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Opened 5 months ago
Last modified 5 months ago
#18022 assigned defect
QScore: model is None
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/gautar/Documents/25HepE525K/Chimera
> sessions/ComparisonWT8actand 9gz1.cxs"
Traceback (most recent call last):
File "C:\Users\gautar\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gautar\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\qscore\ui.py", line 307, in _toggle_save_button_enabled
for atom in model.atoms:
^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'atoms'
Error processing trigger "selected model changed":
AttributeError: 'NoneType' object has no attribute 'atoms'
File "C:\Users\gautar\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\qscore\ui.py", line 307, in _toggle_save_button_enabled
for atom in model.atoms:
^^^^^^^^^^^
See log for complete Python traceback.
Opened 25HepE525K_sharp_273.mrc as #5, grid size 340,340,340, pixel 0.824,
shown at level 0.0385, step 2, values float32
Opened 25hep_WT_conf1.mrc as #2, grid size 400,400,400, pixel 0.83, shown at
level 0.0914, step 2, values float32
Opened 25HepE525K_sharp_272.ccp4 as #9, grid size 340,340,340, pixel 0.824,
shown at level 0.0373, step 2, values float32
Opened 25hep_WT_conf1.pdb map 3 as #10, grid size 98,170,186, pixel 1, shown
at level 0.115, step 1, values float32
Opened 25HepE525K_real_space_refined_231.pdb map 3 as #11, grid size
104,182,170, pixel 1, shown at level 0.113, step 1, values float32
Log from Tue Jun 17 11:50:13 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
> set selectionWidth 4
Done loading forcefield
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\gautar\\\Downloads\\\25hep_WT_conf1.pdb
Chain information for 25hep_WT_conf1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E F | No description available
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> open C:/Users/gautar/Downloads/25hep_WT_conf1.mrc
Opened 25hep_WT_conf1.mrc as #2, grid size 400,400,400, pixel 0.83, shown at
level 0.0412, step 2, values float32
> surface dust #2 size 8.3
> show cartoons
> hide atoms
> volume style image
> volume style surface
> transparency 50
> volume #2 change image level -0.01177,0 level 0.04117,0.8 level 0.6518,1
> volume #2 level 0.07381
> open C:/Users/gautar/Documents/25HepE525K/25HepE525K_sharp_273.ccp4
Opened 25HepE525K_sharp_273.ccp4 as #3, grid size 340,340,340, pixel 0.824,
shown at level 0.00383, step 2, values float32
> select add #3
2 models selected
> select subtract #3
Nothing selected
> select add #2
3 models selected
> select add #1
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> select add #2
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> select subtract #1
3 models selected
> select add #2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-19.866,0,1,0,-42.999,0,0,1,-16.309
> view matrix models #2,1,0,0,-29.92,0,1,0,-38.204,0,0,1,-9.2695
> volume sel style surface
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.95636,-0.29207,0.0079989,24.741,0.255,0.82096,-0.51088,35.299,0.14265,0.49063,0.85961,-91.245
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.95636,-0.29207,0.0079989,28.194,0.255,0.82096,-0.51088,40.964,0.14265,0.49063,0.85961,-101.56
> hide #!1 models
> fitmap #2 inMap #3
Fit map 25hep_WT_conf1.mrc in map 25HepE525K_sharp_273.ccp4 using 41401 points
correlation = 0.7127, correlation about mean = 0.5089, overlap = 1209
steps = 108, shift = 3.27, angle = 6.58 degrees
Position of 25hep_WT_conf1.mrc (#2) relative to 25HepE525K_sharp_273.ccp4 (#3)
coordinates:
Matrix rotation and translation
0.97520003 -0.20606565 0.08075799 -1.84979418
0.21751220 0.82488028 -0.52178631 51.52835827
0.04090656 0.52641188 0.84924507 -89.21663571
Axis 0.92658432 0.03522780 0.37443358
Axis point 0.00000000 159.39636636 47.50633403
Rotation angle (degrees) 34.44569169
Shift along axis -33.30446355
> select add #2
3 models selected
> show #!1 models
> select add #1
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> select add #2
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> hide #!3 models
> view matrix models
> #1,1,0,0,3.3655,0,1,0,2.0103,0,0,1,0.28686,#2,0.9752,-0.20607,0.080758,1.5157,0.21751,0.82488,-0.52179,53.539,0.040907,0.52641,0.84925,-88.93
> select add #2
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> view matrix models
> #1,1,0,0,-0.55337,0,1,0,-0.71138,0,0,1,0.23639,#2,0.9752,-0.20607,0.080758,-2.4032,0.21751,0.82488,-0.52179,50.817,0.040907,0.52641,0.84925,-88.98
> hide #!2 models
> show #!3 models
> view matrix models
> #1,1,0,0,-36.702,0,1,0,-31.63,0,0,1,4.0995,#2,0.9752,-0.20607,0.080758,-38.552,0.21751,0.82488,-0.52179,19.898,0.040907,0.52641,0.84925,-85.117
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.90967,-0.24277,0.33699,-37.121,0.38582,0.79431,-0.46927,17.34,-0.15375,0.5569,0.81622,-33.447,#2,0.84809,-0.21031,0.48632,-81.378,0.52983,0.32867,-0.78183,99.422,0.0045868,0.92073,0.39017,-77.287
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.90967,-0.24277,0.33699,-38.28,0.38582,0.79431,-0.46927,15.465,-0.15375,0.5569,0.81622,-58.956,#2,0.84809,-0.21031,0.48632,-82.538,0.52983,0.32867,-0.78183,97.548,0.0045868,0.92073,0.39017,-102.8
> fitmap #1 inMap #3
Fit molecule 25hep_WT_conf1.pdb (#1) to map 25HepE525K_sharp_273.ccp4 (#3)
using 19469 atoms
average map value = 0.2022, steps = 172
shifted from previous position = 11.7
rotated from previous position = 15.2 degrees
atoms outside contour = 3059, contour level = 0.0038275
Position of 25hep_WT_conf1.pdb (#1) relative to 25HepE525K_sharp_273.ccp4 (#3)
coordinates:
Matrix rotation and translation
0.97452461 -0.20856249 0.08248310 -1.60352266
0.22060372 0.82505126 -0.52021573 50.65054279
0.04044470 0.52515911 0.85004243 -89.05045007
Axis 0.92443764 0.03717507 0.37951688
Axis point 0.00000000 158.68013309 46.38678795
