 0.004369
steps = 448, shift = 19.6, angle = 19.7 degrees
Position of B_DNA.pdb map 10 (#4) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.10582682 -0.40236487 -0.90934220 98.67526880
0.99285210 -0.00799527 0.11908322 258.11265913
-0.05518534 -0.91544449 0.39864268 164.30555976
Axis -0.53448001 -0.44129293 0.72082707
Axis point -16.76138697 218.45094274 -0.00000000
Rotation angle (degrees) 104.58185496
Shift along axis -48.20735562
Average map value = 2.784e-05 for 1312 atoms, 1307 outside contour
Opened A_DNA.pdb map 10 as #5, grid size 52,25,30, pixel 3.33, shown at level
0.0538, step 1, values float32
Opened A_DNA.pdb map 10 as #12, grid size 52,25,30, pixel 3.33, shown at level
0.0538, step 1, values float32
> fitmap #10 inMap #6 resolution 10
Fit map A_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 1378
points
correlation = 0.6458, correlation about mean = 0.3348, overlap = 0.8282
steps = 1248, shift = 14.6, angle = 113 degrees
Position of A_DNA.pdb map 10 (#12) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.54960979 0.38762188 -0.74005296 122.94902316
0.82329761 -0.10093982 0.55856265 269.70589537
0.14181029 -0.91627532 -0.37460567 225.13308384
Axis -0.83194913 -0.49745490 0.24576262
Axis point 0.00000000 196.28129086 65.32711982
Rotation angle (degrees) 117.57878357
Shift along axis -181.12455473
Average map value = 0.002814 for 1722 atoms, 759 outside contour
> volume #12 level 0.2326
> select add #12
1722 atoms, 1930 bonds, 84 residues, 3 models selected
> select subtract #10
2 models selected
> view matrix models
> #12,0.54961,0.38762,-0.74005,126.46,0.8233,-0.10094,0.55856,269.77,0.14181,-0.91628,-0.37461,206.99
> fitmap #10 inMap #6 resolution 10
Fit map A_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 1378
points
correlation = 0.6459, correlation about mean = 0.3344, overlap = 0.8283
steps = 44, shift = 0.0884, angle = 1.19 degrees
Position of A_DNA.pdb map 10 (#5) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.55190192 0.37010664 -0.74727865 123.00874116
0.82237613 -0.09303912 0.56128536 269.77531512
0.13820929 -0.92431858 -0.35571532 225.13409020
Axis -0.83104216 -0.49533916 0.25299813
Axis point 0.00000000 198.62016867 64.02999430
Rotation angle (degrees) 116.64275893
Shift along axis -178.89722436
Average map value = 0.002814 for 1722 atoms, 761 outside contour
> fitmap #8 inMap #6 resolution 10
Fit map B_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 535
points
correlation = 0.09428, correlation about mean = -0.01346, overlap = 0.004369
steps = 448, shift = 19.6, angle = 19.7 degrees
Position of B_DNA.pdb map 10 (#4) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.10582682 -0.40236487 -0.90934220 98.67526880
0.99285210 -0.00799527 0.11908322 258.11265913
-0.05518534 -0.91544449 0.39864268 164.30555976
Axis -0.53448001 -0.44129293 0.72082707
Axis point -16.76138697 218.45094274 -0.00000000
Rotation angle (degrees) 104.58185496
Shift along axis -48.20735562
Average map value = 2.784e-05 for 1312 atoms, 1307 outside contour
> hide #10 models
> hide #8 models
> show #8 models
> select add #8
1312 atoms, 1470 bonds, 64 residues, 3 models selected
> view matrix models
