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Opened 4 months ago
Closed 4 months ago
#18383 closed defect (not a bug)
H-Bonds: acc_phi_psi() bad number of arguments
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/thea/Library/CloudStorage/OneDrive-
> Aarhusuniversitet/Documents/Projects/SM_GM_Erk2-Tornado/P1502_J96_model-
> overlay_ISOLDE.cxs
Opened cryosparc_P1502_J96_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.29, shown at level 0.3, step 1, values float32
Log from Wed Aug 6 16:57:50 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\au759858\\\OneDrive - Aarhus
> universitet\\\Documents\\\Projects\\\SM_GM_Erk2-Tornado\\\P1502_J96_model-
> overlay_ISOLDE.cxs"
Opened cryosparc_P1502_J96_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.29, shown at level 0.3, step 1, values float32
Log from Wed Aug 6 13:50:29 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\au759858\OneDrive - Aarhus
> universitet\Documents\Projects\SM_GM_Erk2-Tornado\P1502_J96_model-
> overlay_ISOLDE.cxs" format session
Opened cryosparc_P1502_J96_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.29, shown at level 0.3, step 1, values float32
Log from Wed Aug 6 12:14:03 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\au759858\\\OneDrive - Aarhus
> universitet\\\Documents\\\Projects\\\SM_GM_Erk2-Tornado\\\P1502_J96_model-
> overlay_ISOLDE.cxs"
Opened cryosparc_P1502_J96_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.29, shown at level 0.306, step 1, values float32
Log from Tue Aug 5 17:41:37 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\au759858\\\OneDrive - Aarhus
> universitet\\\Documents\\\Projects\\\SM_GM_Erk2-Tornado\\\HDOCK prediction
> Tornado C5 Broccoli_Erk2_Isolde3.pdb"
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/cryosparc_P1502_J96_003_volume_map.mrc"
Opened cryosparc_P1502_J96_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.29, shown at level 0.00838, step 2, values float32
> volume #2 step 1
> volume #2 level 0.2
> select clear
[Repeated 1 time(s)]
> select /A:220
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
204 atoms, 205 bonds, 14 residues, 1 model selected
> select up
2840 atoms, 2880 bonds, 176 residues, 1 model selected
> select up
3106 atoms, 3150 bonds, 195 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> transparency sel 70
> select #2
2 models selected
> transparency #2.1 70
> select /A:275
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
62 atoms, 63 bonds, 3 residues, 1 model selected
> select up
2840 atoms, 2880 bonds, 176 residues, 1 model selected
> select up
3106 atoms, 3150 bonds, 195 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> volume #2 level 0.2136
> select up
6853 atoms, 7390 bonds, 213 residues, 1 model selected
> select up
12536 atoms, 13142 bonds, 566 residues, 1 model selected
> select down
6853 atoms, 7390 bonds, 213 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /A:239
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
202 atoms, 203 bonds, 12 residues, 1 model selected
> select up
2840 atoms, 2880 bonds, 176 residues, 1 model selected
> select up
3106 atoms, 3150 bonds, 195 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> volume #2 level 0.2331
Drag select of 5 residues, 2 cryosparc_P1502_J96_003_volume_map.mrc
> select /A:319
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
36 atoms, 36 bonds, 3 residues, 1 model selected
> select up
2840 atoms, 2880 bonds, 176 residues, 1 model selected
> select up
3106 atoms, 3150 bonds, 195 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> volume #2 level 0.2428
> select up
12536 atoms, 13142 bonds, 566 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #2
2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 6 residues, 1 model selected
> select up
2840 atoms, 2880 bonds, 176 residues, 1 model selected
> select up
3106 atoms, 3150 bonds, 195 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> hide sel atoms
> volume #2 level 0.2895
> select clear
> open 1WZY fromDatabase pdb format mmcif
Summary of feedback from opening 1WZY fetched from pdb
---
note | Fetching compressed mmCIF 1wzy from http://files.rcsb.org/download/1wzy.cif
1wzy title:
Crystal structure of human ERK2 complexed with a pyrazolopyridazine derivative
[more info...]