Rotation angle (degrees) 34.43085271
Shift along axis -33.39556831
> show #!2 models
> select subtract #1
3 models selected
> view matrix models
> #2,0.84809,-0.21031,0.48632,-39.896,0.52983,0.32867,-0.78183,119.02,0.0045868,0.92073,0.39017,-87.012
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.91253,-0.40901,0.0018533,63.62,0.39412,0.87809,-0.27135,-35.867,0.10936,0.24835,0.96248,-87.08
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91253,-0.40901,0.0018533,53.231,0.39412,0.87809,-0.27135,-30.988,0.10936,0.24835,0.96248,-66.406
> hide #!1 models
> fitmap #2 inMap #3
Fit map 25hep_WT_conf1.mrc in map 25HepE525K_sharp_273.ccp4 using 41401 points
correlation = 0.7127, correlation about mean = 0.5089, overlap = 1209
steps = 224, shift = 7.56, angle = 20.1 degrees
Position of 25hep_WT_conf1.mrc (#2) relative to 25HepE525K_sharp_273.ccp4 (#3)
coordinates:
Matrix rotation and translation
0.97518916 -0.20608663 0.08083563 -1.85267218
0.21757218 0.82488456 -0.52175453 51.51496547
0.04084657 0.52639695 0.84925720 -89.20708119
Axis 0.92654967 0.03534971 0.37450782
Axis point 0.00000000 159.37517047 47.49975202
Rotation angle (degrees) 34.44541038
Shift along axis -33.30430346
> show #!1 models
> volume sel style surface
> hide #!3 models
> volume sel style surface
> hide #!1 models
> volume sel style surface
> show #!1 models
> show #!3 models
> open
> C:/Users/gautar/Documents/25HepE525K/RealSpaceRefine_231/25HepE525K_real_space_refined_231.pdb
Chain information for 25HepE525K_real_space_refined_231.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F | No description available
> show cartoons
> hide atoms
> select add #2
3 models selected
> select add #2
3 models selected
> hide #!1 models
> hide #!2 models
> select add #2
3 models selected
> select add #2
3 models selected
> hide #!3 models
> hide #!4 models
> select add #2
3 models selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> select add #2
3 models selected
> select add #2
3 models selected
> open C:/Users/gautar/Documents/25HepE525K/25HepE525K_sharp_273.mrc
Opened 25HepE525K_sharp_273.mrc as #5, grid size 340,340,340, pixel 0.824,
shown at level 0.00383, step 2, values float32
> hide #!2 models
> show #!2 models
> hide #!3 models
> select add #2
3 models selected
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!5 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!3 models
> volume #2 level 0.09191
> hide #!4 models
> show #!4 models
> show #!5 models
> transparency sel 0
> hide #!4 models
> hide #!1 models
> show #!1 models
> transparency sel 50
> show #!4 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> transparency sel 0
> transparency sel 50
> select add #2
3 models selected
> hide #!2 models
> transparency #5.1 50
> show #!2 models
> volume #2 level 0.1161
> volume #3 level 0.1253
> hide #!1 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> volume #5 level 0.1079
> show #!1 models
> hide #!5 models
> volume #2 level 0.08634
> hide #!2 models
> show #!1 atoms
> hide #!1 atoms
> show #!1 atoms
> style #!1 ball
Changed 19469 atom styles
> show #!2 models
> open C:/Users/gautar/Documents/25HepE525K/25Hep-WT-conf1-refined.pdb
Summary of feedback from opening C:/Users/gautar/Documents/25HepE525K/25Hep-
WT-conf1-refined.pdb
---
warnings | Start residue of secondary structure not found: HELIX 57 57 ASP B 945 GLU B 949 1 5
Start residue of secondary structure not found: HELIX 58 58 ARG B 952 LEU B
961 1 10
End residue of secondary structure not found: HELIX 106 106 ASP A 906 THR A
960 1 55
Start residue of secondary structure not found: HELIX 107 107 LEU A 961 LYS A
963 1 3
Chain information for 25Hep-WT-conf1-refined.pdb #6
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E F | No description available
> select add #6
19469 atoms, 19828 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> view matrix models
> #2,0.97519,-0.20609,0.080836,-25.684,0.21757,0.82488,-0.52175,11.944,0.040847,0.5264,0.84926,-116.22,#6,1,0,0,-23.832,0,1,0,-39.571,0,0,1,-27.016
> undo
> hide #!2 models
> show #!5 models
> hide #!1 models
> view matrix models
> #2,0.97519,-0.20609,0.080836,-24.525,0.21757,0.82488,-0.52175,13.725,0.040847,0.5264,0.84926,-114.54,#6,1,0,0,-22.672,0,1,0,-37.79,0,0,1,-25.328
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75246,-0.62184,0.21707,77.789,0.48049,0.29286,-0.82666,117.73,0.45047,0.72633,0.51916,-178.6,#6,0.87949,-0.46248,-0.11225,93.229,0.34139,0.77743,-0.52825,31.189,0.33158,0.42627,0.84163,-124.87
> fitmap #6 inMap #5
Fit molecule 25Hep-WT-conf1-refined.pdb (#6) to map 25HepE525K_sharp_273.mrc
(#5) using 19469 atoms
average map value = 0.2008, steps = 192
shifted from previous position = 11.3
rotated from previous position = 19.2 degrees
atoms outside contour = 9854, contour level = 0.10795
Position of 25Hep-WT-conf1-refined.pdb (#6) relative to
25HepE525K_sharp_273.mrc (#5) coordinates:
Matrix rotation and translation
0.97458785 -0.20834127 0.08229476 -1.61543684
0.22031168 0.82504662 -0.52034684 50.70528086
0.04051271 0.52525421 0.84998043 -89.07352338
Axis 0.92463362 0.03694822 0.37906133
Axis point 0.00000000 158.75268004 46.43914586
Rotation angle (degrees) 34.43102490
Shift along axis -33.38454608
> show sel cartoons
> hide sel atoms
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!6 models
> view matrix models
> #2,0.87123,0.061431,0.48701,-100.84,0.20082,0.8607,-0.46783,8.529,-0.44791,0.50539,0.73753,-31.633,#6,0.74015,0.2398,0.62822,-98.769,-0.29217,0.95614,-0.020755,40.131,-0.60565,-0.16818,0.77776,101.82
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.87123,0.061431,0.48701,-98.565,0.20082,0.8607,-0.46783,29.366,-0.44791,0.50539,0.73753,13.29,#6,0.74015,0.2398,0.62822,-96.495,-0.29217,0.95614,-0.020755,60.968,-0.60565,-0.16818,0.77776,146.74
> fitmap #2 inMap #5