> #8,0.42611,-0.35419,-0.83245,113.84,0.90435,0.19134,0.3815,261.54,0.024153,-0.91539,0.40184,180.19,#12,0.54961,0.38762,-0.74005,125.93,0.8233,-0.10094,0.55856,270.57,0.14181,-0.91628,-0.37461,211.52
> undo
> select subtract #12
1312 atoms, 1470 bonds, 64 residues, 1 model selected
> view matrix models
> #8,0.42611,-0.35419,-0.83245,113.79,0.90435,0.19134,0.3815,262.21,0.024153,-0.91539,0.40184,181.97
> undo
> hide #8 models
> show #8 models
> select subtract #8
Nothing selected
> select add #8
1312 atoms, 1470 bonds, 64 residues, 1 model selected
> hide #!4 models
> select subtract #8
Nothing selected
> select add #8
1312 atoms, 1470 bonds, 64 residues, 1 model selected
> view matrix models
> #8,0.42611,-0.35419,-0.83245,106.61,0.90435,0.19134,0.3815,263.14,0.024153,-0.91539,0.40184,221.52
> fitmap #8 inMap #6 resolution 10
Fit map B_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 535
points
correlation = 0.811, correlation about mean = 0.2909, overlap = 0.6815
steps = 596, shift = 19.4, angle = 33 degrees
Position of B_DNA.pdb map 10 (#4) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.37407360 0.17714676 -0.91032302 114.96991669
0.92394806 0.01341363 0.38228272 245.98889095
0.07993088 -0.98409305 -0.15865672 224.75906474
Axis -0.74044467 -0.53662267 0.40469471
Axis point 0.00000000 205.36106857 63.63086024
Rotation angle (degrees) 112.68004634
Shift along axis -126.17327291
Average map value = 0.003559 for 1312 atoms, 432 outside contour
> fitmap #10 inMap #6 resolution 10
Fit map A_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 1378
points
correlation = 0.6461, correlation about mean = 0.334, overlap = 0.8285
steps = 64, shift = 0.204, angle = 2.36 degrees
Position of A_DNA.pdb map 10 (#5) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.55588260 0.33500160 -0.76076836 123.08234928
0.82091996 -0.07732810 0.56578336 269.96186728
0.13070956 -0.93903904 -0.31799484 225.13335981
Axis -0.82896298 -0.49108930 0.26767832
Axis point 0.00000000 203.33326766 61.35325018
Rotation angle (degrees) 114.81692190
Shift along axis -174.34277709
Average map value = 0.002815 for 1722 atoms, 761 outside contour
> fitmap #10 inMap #6 resolution 10
Fit map A_DNA.pdb map 10 in map run_eq3_it025_class006.mrc gaussian using 1378
points
correlation = 0.6464, correlation about mean = 0.3337, overlap = 0.8286
steps = 48, shift = 0.133, angle = 1.26 degrees
Position of A_DNA.pdb map 10 (#5) relative to run_eq3_it025_class006.mrc
gaussian (#6) coordinates:
Matrix rotation and translation
0.55842576 0.31598303 -0.76701723 123.13581749
0.81982648 -0.06902883 0.56843610 270.08315817
0.12666985 -0.94625038 -0.29759873 225.13248532
Axis -0.82795593 -0.48850606 0.27541025
Axis point 0.00000000 205.90965936 59.82523381
Rotation angle (degrees) 113.83479702
Shift along axis -171.88449718
Average map value = 0.002815 for 1722 atoms, 763 outside contour
> save D:/HBc_Mature/2025_0520/Fig3_A-form_B-form_DNA/Fig_FC/FC3.cxs
> includeMaps true
——— End of log from Fri Jul 17 22:49:11 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show Orthopick
> ui tool show LocScale-SURFER
LocScale-SURFER tool initialized.
Segment and hide micelle densities in cryo-EM maps.
