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Opened 3 months ago
Closed 3 months ago
#18407 closed defect (duplicate)
QScore: scores 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: macOS-15.5-x86_64-i386-64bit
ChimeraX Version: 1.10.dev202503110047 (2025-03-11 00:47:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.dev202503110047 (2025-03-11)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Mon Aug 4 11:11:34 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Mon Aug 4 11:04:40 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Aug 3 18:22:11 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Aug 3 18:03:16 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Aug 3 17:32:55 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Thu Jul 31 22:16:36 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Jul 27 17:08:25 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Jul 27 15:20:49 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sat Jul 26 20:18:07 2025
> cofr centerOfView
UCSF ChimeraX version: 1.11.dev202506260705 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job603_Refine3D_10A.mrc"
Opened Job603_Refine3D_10A.mrc as #1, grid size 480,480,480, pixel 1.4, shown
at level 0.0289, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job603_Refine3D_8A.mrc"
Opened Job603_Refine3D_8A.mrc as #2, grid size 480,480,480, pixel 1.4, shown
at level 0.0285, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job603_Refine3D_6A.mrc"
Opened Job603_Refine3D_6A.mrc as #3, grid size 480,480,480, pixel 1.4, shown
at level 0.0279, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job603_locres_filtered.mrc"
Opened Job603_locres_filtered.mrc as #4, grid size 480,480,480, pixel 1.4,
shown at level 0.0268, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job603_highRes.mrc"
Opened Job603_highRes.mrc as #5, grid size 480,480,480, pixel 1.4, shown at
level 0.00562, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job603_Refine3D.mrc"
Opened Job603_Refine3D.mrc as #6, grid size 480,480,480, pixel 1.4, shown at
level 0.0271, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job588_Refine3D_10A.mrc"
Opened Job588_Refine3D_10A.mrc as #7, grid size 416,416,416, pixel 0.84, shown
at level 0.00436, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job588_Refine3D_8A.mrc"
Opened Job588_Refine3D_8A.mrc as #8, grid size 416,416,416, pixel 0.84, shown
at level 0.00439, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job588_Refine3D_6A.mrc"
Opened Job588_Refine3D_6A.mrc as #9, grid size 416,416,416, pixel 0.84, shown
at level 0.00439, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job588_highRes.mrc"
Opened Job588_highRes.mrc as #10, grid size 416,416,416, pixel 0.84, shown at
level 0.0101, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job588_locres_filtered.mrc"
Opened Job588_locres_filtered.mrc as #11, grid size 416,416,416, pixel 0.84,
shown at level 0.00415, step 2, values float32
> open
> "/Users/rjk/FKBP11/FKBP11_EM/2023_12_15_FKBP11_2/SuperResolutionProcessing/Latest
> maps/unaligned/Job588_Refine3D.mrc"
Opened Job588_Refine3D.mrc as #12, grid size 416,416,416, pixel 0.84, shown at
level 0.00443, step 2, values float32
> open "/Users/rjk/FKBP11/FKBP11_EM/FKBP11_deposition/July
> 2025/RTC_real_space_refined_172_aligned.cif"
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_deposition/July
2025/RTC_real_space_refined_172_aligned.cif
---
warnings | Unknown polymer entity '1' on line 344
Unknown polymer entity '2' on line 2539
Unknown polymer entity '3' on line 5044
Unknown polymer entity '4' on line 7985
Unknown polymer entity '5' on line 10319
65 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Atom HO5' is not in the residue template for C /L5:1
Atom HO5' is not in the residue template for C /L8:1
Chain information for RTC_real_space_refined_172_aligned.cif #13
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
u3 | No description available
v3 | No description available
y3 | No description available
> open "/Users/rjk/FKBP11/FKBP11_EM/FKBP11_deposition/July
> 2025/Translocon_real_space_refined_174_aligned.cif"
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_deposition/July
2025/Translocon_real_space_refined_174_aligned.cif
---
warnings | Unknown polymer entity '1' on line 218
Unknown polymer entity '2' on line 2413
Unknown polymer entity '3' on line 4918
Unknown polymer entity '4' on line 7859
Unknown polymer entity '5' on line 10193
15 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Chain information for Translocon_real_space_refined_174_aligned.cif #14
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
y3 | No description available
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> volume #4 step 1
> volume #6 step 1
> volume #12 step 1
> select add #14
74601 atoms, 75451 bonds, 14 pseudobonds, 4690 residues, 2 models selected
> select add #13
400757 atoms, 413750 bonds, 1505 pseudobonds, 20841 residues, 5 models
selected
> select add #12
400757 atoms, 413750 bonds, 1505 pseudobonds, 20841 residues, 7 models
selected
> select add #11
400757 atoms, 413750 bonds, 1505 pseudobonds, 20841 residues, 9 models
selected
> select add #10
400757 atoms, 413750 bonds, 1505 pseudobonds, 20841 residues, 11 models
selected
> select add #9
400757 atoms, 413750 bonds, 1505 pseudobonds, 20841 residues, 13 models
selected
> select subtract #13
74601 atoms, 75451 bonds, 14 pseudobonds, 4690 residues, 10 models selected
> hide #!13 models