Fit map 25hep_WT_conf1.mrc in map 25HepE525K_sharp_273.mrc using 33578 points
correlation = 0.7253, correlation about mean = 0.4809, overlap = 1175
steps = 312, shift = 10.4, angle = 29.1 degrees
Position of 25hep_WT_conf1.mrc (#2) relative to 25HepE525K_sharp_273.mrc (#5)
coordinates:
Matrix rotation and translation
0.97513265 -0.20629868 0.08097621 -1.83424539
0.21782718 0.82484248 -0.52171466 51.46242453
0.04083642 0.52637982 0.84926830 -89.20485130
Axis 0.92639485 0.03547895 0.37487842
Axis point 0.00000000 159.32080080 47.41700790
Rotation angle (degrees) 34.44984091
Shift along axis -33.31437654
> show #!1 models
> show #!6 models
> select subtract #6
3 models selected
> hide #!5 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> select add #6
19469 atoms, 19828 bonds, 4 pseudobonds, 2415 residues, 5 models selected
> view matrix models
> #2,0.97513,-0.2063,0.080976,-26.526,0.21783,0.82484,-0.52171,8.9588,0.040836,0.52638,0.84927,-102.48,#6,0.74015,0.2398,0.62822,-121.19,-0.29217,0.95614,-0.020755,18.464,-0.60565,-0.16818,0.77776,133.46
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.037802,-0.99915,-0.016505,326.58,0.21885,0.024393,-0.97545,228.5,0.97503,0.033262,0.21958,-102.19,#6,0.74081,-0.62339,-0.25018,169,0.41582,0.7181,-0.55806,31.411,0.52754,0.30938,0.79119,-134.51
> view matrix models
> #2,-0.13408,-0.98341,0.12221,337.05,0.19756,-0.14737,-0.96915,264,0.97108,-0.1058,0.21404,-74.507,#6,0.57884,-0.77427,-0.25584,221.75,0.52281,0.59315,-0.61224,43.77,0.62579,0.22063,0.74813,-128.62
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.13408,-0.98341,0.12221,325.13,0.19756,-0.14737,-0.96915,276.22,0.97108,-0.1058,0.21404,-62.98,#6,0.57884,-0.77427,-0.25584,209.83,0.52281,0.59315,-0.61224,55.995,0.62579,0.22063,0.74813,-117.1
> fitmap #6 inMap #5
Fit molecule 25Hep-WT-conf1-refined.pdb (#6) to map 25HepE525K_sharp_273.mrc
(#5) using 19469 atoms
average map value = 0.2008, steps = 412
shifted from previous position = 4.5
rotated from previous position = 45.4 degrees
atoms outside contour = 9851, contour level = 0.10795
Position of 25Hep-WT-conf1-refined.pdb (#6) relative to
25HepE525K_sharp_273.mrc (#5) coordinates:
Matrix rotation and translation
0.97457903 -0.20835613 0.08236165 -1.62102440
0.22036169 0.82506579 -0.52029526 50.68621742
0.04045293 0.52521820 0.85000552 -89.06204907
Axis 0.92459844 0.03706192 0.37913603
Axis point 0.00000000 158.72988982 46.42808400
Rotation angle (degrees) 34.42922938
Shift along axis -33.38690037
> show #!2 models
> select subtract #6
3 models selected
> hide #!6 models
> view matrix models
> #2,-0.13408,-0.98341,0.12221,319.61,0.19756,-0.14737,-0.96915,297.37,0.97108,-0.1058,0.21404,-62.9
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.9639,-0.23314,0.12858,14.126,0.25611,0.67995,-0.68708,102.45,0.072763,0.69521,0.71512,-133.99
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.9639,-0.23314,0.12858,14.668,0.25611,0.67995,-0.68708,99.364,0.072763,0.69521,0.71512,-105
> fitmap #2 inMap #5
Fit map 25hep_WT_conf1.mrc in map 25HepE525K_sharp_273.mrc using 33578 points
correlation = 0.406, correlation about mean = 0.09803, overlap = 406.7
steps = 160, shift = 17.6, angle = 13 degrees
Position of 25hep_WT_conf1.mrc (#2) relative to 25HepE525K_sharp_273.mrc (#5)
coordinates:
Matrix rotation and translation
0.97849271 -0.12908159 0.16090353 -26.25809421
0.19693977 0.81664315 -0.54250224 68.89005034
-0.06137372 0.56252280 0.82450067 -74.77914575
Axis 0.94176002 0.18943627 0.27785242
Axis point 0.00000000 144.79002866 89.38243641
Rotation angle (degrees) 35.92182016
Shift along axis -32.45611545
> show #!6 models
> show #!1 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> fitmap #6 inMap #2
Fit molecule 25Hep-WT-conf1-refined.pdb (#6) to map 25hep_WT_conf1.mrc (#2)
using 19469 atoms
average map value = 0.1528, steps = 144
shifted from previous position = 9.52
rotated from previous position = 6.54 degrees
atoms outside contour = 5434, contour level = 0.086342
Position of 25Hep-WT-conf1-refined.pdb (#6) relative to 25hep_WT_conf1.mrc
(#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00001064 0.00007043 -0.01866885
0.00001064 1.00000000 0.00002829 0.00067846
-0.00007043 -0.00002829 1.00000000 0.01639743
Axis -0.36914921 0.91894444 0.13881634
Axis point 213.50668470 0.00000000 213.75354447
Rotation angle (degrees) 0.00439137
Shift along axis 0.00979129
> show #!1 models
> hide #!6 models
> fitmap #1 inMap #2
Fit molecule 25hep_WT_conf1.pdb (#1) to map 25hep_WT_conf1.mrc (#2) using
19469 atoms
average map value = 0.1541, steps = 128
shifted from previous position = 9.5
rotated from previous position = 6.54 degrees
atoms outside contour = 5264, contour level = 0.086342
Position of 25hep_WT_conf1.pdb (#1) relative to 25hep_WT_conf1.mrc (#2)
coordinates:
Matrix rotation and translation
1.00000000 0.00000755 0.00008759 -0.02505777
-0.00000756 1.00000000 0.00011458 -0.02184863
-0.00008759 -0.00011458 1.00000000 0.02783871
Axis -0.79335868 0.60650199 -0.05231952
Axis point 0.00000000 245.31239978 218.08355698
Rotation angle (degrees) 0.00827461
Shift along axis 0.00517206
> show #!6 models
> hide #!2 models
> color #6 #454fdeff
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> open C:/Users/gautar/Documents/25HepE525K/8ACT.cif-coot-0.pdb
Summary of feedback from opening
C:/Users/gautar/Documents/25HepE525K/8ACT.cif-coot-0.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA1 4 ASP A 34 PRO A 38 0
Start residue of secondary structure not found: SHEET 2 AA1 4 PHE A 44 GLU A
53 -1
Start residue of secondary structure not found: SHEET 3 AA1 4 LYS A 56 THR A
61 -1
Start residue of secondary structure not found: SHEET 4 AA1 4 THR A 66 LYS A
70 -1
Start residue of secondary structure not found: SHEET 1 AA2 7 TYR A 113 SER A
116 0
48 messages similar to the above omitted
Chain information for 8ACT.cif-coot-0.pdb #7
