![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5532 closed defect (fixed)
Region bound checking using None
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3rc202110301701 (2021-10-30 17:01:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3rc202110301701 (2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/courtneykarl/Desktop/RIP.cxs
Opened emdb 30209 as #3, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Opened emdb 30209 as #4, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Log from Wed Nov 3 04:32:36 2021UCSF ChimeraX version: 1.3rc202110301701
(2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/courtneykarl/Desktop/colors.cxs format session
Opened emdb 30209 as #3, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Opened emdb 30209 as #4, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Log from Wed Nov 3 02:36:47 2021UCSF ChimeraX version: 1.3rc202110301701
(2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/courtneykarl/Desktop/yeet.cxs format session
Opened emdb 30209 as #3, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Opened emdb 30209 as #4, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Log from Wed Nov 3 02:36:28 2021UCSF ChimeraX version: 1.3rc202110301701
(2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/courtneykarl/Desktop/meh.cxs format session
Opened emdb 30209 as #3, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Opened emdb 30209 as #4, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
Log from Wed Nov 3 01:05:02 2021 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.3rc202110301701 (2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> ui windowfill toggle
[Repeated 1 time(s)]
> open /Users/courtneykarl/Desktop/7btf.cif.gz
File reader requires uncompressed file;
'/Users/courtneykarl/Desktop/7btf.cif.gz' is compressed
> open /Users/courtneykarl/Desktop/7btf.cif
Summary of feedback from opening /Users/courtneykarl/Desktop/7btf.cif
---
note | Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
7btf.cif title:
SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors in reduced
condition [more info...]
Chain information for 7btf.cif #1
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2
B D | Non-structural protein 8 | R1AB_SARS2
C | Non-structural protein 7 | R1AB_SARS2
Non-standard residues in 7btf.cif #1
---
ZN — zinc ion
> select /A:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
7378 atoms, 7562 bonds, 917 residues, 1 model selected
> select down
141 atoms, 144 bonds, 16 residues, 1 model selected
> select /B:67-192
983 atoms, 997 bonds, 126 residues, 1 model selected
> hide target m
> show target m
> hide sel cartoons
> select /D:84-191
805 atoms, 817 bonds, 1 pseudobond, 104 residues, 2 models selected
> hide sel cartoons
> select /C:1-68
519 atoms, 522 bonds, 68 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
> hide sel surfaces
> select /A:4-932
7376 atoms, 7562 bonds, 1 pseudobond, 915 residues, 2 models selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> rainbow sel
[Repeated 1 time(s)]
> view clip false
[Repeated 1 time(s)]
> color (#!1 & sel) cyan
> color (#!1 & sel) blue
> color (#!1 & sel) medium blue
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select up
141 atoms, 144 bonds, 1 pseudobond, 16 residues, 3 models selected
> select up
7378 atoms, 7562 bonds, 1 pseudobond, 917 residues, 3 models selected
> select down
141 atoms, 144 bonds, 1 pseudobond, 16 residues, 3 models selected
> 183
Unknown command: 183
> ui tool show AlphaFold
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select up
141 atoms, 144 bonds, 1 pseudobond, 16 residues, 3 models selected
> select up
7378 atoms, 7562 bonds, 1 pseudobond, 917 residues, 3 models selected
> select down
141 atoms, 144 bonds, 1 pseudobond, 16 residues, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
> select down
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 3 models selected
>
Incomplete command: alphafold
> alphafold fetch Q13546
Fetching compressed AlphaFold Q13546 from
https://alphafold.ebi.ac.uk/files/AF-Q13546-F1-model_v1.cif