Chain information for 1wzy #3
---
Chain | Description | UniProt
A | Mitogen-activated protein kinase 1 | MK01_HUMAN 1-360
Non-standard residues in 1wzy #3
---
F29 —
1-allyl-5-(2-phenylpyrazolo[1,5-A]pyridin-3-yl)-1H-pyrazolo[3,4-C]pyridazin-3-amine
(FR296110)
> mmaker #3 to #1
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 HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb, chain A (#1)
with 1wzy, chain A (#3), sequence alignment score = 1729.6
RMSD between 304 pruned atom pairs is 0.762 angstroms; (across all 350 pairs:
2.276)
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.1906, steps = 96
shifted from previous position = 1.42
rotated from previous position = 28.7 degrees
atoms outside contour = 2605, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.24025950 0.96410889 0.11300188 179.62804856
0.33700202 0.02632708 -0.94113576 233.80265049
-0.91033236 0.26419867 -0.31858131 159.26004068
Axis 0.70861493 0.60161719 -0.36867551
Axis point 0.00000000 -52.31587489 168.80020798
Rotation angle (degrees) 121.73540971
Shift along axis 209.23153430
> hide #1 models
> select add #3
3116 atoms, 2948 bonds, 592 residues, 1 model selected
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.22, steps = 668
shifted from previous position = 13.2
rotated from previous position = 106 degrees
atoms outside contour = 2199, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.43767083 -0.19654138 0.87739143 170.90277173
-0.04898107 0.96915624 0.24153061 186.44013355
-0.89780014 -0.14868647 0.41454461 137.24398504
Axis -0.21398715 0.97347912 0.08091909
Axis point 204.97264786 0.00000000 -101.47026326
Rotation angle (degrees) 65.75207430
Shift along axis 156.03023857
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.22, steps = 48
shifted from previous position = 0.0272
rotated from previous position = 0.0634 degrees
atoms outside contour = 2198, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.43847364 -0.19695647 0.87689738 170.90806003
-0.04909973 0.96898536 0.24219124 186.43244897
-0.89740185 -0.14924990 0.41520403 137.23643287
Axis -0.21472695 0.97330052 0.08110754
Axis point 205.12405031 0.00000000 -101.72076124
Rotation angle (degrees) 65.71149439
Shift along axis 155.88714152
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.22, steps = 260
shifted from previous position = 12.4
rotated from previous position = 48 degrees
atoms outside contour = 2199, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.38333465 -0.73235594 0.56276933 188.59387847
0.66207590 0.64272746 0.38543081 198.02930080
-0.64397985 0.22484703 0.73125493 125.14639614
Axis -0.08675173 0.65191877 0.75331006
Axis point 39.14223396 249.07954850 -0.00000000
Rotation angle (degrees) 67.74938696
Shift along axis 207.01221288
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.22, steps = 364
shifted from previous position = 13.4
rotated from previous position = 113 degrees
atoms outside contour = 2198, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.15486860 -0.83734022 -0.52428720 219.71289569
0.26590820 0.54643546 -0.79416693 225.32844174
0.95147703 -0.01642075 0.30728133 174.70670519
Axis 0.38887667 -0.73788892 0.55162929
Axis point 56.17619620 0.00000000 316.98405911
Rotation angle (degrees) 89.75404589
Shift along axis 15.54719658
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.2064, steps = 144
shifted from previous position = 3.82
rotated from previous position = 43.8 degrees
atoms outside contour = 2351, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.16142024 -0.98383359 0.07755622 203.28220184
0.72055270 0.06379368 -0.69045940 234.00661059
0.67434955 0.16733747 0.71920154 153.87848555
Axis 0.42906417 -0.29851197 0.85252246
Axis point -95.85723220 223.54157419 0.00000000
Rotation angle (degrees) 91.59258455
Shift along axis 148.55219905
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.2064, steps = 96
shifted from previous position = 13.3
rotated from previous position = 18.3 degrees
atoms outside contour = 2353, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.45515236 -0.89017195 0.02074174 225.55362172
0.60538314 0.29228730 -0.74032384 231.19769304
0.65295298 0.34951685 0.67193034 156.51938269
Axis 0.55730991 -0.32329274 0.76477936
Axis point -175.88503533 254.18999992 0.00000000
Rotation angle (degrees) 77.89610680
Shift along axis 170.66152570
> fitmap #3 inMap #2
Fit molecule 1wzy (#3) to map cryosparc_P1502_J96_003_volume_map.mrc (#2)
using 3116 atoms
average map value = 0.1906, steps = 148
shifted from previous position = 3.46
rotated from previous position = 40.9 degrees
atoms outside contour = 2605, contour level = 0.28953
Position of 1wzy (#3) relative to cryosparc_P1502_J96_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.20385960 -0.96129670 -0.18533734 219.59363517
0.04092672 0.19751555 -0.97944505 217.61025252
0.97814430 0.19208402 0.07960816 185.17351890
Axis 0.60654422 -0.60237776 0.51888838
Axis point 0.00000000 133.00980600 173.59000231
Rotation angle (degrees) 105.04089118
Shift along axis 98.19406037
> show #1 models
> mmaker #1/a to #3