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show #!1,6-7 cartoons
Computing secondary structure
> hide #!1,6-7 atoms
> show #!2 models
> hide #!1 models
> hide #!6 models
> fitmap #7 inMap #2
Fit molecule 8ACT.cif-coot-0.pdb (#7) to map 25hep_WT_conf1.mrc (#2) using
18834 atoms
average map value = 0.1289, steps = 116
shifted from previous position = 9.54
rotated from previous position = 6.63 degrees
atoms outside contour = 7483, contour level = 0.086342
Position of 8ACT.cif-coot-0.pdb (#7) relative to 25hep_WT_conf1.mrc (#2)
coordinates:
Matrix rotation and translation
0.97721131 0.20742107 0.04510620 -5.36933358
-0.19973504 0.82657259 0.52619738 3.20817983
0.07186088 -0.52321531 0.84916534 104.26276410
Axis -0.93202589 -0.02376191 -0.36161183
Axis point 0.00000000 162.51159141 48.94469584
Rotation angle (degrees) 34.26171979
Shift along axis -32.77452321
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98833,-0.12968,-0.07989,12.371,0.056169,0.79786,-0.60022,104.59,0.14158,0.58873,0.79583,-107.46
> view matrix models
> #2,0.99375,0.038287,0.10482,-47.392,0.025313,0.83748,-0.54587,93.936,-0.10869,0.54512,0.83128,-65.288
> undo
> show #!5 models
> hide #!2 models
> fitmap #7 inMap #5
Fit molecule 8ACT.cif-coot-0.pdb (#7) to map 25HepE525K_sharp_273.mrc (#5)
using 18834 atoms
average map value = 0.2023, steps = 128
shifted from previous position = 9.47
rotated from previous position = 6.34 degrees
atoms outside contour = 9556, contour level = 0.10795
Position of 8ACT.cif-coot-0.pdb (#7) relative to 25HepE525K_sharp_273.mrc (#5)
coordinates:
Matrix rotation and translation
0.99993898 -0.00883989 0.00662534 0.20813860
0.00883481 0.99996066 0.00079636 -1.25397721
-0.00663212 -0.00073778 0.99997774 1.13610400
Axis -0.06926926 0.59860049 0.79804713
Axis point 151.63627638 23.60833942 0.00000000
Rotation angle (degrees) 0.63449030
Shift along axis 0.14161555
> hide #!5 models
> show #!2 models
> show #!1 models
> show #!6 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> show #!5 models
> show #!2 models
> fitmap #2 inMap #5
Fit map 25hep_WT_conf1.mrc in map 25HepE525K_sharp_273.mrc using 33578 points
correlation = 0.7251, correlation about mean = 0.4801, overlap = 1175
steps = 152, shift = 9.14, angle = 11.6 degrees
Position of 25hep_WT_conf1.mrc (#2) relative to 25HepE525K_sharp_273.mrc (#5)
coordinates:
Matrix rotation and translation
0.97513458 -0.20626183 0.08104680 -1.85570310
0.21782918 0.82479144 -0.52179452 51.48651902
0.04077959 0.52647424 0.84921251 -89.18402047
Axis 0.92642367 0.03558676 0.37479697
Axis point 0.00000000 159.27679852 47.46189401
Rotation angle (degrees) 34.45515360
Shift along axis -33.31282928
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!2 models
> fitmap #6 inMap #5
Fit molecule 25Hep-WT-conf1-refined.pdb (#6) to map 25HepE525K_sharp_273.mrc
(#5) using 19469 atoms
average map value = 0.06988, steps = 48
shifted from previous position = 0.866
rotated from previous position = 0.541 degrees
atoms outside contour = 15574, contour level = 0.10795
Position of 25Hep-WT-conf1-refined.pdb (#6) relative to
25HepE525K_sharp_273.mrc (#5) coordinates:
Matrix rotation and translation
0.97995580 -0.12106726 0.15820663 -26.79136169
0.18856844 0.81985458 -0.54062964 68.94864723
-0.06425388 0.55962593 0.82625072 -74.51178802
Axis 0.94487792 0.19104472 0.26590907
Axis point 0.00000000 145.96323685 90.18927866
Rotation angle (degrees) 35.60690956
Shift along axis -31.95565133
> fitmap #6 inMap #5
Fit molecule 25Hep-WT-conf1-refined.pdb (#6) to map 25HepE525K_sharp_273.mrc
(#5) using 19469 atoms
average map value = 0.06988, steps = 28
shifted from previous position = 0.0142
rotated from previous position = 0.0041 degrees
atoms outside contour = 15579, contour level = 0.10795
Position of 25Hep-WT-conf1-refined.pdb (#6) relative to
25HepE525K_sharp_273.mrc (#5) coordinates:
Matrix rotation and translation
0.97995788 -0.12107957 0.15818433 -26.79602019
0.18857042 0.81981747 -0.54068522 68.95405362
-0.06421634 0.55967763 0.82621861 -74.52365031
Axis 0.94489398 0.19097796 0.26589994
Axis point 0.00000000 145.96805838 90.17827564
Rotation angle (degrees) 35.61021297
Shift along axis -31.96652762
> show #!2 models
> hide #!6 models
> hide #!2 models
> close #2
> open C:/Users/gautar/Downloads/25hep_WT_conf1.mrc
Opened 25hep_WT_conf1.mrc as #2, grid size 400,400,400, pixel 0.83, shown at
level 0.0412, step 2, values float32
> surface dust #5 size 8.24
> surface dust #2 size 8.3
> select add #5
2 models selected
> view matrix models
> #5,0.95937,0.11874,-0.25594,27.324,0.091386,0.72745,0.68005,-76.478,0.26693,-0.67581,0.68704,107.51
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95937,0.11874,-0.25594,17.426,0.091386,0.72745,0.68005,-58.522,0.26693,-0.67581,0.68704,109.16
> view matrix models
> #5,0.95937,0.11874,-0.25594,48.616,0.091386,0.72745,0.68005,-46.779,0.26693,-0.67581,0.68704,107.88
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.89958,0.098647,-0.42547,85.389,0.16994,0.81833,0.54905,-50.776,0.40233,-0.56622,0.71939,68.654
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.89958,0.098647,-0.42547,84.579,0.16994,0.81833,0.54905,-52.793,0.40233,-0.56622,0.71939,82.42
> fitmap #5 inMap #2
Fit map 25HepE525K_sharp_273.mrc in map 25hep_WT_conf1.mrc using 20877 points
correlation = 0.8252, correlation about mean = 0.4278, overlap = 1202
steps = 268, shift = 5.15, angle = 29.1 degrees
Position of 25HepE525K_sharp_273.mrc (#5) relative to 25hep_WT_conf1.mrc (#2)
coordinates:
Matrix rotation and translation
0.97466150 0.21981384 0.04143484 -6.02312426
-0.20835136 0.82473473 0.52573981 4.49108435
0.08139214 -0.52105135 0.84963569 102.61446089
Axis -0.92499077 -0.03530803 -0.37834563
Axis point 0.00000000 159.18089780 46.76738294
Rotation angle (degrees) 34.46055250
Shift along axis -33.41096938