> ui mousemode right "translate selected models"
> view matrix models
> #9,1,0,0,50.308,0,1,0,191.01,0,0,1,12.895,#10,1,0,0,50.308,0,1,0,191.01,0,0,1,12.895,#11,1,0,0,50.308,0,1,0,191.01,0,0,1,12.895,#12,1,0,0,50.308,0,1,0,191.01,0,0,1,12.895,#14,1,0,0,50.308,0,1,0,191.01,0,0,1,12.895
> undo
> select add #8
74601 atoms, 75451 bonds, 14 pseudobonds, 4690 residues, 12 models selected
> select add #7
74601 atoms, 75451 bonds, 14 pseudobonds, 4690 residues, 14 models selected
> view matrix models
> #7,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54,#8,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54,#9,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54,#10,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54,#11,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54,#12,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54,#14,1,0,0,154.44,0,1,0,315.68,0,0,1,128.54
> view matrix models
> #7,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77,#8,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77,#9,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77,#10,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77,#11,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77,#12,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77,#14,1,0,0,147.82,0,1,0,318.08,0,0,1,124.77
> select clear
> volume #10 step 1
> volume #11 step 1
> volume #7 step 1
> volume #8 step 1
> volume #9 step 1
> volume #5 step 1
> hide #!14 atoms
> show #!14 cartoons
> ui tool show "Fit in Map"
> fitmap #7 inMap #4
Fit map Job588_Refine3D_10A.mrc in map Job603_locres_filtered.mrc using 720362
points
correlation = 0.8769, correlation about mean = 0.2894, overlap = 88.97
steps = 96, shift = 12.5, angle = 0.524 degrees
Position of Job588_Refine3D_10A.mrc (#7) relative to
Job603_locres_filtered.mrc (#4) coordinates:
Matrix rotation and translation
0.99995821 0.00245470 0.00880588 139.99497898
-0.00245457 0.99999699 -0.00002554 319.82343763
-0.00880592 0.00000392 0.99996123 137.18850609
Axis 0.00161100 0.96327507 -0.26851171
Axis point 23926.01487219 0.00000000 -15734.69273338
Rotation angle (degrees) 0.52378401
Shift along axis 271.46675631
> fitmap #8 inMap #4
Fit map Job588_Refine3D_8A.mrc in map Job603_locres_filtered.mrc using 718831
points
correlation = 0.8861, correlation about mean = 0.3744, overlap = 94.7
steps = 92, shift = 12.5, angle = 0.517 degrees
Position of Job588_Refine3D_8A.mrc (#8) relative to Job603_locres_filtered.mrc
(#4) coordinates:
Matrix rotation and translation
0.99995937 0.00160364 0.00887016 140.10343523
-0.00159972 0.99999862 -0.00044888 319.84095734
-0.00887087 0.00043467 0.99996056 137.15297311
Axis 0.04895090 0.98290690 -0.17747630
Axis point 21463.33877410 0.00000000 -14058.18406215
Rotation angle (degrees) 0.51708873
Shift along axis 296.89067203
> fitmap #7 inMap #4
Fit map Job588_Refine3D_10A.mrc in map Job603_locres_filtered.mrc using 720362
points
correlation = 0.8769, correlation about mean = 0.2894, overlap = 88.97
steps = 28, shift = 0.00201, angle = 0.0028 degrees
Position of Job588_Refine3D_10A.mrc (#7) relative to
Job603_locres_filtered.mrc (#4) coordinates:
Matrix rotation and translation
0.99995812 0.00242644 0.00882396 139.99521395
-0.00242600 0.99999706 -0.00006070 319.82424010
-0.00882408 0.00003929 0.99996107 137.18434388
Axis 0.00546281 0.96420190 -0.26511290
Axis point 23810.52804039 0.00000000 -15583.48139713
Rotation angle (degrees) 0.52435726
Shift along axis 272.77056858
> fitmap #9 inMap #4
Fit map Job588_Refine3D_6A.mrc in map Job603_locres_filtered.mrc using 718579
points
correlation = 0.89, correlation about mean = 0.4088, overlap = 98.21
steps = 108, shift = 12.5, angle = 0.503 degrees
Position of Job588_Refine3D_6A.mrc (#9) relative to Job603_locres_filtered.mrc
(#4) coordinates:
Matrix rotation and translation
0.99996161 0.00109363 0.00869424 140.22322400
-0.00108898 0.99999926 -0.00053913 319.83159854
-0.00869482 0.00052964 0.99996206 137.12104114
Axis 0.06087039 0.99037484 -0.12430796
Axis point 20237.87787717 0.00000000 -13880.83400782
Rotation angle (degrees) 0.50300798
Shift along axis 308.24337434
> fitmap #10 inMap #4
Fit map Job588_highRes.mrc in map Job603_locres_filtered.mrc using 718354
points
correlation = 0.6829, correlation about mean = 0.3699, overlap = 3603
steps = 140, shift = 12.6, angle = 0.548 degrees
Position of Job588_highRes.mrc (#10) relative to Job603_locres_filtered.mrc
(#4) coordinates:
Matrix rotation and translation
0.99995522 0.00041275 0.00945462 140.23841499
-0.00039923 0.99999890 -0.00143162 320.07840718
-0.00945520 0.00142779 0.99995428 137.20716725
Axis 0.14937874 0.98786975 -0.04241861
Axis point 16043.75446929 0.00000000 -9522.03267705
Rotation angle (degrees) 0.54838651
Shift along axis 331.32427808
> fitmap #11 inMap #4
Fit map Job588_locres_filtered.mrc in map Job603_locres_filtered.mrc using
717862 points
correlation = 0.9491, correlation about mean = 0.4281, overlap = 117.8
steps = 140, shift = 12.5, angle = 0.522 degrees
Position of Job588_locres_filtered.mrc (#11) relative to
Job603_locres_filtered.mrc (#4) coordinates:
Matrix rotation and translation
0.99995852 0.00068916 0.00908206 140.21341432
-0.00068764 0.99999975 -0.00016980 319.74466251
-0.00908218 0.00016354 0.99995874 137.24603744
Axis 0.01829599 0.99697280 -0.07556775
Axis point 17765.90686468 0.00000000 -14730.89764199
Rotation angle (degrees) 0.52195450
Shift along axis 310.97070230
> fitmap #12 inMap #4