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 1wzy, chain A (#3) with HDOCK prediction Tornado C5
Broccoli_Erk2_Isolde3.pdb, chain A (#1), sequence alignment score = 1729.6
RMSD between 304 pruned atom pairs is 0.762 angstroms; (across all 350 pairs:
2.276)
> show #1 models
> undo
[Repeated 2 time(s)]
> redo
[Repeated 2 time(s)]
> select #1/B:197
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
6853 atoms, 7390 bonds, 213 residues, 1 model selected
> fitmap #1 inMap #2
Fit molecule HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb (#1) to map
cryosparc_P1502_J96_003_volume_map.mrc (#2) using 12536 atoms
average map value = 0.2549, steps = 204
shifted from previous position = 12.6
rotated from previous position = 28.5 degrees
atoms outside contour = 7863, contour level = 0.28953
Position of HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb (#1)
relative to cryosparc_P1502_J96_003_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99997407 0.00702256 0.00159771 -1.54830948
-0.00703022 0.99996356 0.00484273 0.32955687
-0.00156364 -0.00485384 0.99998700 0.78325699
Axis -0.55843931 0.18206686 -0.80931897
Axis point 38.32416846 197.49879216 0.00000000
Rotation angle (degrees) 0.49743977
Shift along axis 0.29073352
> select #1/A:41
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 6 residues, 1 model selected
> select up
2843 atoms, 2872 bonds, 177 residues, 1 model selected
> select up
2936 atoms, 2965 bonds, 183 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> hide #3 models
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/HDOCK prediction Tornado
> C5 Broccoli_Erk2_Isolde4.pdb"
> open 8k7W fromDatabase pdb format mmcif
Summary of feedback from opening 8k7W fetched from pdb
---
notes | Fetching compressed mmCIF 8k7w from http://files.rcsb.org/download/8k7w.cif
Fetching CCD K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif
8k7w title:
Crystal structure of Broccoli aptamer with DFHBI-1T [more info...]
Chain information for 8k7w #4
---
Chain | Description
A | RNA (49-MER)
Non-standard residues in 8k7w #4
---
2ZY —
(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one
K — potassium ion
NA — sodium ion
8k7w mmCIF Assemblies
---
1| author_and_software_defined_assembly
> mmaker #4 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb, chain B (#1)
with 8k7w, chain A (#4), sequence alignment score = 191.1
RMSD between 12 pruned atom pairs is 1.274 angstroms; (across all 49 pairs:
14.525)
> select #4/A:3
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1053 atoms, 1177 bonds, 49 residues, 1 model selected
> undo
[Repeated 4 time(s)]
> select up
1094 atoms, 1200 bonds, 69 residues, 1 model selected
> select up
16746 atoms, 17290 bonds, 1227 residues, 5 models selected
> select down
1094 atoms, 1200 bonds, 69 residues, 1 model selected
> SEQUENCE CHAIN #4
Unknown command: SEQUENCE CHAIN #4
> sequence chain #4
Alignment identifier is 4/A
> sequence chain #1/B
Alignment identifier is 1/B
> select #4/A:25
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/A:25-28
82 atoms, 90 bonds, 4 residues, 1 model selected
> select #4/A:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/A:20-21
42 atoms, 46 bonds, 2 residues, 1 model selected
> select #4/A:18
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/A:18-27
209 atoms, 232 bonds, 7 pseudobonds, 10 residues, 2 models selected
> select #1/B:181
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/B:181-186
187 atoms, 200 bonds, 6 residues, 1 model selected
> select #1/B:93
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:93-97
155 atoms, 165 bonds, 5 residues, 1 model selected
> select #1/B:100-101
63 atoms, 67 bonds, 2 residues, 1 model selected
> select #1/B:100-104
160 atoms, 172 bonds, 5 residues, 1 model selected
> select #1/B:81
34 atoms, 36 bonds, 1 residue, 1 model selected
> select #1/B:81-84
126 atoms, 134 bonds, 4 residues, 1 model selected
> select #1/B:60
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:60-63
124 atoms, 132 bonds, 4 residues, 1 model selected
> select #1/B:53
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/B:53-84
1023 atoms, 1102 bonds, 32 residues, 1 model selected
> select #1/B:84
31 atoms, 32 bonds, 1 residue, 1 model selected
> select #1/B:41-84
1413 atoms, 1523 bonds, 44 residues, 1 model selected
> select #1/B:84
31 atoms, 32 bonds, 1 residue, 1 model selected
> select #1/B:38-84
1511 atoms, 1629 bonds, 47 residues, 1 model selected
> select clear
> select #4/A:39
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1053 atoms, 1177 bonds, 49 residues, 1 model selected
> select up
1094 atoms, 1200 bonds, 69 residues, 1 model selected
> volume #2 level 0.3061
> select up
16746 atoms, 17290 bonds, 1227 residues, 5 models selected
> select up
16746 atoms, 17290 bonds, 1227 residues, 5 models selected
> hide sel & #1#!4 atoms
> show sel & #1#!4 atoms
> graphics silhouettes true
> color (#1#!4 & sel) white
> select #1/A:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 6 residues, 1 model selected
> select up
2843 atoms, 2872 bonds, 177 residues, 1 model selected
> select up
2936 atoms, 2965 bonds, 183 residues, 1 model selected