> select subtract #5
Nothing selected
> volume #2 level 0.09879
> volume #5 level 0.1114
> volume #2 level 0.1211
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.06908
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> select add #1
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 2 models selected
> view matrix models
> #1,0.97848,-0.12909,0.16097,-29.431,0.19698,0.81671,-0.54239,79.819,-0.06145,0.56243,0.82456,-66.739
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92929,-0.24062,-0.28021,70.473,0.24308,0.96964,-0.026498,-38.902,0.27808,-0.043487,0.95957,-43.375
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.92929,-0.24062,-0.28021,101.66,0.24308,0.96964,-0.026498,-26.078,0.27808,-0.043487,0.95957,-45.239
> view matrix models
> #1,0.92929,-0.24062,-0.28021,96.803,0.24308,0.96964,-0.026498,-23.399,0.27808,-0.043487,0.95957,-29.882
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98406,-0.17512,-0.031065,35.538,0.17682,0.98212,0.064557,-29.719,0.019205,-0.069021,0.99743,10.582
> fitmap #1 inMap #2
Fit molecule 25hep_WT_conf1.pdb (#1) to map 25hep_WT_conf1.mrc (#2) using
19469 atoms
average map value = 0.1541, steps = 148
shifted from previous position = 7.65
rotated from previous position = 10.9 degrees
atoms outside contour = 2981, contour level = 0.069078
Position of 25hep_WT_conf1.pdb (#1) relative to 25hep_WT_conf1.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999999 0.00003328 0.00011029 -0.03225655
-0.00003329 1.00000000 0.00005292 0.00520329
-0.00011029 -0.00005293 0.99999999 0.02583606
Axis -0.41746317 0.86994606 -0.26252304
Axis point 260.92143344 0.00000000 250.05054091
Rotation angle (degrees) 0.00726391
Shift along axis 0.01120995
> select subtract #1
Nothing selected
> show #!6 models
> select add #6
19469 atoms, 19828 bonds, 4 pseudobonds, 2415 residues, 2 models selected
> hide #!1 models
> view matrix models
> #6,0.90802,-0.21779,-0.35787,86.866,0.253,0.96595,0.054082,-64.817,0.3339,-0.13965,0.93221,-40.378
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.90802,-0.21779,-0.35787,80.917,0.253,0.96595,0.054082,-61.081,0.3339,-0.13965,0.93221,-23.955
> view matrix models
> #6,0.90802,-0.21779,-0.35787,101.82,0.253,0.96595,0.054082,-64.77,0.3339,-0.13965,0.93221,-25.956
> view matrix models
> #6,0.90802,-0.21779,-0.35787,93.252,0.253,0.96595,0.054082,-52.104,0.3339,-0.13965,0.93221,-13.611
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.98054,0.013282,0.19586,-49.246,-0.050499,0.9812,0.18627,-26.833,-0.18971,-0.19254,0.96278,76.028
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.98054,0.013282,0.19586,-45.775,-0.050499,0.9812,0.18627,-31.977,-0.18971,-0.19254,0.96278,70.892
> view matrix models
> #6,0.98054,0.013282,0.19586,-25.97,-0.050499,0.9812,0.18627,-18.898,-0.18971,-0.19254,0.96278,61.844
> fitmap #6 inMap #2
Fit molecule 25Hep-WT-conf1-refined.pdb (#6) to map 25hep_WT_conf1.mrc (#2)
using 19469 atoms
average map value = 0.1528, steps = 188
shifted from previous position = 9.49
rotated from previous position = 15.8 degrees
atoms outside contour = 3149, contour level = 0.069078
Position of 25Hep-WT-conf1-refined.pdb (#6) relative to 25hep_WT_conf1.mrc
(#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00005368 0.00004141 -0.00468633
0.00005368 0.99999999 0.00005764 -0.02151061
-0.00004141 -0.00005764 0.99999999 0.01055998
Axis -0.64771250 0.46534227 0.60326203
Axis point 0.00000000 189.51657456 368.32019957
Rotation angle (degrees) 0.00509870
Shift along axis -0.00060396
> select subtract #6
Nothing selected
> show #!1 models
> transparency #2.1 50
> volume #2 level 0.09136
> show #!1,6 atoms
> style #!1,6 ball
Changed 38938 atom styles
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!1 models
> select add #7
18834 atoms, 19195 bonds, 9 pseudobonds, 2328 residues, 2 models selected
> view matrix models
> #7,0.99994,-0.0088399,0.0066253,5.6064,0.0088348,0.99996,0.00079636,2.3837,-0.0066321,-0.00073778,0.99998,-3.4969
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.6737,0.63388,-0.37989,16.315,-0.53151,0.77278,0.34687,57.074,0.51344,-0.031772,0.85753,-48.993
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.6737,0.63388,-0.37989,3.6266,-0.53151,0.77278,0.34687,74.173,0.51344,-0.031772,0.85753,-34.977
> view matrix models
> #7,0.6737,0.63388,-0.37989,11.027,-0.53151,0.77278,0.34687,74.478,0.51344,-0.031772,0.85753,-37.25
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.97914,-0.1909,0.069548,19.732,0.088867,0.71022,0.69835,-53.985,-0.18271,-0.6776,0.71237,171.79
> view matrix models
> #7,0.98332,-0.11164,0.14361,-3.198,0.013405,0.83184,0.55485,-39.577,-0.1814,-0.54367,0.81946,136.53
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.98332,-0.11164,0.14361,31.282,0.013405,0.83184,0.55485,-37.414,-0.1814,-0.54367,0.81946,128.26
> view matrix models
> #7,0.98332,-0.11164,0.14361,22.262,0.013405,0.83184,0.55485,-32.833,-0.1814,-0.54367,0.81946,142.54
> fitmap #7 inMap #2
Fit molecule 8ACT.cif-coot-0.pdb (#7) to map 25hep_WT_conf1.mrc (#2) using
18834 atoms
average map value = 0.1289, steps = 220
shifted from previous position = 4.64
rotated from previous position = 19.2 degrees
atoms outside contour = 8147, contour level = 0.091363
Position of 8ACT.cif-coot-0.pdb (#7) relative to 25hep_WT_conf1.mrc (#2)
coordinates:
Matrix rotation and translation
0.97722521 0.20736870 0.04504565 -5.34931697
-0.19966065 0.82660163 0.52617998 3.19126909
0.07187846 -0.52319019 0.84917932 104.25011677
Axis -0.93205733 -0.02383307 -0.36152609
Axis point 0.00000000 162.49196050 48.96766395
Rotation angle (degrees) 34.25882245
Shift along axis -32.77932492
> show #!1 models
> select subtract #7
Nothing selected
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!6 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> select add #7