Use unsharpened halfmaps as input, and optionally a mask map to speed up
computation. Recommended to use GPUs
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> undo
> color #6 #61616133 models
> hide sel atoms
[Repeated 2 time(s)]
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> select add #8.1
1312 atoms, 1470 bonds, 64 residues, 5 models selected
> select subtract #8.1
656 atoms, 735 bonds, 32 residues, 3 models selected
> hide #!8.1 models
> show #8.1 models
> close #8.1
> close #8.2
> ui tool show "Minimize Structure"
> minimize #8
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Summary of feedback from adding hydrogens to B_DNA.pdb #8
---
warnings | Not adding hydrogens to B_DNA.pdb #8/A A 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A A 1 C2' because it is missing heavy-
atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A C 3 C2' because it is missing heavy-
atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A G 4 C2' because it is missing heavy-
atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A A 5 C2' because it is missing heavy-
atom bond partners
45 messages similar to the above omitted
notes | No usable SEQRES records for B_DNA.pdb (#8) chain A; guessing termini instead
No usable SEQRES records for B_DNA.pdb (#8) chain B; guessing termini instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
96 hydrogen bonds
626 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
B_DNA.pdb #8: B_DNA.pdb #8/A A 1: -1.1436, B_DNA.pdb #8/A C 3: -1.1436,
B_DNA.pdb #8/A G 4: -1.1436, B_DNA.pdb #8/A A 5: -1.1436, B_DNA.pdb #8/A C 7:
-1.1436, B_DNA.pdb #8/A G 8: -1.1436, B_DNA.pdb #8/A A 9: -1.1436, B_DNA.pdb
#8/A C 11: -1.1436, B_DNA.pdb #8/A G 12: -1.1436, B_DNA.pdb #8/A A 13:
-1.1436, B_DNA.pdb #8/A C 15: -1.1436, B_DNA.pdb #8/A G 16: -1.1436, B_DNA.pdb
#8/A A 17: -1.1436, B_DNA.pdb #8/A C 19: -1.1436, B_DNA.pdb #8/A G 20:
-1.1436, B_DNA.pdb #8/A A 21: -1.1436, B_DNA.pdb #8/A C 23: -1.1436, B_DNA.pdb
#8/A G 24: -1.1436, B_DNA.pdb #8/A A 25: -1.1436, B_DNA.pdb #8/A C 27:
-1.1436, B_DNA.pdb #8/A G 28: -1.1436, B_DNA.pdb #8/A A 29: -1.1436, B_DNA.pdb
#8/A C 31: -1.1436, B_DNA.pdb #8/A G 32: -0.8357, B_DNA.pdb #8/B C 1: -1.1436,
B_DNA.pdb #8/B G 2: -1.1436, B_DNA.pdb #8/B A 3: -1.1436, B_DNA.pdb #8/B C 5:
-1.1436, B_DNA.pdb #8/B G 6: -1.1436, B_DNA.pdb #8/B A 7: -1.1436, B_DNA.pdb
#8/B C 9: -1.1436, B_DNA.pdb #8/B G 10: -1.1436, B_DNA.pdb #8/B A 11: -1.1436,
B_DNA.pdb #8/B C 13: -1.1436, B_DNA.pdb #8/B G 14: -1.1436, B_DNA.pdb #8/B A
15: -1.1436, B_DNA.pdb #8/B C 17: -1.1436, B_DNA.pdb #8/B G 18: -1.1436,
B_DNA.pdb #8/B A 19: -1.1436, B_DNA.pdb #8/B C 21: -1.1436, B_DNA.pdb #8/B G
22: -1.1436, B_DNA.pdb #8/B A 23: -1.1436, B_DNA.pdb #8/B C 25: -1.1436,
B_DNA.pdb #8/B G 26: -1.1436, B_DNA.pdb #8/B A 27: -1.1436, B_DNA.pdb #8/B C
29: -1.1436, B_DNA.pdb #8/B G 30: -1.1436, B_DNA.pdb #8/B A 31: -1.1436, and
B_DNA.pdb #8/B T 32: -0.6921
Dock prep finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 203, in _minimize
cx_atom = name_lookup[cx_res][omm_atom.name]
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
KeyError: 'OP3'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 116, in minimize
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in cmd_minimize
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 150, in prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps
callback()
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 149, in <lambda>
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 45, in <lambda>
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 207, in _minimize
omm_atom.type = prefix + op2.gaff_type
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'gaff_type'
AttributeError: 'NoneType' object has no attribute 'gaff_type'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 207, in _minimize
omm_atom.type = prefix + op2.gaff_type
^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Minimize Structure"
> minimize #8 logEnergy true
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Summary of feedback from adding hydrogens to B_DNA.pdb #8