Fit map Job588_Refine3D.mrc in map Job603_locres_filtered.mrc using 718343
points
correlation = 0.8904, correlation about mean = 0.3984, overlap = 103.1
steps = 108, shift = 12.5, angle = 0.502 degrees
Position of Job588_Refine3D.mrc (#12) relative to Job603_locres_filtered.mrc
(#4) coordinates:
Matrix rotation and translation
0.99996180 0.00075567 0.00870799 140.29836412
-0.00075058 0.99999955 -0.00058714 319.82967729
-0.00870843 0.00058059 0.99996191 137.13736849
Axis 0.06664981 0.99406576 -0.08597126
Axis point 18921.80336425 0.00000000 -13613.70524349
Rotation angle (degrees) 0.50192860
Shift along axis 315.49271925
> volume #10 level 0.07013
> fitmap #14 inMap #10
Fit molecule Translocon_real_space_refined_174_aligned.cif (#14) to map
Job588_highRes.mrc (#10) using 74601 atoms
average map value = 0.1407, steps = 132
shifted from previous position = 12.6
rotated from previous position = 0.548 degrees
atoms outside contour = 44347, contour level = 0.070129
Position of Translocon_real_space_refined_174_aligned.cif (#14) relative to
Job588_highRes.mrc (#10) coordinates:
Matrix rotation and translation
1.00000000 -0.00002090 -0.00001559 0.02131732
0.00002090 1.00000000 -0.00002889 0.00734750
0.00001559 0.00002889 1.00000000 -0.01554749
Axis 0.74238709 -0.40055865 0.53704206
Axis point 0.00000000 622.35122670 317.11787613
Rotation angle (degrees) 0.00222996
Shift along axis 0.00453294
> volume #11 color silver
> volume #11 color #c0c0c040
> volume #11 level 0.004927
> volume #4 color #b2b2ff40
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> show #!13 models
> hide atoms
> show cartoons
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!14 models
> show #!14 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!4 models
> show #!5 models
> volume #5 level 0.05504
> volume #6 level 0.02659
> volume #6 color #ffb2b240
> volume #5 color #ffb2ff40
> volume #3 color #b2ffff40
> volume #2 color #ffffb240
> volume #1 color #b2b2b240
> volume #7 color #b2ffb240
> volume #8 color #e5bf9940
> volume #9 color #99bfe540
> volume #10 color #cccc9940
> volume #12 color #ffffb240
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> select H
180293 atoms, 20609 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> hide #!13 models
> show #!12 models
> volume #11 level 0.004225
> cofr
Center of rotation: 321.35 430.43 353.65 center of view
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> volume #10 level 0.1602
> color #13 light grey
> color #13/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #13/5-8 tan
> color #13/D-F khaki
> color #13/G goldenrod
> color #13/A medium purple
> color #13/B cornflower blue
> color #13/y3 violet
> color #14 light grey
> color #14/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #14/5-8 tan
> color #14/D-F khaki
> color #14/G goldenrod
> color #14/A medium purple
> color #14/B cornflower blue
> color #14/y3 violet
> select clear
> show #!13 models
> hide #!14 models
> show #!14 models
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> volume #10 level 0.1903
> show #!5 models
> hide #!10 models
> select add #14
37168 atoms, 38018 bonds, 14 pseudobonds, 4690 residues, 2 models selected
> select subtract #14
Nothing selected
> select add #13
183296 atoms, 195439 bonds, 1491 pseudobonds, 16151 residues, 3 models
selected
> select add #14
220464 atoms, 233457 bonds, 1505 pseudobonds, 20841 residues, 5 models
selected
> show (#!13-14 & sel-residues & sidechain) target ab
> style sel stick
Changed 220464 atom styles
> select clear
> color byhetero
> select clear
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> hide cartoons
> show cartoons
> hide atoms
> volume #4 level 0.02203
> volume #4 level 0.02303
> show cartoons
> show atoms
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> ui tool show "Volume Viewer"
> hide atoms
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> show #!13 models
> hide #!13 models
> show #!13 models
> dssp
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> show #!14 models
> hide #!10 models
> show #!13 models
> hide #!14 models
> graphics silhouettes true
> show #!10 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Sat Jul 26 20:18:07 2025 ———
> view name session-start
opened ChimeraX session
> show #!14 models
> hide #!14 models
> show #!14 models
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_177/RTC_real_space_refined_177.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_177/RTC_real_space_refined_177.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 499
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Atom HO5' is not in the residue template for C /L5:1
Atom HO5' is not in the residue template for C /L8:1
Skipping chem_comp category: Missing column 'type' on line 327058
Skipping chem_comp category: Missing column 'type' on line 327324
Skipping chem_comp category: Missing column 'type' on line 327616
Skipping chem_comp category: Missing column 'type' on line 327898
Skipping chem_comp category: Missing column 'type' on line 328150
6 messages similar to the above omitted
Chain information for RTC_real_space_refined_177.cif #15
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
u3 | No description available
v3 | No description available
y3 | No description available
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_180/Translocon_real_space_refined_180.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_180/Translocon_real_space_refined_180.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 416