18834 atoms, 19195 bonds, 9 pseudobonds, 2328 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 18834 atom styles
> select subtract #7
Nothing selected
> show #!2 models
> color #7 #c40fcaff
> hide #!2 models
> hide #!7 models
> select add #1
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 2 models selected
> hide sel atoms
> select subtract #1
Nothing selected
> ui mousemode right select
> select #1/A:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select #1/B:874
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!7 models
> hide sel atoms
> show sel cartoons
> select add #7
18843 atoms, 19203 bonds, 9 pseudobonds, 2329 residues, 3 models selected
> hide sel atoms
> select subtract #7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1
19469 atoms, 19827 bonds, 4 pseudobonds, 2415 residues, 2 models selected
> select subtract #1
Nothing selected
> select #7/A:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:874
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:874
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #1/A:450@NZ #1/B:874@OE1
Distance between 25hep_WT_conf1.pdb #1/A LYS 450 NZ and /B GLU 874 OE1:
11.553Å
> distance #7/A:450@NZ #7/B:874@OE2
Distance between 8ACT.cif-coot-0.pdb #7/A LYS 450 NZ and /B GLU 874 OE2:
2.960Å
> ui mousemode right select
> select #7/A:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:875
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> style sel sphere
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> show sel atoms
Drag select of 1 residues
> ui mousemode right distance
> distance #1/A:450@NZ #1/B:875@OE2
Distance between 25hep_WT_conf1.pdb #1/A LYS 450 NZ and /B GLU 875 OE2: 2.626Å
> show #!4 models
> show #!2 models
> select add #7
18834 atoms, 19195 bonds, 10 pseudobonds, 2328 residues, 3 models selected
> select subtract #7
Nothing selected
> select add #4
19105 atoms, 19459 bonds, 4 pseudobonds, 2372 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,24.955,0,1,0,14.017,0,0,1,-0.49099
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.97824,-0.20324,-0.041637,63.279,0.16131,0.61893,0.76871,-70.401,-0.13046,-0.7587,0.63824,180.65
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97824,-0.20324,-0.041637,54.997,0.16131,0.61893,0.76871,-60.152,-0.13046,-0.7587,0.63824,184.18
> view matrix models
> #4,0.97824,-0.20324,-0.041637,59.892,0.16131,0.61893,0.76871,-50.775,-0.13046,-0.7587,0.63824,179.88
> hide #!1 models
> hide #!7 models
> hide #!8 models
> fitmap #4 inMap #2
Fit molecule 25HepE525K_real_space_refined_231.pdb (#4) to map
25hep_WT_conf1.mrc (#2) using 19105 atoms
average map value = 0.1301, steps = 352
shifted from previous position = 16.7
rotated from previous position = 30.9 degrees
atoms outside contour = 8302, contour level = 0.091363
Position of 25HepE525K_real_space_refined_231.pdb (#4) relative to
25hep_WT_conf1.mrc (#2) coordinates:
Matrix rotation and translation
0.97554346 0.21604514 0.04049002 -5.55578166
-0.20486742 0.82693001 0.52365645 4.05789244
0.07965102 -0.51914472 0.85096678 102.38794422
Axis -0.92674758 -0.03480276 -0.37406911
Axis point 0.00000000 159.67494104 47.23654295
Rotation angle (degrees) 34.23672393
Shift along axis -33.29258544
> show #!1 models
> show #!7 models
> select subtract #4
Nothing selected
> color #4 lime
> volume #2 level 0.1341
> volume #2 level 0.1396
> hide #!2 models
> ui mousemode right select
> select #4/B:874
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select #4/A:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select clear
> ui mousemode right distance
> distance #4/A:450@NZ #4/B:874@OE1
Distance between 25HepE525K_real_space_refined_231.pdb #4/A LYS 450 NZ and /B
GLU 874 OE1: 6.942Å
> distance #4/A:450@NZ #4/B:874@OE1
Distance already exists; modify distance properties with 'distance style'
> ui tool show Distances
> ~distance #4/A:450@NZ #4/B:874@OE1
> distance #4/A:450@NZ #4/B:874@OE1
Distance between 25HepE525K_real_space_refined_231.pdb #4/A LYS 450 NZ and /B
GLU 874 OE1: 6.942Å
> show #!8 models
> ui mousemode right select
> select #4/B:875
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> ui mousemode right distance
> distance #4/A:450@NZ #4/B:875@OE1
Distance between 25HepE525K_real_space_refined_231.pdb #4/A LYS 450 NZ and /B
GLU 875 OE1: 5.467Å
> distance #4/A:450@NZ #4/B:874@OE2
Distance between 25HepE525K_real_space_refined_231.pdb #4/A LYS 450 NZ and /B
GLU 874 OE2: 5.098Å
> show #!5 models
> volume #5 level 0.01077
> hide #!7 models
> show #!2 models
> hide #!5 models
> volume #2 level 0.1248
> volume #2 level 0.06536
> select add #1
19478 atoms, 19835 bonds, 6 pseudobonds, 2416 residues, 4 models selected
> show sel atoms
> select subtract #1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4
19105 atoms, 19459 bonds, 7 pseudobonds, 2372 residues, 3 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> open C:/Users/gautar/Downloads/25HepE525K_sharp_272.ccp4
Opened 25HepE525K_sharp_272.ccp4 as #9, grid size 340,340,340, pixel 0.824,
shown at level 0.0497, step 2, values float32
> surface dust #2 size 8.3
> surface dust #9 size 8.24
> select add #9
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-0.11212,0,1,0,10.592,0,0,1,-3.6359
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.91279,0.18514,-0.36406,39.314,0.012372,0.87842,0.47773,-44.664,0.40824,-0.44057,0.79952,33.816
> view matrix models
> #9,0.92426,0.33295,-0.1868,-9.9634,-0.16839,0.79466,0.58324,-23.515,0.34263,-0.50761,0.79053,53.816
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.92426,0.33295,-0.1868,26.913,-0.16839,0.79466,0.58324,-16.133,0.34263,-0.50761,0.79053,68.177
> view matrix models
> #9,0.92426,0.33295,-0.1868,21.381,-0.16839,0.79466,0.58324,-4.1353,0.34263,-0.50761,0.79053,71.387
> hide #!1 models
> show #!5 models
> hide #!8 models
> select subtract #9
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.