Chain information for AlphaFold Q13546 #2
---
Chain | Description | UniProt
A | Receptor-interacting serine/threonine-protein kinase 1 | RIPK1_HUMAN
> select ::name="PRO"
546 atoms, 548 bonds, 78 residues, 2 models selected
> select ::name="SER"
786 atoms, 669 bonds, 131 residues, 2 models selected
> select down
786 atoms, 669 bonds, 131 residues, 4 models selected
> select down
786 atoms, 669 bonds, 131 residues, 4 models selected
> select down
786 atoms, 669 bonds, 131 residues, 4 models selected
> select down
786 atoms, 669 bonds, 131 residues, 4 models selected
> select down
786 atoms, 669 bonds, 131 residues, 4 models selected
> select down
786 atoms, 669 bonds, 131 residues, 4 models selected
> select S321
Expected an objects specifier or a keyword
> select AlphaFold Q13546 S321
Expected an objects specifier or a keyword
> select #AlphaFold Q13546 :S321
Expected an objects specifier or a keyword
> select#AlphaFold_Q13546:S321
Unknown command: select#AlphaFold_Q13546:S321
> select#AlphaFoldQ13546:S321
Unknown command: select#AlphaFoldQ13546:S321
> select:S321
Unknown command: select:S321
> select:321
Unknown command: select:321
> select #1/C
519 atoms, 522 bonds, 68 residues, 1 model selected
> select #2/A
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> select up
15015 atoms, 15347 bonds, 1886 residues, 2 models selected
> select up
15015 atoms, 15347 bonds, 10 pseudobonds, 1886 residues, 6 models selected
> select up
15015 atoms, 15347 bonds, 10 pseudobonds, 1886 residues, 6 models selected
> select down
15015 atoms, 15347 bonds, 1886 residues, 4 models selected
> select down
5330 atoms, 5449 bonds, 671 residues, 3 models selected
> select up
15015 atoms, 15347 bonds, 1886 residues, 2 models selected
> select clear
> select :321
19 atoms, 18 bonds, 2 residues, 2 models selected
> select #2 :321
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #2 :332
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel magenta
> select #2 :334
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #2 :336
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel magenta
> select #1 :35-39
89 atoms, 90 bonds, 10 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :48-49
35 atoms, 35 bonds, 4 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :50-52
50 atoms, 48 bonds, 6 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :55
19 atoms, 17 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :71
19 atoms, 18 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :73
18 atoms, 16 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :74
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :75
21 atoms, 20 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :79
17 atoms, 15 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :83
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :116
25 atoms, 24 bonds, 3 residues, 1 model selected
> color (#!1 & sel) orange
[Repeated 1 time(s)]
> select #1 :119
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :120-123
88 atoms, 88 bonds, 11 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :204
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) orange
> select #1 :206
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) orange
> select #1 :208-209
16 atoms, 15 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :217-218
20 atoms, 20 bonds, 2 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :220-222
23 atoms, 23 bonds, 3 residues, 1 model selected
> color (#!1 & sel) orange
> select #1 :236
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) orange
> select #1 :323
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
> select #2 : 1-303
2415 atoms, 2462 bonds, 303 residues, 1 model selected
> color sel red
> color sel purple
> select #2 : 166
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel lime
> style sel sphere
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> style sel sphere
Changed 5330 atom styles
> style sel sphere
Changed 5330 atom styles
> style sel stick
Changed 5330 atom styles
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> select #1
9685 atoms, 9898 bonds, 10 pseudobonds, 1215 residues, 3 models selected