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "5", on line 170
Invalid residue range for struct_conf "2": invalid chain "5", on line 171
Invalid residue range for struct_conf "3": invalid chain "6", on line 172
Invalid residue range for struct_conf "4": invalid chain "6", on line 173
Invalid residue range for struct_conf "5": invalid chain "6", on line 174
10 messages similar to the above omitted
Bad residue range for struct_conf "22" on line 191
Bad residue range for struct_conf "31" on line 200
Bad residue range for struct_conf "40" on line 209
Bad residue range for struct_conf "41" on line 210
Bad residue range for struct_conf "42" on line 211
53 messages similar to the above omitted
Invalid residue range for struct_conf "116": invalid chain "K2", on line 285
Invalid residue range for struct_conf "117": invalid chain "K2", on line 286
Invalid residue range for struct_conf "118": invalid chain "L2", on line 287
Invalid residue range for struct_conf "119": invalid chain "L2", on line 288
Invalid residue range for struct_conf "120": invalid chain "L2", on line 289
5 messages similar to the above omitted
Bad residue range for struct_conf "129" on line 298
Bad residue range for struct_conf "130" on line 299
Bad residue range for struct_conf "131" on line 300
Invalid residue range for struct_conf "132": invalid chain "N2", on line 301
Invalid residue range for struct_conf "133": invalid chain "N2", on line 302
Invalid residue range for struct_conf "134": invalid chain "N2", on line 303
Invalid residue range for struct_conf "135": invalid chain "N2", on line 304
Invalid residue range for struct_conf "136": invalid chain "N2", on line 305
61 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Skipping chem_comp category: Missing column 'type' on line 75414
Skipping chem_comp category: Missing column 'type' on line 75648
Skipping chem_comp category: Missing column 'type' on line 75836
Skipping chem_comp category: Missing column 'type' on line 75979
Skipping chem_comp category: Missing column 'type' on line 76213
Chain information for Translocon_real_space_refined_180.cif #16
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
y3 | No description available
> hide atoms
> show cartoons
Computing secondary structure
> dssp
> select add #16
74598 atoms, 75447 bonds, 14 pseudobonds, 4690 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,188.33,0,1,0,310.55,0,0,1,55.917
> view matrix models #16,1,0,0,139.09,0,1,0,320.8,0,0,1,133.66
> select subtract #16
Nothing selected
> hide #!10 models
> show #!10 models
> ui tool show "Fit in Map"
> fitmap #16 inMap #10
Fit molecule Translocon_real_space_refined_180.cif (#16) to map
Job588_highRes.mrc (#10) using 74598 atoms
average map value = 0.1403, steps = 100
shifted from previous position = 3.7
rotated from previous position = 0.649 degrees
atoms outside contour = 55837, contour level = 0.19028
Position of Translocon_real_space_refined_180.cif (#16) relative to
Job588_highRes.mrc (#10) coordinates:
Matrix rotation and translation
0.99999835 -0.00012532 0.00181416 -0.32073347
0.00012460 0.99999991 0.00039404 -0.11515200
-0.00181421 -0.00039382 0.99999828 0.34356313
Axis -0.21171613 0.97502095 0.06715976
Axis point 189.99181370 0.00000000 179.45345335
Rotation angle (degrees) 0.10660795
Shift along axis -0.02129754
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!10 models
> hide #!16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!14 models
> show #!16 models
> select ligand
1582 atoms, 1642 bonds, 88 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 1582 atom styles
> select clear
> hide #!14 models
> hide #!13 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!10 models
> show #!11 models
> hide #!10 models
> volume #11 level 0.005815
> select /y3
12340 atoms, 12420 bonds, 16 pseudobonds, 1100 residues, 8 models selected
> show sel & #!16 atoms
> style sel & #!16 stick
Changed 4112 atom styles
> color sel & #!16 byhetero
> select H
180302 atoms, 20609 residues, 2 models selected
> hide sel & #!16 atoms
> select clear
> show #!14 models
> select #14/y3
2058 atoms, 2078 bonds, 4 pseudobonds, 275 residues, 2 models selected
> show sel atoms
> select #11
2 models selected
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!16 models
> show #!16 models
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> volume #11 level 0.00656
> show #!10 models
> hide #!11 models
> hide #!14 models
> close #13-14
> color #15 light grey
> color #15/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #15/5-8 tan
> color #15/D-F khaki
> color #15/G goldenrod
> color #15/A medium purple
> color #15/B cornflower blue
> color #15/y3 violet
> color #16 light grey
> color #16/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #16/5-8 tan
> color #16/D-F khaki
> color #16/G goldenrod
> color #16/A medium purple
> color #16/B cornflower blue
> color #16/y3 violet
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> volume #10 level 0.22
> volume #10 level 0.1531
> color #!16 byhetero
> select clear
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> rename #15 id #13
> rename #16 id #14
> volume #10 level 0.101
> select /y3
8224 atoms, 8264 bonds, 8 pseudobonds, 550 residues, 4 models selected
> hide sel & #!14 atoms
> select clear
> volume #10 level 0.1233
> volume #11 level 0.003777
> show #!13 models