> select up
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> hide sel atoms
> ui tool show "Color Actions"
QWindowsWindow::setGeometry: Unable to set geometry 316x649+1043+390 (frame:
334x696+1034+352) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 314x641+1044+397 (frame:
332x688+1035+359) margins: 9, 38, 9, 9 minimum size: 253x519 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=334, y=696)))
> color sel fire brick
> color sel maroon
> color sel dark red
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #4
Alignment identifier is 4/A
> select #1/B:38
34 atoms, 36 bonds, 1 residue, 1 model selected
> select #1/B:38-84
1511 atoms, 1629 bonds, 47 residues, 1 model selected
> color sel forest green
> select #4/A:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/A:1-49
1053 atoms, 1177 bonds, 54 pseudobonds, 49 residues, 2 models selected
> color sel lime green
> select #1/B:162
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/B:157-162
199 atoms, 216 bonds, 6 residues, 1 model selected
> select #1/B:171
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:145-171
863 atoms, 930 bonds, 27 residues, 1 model selected
> select #1/B:171
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:114-171
1871 atoms, 2020 bonds, 58 residues, 1 model selected
> color sel dark red
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/P1502_J96_model-
> overlay_ISOLDE.cxs"
——— End of log from Tue Aug 5 17:41:37 2025 ———
opened ChimeraX session
> hide #!4 models
> select clear
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE.png"
> width 1000 height 723 supersample 3 transparentBackground true
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE_aptamer.png"
> width 1000 height 723 supersample 3 transparentBackground true
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE_broccoli.png"
> width 1000 height 723 supersample 3
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE_broccoli.png"
> width 1000 height 723 supersample 3 transparentBackground true
> show #!4 models
> select #1/B:38
34 atoms, 36 bonds, 1 residue, 1 model selected
> select #1/B:38-84
1511 atoms, 1629 bonds, 47 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE_realbroccoli.png"
> width 1000 height 723 supersample 3 transparentBackground true
> hide #!4 models
> show sel cartoons
> show sel atoms
> select clear
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE_broccoli.png"
> width 1000 height 723 supersample 3 transparentBackground true
> select #1/B:38
34 atoms, 36 bonds, 1 residue, 1 model selected
> select #1/B:38-84
1511 atoms, 1629 bonds, 47 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!4 models
> select add #4
2605 atoms, 2829 bonds, 72 pseudobonds, 116 residues, 4 models selected
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.50424,-0.13022,0.85369,185.1,-0.84718,0.26626,-0.45978,159.18,-0.16743,-0.95506,-0.24458,245.69
> view name broccoli
> view matrix models
> #4,-0.46715,-0.13742,0.87344,184.12,-0.8604,0.2982,-0.41326,158.23,-0.20367,-0.94456,-0.25754,246.5
> view matrix models
> #4,-0.46715,-0.13742,0.87344,184.56,-0.8604,0.2982,-0.41326,159.96,-0.20367,-0.94456,-0.25754,246.29
> view matrix models
> #4,-0.37281,-0.18936,0.90838,182.59,-0.85149,0.45884,-0.25382,155.56,-0.36874,-0.86811,-0.3323,250.12
> view matrix models
> #4,-0.37281,-0.18936,0.90838,181.68,-0.85149,0.45884,-0.25382,156.01,-0.36874,-0.86811,-0.3323,249.96
> view matrix models
> #4,-0.39423,-0.16906,0.90333,182.02,-0.84004,0.46494,-0.27959,156.33,-0.37272,-0.86905,-0.32531,249.88
> view matrix models
> #4,-0.39423,-0.16906,0.90333,182.16,-0.84004,0.46494,-0.27959,155.68,-0.37272,-0.86905,-0.32531,250.07
> view matrix models
> #4,-0.46021,-0.18519,0.86828,184.05,-0.86981,0.29001,-0.39917,159.66,-0.17788,-0.93894,-0.29455,246.66
> volume #2 level 0.2659
> view matrix models
> #4,-0.62746,-0.7482,-0.21561,212.75,-0.76694,0.6417,0.0051357,147.48,0.13451,0.16858,-0.97647,249.35
> view matrix models
> #4,-0.62746,-0.7482,-0.21561,213.52,-0.76694,0.6417,0.0051357,147.72,0.13451,0.16858,-0.97647,248.02
> view matrix models
> #4,-0.62152,-0.75511,-0.20861,213.32,-0.77469,0.63201,0.020359,147.59,0.11647,0.17426,-0.97779,248.31
> view matrix models
> #4,-0.62152,-0.75511,-0.20861,213.69,-0.77469,0.63201,0.020359,148,0.11647,0.17426,-0.97779,247.91
> view matrix models
> #4,-0.62927,-0.76563,-0.13357,212.3,-0.76831,0.63873,-0.041588,149.14,0.11716,0.076456,-0.99017,248.73
> view matrix models
> #4,-0.62927,-0.76563,-0.13357,208.79,-0.76831,0.63873,-0.041588,149.27,0.11716,0.076456,-0.99017,249.63
> view matrix models
> #4,-0.62868,-0.75792,-0.17414,209.59,-0.74143,0.65172,-0.15983,151.25,0.23463,0.028633,-0.97166,247.61
> view matrix models
> #4,-0.62868,-0.75792,-0.17414,209.28,-0.74143,0.65172,-0.15983,150.13,0.23463,0.028633,-0.97166,246.74
> view broccoli
> select clear
> select add #4
1094 atoms, 1200 bonds, 72 pseudobonds, 69 residues, 3 models selected
> view matrix models
> #4,-0.50424,-0.13022,0.85369,184.96,-0.84718,0.26626,-0.45978,159.08,-0.16743,-0.95506,-0.24458,245.12
> select subtract #4