> hide #!5 models
> select add #9
2 models selected
> fitmap #9 inMap #2
Fit map 25HepE525K_sharp_272.ccp4 in map 25hep_WT_conf1.mrc using 49084 points
correlation = 0.8445, correlation about mean = 0.6048, overlap = 683.5
steps = 208, shift = 4.24, angle = 15.4 degrees
Position of 25HepE525K_sharp_272.ccp4 (#9) relative to 25hep_WT_conf1.mrc (#2)
coordinates:
Matrix rotation and translation
0.97355380 0.22446850 0.04250740 -6.55450183
-0.21275346 0.82300609 0.52668486 5.35887661
0.08324031 -0.52179965 0.84899716 102.60932155
Axis -0.92237368 -0.03583359 -0.38463327
Axis point 0.00000000 158.71535483 45.44892293
Rotation angle (degrees) 34.63609000
Shift along axis -33.61328702
> select subtract #9
Nothing selected
> show #!1 models
> show #!6 models
> show #!7 models
> volume #9 level 0.08944
> transparency #2.1#9.1 0
> transparency #2.1#9.1 50
> hide #!6 models
> show #!4 models
> select add #4
19105 atoms, 19459 bonds, 7 pseudobonds, 2372 residues, 3 models selected
> show sel atoms
> style sel ball
Changed 19105 atom styles
> show sel cartoons
> select subtract #4
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!9 models
> ui mousemode right distance
> distance #4/A:525@NZ #4/B:903@OE2
Distance between 25HepE525K_real_space_refined_231.pdb #4/A LYS 525 NZ and /B
GLU 903 OE2: 4.207Å
> ui mousemode right distance
> distance #4/A:525@NZ #4/B:903@OE2
Distance already exists; modify distance properties with 'distance style'
> ~distance #4/A:525@NZ #4/B:903@OE2
> distance #4/A:525@NZ #4/B:903@OE2
Distance between 25HepE525K_real_space_refined_231.pdb #4/A LYS 525 NZ and /B
GLU 903 OE2: 4.207Å
> show #!8 models
> show #!9 models
> hide #!2 models
> hide #!7 models
> show #!2 models
> molmap #1 3.0
Opened 25hep_WT_conf1.pdb map 3 as #10, grid size 98,170,186, pixel 1, shown
at level 0.115, step 1, values float32
> hide #!1 models
> hide #!4 models
> hide #!9 models
> show #!1 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> molmap #4 3.0
Opened 25HepE525K_real_space_refined_231.pdb map 3 as #11, grid size
104,182,170, pixel 1, shown at level 0.113, step 1, values float32
> hide #!4 models
> hide #!1 models
> hide #!10 models
> volume #9 level 0.06958
> show #!4 models
> hide #!11 models
> show #!11 models
> show #!10 models
> hide #!11 models
> hide #!4 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> show #!2 models
> show #!9 models
> hide #!2 models
> hide #!10 models
> show #!4 models
> volume #9 level 0.1143
> volume #9 level 0.07951
> show #!2 models
> volume #2 level 0.09879
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> volume #9 level 0.06462
> show #!1 models
> show #!2 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!7 models
> select add #7
18834 atoms, 19195 bonds, 10 pseudobonds, 2328 residues, 3 models selected
> show sel atoms
> select subtract #7
Nothing selected
> hide #!7 models
> select add #1
19469 atoms, 19827 bonds, 6 pseudobonds, 2415 residues, 3 models selected
> hide sel atoms
> select subtract #1
Nothing selected
> volume #2 level 0.07094
> show #!4 models
> select add #4
19105 atoms, 19459 bonds, 8 pseudobonds, 2372 residues, 3 models selected
> hide sel atoms
> select subtract #4
Nothing selected
> show #!5 models
> hide #!5 models
> show #!9 models
> hide #!2 models
> volume #9 level 0.04475
> show #!5 models
> hide #!9 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!7 models
> select add #7
18834 atoms, 19195 bonds, 10 pseudobonds, 2328 residues, 3 models selected
> hide sel atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!9 models
> volume #9 level 0.03482
> select add #8
18834 atoms, 19195 bonds, 16 pseudobonds, 2328 residues, 4 models selected
> select subtract #8
18834 atoms, 19195 bonds, 9 pseudobonds, 2328 residues, 2 models selected
> hide #!7 models
> hide #!4 models
> volume #9 level 0.04972
> show #!2 models
> select subtract #7
Nothing selected
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!7 models
> hide #!7 models
> show #!9 models
> volume #9 level 0.05965
> hide #!1 models
> hide #!4 models
> open
> C:/Users/gautar/Documents/25HepE525K/SequenceFromMap_130/sequence_from_map.pdb
Summary of feedback from opening
C:/Users/gautar/Documents/25HepE525K/SequenceFromMap_130/sequence_from_map.pdb
---
warning | Ignored bad PDB record found on line 4349
Chain information for sequence_from_map.pdb #12
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> close #12
> show #!3 models
> open
> C:/Users/gautar/Documents/25HepE525K/SequenceFromMap_130/sequence_from_map.pdb
Summary of feedback from opening
C:/Users/gautar/Documents/25HepE525K/SequenceFromMap_130/sequence_from_map.pdb
---
warning | Ignored bad PDB record found on line 4349
Chain information for sequence_from_map.pdb #12
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> transparency #2.1#3.1#9.1 0
> transparency #2.1#3.1#9.1 50
> volume #11 level 0.1131
> hide #12 models
> hide #!11 models
> hide #!3 models
> fitmap #2 inMap #9
Fit map 25hep_WT_conf1.mrc in map 25HepE525K_sharp_272.ccp4 using 43469 points
correlation = 0.8362, correlation about mean = 0.6307, overlap = 653.6
steps = 36, shift = 0.0394, angle = 0.0627 degrees
Position of 25hep_WT_conf1.mrc (#2) relative to 25HepE525K_sharp_272.ccp4 (#9)
coordinates:
Matrix rotation and translation
0.97330830 -0.21365265 0.08380637 -0.92875440
0.22552595 0.82272289 -0.52179027 50.43461287
0.04253246 0.52676331 0.84894724 -89.67422678
Axis 0.92175557 0.03628280 0.38607023
Axis point 0.00000000 158.52031303 45.13956879
Rotation angle (degrees) 34.66524471
Shift along axis -33.64672493
> show #!1 models
> hide #!2 models
> show #!4 models
> volume #9 level 0.06958
> volume #9 level 0.02737
> select add #1
19469 atoms, 19827 bonds, 6 pseudobonds, 2415 residues, 3 models selected
> hide sel atoms
> show sel atoms
> select subtract #1
Nothing selected
> show #!2 models
> hide #!9 models
> volume #2 level 0.09508
> show #!9 models
> hide #!9 models
> show #!5 models
> volume #5 level 0.01771
> select add #4
19105 atoms, 19459 bonds, 8 pseudobonds, 2372 residues, 3 models selected
> show sel atoms
> select subtract #4
Nothing selected
> hide #!2 models
> hide #!4 models
> volume #2 level 0.09136
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!4 models
> hide #!1 models
> volume #5 level 0.03853
> show #!9 models
> hide #!5 models
> volume #9 level 0.03731
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!9 models
> show #!7 models
> open 9gz1 fromDatabase pdb format mmcif
9gz1 title:
Beta-cardiac myosin interacting heads motif complexed to mavacamten [more
info...]