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Sun Jul 27 15:20:49 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_182/RTC_fixed_real_space_refined_182.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_182/RTC_fixed_real_space_refined_182.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 417
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Atom HO5' is not in the residue template for C /L5:1
Atom HO5' is not in the residue template for C /L8:1
Skipping chem_comp category: Missing column 'type' on line 326899
Skipping chem_comp category: Missing column 'type' on line 327191
Skipping chem_comp category: Missing column 'type' on line 327473
Skipping chem_comp category: Missing column 'type' on line 327725
Skipping chem_comp category: Missing column 'type' on line 327752
5 messages similar to the above omitted
Chain information for RTC_fixed_real_space_refined_182.cif #15
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
u3 | No description available
v3 | No description available
y3 | No description available
> hide #!14 models
> show #!13,15 cartoons
Computing secondary structure
> hide #!13,15 atoms
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> close #13
> rename #15 id #13
> color #13 light grey
> color #13/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #13/5-8 tan
> color #13/D-F khaki
> color #13/G goldenrod
> color #13/A medium purple
> color #13/B cornflower blue
> color #13/y3 violet
> select clear
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> select ligand
1034 atoms, 1064 bonds, 44 residues, 2 models selected
> show sel & #!13 atoms
> select clear
> hide #!11 models
> color #!13 byhetero
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> dssp
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
Drag select of 30 residues
> select clear
> show #!10 models
> hide #!13 models
> hide #!10 models
> show #!13 models
> show #!11 models
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Sun Jul 27 17:08:25 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/Translocon_real_space_refined_180-coot-0.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/Translocon_real_space_refined_180-coot-0.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 19
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Chain information for Translocon_real_space_refined_180-coot-0.cif #15
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
y3 | No description available
> ui tool show Matchmaker
> matchmaker #!15 to #14
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Translocon_real_space_refined_180.cif, chain I (#14) with
Translocon_real_space_refined_180-coot-0.cif, chain I (#15), sequence
alignment score = 3684.1
RMSD between 701 pruned atom pairs is 0.006 angstroms; (across all 701 pairs:
0.006)
> matchmaker #!15 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Translocon_real_space_refined_180.cif, chain I (#14) with
Translocon_real_space_refined_180-coot-0.cif, chain I (#15), sequence
alignment score = 3684.1
RMSD between 701 pruned atom pairs is 0.006 angstroms; (across all 701 pairs:
0.006)
> hide atoms
> show cartoons
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> close #14
> rename #15 id #14
> rename #14 Translocon_real_space_refined.cif
> rename #13 60S_translocon_model.cif
> rename #14 Translocon_only_model.cif
> color #14 light grey
> color #14/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #14/5-8 tan
> color #14/D-F khaki
> color #14/G goldenrod
> color #14/A medium purple
> color #14/B cornflower blue
> color #14/y3 violet
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> volume #11 level 0.005232
> hide #!13 models
> select #14/y3:2-79
438 atoms, 439 bonds, 55 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 438 atom styles
> color sel byhetero
> select clear
> show #!13 models
> hide #!13 models
> select ligand
791 atoms, 821 bonds, 44 residues, 2 models selected
> style sel & #!14 stick
Changed 273 atom styles
> select clear
Drag select of 11 Job588_locres_filtered.mrc , 31 atoms, 20 residues, 23 bonds
> select clear
> select #13,14
363325 atoms, 376316 bonds, 756 pseudobonds, 20841 residues, 5 models selected
> select ligand
791 atoms, 821 bonds, 44 residues, 2 models selected
> show sel & #!14 atoms
> select clear
> hide #!11 models
> show #!11 models
> hide #!14 models
> show #!14 models
> select add #11
2 models selected
> select add #14
37161 atoms, 38010 bonds, 14 pseudobonds, 4690 residues, 4 models selected
> color sel byhetero
> select subtract #14
2 models selected
> select subtract #11
Nothing selected
> select clear
> volume #11 level 0.003878
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs"
——— End of log from Thu Jul 31 22:16:36 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_193/RTC_real_space_refined_193.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_193/RTC_real_space_refined_193.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 417
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Atom HO5' is not in the residue template for C /L5:1
Atom HO5' is not in the residue template for C /L8:1
Skipping chem_comp category: Missing column 'type' on line 326898
Skipping chem_comp category: Missing column 'type' on line 327190
Skipping chem_comp category: Missing column 'type' on line 327472
Skipping chem_comp category: Missing column 'type' on line 327724
Skipping chem_comp category: Missing column 'type' on line 327751
5 messages similar to the above omitted
Chain information for RTC_real_space_refined_193.cif #15
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
u3 | No description available
v3 | No description available