Nothing selected
> volume #2 level 0.25
> volume #2 level 0.4
> volume #2 level 0.3
> view broccoli
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_model_ISOLDE_realbroccoli2.png"
> width 1000 height 723 supersample 3 transparentBackground true
> view matrix models #2,1,0,0,-3.4215,0,1,0,5.142,0,0,1,22.496
> undo
> open "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/HDOCK prediction Tornado
> C5 Broccoli_Erk2.pdb"
Summary of feedback from opening C:/Users/au759858/OneDrive - Aarhus
universitet/Documents/Projects/SM_GM_Erk2-Tornado/HDOCK prediction Tornado C5
Broccoli_Erk2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 4
Duplicate atom serial number found: 8
Duplicate atom serial number found: 10
1916 messages similar to the above omitted
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb #5
---
Chain | Description
A | No description available
B | No description available
> mmaker #5 to #1
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 HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb, chain A (#1)
with HDOCK prediction Tornado C5 Broccoli_Erk2.pdb, chain A (#5), sequence
alignment score = 1781.5
RMSD between 352 pruned atom pairs is 0.125 angstroms; (across all 352 pairs:
0.125)
> mmaker #5/B to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb, chain B (#1)
with HDOCK prediction Tornado C5 Broccoli_Erk2.pdb, chain B (#5), sequence
alignment score = 852
RMSD between 6 pruned atom pairs is 1.554 angstroms; (across all 213 pairs:
28.317)
> hide #!2 models
> show #!2 models
> hide #1 models
> select clear
> select #5/B:210
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
4557 atoms, 5094 bonds, 213 residues, 1 model selected
> select up
7444 atoms, 8049 bonds, 566 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray
> select #5/A
2887 atoms, 2955 bonds, 353 residues, 1 model selected
> color sel dark red
> hide #5.1 models
> sequence chain #5
Chains must have same sequence
> sequence chain #5/B
Alignment identifier is 5/B
> select #5/B:38
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:38-84
1007 atoms, 1125 bonds, 47 residues, 1 model selected
> color sel green
> color sel lawn green
> color sel forest green
> show #1 models
> hide #!2 models
> show #!2 models
> select #5/B:114
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/B:114-171
1244 atoms, 1393 bonds, 58 residues, 1 model selected
> color sel fire brick
> color sel dark red
> hide #1 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> select clear
> hide #!5 models
> select add #2
2 models selected
> transparency #2.1 50
> select clear
> view name front
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map.png" width 1000
> height 723 supersample 3 transparentBackground true
> show #!5 models
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map_HDOCKmodel.png"
> width 1000 height 723 supersample 3 transparentBackground true
> turn y 90
> view front
> turn y 60
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map_HDOCKmodel2.png"
> width 1000 height 723 supersample 3 transparentBackground true
> hide #!5 models
> select #2
2 models selected
> transparency #2.1 50
> select clear
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map2.png" width 1000
> height 723 supersample 3 transparentBackground true
> view name side
> show #1 models
> select add #1
12536 atoms, 13142 bonds, 566 residues, 1 model selected
> show sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> select #1/a
5683 atoms, 5752 bonds, 353 residues, 1 model selected
> hide sel atoms
> select clear
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map_model2.png" width
> 1000 height 723 supersample 3 transparentBackground true
> view front
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map_model.png" width
> 1000 height 723 supersample 3 transparentBackground true
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/P1502_J96_model-
> overlay_ISOLDE.cxs"
——— End of log from Wed Aug 6 12:14:03 2025 ———
opened ChimeraX session
> show #!4 models
> select #5/B:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:8
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:8
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:54
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:54
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:56
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:56-58
60 atoms, 65 bonds, 3 residues, 1 model selected
> select #5/B:42
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:42-45
86 atoms, 96 bonds, 4 residues, 1 model selected
> select #5/B:6
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:6-8
66 atoms, 73 bonds, 3 residues, 1 model selected
> select #5/B:13
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:13-23
231 atoms, 256 bonds, 11 residues, 1 model selected
> select #4/A:7
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4/A:7-8
43 atoms, 47 bonds, 2 residues, 1 model selected
> select #4/A:8
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/A:8
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:43
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:43