> show sel surfaces
> select #1/C
519 atoms, 522 bonds, 68 residues, 1 model selected
> hide sel cartoons
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/B#1/D
1788 atoms, 1814 bonds, 1 pseudobond, 230 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> hide sel surfaces
> select #1-2
12708 atoms, 13011 bonds, 9 pseudobonds, 1588 residues, 4 models selected
> ui tool show ViewDockX
No suitable models found for ViewDockX
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> hide sel surfaces
> select #1-2
12708 atoms, 13011 bonds, 9 pseudobonds, 1588 residues, 4 models selected
> ui tool show ViewDockX
No suitable models found for ViewDockX
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> show sel surfaces
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> surface style #1 solid
> ui tool show "Fit in Map"
> select #1-2
12708 atoms, 13011 bonds, 9 pseudobonds, 1588 residues, 4 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui tool show "Map Coordinates"
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> volume region all imageMode "full region"
No volumes specified
> ui mousemode right "move markers"
> hide sel surfaces
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> hide sel surfaces
> select none
Expected an objects specifier or a keyword
> select cancel
Expected an objects specifier or a keyword
> select clear
> open 30209 fromDatabase emdb
Summary of feedback from opening 30209 fetched from emdb
---
note | Fetching compressed map 30209 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30209/map/emd_30209.map.gz
Opened emdb 30209 as #3, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
> open 30209 fromDatabase emdb
Opened emdb 30209 as #4, grid size 192,192,192, pixel 1.01, shown at level
0.0225, step 1, values float32
> save /Users/courtneykarl/Desktop/meh.cxs
——— End of log from Wed Nov 3 01:05:02 2021 ———
opened ChimeraX session
> hide #!1 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> ui mousemode right select
> select #4
2 models selected
> select clear
[Repeated 2 time(s)]
> select #4
2 models selected
> select #2/A:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select down
Nothing selected
> select #2/A:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
59 atoms, 59 bonds, 7 residues, 2 models selected
> select up
5330 atoms, 5449 bonds, 671 residues, 2 models selected
> select up
5330 atoms, 5449 bonds, 671 residues, 2 models selected
> select up
12708 atoms, 13011 bonds, 1588 residues, 7 models selected
> select #4
2 models selected
> select #4
2 models selected
> volume sel style surface
> surface dust #4 size 10.1
> color zone #4 near #2 distance 6.08
> select clear
> select #2/A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
158 atoms, 160 bonds, 18 residues, 2 models selected
> select up
5330 atoms, 5449 bonds, 671 residues, 2 models selected
> select up
5330 atoms, 5449 bonds, 671 residues, 2 models selected
> select down
1 model selected
> select clear
> select #2/A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
158 atoms, 160 bonds, 18 residues, 2 models selected
> select up
5330 atoms, 5449 bonds, 671 residues, 2 models selected
> show sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> select #4
2 models selected
> show #!1 models
> select clear
[Repeated 1 time(s)]
> select #1/A:468
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
140 atoms, 142 bonds, 16 residues, 2 models selected
> select up
7378 atoms, 7562 bonds, 917 residues, 2 models selected
> show sel surfaces
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,74.61,0,1,0,-83.232,0,0,1,-39.615
> ui mousemode right select
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.43603,-0.70983,0.5532,67.98,0.27399,0.69024,0.66971,-63.95,-0.85721,-0.14044,0.49545,147.66
> view matrix models
> #4,0.85532,-0.27114,-0.44149,85.361,0.46714,0.035051,0.88349,-39.943,-0.22407,-0.9619,0.15664,201.6
> view matrix models
> #4,0.86476,-0.20813,-0.45703,79.84,0.49008,0.15104,0.85849,-51.007,-0.10965,-0.96637,0.23261,183.3
> view matrix models