---
warnings | Not adding hydrogens to B_DNA.pdb #8/A A 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A A 1 C2' because it is missing heavy-
atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A C 3 C2' because it is missing heavy-
atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A G 4 C2' because it is missing heavy-
atom bond partners
Not adding hydrogens to B_DNA.pdb #8/A A 5 C2' because it is missing heavy-
atom bond partners
45 messages similar to the above omitted
notes | No usable SEQRES records for B_DNA.pdb (#8) chain A; guessing termini instead
No usable SEQRES records for B_DNA.pdb (#8) chain B; guessing termini instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
96 hydrogen bonds
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
B_DNA.pdb #8: B_DNA.pdb #8/A A 1: -1.1436, B_DNA.pdb #8/A C 3: -1.1436,
B_DNA.pdb #8/A G 4: -1.1436, B_DNA.pdb #8/A A 5: -1.1436, B_DNA.pdb #8/A C 7:
-1.1436, B_DNA.pdb #8/A G 8: -1.1436, B_DNA.pdb #8/A A 9: -1.1436, B_DNA.pdb
#8/A C 11: -1.1436, B_DNA.pdb #8/A G 12: -1.1436, B_DNA.pdb #8/A A 13:
-1.1436, B_DNA.pdb #8/A C 15: -1.1436, B_DNA.pdb #8/A G 16: -1.1436, B_DNA.pdb
#8/A A 17: -1.1436, B_DNA.pdb #8/A C 19: -1.1436, B_DNA.pdb #8/A G 20:
-1.1436, B_DNA.pdb #8/A A 21: -1.1436, B_DNA.pdb #8/A C 23: -1.1436, B_DNA.pdb
#8/A G 24: -1.1436, B_DNA.pdb #8/A A 25: -1.1436, B_DNA.pdb #8/A C 27:
-1.1436, B_DNA.pdb #8/A G 28: -1.1436, B_DNA.pdb #8/A A 29: -1.1436, B_DNA.pdb
#8/A C 31: -1.1436, B_DNA.pdb #8/A G 32: -0.8357, B_DNA.pdb #8/B C 1: -1.1436,
B_DNA.pdb #8/B G 2: -1.1436, B_DNA.pdb #8/B A 3: -1.1436, B_DNA.pdb #8/B C 5:
-1.1436, B_DNA.pdb #8/B G 6: -1.1436, B_DNA.pdb #8/B A 7: -1.1436, B_DNA.pdb
#8/B C 9: -1.1436, B_DNA.pdb #8/B G 10: -1.1436, B_DNA.pdb #8/B A 11: -1.1436,
B_DNA.pdb #8/B C 13: -1.1436, B_DNA.pdb #8/B G 14: -1.1436, B_DNA.pdb #8/B A
15: -1.1436, B_DNA.pdb #8/B C 17: -1.1436, B_DNA.pdb #8/B G 18: -1.1436,
B_DNA.pdb #8/B A 19: -1.1436, B_DNA.pdb #8/B C 21: -1.1436, B_DNA.pdb #8/B G
22: -1.1436, B_DNA.pdb #8/B A 23: -1.1436, B_DNA.pdb #8/B C 25: -1.1436,
B_DNA.pdb #8/B G 26: -1.1436, B_DNA.pdb #8/B A 27: -1.1436, B_DNA.pdb #8/B C
29: -1.1436, B_DNA.pdb #8/B G 30: -1.1436, B_DNA.pdb #8/B A 31: -1.1436, and
B_DNA.pdb #8/B T 32: -0.6921
Dock prep finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 203, in _minimize
cx_atom = name_lookup[cx_res][omm_atom.name]
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
KeyError: 'OP3'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 116, in minimize
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in cmd_minimize
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 150, in prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps
callback()
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 149, in <lambda>
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 45, in <lambda>
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 207, in _minimize
omm_atom.type = prefix + op2.gaff_type
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'gaff_type'
AttributeError: 'NoneType' object has no attribute 'gaff_type'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 207, in _minimize
omm_atom.type = prefix + op2.gaff_type
^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 596.08
OpenGL renderer: NVIDIA RTX 2000 Ada Generation Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 3591
OS: Microsoft Windows 11 Pro (Build 22631.5771)
Memory: 33,777,467,392
MaxProcessMemory: 137,438,953,344
CPU: 22 Intel(R) Core(TM) Ultra 9 185H
OSLanguage: en-US
Installed Packages:
absl-py: 2.5.0
accessible-pygments: 0.0.5
aiobotocore: 3.8.0
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aioitertools: 0.13.0
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asciitree: 0.3.3
asttokens: 3.0.1
asyncssh: 2.24.0
attrs: 26.1.0
babel: 2.18.0
backoff: 2.2.1
beautifulsoup4: 4.13.5
biopython: 1.83
blockdiag: 3.0.0
blosc2: 4.4.3
boto3: 1.43.46
botocore: 1.43.46
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
cffi: 2.1.0
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.7.0