30 atoms, 31 bonds, 1 residue, 1 model selected
> hide #!4 models
> select #1/B:73
34 atoms, 36 bonds, 1 residue, 1 model selected
> hide #!2 models
> ui mousemode right "tape measure"
> select ::name="LYS"
920 atoms, 854 bonds, 69 residues, 3 models selected
> color (#1 & sel) orange
> select #1/B:43
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:43
30 atoms, 31 bonds, 1 residue, 1 model selected
> marker segment #6 position 192.7,175.9,166.2 toPosition 207.4,142.3,232.8
> color yellow radius 0.1 label 76.01 labelHeight 7.601 labelColor yellow
> marker delete #6
> marker segment #6 position 192.7,175.9,166.2 toPosition 195.8,144.1,243.8
> color yellow radius 0.1 label 83.9 labelHeight 8.39 labelColor yellow
> marker delete #6
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 34 atom styles
> marker segment #6 position 192.7,175.9,166.2 toPosition 194.7,144.7,236.9
> color yellow radius 0.1 label 77.29 labelHeight 7.729 labelColor yellow
> nucleotides sel stubs
> select clear
[Repeated 1 time(s)]
> nucleotides sel atoms
> style nucleic & sel stick
Changed 34 atom styles
> select clear
> marker delete #6
> select clear
> marker segment #6 position 193.1,223.3,258.2 toPosition 193.2,213.2,170.8
> color yellow radius 0.1 label 87.94 labelHeight 8.794 labelColor yellow
> marker delete #6
> marker segment #6 position 194.7,213.6,174.3 toPosition 195.7,225.5,259.1
> color yellow radius 0.1 label 85.55 labelHeight 8.555 labelColor yellow
> select #1/B:43
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/B:43
30 atoms, 31 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 34 atom styles
> marker segment #6 position 192.7,175.9,166.2 toPosition 194.7,144.7,236.9
> color yellow radius 0.1 label 77.29 labelHeight 7.729 labelColor yellow
> select #1/B:8
34 atoms, 36 bonds, 1 residue, 1 model selected
> select add #1/B:73
68 atoms, 72 bonds, 2 residues, 1 model selected
> nucleotides sel stubs
> show #!4 models
> hide #!4 models
> show #!2 models
> view front
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map_model.png" width
> 1000 height 723 supersample 3 transparentBackground true
> select clear
> view front
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/J96_map_model.png" width
> 1000 height 723 supersample 3 transparentBackground true
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/P1502_J96_model-
> overlay_ISOLDE.cxs"
——— End of log from Wed Aug 6 13:50:29 2025 ———
opened ChimeraX session
> show #!5 models
> hide #!5 models
> open "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/HDOCK prediction Tornado
> C5 Broccoli_Erk2.pdb"
Summary of feedback from opening C:/Users/au759858/OneDrive - Aarhus
universitet/Documents/Projects/SM_GM_Erk2-Tornado/HDOCK prediction Tornado C5
Broccoli_Erk2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 4
Duplicate atom serial number found: 8
Duplicate atom serial number found: 10
1916 messages similar to the above omitted
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb #7
---
Chain | Description
A | No description available
B | No description available
> mmaker #7 to #5
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 HDOCK prediction Tornado C5 Broccoli_Erk2.pdb, chain A (#5) with
HDOCK prediction Tornado C5 Broccoli_Erk2.pdb, chain A (#7), sequence
alignment score = 1826.9
RMSD between 352 pruned atom pairs is 0.000 angstroms; (across all 352 pairs:
0.000)
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> split #7
Split HDOCK prediction Tornado C5 Broccoli_Erk2.pdb (#7) into 2 models
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb A #7.1
---
Chain | Description
A | No description available
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #7.2
---
Chain | Description
B | No description available
> hide #7.2 models
> show #7.2 models
> hide #7.1 models
> show #7.1 models
> mmaker #7.1 to #1
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 HDOCK prediction Tornado C5 Broccoli_Erk2_Isolde3.pdb, chain A (#1)
with HDOCK prediction Tornado C5 Broccoli_Erk2.pdb A, chain A (#7.1), sequence
alignment score = 1781.5
RMSD between 352 pruned atom pairs is 0.125 angstroms; (across all 352 pairs:
0.125)
> select #7.2/B:99
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7.2/B:98
20 atoms, 21 bonds, 1 residue, 1 model selected
> sequence chain #7.2
Alignment identifier is 7.2/B
> select #7.2/B:24
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #7.2/B:98
40 atoms, 42 bonds, 2 residues, 1 model selected
> select #7.2/B:98
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:98-213
2487 atoms, 2782 bonds, 116 residues, 1 model selected
> select #7.2/B:24
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:1-24
511 atoms, 569 bonds, 24 residues, 1 model selected
> select #7.2/B:1-24,98-213
2998 atoms, 3351 bonds, 140 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> select #7.2/B:98
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:98-213
2487 atoms, 2782 bonds, 116 residues, 1 model selected
> select #7.2/B:98
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:98-147
1081 atoms, 1211 bonds, 50 residues, 1 model selected