y3 | No description available
> hide #!14-15 atoms
> show #!14-15 cartoons
Computing secondary structure
> hide #!15 models
> show #!15 models
> show #!13 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> close #13
> rename #15 id #13
> rename #13 60S+translocon_model.cif
> color #13 light grey
> color #13/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #13/5-8 tan
> color #13/D-F khaki
> color #13/G goldenrod
> color #13/A medium purple
> color #13/B cornflower blue
> color #13/y3 violet
> hide #!13 models
> show #!13 models
> show #!14 models
> hide #!13 models
> show #!13 models
> select ligand
791 atoms, 821 bonds, 44 residues, 2 models selected
> show sel atoms
> select clear
> hide #!13 models
> show #!13 models
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Sun Aug 3 17:32:55 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_193/RTC_real_space_refined_193.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_193/RTC_real_space_refined_193.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 417
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Atom HO5' is not in the residue template for C /L5:1
Atom HO5' is not in the residue template for C /L8:1
Skipping chem_comp category: Missing column 'type' on line 326898
Skipping chem_comp category: Missing column 'type' on line 327190
Skipping chem_comp category: Missing column 'type' on line 327472
Skipping chem_comp category: Missing column 'type' on line 327724
Skipping chem_comp category: Missing column 'type' on line 327751
5 messages similar to the above omitted
Chain information for RTC_real_space_refined_193.cif #15
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
u3 | No description available
v3 | No description available
y3 | No description available
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_202/Translocon_real_space_refined_202.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_202/Translocon_real_space_refined_202.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 135
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Skipping chem_comp category: Missing column 'type' on line 75015
Skipping chem_comp category: Missing column 'type' on line 75203
Skipping chem_comp category: Missing column 'type' on line 75346
Skipping chem_comp category: Missing column 'type' on line 75580
Chain information for Translocon_real_space_refined_202.cif #16
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
y3 | No description available
> hide #!13 models
> hide #!14 models
> hide #!15-16 atoms
> show #!15-16 cartoons
Computing secondary structure
[Repeated 1 time(s)]
> show #!14 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> select ligand
1825 atoms, 1885 bonds, 88 residues, 4 models selected
> show sel & #!15-16 cartoons
> show sel & #!15-16 atoms
> select clear
> close #13-14
> rename #15 id #13
> rename #16 id #14
> rename #13 60S_and_translocon_model
> rename #14 Translocon_only_model
> windowsize 800 800
> color #13 light grey
> color #13/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #13/5-8 tan
> color #13/D-F khaki
> color #13/G goldenrod
> color #13/A medium purple
> color #13/B cornflower blue
> color #13/y3 violet
> color #14 light grey
> color #14/K2,M2,L2,O2,N2,P2,I,J,N light green
> color #14/5-8 tan
> color #14/D-F khaki
> color #14/G goldenrod
> color #14/A medium purple
> color #14/B cornflower blue
> color #14/y3 violet
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> show #!4 models
> hide #!4 models
> color byhetero
> select clear
Drag select of 11 Job588_locres_filtered.mrc , 10 residues
> select clear
> volume #11 level 0.004881
> volume #11 level 0.003276
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Sun Aug 3 18:03:16 2025 ———
> view name session-start
opened ChimeraX session
> select H
180314 atoms, 20609 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs"
——— End of log from Sun Aug 3 18:22:11 2025 ———
> view name session-start
opened ChimeraX session
> rename #1 id #20
> rename #6 id #1
> rename #2 id #23
> rename #3 id #2
> rename #23 id #3
> rename #5 id #6
> rename #4 id #5
> rename #20 id #4
> rename #7 id #20
> rename #12 id #7
> rename #8 id #29
> rename #9 id #8
> rename #29 id #9
> rename #10 id #21
> rename #20 id #10
> rename #21 id #12
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 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
> show #!11 models
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Mon Aug 4 11:04:40 2025 ———
> view name session-start
opened ChimeraX session
> hide #!11 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!14 models
> show #!14 models
> show #!14 cartoons
> select add #14
37161 atoms, 38010 bonds, 14 pseudobonds, 4690 residues, 2 models selected
> show sel cartoons
> cartoon #14
> select #14
37161 atoms, 38010 bonds, 14 pseudobonds, 4690 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> open
> /Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_202/Translocon_real_space_refined_202.cif
Summary of feedback from opening
/Users/rjk/FKBP11/FKBP11_EM/FKBP11_phenix/RealSpaceRefine_202/Translocon_real_space_refined_202.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 135
Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom C01 is not in the residue template for ELU /I:801
Skipping chem_comp category: Missing column 'type' on line 75015
Skipping chem_comp category: Missing column 'type' on line 75203
Skipping chem_comp category: Missing column 'type' on line 75346