> #4,0.80859,-0.30491,-0.50319,99.443,0.53168,0.012381,0.84686,-40.226,-0.25199,-0.9523,0.17213,201.78
> view matrix models
> #4,0.94936,-0.17164,-0.26316,48.431,0.26129,-0.033831,0.96467,-21.557,-0.17448,-0.98458,0.012731,213.64
> view matrix models
> #4,0.85997,-0.26954,-0.43337,83.931,0.43617,-0.052734,0.89832,-29.84,-0.26499,-0.96154,0.072215,214.08
> view matrix models
> #4,-0.80273,-0.070943,-0.59211,240.93,-0.054424,-0.98004,0.1912,180.25,-0.59386,0.18571,0.78284,61.081
> view matrix models
> #4,-0.91815,0.34015,-0.20321,172.25,-0.3386,-0.93993,-0.043451,227.53,-0.20578,0.02891,0.97817,19.226
> view matrix models
> #4,-0.89804,0.37191,-0.23498,170.42,-0.40549,-0.90692,0.1143,214.74,-0.1706,0.19793,0.96526,0.5489
> view matrix models
> #4,-0.80931,0.48013,-0.33837,161.72,-0.50549,-0.8627,-0.015075,233.17,-0.29915,0.15884,0.94089,19.258
> view matrix models
> #4,-0.96737,0.086325,-0.23822,205.47,-0.12191,-0.98277,0.1389,192.34,-0.22212,0.16341,0.96123,9.3169
> view matrix models
> #4,-0.95726,-0.19648,-0.21224,229.63,0.16763,-0.97491,0.14648,162.87,-0.23569,0.10464,0.96618,15.893
> view matrix models
> #4,-0.9362,-0.20666,-0.2843,235.9,0.17447,-0.97543,0.13453,163.47,-0.30511,0.076342,0.94925,27.086
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.9362,-0.20666,-0.2843,257.67,0.17447,-0.97543,0.13453,134.13,-0.30511,0.076342,0.94925,-1.0505
> view matrix models
> #4,-0.9362,-0.20666,-0.2843,258.48,0.17447,-0.97543,0.13453,131.03,-0.30511,0.076342,0.94925,-4.4043
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.33077,0.86452,-0.37841,40.636,0.93267,-0.23833,0.27079,-28.296,0.14392,-0.4425,-0.88515,189.29
> view matrix models
> #4,0.53023,0.82517,-0.19483,6.6383,0.47429,-0.098194,0.87488,-59.112,0.70279,-0.55629,-0.44343,101.75
> view matrix models
> #4,0.73289,0.67665,0.070842,-25.279,0.32141,-0.43613,0.84053,-7.7026,0.59964,-0.59324,-0.53712,124.83
> view matrix models
> #4,0.39105,0.91959,0.037826,-12.806,0.69196,-0.32085,0.64672,-35.107,0.60686,-0.22672,-0.76179,110.94
> view matrix models
> #4,0.80102,-0.46331,0.3791,48.8,-0.37443,0.10637,0.92113,-2.0169,-0.46709,-0.87979,-0.088269,210.34
> view matrix models
> #4,0.54243,-0.83017,-0.12875,161.28,0.30932,0.054868,0.94937,-65.783,-0.78108,-0.5548,0.28655,170.7
> view matrix models
> #4,0.23317,0.68008,0.69507,-40.729,-0.96862,0.2257,0.1041,126.46,-0.086082,-0.69753,0.71137,74.575
> view matrix models
> #4,-0.92304,0.36671,-0.11624,183.87,-0.36411,-0.93033,-0.043716,196.64,-0.12417,0.0019723,0.99226,-18.92
> view matrix models
> #4,-0.94539,0.29228,-0.14429,196.18,-0.29264,-0.95603,-0.019191,189.78,-0.14356,0.024083,0.98935,-18.926
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.94539,0.29228,-0.14429,275.18,-0.29264,-0.95603,-0.019191,157.37,-0.14356,0.024083,0.98935,-12.565
> view matrix models
> #4,-0.94539,0.29228,-0.14429,268.89,-0.29264,-0.95603,-0.019191,163.78,-0.14356,0.024083,0.98935,-4.4736
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.82572,0.55614,0.094262,207.24,-0.55246,-0.83109,0.063888,168.15,0.11387,0.00067769,0.9935,-27.429
> view matrix models
> #4,-0.79911,0.59674,0.072891,202.85,-0.59367,-0.80241,0.060679,169.63,0.094698,0.0052158,0.99549,-26.228
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.79911,0.59674,0.072891,188.17,-0.59367,-0.80241,0.060679,171.7,0.094698,0.0052158,0.99549,-43.816
> view matrix models
> #4,-0.79911,0.59674,0.072891,183.36,-0.59367,-0.80241,0.060679,207.94,0.094698,0.0052158,0.99549,-57.538
> view matrix models
> #4,-0.79911,0.59674,0.072891,181.06,-0.59367,-0.80241,0.060679,206.56,0.094698,0.0052158,0.99549,-49.532
> view matrix models
> #4,-0.79911,0.59674,0.072891,186.17,-0.59367,-0.80241,0.060679,212.39,0.094698,0.0052158,0.99549,-39.645
> view matrix models
> #4,-0.79911,0.59674,0.072891,182.09,-0.59367,-0.80241,0.060679,233.7,0.094698,0.0052158,0.99549,-38.336
> view matrix models
> #4,-0.79911,0.59674,0.072891,192.68,-0.59367,-0.80241,0.060679,218.29,0.094698,0.0052158,0.99549,-39.712
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.97179,0.18695,-0.14379,271.55,-0.20294,-0.97345,0.10587,192.8,-0.12018,0.13207,0.98393,-30.265