> rename #7 "HDOCK prediction Tornado C5 Broccoli_Erk2_handmodelled.pdb"
> save "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/P1502_J96_model-
> overlay_ISOLDE.cxs"
——— End of log from Wed Aug 6 16:57:50 2025 ———
opened ChimeraX session
> view matrix models
> #7.2,0.096805,0.23982,-0.96598,216.06,-0.97931,-0.15035,-0.13547,226.62,-0.17773,0.9591,0.22031,143.55
> undo
> ui mousemode right "translate selected atoms"
> hide #1 models
> ui mousemode right translate
> select #7.2/B:110
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:110-112
63 atoms, 69 bonds, 3 residues, 1 model selected
> select #7.2/B:169-170
40 atoms, 43 bonds, 2 residues, 1 model selected
> select #7.2/B:110-170
1310 atoms, 1467 bonds, 61 residues, 1 model selected
> select #7.2/B:177
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:110-177
1459 atoms, 1633 bonds, 68 residues, 1 model selected
> ui mousemode right "translate selected atoms"
Drag select of 2 cryosparc_P1502_J96_003_volume_map.mrc , 670 atoms, 48
residues, 739 bonds
> select up
4557 atoms, 5094 bonds, 213 residues, 3 models selected
Drag select of 2 cryosparc_P1502_J96_003_volume_map.mrc , 696 atoms, 52
residues, 765 bonds
> select up
4557 atoms, 5094 bonds, 213 residues, 1 model selected
> select down
1121 atoms, 765 bonds, 52 residues, 1 model selected
> select up
4557 atoms, 5094 bonds, 213 residues, 1 model selected
> select down
1121 atoms, 765 bonds, 52 residues, 1 model selected
> select #7.2/B:112
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7.2/B:112-173
1330 atoms, 1489 bonds, 62 residues, 1 model selected
> select #7.2/B:133
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:133-136
80 atoms, 87 bonds, 4 residues, 1 model selected
> select #7.2/B:145
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7.2/B:133-145
278 atoms, 310 bonds, 13 residues, 1 model selected
> select #7.2/B:111-112
43 atoms, 47 bonds, 2 residues, 1 model selected
> select #7.2/B:111-132
482 atoms, 541 bonds, 22 residues, 1 model selected
> select #7.2/B:146-147
42 atoms, 46 bonds, 2 residues, 1 model selected
> select #7.2/B:146-149
85 atoms, 94 bonds, 4 residues, 1 model selected
> select #7.2/B:111
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:111-132
482 atoms, 541 bonds, 22 residues, 1 model selected
> select #7.2/B:111-132,146-171
1032 atoms, 1155 bonds, 48 residues, 1 model selected
> select #7.2/B:111-132,146-173
1072 atoms, 1199 bonds, 50 residues, 1 model selected
Drag select of 3 atoms, 3 residues, 4 bonds
> select #7.2/B:111
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:111-132
482 atoms, 541 bonds, 22 residues, 1 model selected
> select #7.2/B:146-147
42 atoms, 46 bonds, 2 residues, 1 model selected
> select #7.2/B:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:146-180
739 atoms, 824 bonds, 35 residues, 1 model selected
> select #7.2/B:173
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:146-173
590 atoms, 658 bonds, 28 residues, 1 model selected
> select #7.2/B:114-132,146-173
1006 atoms, 1125 bonds, 47 residues, 1 model selected
> select #7.2/B:111-132,146-173
1072 atoms, 1199 bonds, 50 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right "translate selected atoms"
> select subtract #7.2/B:111
1052 atoms, 1177 bonds, 49 residues, 1 model selected
> select #7.2/B:112
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7.2/B:113
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7.2/B:113-132
439 atoms, 493 bonds, 20 residues, 1 model selected
> select #7.2/B:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7.2/B:146-150
105 atoms, 116 bonds, 5 residues, 1 model selected
> select #7.2/B:118
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7.2/B:118-132
327 atoms, 366 bonds, 15 residues, 1 model selected
> select #7.2/B:114-132
416 atoms, 467 bonds, 19 residues, 1 model selected
> select #7.2/B:114-132,146-174
1029 atoms, 1151 bonds, 48 residues, 1 model selected
> select #7.2/B:114-132,146-174
1029 atoms, 1151 bonds, 48 residues, 1 model selected
> select #7.2/B:114-132,146-174
1029 atoms, 1151 bonds, 48 residues, 1 model selected
> select subtract #7.2/B:174
1006 atoms, 1125 bonds, 47 residues, 1 model selected
Drag select of 2 cryosparc_P1502_J96_003_volume_map.mrc , 1035 atoms, 68
residues, 1136 bonds
> select clear
> save "/Users/thea/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/P1502_J96_model-
> overlay_ISOLDE.cxs"
> isolde start
> set selectionWidth 4
Done loading forcefield
> 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
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> undo
> select up
4557 atoms, 5094 bonds, 213 residues, 1 model selected
> select down
1435 atoms, 67 residues, 1 model selected
> undo
> ui mousemode right translate
> select clear
> clipper associate #2 toModel #8
Opened cryosparc_P1502_J96_003_volume_map.mrc as #8.1.1.1, grid size
300,300,300, pixel 1.29, shown at step 1, values float32
> dinstances nucleic
Unknown command: isolde restrain dinstances nucleic
> isolde restrain distances nucleic
Restrained residues must be from a single model!