Skipping chem_comp category: Missing column 'type' on line 75580
Chain information for Translocon_real_space_refined_202.cif #15
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K2 | No description available
L2 | No description available
M2 | No description available
N | No description available
N2 | No description available
O2 | No description available
P2 | No description available
y3 | No description available
> show #!13 models
> ui tool show Matchmaker
> matchmaker #!15 to #14
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Translocon_only_model, chain I (#14) with
Translocon_real_space_refined_202.cif, chain I (#15), sequence alignment score
= 3684.1
RMSD between 701 pruned atom pairs is 0.000 angstroms; (across all 701 pairs:
0.000)
> matchmaker #!15 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Translocon_only_model, chain I (#14) with
Translocon_real_space_refined_202.cif, chain I (#15), sequence alignment score
= 3684.1
RMSD between 701 pruned atom pairs is 0.000 angstroms; (across all 701 pairs:
0.000)
> select add #15
111762 atoms, 113460 bonds, 28 pseudobonds, 9380 residues, 4 models selected
> select subtract #14
74601 atoms, 75450 bonds, 14 pseudobonds, 4690 residues, 2 models selected
> select subtract #15
Nothing selected
> hide atoms
> show cartoons
> hide #!14 models
> show #!14 models
> close #15
> ui tool show Matchmaker
> matchmaker #!14 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60S_and_translocon_model, chain I (#13) with Translocon_only_model,
chain I (#14), sequence alignment score = 3694.3
RMSD between 701 pruned atom pairs is 0.093 angstroms; (across all 701 pairs:
0.093)
> matchmaker #!14 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60S_and_translocon_model, chain I (#13) with Translocon_only_model,
chain I (#14), sequence alignment score = 3694.3
RMSD between 701 pruned atom pairs is 0.093 angstroms; (across all 701 pairs:
0.093)
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #14/y3
2058 atoms, 2078 bonds, 4 pseudobonds, 275 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 2058 atom styles
> show #!11 models
> select clear
> volume #11 level 0.005182
> show #!13 models
> select #13/y3
2058 atoms, 2078 bonds, 4 pseudobonds, 275 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 2058 atom styles
> select clear
> hide atoms
> select ligand
548 atoms, 578 bonds, 44 residues, 2 models selected
> show sel atoms
> select clear
> hide #!14 models
> show #!14 models
> volume #11 level 0.003677
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
> volume #11 level 0.003226
> save "/Users/rjk/MANUSCRIPTS/GRP94 manuscript/Nature
> revision/ChimeraX_session_for_referees.cxs" includeMaps true
——— End of log from Mon Aug 4 11:11:34 2025 ———
> view name session-start
opened ChimeraX session
> volume #11 level 0.004379
> volume #11 level 0.003527
> volume #11 level 0.00468
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> show #!11 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> volume #11 level 0.003828
> volume #11 level 0.003727
> volume #11 level 0.004329
> volume #11 level 0.004078
> volume #11 level 0.003777
> fitmap #13 inMap #11
Fit molecule 60S_and_translocon_model (#13) to map Job588_locres_filtered.mrc
(#11) using 183289 atoms
average map value = 0.001843, steps = 416
shifted from previous position = 0.228
rotated from previous position = 0.106 degrees
atoms outside contour = 151650, contour level = 0.0037775
Position of 60S_and_translocon_model (#13) relative to
Job588_locres_filtered.mrc (#11) coordinates:
Matrix rotation and translation
0.99995181 0.00095844 -0.00977004 -139.28648229
-0.00096144 0.99999949 -0.00030220 -319.34846704
0.00976975 0.00031158 0.99995223 -138.91303988
Axis 0.03124559 -0.99472170 -0.09773663
Axis point 10873.42114834 0.00000000 -15355.54046691
Rotation angle (degrees) 0.56275298
Shift along axis 326.88765422
> toolshed show
Downloading bundle ChimeraX_QScore-1.2-cp311-cp311-macosx_10_13_universal2.whl
Installed ChimeraX-QScore (1.2)
Downloading bundle ChimeraX_QScore-1.2-cp311-cp311-macosx_10_13_universal2.whl
Bundle installation canceled
> ui tool show "Model-map Q-Score"
Matplotlib is building the font cache; this may take a moment.
> show #!14 models
> hide #!13 models
> style #14 stick
Changed 37161 atom styles
> color #14 byhetero
> select #14/y3
2058 atoms, 2078 bonds, 4 pseudobonds, 275 residues, 2 models selected
> select add #1
2058 atoms, 2078 bonds, 4 pseudobonds, 275 residues, 4 models selected
> select subtract #1
2058 atoms, 2078 bonds, 4 pseudobonds, 275 residues, 2 models selected
> hide #!11 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> transparency #7 60
> qscore #14 toVolume #7 useGui false pointsPerShell 8 shellRadiusStep 0.100
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false assignAttr
> false
WARNING: the following residues in #14 have atoms outside the bounds of volume
#7 and will be excluded from the Q-score calculation:
#14/5-B,D-G,I-J,K2,L2-P2,K,C,H,L/y3:25-599
Overall mean Q-Score: 0.17
/Users/friedrich/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/qscore/ui.py:577: UserWarning: Attempting to set identical
low and high xlims makes transformation singular; automatically expanding.
self.axes.set_xlim([resnum.min(), resnum.max()])
/Users/friedrich/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/qscore/ui.py:566: UserWarning: Attempting to set identical
low and high xlims makes transformation singular; automatically expanding.