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Clipper: 0.27
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-copick: 1.12.0
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-CubeNTube: 1.1.0
ChimeraX-DAQplugin: 1.0.7
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-InstantMap: 1.0.1
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.12.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LigandRecognizer: 0.2
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-locscalesurfer: 0.1.4
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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-OME-Zarr: 0.7.0
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-ProNA3D: 0.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RMF: 0.16
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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
click: 8.4.2
click: 8.4.1
cloudpickle: 3.1.2
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
copick: 1.26.0
copick-shared-ui: 0.6.0
coverage: 7.14.1
cryoet_data_portal: 4.8.0
cryptography: 49.0.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
dask: 2026.7.1
debugpy: 1.8.21
decorator: 5.3.1
deepmerge: 2.1.0
Deprecated: 1.3.1
DiffFit: 0.7.0
distinctipy: 1.3.4
distributed: 2026.7.1
docutils: 0.21.2
dynamotable: 0.3.0
einops: 0.8.2
emfile: 0.3.0
etils: 1.14.0
executing: 2.2.1
fasteners: 0.20
filelock: 3.19.1
finufft: 2.5.1
flatbuffers: 25.12.19
fonttools: 4.63.0
frozenlist: 1.8.0
fsspec: 2026.6.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
glfw: 2.10.0
gql: 3.5.3
grako: 3.16.5
graphql-core: 3.2.6
h11: 0.16.0
h5py: 3.16.0
hatchling: 1.31.0
hf-xet: 1.5.2
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
huggingface_hub: 1.24.0
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
ImageIO: 2.37.3
imagesize: 2.0.0
importlib_metadata: 9.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jmespath: 1.1.0
jsonpath-rw: 1.4.0
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
lazy-loader: 0.5
line_profiler: 5.0.0
linkify-it-py: 2.1.0
llvmlite: 0.48.0
locket: 1.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
mdit-py-plugins: 0.6.1
mdurl: 0.1.2
mlcroissant: 1.1.0
mpmath: 1.3.0
mrcfile: 1.5.4
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.66.0
numcodecs: 0.15.1
numexpr: 2.14.1
numpy: 1.26.4
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
ome-zarr: 0.10.3
onnxruntime-directml: 1.24.4
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
pandas: 3.0.3
pandas-stubs: 3.0.3.260530
ParmEd: 4.2.2
parso: 0.8.7
partd: 1.4.2
pathspec: 1.1.1
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
ply: 3.11
prompt_toolkit: 3.0.52
propcache: 0.5.2
protobuf: 7.35.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 25.0.0
pybind11: 3.0.1
pycollada: 0.8
pycparser: 3.0
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.20.0
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pyspnego: 0.12.1
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pywin32: 311
PyYAML: 6.0.3
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
rdflib: 7.6.0
referencing: 0.37.0
requests: 2.32.5
requests-toolbelt: 1.0.0
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 2026.5.1
s3fs: 2026.6.0
s3transfer: 0.19.1
safetensors: 0.8.0
scikit-image: 0.26.0
scipy: 1.16.3
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
smbprotocol: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.4
sshfs: 2025.11.0
sspilib: 0.5.0
stack-data: 0.6.3
starfile: 0.5.13
starlette: 1.3.0
strcase: 1.0.0
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tblib: 3.2.2
tcia_utils: 3.2.1
textual: 8.2.8
threadpoolctl: 3.6.0
tifffile: 2025.3.13
timm: 1.0.28
tinyarray: 1.2.5
toolz: 1.1.0
torch: 2.9.1
torchvision: 0.24.1
tornado: 6.5.7
tqdm: 4.67.3
tqdm: 4.68.2
traitlets: 5.14.3
trimesh: 4.12.2
trove-classifiers: 2026.6.1.19
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.2
uc-micro-py: 2.0.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
WMI: 1.5.1
wrapt: 2.2.2
yarl: 1.24.2
zarr: 2.18.7
zict: 3.0.0
zipp: 4.1.0
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