Chain information for 9gz1 #13
---
Chain | Description | UniProt
A B | Myosin-7 | MYH7_HUMAN 2-1138
C E | Myosin light chain 1/3, skeletal muscle isoform | MYL1_MOUSE 1-187
D F | Myosin regulatory light chain 11 | MYL11_MOUSE 1-168
Non-standard residues in 9gz1 #13
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
PO4 — phosphate ion
XB2 —
6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione
> select add #13
19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,1.1595,0,1,0,9.2472,0,0,1,6.2865
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.9997,-0.015508,-0.019128,6.449,0.024624,0.63674,0.77069,-54.363,0.00022758,-0.77093,0.63693,178.79
> view matrix models
> #13,-0.95645,-0.046355,0.28819,251.21,-0.04869,0.99881,-0.00093623,16.692,-0.28781,-0.014928,-0.95757,344.4
> view matrix models
> #13,-0.98087,0.025873,0.19294,258.01,0.01928,0.99917,-0.035973,11.952,-0.19371,-0.031565,-0.98055,336.63
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.98087,0.025873,0.19294,280.62,0.01928,0.99917,-0.035973,16.477,-0.19371,-0.031565,-0.98055,334.53
> view matrix models
> #13,-0.98087,0.025873,0.19294,279.47,0.01928,0.99917,-0.035973,23.143,-0.19371,-0.031565,-0.98055,346.94
> view matrix models
> #13,-0.98087,0.025873,0.19294,279.78,0.01928,0.99917,-0.035973,19.778,-0.19371,-0.031565,-0.98055,348.3
> hide #!7 models
> hide #!1 models
> fitmap #13 inMap #2
Fit molecule 9gz1 (#13) to map 25hep_WT_conf1.mrc (#2) using 19295 atoms
average map value = 0.1055, steps = 188
shifted from previous position = 2.11
rotated from previous position = 11.1 degrees
atoms outside contour = 10486, contour level = 0.091363
Position of 9gz1 (#13) relative to 25hep_WT_conf1.mrc (#2) coordinates:
Matrix rotation and translation
-0.99815510 0.05451391 0.02673429 301.16123390
0.05050823 0.98987280 -0.13266807 31.03763648
-0.03369579 -0.13107299 -0.99079994 339.67636329
Axis 0.02632851 0.99746439 -0.06611804
Axis point 152.75872676 0.00000000 168.58314411
Rotation angle (degrees) 178.26413969
Shift along axis 16.42932781
> show #!1 models
> show #!7 models
> select subtract #13
Nothing selected
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!2 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> hide #!13 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!2 models
> show #!13 models
> hide #!7 models
> hide #!13 models
> show #!2 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> show #!13 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> ui mousemode right select
> select #13/A:526
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select #13/B:903
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!2 models
> show #!6 models
> hide #!2 models
> show sel cartoons
> select add #6
19478 atoms, 19836 bonds, 4 pseudobonds, 2416 residues, 3 models selected
> select add #1
38947 atoms, 39663 bonds, 10 pseudobonds, 4831 residues, 6 models selected
> select add #13
58233 atoms, 59306 bonds, 27 pseudobonds, 7223 residues, 8 models selected
> hide sel atoms
> show #!3 models
> hide #!3 models
> close #3
> show #!4 models
> hide sel atoms
> show sel cartoons
> select subtract #6
38764 atoms, 39478 bonds, 23 pseudobonds, 4808 residues, 6 models selected
> select add #4
57869 atoms, 58937 bonds, 31 pseudobonds, 7180 residues, 8 models selected
> hide sel atoms
> select subtract #4
38764 atoms, 39478 bonds, 23 pseudobonds, 4808 residues, 6 models selected
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> show #!7 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #12 models
> hide #12 models
> close #12
> select subtract #13
19469 atoms, 19827 bonds, 6 pseudobonds, 2415 residues, 3 models selected
> select subtract #1
Nothing selected
> show #!2 models
> open C:/Users/gautar/Documents/25HepE525K/25Hep-WT-conf1-refined052025.pdb
Summary of feedback from opening C:/Users/gautar/Documents/25HepE525K/25Hep-
WT-conf1-refined052025.pdb
---
warnings | Start residue of secondary structure not found: HELIX 57 57 ASP B 945 GLU B 949 1 5
Start residue of secondary structure not found: HELIX 58 58 ARG B 952 LEU B
961 1 10
End residue of secondary structure not found: HELIX 106 106 ASP A 906 THR A
960 1 55
Start residue of secondary structure not found: HELIX 107 107 LEU A 961 LYS A
963 1 3
Chain information for 25Hep-WT-conf1-refined052025.pdb #3
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E F | No description available
> show cartoons
> hide atoms
> color #1 #de594dff
> color #3 #dddea3ff
> color #13 #5566faff
> hide #!2 models
> hide #!4 models
> ui mousemode right label
> label #13/B:844
> label #1/B:844
> label #7/B:848
> ui mousemode right "move label"
> save "C:/Users/gautar/Documents/25HepE525K/Chimera
> sessions/ComparisonWT8actand 9gz1.cxs"
——— End of log from Tue Jun 17 11:50:13 2025 ———
opened ChimeraX session
OpenGL version: 3.3.0 - Build 32.0.101.6104
OpenGL renderer: Intel(R) Arc(TM) 140T GPU (16GB)
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS Vivobook S 16 S5606CA_S5606CA
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 33,685,598,208
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) Ultra 9 285H
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-clix: 0.2.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
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-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-RealSense: 1.9
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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-StarMap: 1.2.15
ChimeraX-StdCommands: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
pyqtgraph: 0.13.7
pyrealsense2: 2.55.1.6486
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.20
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
zipp: 3.19.2
Change History (1)
comment:1 by , 5 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → QScore: model is None |
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