axes.set_xlim([new_xmin, new_xmax])
> qscore #14 toVolume #7 useGui false pointsPerShell 8 shellRadiusStep 0.025
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false assignAttr
> false
WARNING: the following residues in #14 have atoms outside the bounds of volume
#7 and will be excluded from the Q-score calculation:
#14/5-B,D-G,I-J,K2,L2-P2,K,C,H,L/y3:25-599
Overall mean Q-Score: 0.17
> qscore #14 toVolume #7 useGui false pointsPerShell 8 shellRadiusStep 0.025
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false assignAttr
> false
WARNING: the following residues in #14 have atoms outside the bounds of volume
#7 and will be excluded from the Q-score calculation:
#14/5-B,D-G,I-J,K2,L2-P2,K,C,H,L/y3:25-599
Overall mean Q-Score: 0.17
> select clear
> qscore #14 toVolume #7 useGui false pointsPerShell 8 shellRadiusStep 0.025
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false assignAttr
> false
WARNING: the following residues in #14 have atoms outside the bounds of volume
#7 and will be excluded from the Q-score calculation:
#14/5-B,D-G,I-J,K2,L2-P2,K,C,H,L/y3:25-599
Overall mean Q-Score: 0.17
> show #!7 models
> qscore #14 toVolume #7 useGui false pointsPerShell 8 shellRadiusStep 0.025
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false assignAttr
> false
WARNING: the following residues in #14 have atoms outside the bounds of volume
#7 and will be excluded from the Q-score calculation:
#14/5-B,D-G,I-J,K2,L2-P2,K,C,H,L/y3:25-599
Overall mean Q-Score: 0.17
> qscore #14 toVolume #7 useGui false pointsPerShell 8 shellRadiusStep 0.025
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails true assignAttr
> false
WARNING: the following residues in #14 have atoms outside the bounds of volume
#7 and will be excluded from the Q-score calculation:
#14/5-B,D-G,I-J,K2,L2-P2,K,C,H,L/y3:25-599
Chain Number Name Qavg Qworst Qbb Qsc
-------------------------------------------------------
5 77 PRO "N/A" "N\A" "N/A" "N/A"
Traceback (most recent call last):
File "/Users/friedrich/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/qscore/ui.py", line
248, in recalc
residue_map, (query_atoms, atom_scores) = run_chimerax_command(self.session,
f'qscore #{m.id_string} to #{v.id_string} useGui false pointsPerShell
{self.points_per_shell} shellRadiusStep {self.shell_radius_step:.3f}
maxShellRadius {self.max_shell_radius:.2f} referenceGaussianSigma
{self.reference_sigma:.2f} logDetails {log_details} {outputfile_text}
assignAttr {self.assign_attr}', log=echo_command)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3215, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/friedrich/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/qscore/cmd.py", line
40, in qscore
residue_map, (query_atoms, atom_scores) = q_score(residues, to_volume,
ref_sigma=reference_gaussian_sigma,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/friedrich/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/qscore/qscore.py",
line 256, in q_score
report_results(residue_scores, query_atoms, q_scores, oob_residues,
log=log_details, filename=output_file)
File "/Users/friedrich/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/qscore/qscore.py",
line 287, in report_results
qavg, qworst = scores
^^^^^^^^^^^^
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File "/Users/friedrich/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/qscore/qscore.py",
line 287, in report_results
qavg, qworst = scores
^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 570X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 32 GB
System Firmware Version: 2075.100.3.0.3
OS Loader Version: 583~1350
SMC Version (system): 2.46f12
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 75 days, 1 hour, 1 minute
Graphics/Displays:
Radeon Pro 570X:
Chipset Model: Radeon Pro 570X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A14GL-003
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiobotocore: 2.21.1
aiohappyeyeballs: 2.6.1
aiohttp: 3.11.13
aioitertools: 0.12.0
aiosignal: 1.3.2
alabaster: 1.0.0
annotated-types: 0.7.0
appdirs: 1.4.4
appnope: 0.1.4
asciitree: 0.3.3
asttokens: 3.0.0
attrs: 25.3.0
auditwheel: 6.2.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.0
botocore: 1.37.1
build: 1.2.2.post1
certifi: 2023.11.17
cffi: 1.17.1
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
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-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202503110047
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.7
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: 2.15
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-OME-Zarr: 0.5.5
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17
ChimeraX-Shape: 1.1
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-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.44
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
click: 8.1.8
cloudpickle: 3.1.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.6.12
cryptography: 44.0.2
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
dask: 2025.2.0
debugpy: 1.8.13
decorator: 5.2.1
Deprecated: 1.2.18
distributed: 2025.2.0
docutils: 0.21.2
executing: 2.2.0
fasteners: 0.19
filelock: 3.17.0
fonttools: 4.56.0
frozenlist: 1.5.0
fsspec: 2025.3.0
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imageio: 2.37.0
imagesize: 1.4.1
importlib_metadata: 8.6.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.6
jmespath: 1.0.1
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
lazy_loader: 0.4
line_profiler: 4.2.0
locket: 1.0.0
lxml: 5.3.1
lz4: 4.4.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.1.0
multidict: 6.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numcodecs: 0.15.1
numexpr: 2.10.2
numpy: 1.26.4
ome-zarr: 0.10.3
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
partd: 1.4.2
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.50
propcache: 0.3.0
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 19.0.1
pycollada: 0.8
pycparser: 2.22
pydantic: 2.10.6
pydantic_core: 2.27.2
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pyspnego: 0.11.2
pytest: 8.3.5
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
PyYAML: 6.0.2
pyzmq: 26.2.1
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
s3fs: 2025.3.0
scikit-image: 0.25.2
scipy: 1.14.0
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
smbprotocol: 1.15.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.1.3
sphinx-autodoc-typehints: 3.0.1
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
stack-data: 0.6.3
starfile: 0.5.12
superqt: 0.7.1
tables: 3.10.2
tblib: 3.0.0
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toolz: 1.0.0
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
wrapt: 1.17.2
yarl: 1.18.3
zarr: 2.18.4
zict: 3.0.0
zipp: 3.21.0
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → QScore: scores is None |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Looks like a duplicate of #17983