> select up
4557 atoms, 5094 bonds, 213 residues, 1 model selected
> isolde restrain distances nucleic
Restrained residues must be from a single model!
> isolde restrain distances nucleic sel
Expected ',' or a keyword
> isolde restrain distances nucleic #7.1
Expected ',' or a keyword
> addh #8.2
Summary of feedback from adding hydrogens to HDOCK prediction Tornado C5
Broccoli_Erk2.pdb B #8.2
---
warnings | Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C2 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 N3 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C6 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 46 C5 because it is missing heavy-atom bond partners
2 messages similar to the above omitted
notes | No usable SEQRES records for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B (#8.2) chain B; guessing termini instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
donor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B A 72 N6
acceptor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 46 N7
Traceback (most recent call last):
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table
self._ask_to_add_hydrogens_if_necessary(residues)
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary
run(self.session, f'addh #{residues.unique_structures[0].id_string}')
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> addh #8.2
Summary of feedback from adding hydrogens to HDOCK prediction Tornado C5
Broccoli_Erk2.pdb B #8.2
---
warnings | Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C2 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 N3 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C6 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 46 C5 because it is missing heavy-atom bond partners
2 messages similar to the above omitted
notes | No usable SEQRES records for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B (#8.2) chain B; guessing termini instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
donor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B A 72 N6
acceptor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 46 N7
Traceback (most recent call last):
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table
self._ask_to_add_hydrogens_if_necessary(residues)
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary
run(self.session, f'addh #{residues.unique_structures[0].id_string}')
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> addh #8.2
Summary of feedback from adding hydrogens to HDOCK prediction Tornado C5
Broccoli_Erk2.pdb B #8.2
---
warnings | Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C2 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 N3 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C6 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 46 C5 because it is missing heavy-atom bond partners
2 messages similar to the above omitted
notes | No usable SEQRES records for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B (#8.2) chain B; guessing termini instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
donor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B A 72 N6
acceptor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 46 N7
Traceback (most recent call last):
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table
self._ask_to_add_hydrogens_if_necessary(residues)
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary
run(self.session, f'addh #{residues.unique_structures[0].id_string}')
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> isolde sim start #8.2/B:118-121,156-157,159,165
Sim termination reason: None
ISOLDE: stopped sim
> select up
6559 atoms, 7096 bonds, 213 residues, 1 model selected
> isolde sim start #8.2/B
Sim termination reason: None
ISOLDE: stopped sim
> addh #8.2
Summary of feedback from adding hydrogens to HDOCK prediction Tornado C5
Broccoli_Erk2.pdb B #8.2
---
warnings | Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 1 P because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C2 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 N3 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 45 C6 because it is missing heavy-atom bond partners
Not adding hydrogens to HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B
G 46 C5 because it is missing heavy-atom bond partners
2 messages similar to the above omitted
notes | No usable SEQRES records for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B (#8.2) chain B; guessing termini instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
donor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B A 72 N6
acceptor: HDOCK prediction Tornado C5 Broccoli_Erk2.pdb B #8.2/B G 46 N7
Traceback (most recent call last):
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table
self._ask_to_add_hydrogens_if_necessary(residues)
File "/Users/thea/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary
run(self.session, f'addh #{residues.unique_structures[0].id_string}')
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11B0000TD/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 3 days, 1 hour, 11 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-Clipper: 0.23.1
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → H-Bonds: acc_phi_psi() bad number of arguments |
comment:2 by , 4 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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