> view matrix models
> #4,-0.90946,0.41461,-0.031372,231.78,-0.41323,-0.90964,-0.042396,221.86,-0.046115,-0.025594,0.99861,-23.42
> view matrix models
> #4,-0.90705,0.10606,-0.40744,299.99,-0.11039,-0.9938,-0.012947,197.92,-0.40629,0.033232,0.91314,14.218
> view matrix models
> #4,-0.85217,0.16594,-0.49627,297.82,-0.1629,-0.98539,-0.049753,205.9,-0.49727,0.038444,0.86674,27.19
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.85217,0.16594,-0.49627,334.31,-0.1629,-0.98539,-0.049753,168.38,-0.49727,0.038444,0.86674,40.58
> view matrix models
> #4,-0.85217,0.16594,-0.49627,328.22,-0.1629,-0.98539,-0.049753,206.74,-0.49727,0.038444,0.86674,49.892
> view matrix models
> #4,-0.85217,0.16594,-0.49627,327.78,-0.1629,-0.98539,-0.049753,206.97,-0.49727,0.038444,0.86674,50.593
> view matrix models
> #4,-0.85217,0.16594,-0.49627,323.52,-0.1629,-0.98539,-0.049753,231.72,-0.49727,0.038444,0.86674,57.127
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.79658,-0.12611,-0.59124,356.47,0.19484,-0.97937,-0.053618,197.01,-0.57228,-0.15791,0.80471,89.932
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.79658,-0.12611,-0.59124,366.01,0.19484,-0.97937,-0.053618,123.66,-0.57228,-0.15791,0.80471,79.573
> view matrix models
> #4,-0.79658,-0.12611,-0.59124,420.76,0.19484,-0.97937,-0.053618,164.72,-0.57228,-0.15791,0.80471,46.896
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.69938,0.56047,-0.44354,329,-0.18149,-0.73948,-0.64825,237.79,-0.69132,-0.37288,0.6189,98.334
> view matrix models
> #4,-0.59529,0.64389,-0.48065,314.53,-0.46677,-0.76403,-0.44541,247.15,-0.65403,-0.040789,0.75537,48.289
> view matrix models
> #4,-0.8407,0.014963,-0.54129,406.1,0.11237,-0.97304,-0.20143,187.05,-0.52971,-0.23017,0.81635,48.704
> view matrix models
> #4,-0.35837,-0.91769,-0.17152,413.63,0.39972,-0.31685,0.86013,-12.773,-0.84368,0.23969,0.48037,66.942
> view matrix models
> #4,0.68152,-0.51599,0.51893,203.84,-0.24458,0.50773,0.82607,-28.122,-0.68972,-0.6899,0.21982,169.79
> view matrix models
> #4,0.51116,-0.80264,0.3074,269.88,0.13382,0.42761,0.894,-63.649,-0.84901,-0.41584,0.32598,147.48
> view matrix models
> #4,0.91095,0.30633,-0.27627,181.64,0.0069762,0.65819,0.75282,-59.731,0.41245,-0.68771,0.59744,24.945
> view matrix models
> #4,0.76861,-0.15834,-0.61982,275.84,0.63125,0.34485,0.6947,-83.292,0.10375,-0.92521,0.365,101.62
> view matrix models
> #4,0.96194,0.0015146,-0.27327,206.34,0.25902,0.31371,0.91351,-66.522,0.08711,-0.94952,0.30137,112.07
> view matrix models
> #4,0.72377,-0.5192,-0.45453,298.83,0.58232,0.10615,0.806,-66.426,-0.37023,-0.84804,0.37916,138.33
> view matrix models
> #4,0.61753,-0.57659,-0.53497,322.87,0.64748,-0.013507,0.76196,-56.498,-0.44657,-0.81692,0.36499,144.08
> view matrix models
> #4,0.67343,-0.66657,-0.31963,304.47,0.55861,0.17565,0.81062,-71.431,-0.4842,-0.72445,0.49064,125.88
> view matrix models
> #4,0.60619,0.70912,0.36012,106.94,-0.41165,-0.10768,0.90496,40.412,0.6805,-0.69682,0.22663,37.595
> view matrix models
> #4,0.76529,0.57369,0.29191,111.81,-0.32132,-0.052471,0.94552,22.164,0.55775,-0.81739,0.14418,69.637
> view matrix models
> #4,0.72496,0.55699,0.40521,105.84,-0.47517,-0.021466,0.87963,40.645,0.49864,-0.83024,0.2491,65.959
> view matrix models
> #4,0.86082,-0.40657,-0.30609,259.49,-0.40945,-0.1961,-0.89101,231.06,0.30223,0.89232,-0.33528,-24.939
> view matrix models
> #4,0.38698,-0.91895,0.076069,316.74,-0.785,-0.3716,-0.49568,244.41,0.48377,0.1321,-0.86517,85.938
> view matrix models
> #4,0.23888,-0.95176,0.19257,322.43,-0.63906,-0.30339,-0.70679,245.06,0.73112,0.045772,-0.68071,51.842
> view matrix models
> #4,0.46239,0.87703,0.13042,127.63,0.81584,-0.36321,-0.44999,84.531,-0.34729,0.31447,-0.88346,150.06
> view matrix models
> #4,0.48878,0.83487,0.25315,116.77,0.82701,-0.35102,-0.43914,81.156,-0.27776,0.424,-0.86202,130.42
> ui mousemode right select
> select up
12708 atoms, 13011 bonds, 1588 residues, 6 models selected
> select down
4 models selected
> hide #!2 models
> select up
12708 atoms, 13011 bonds, 1588 residues, 6 models selected
> fitmap #1 inMap #4
Fit molecule 7btf.cif (#1) to map emdb 30209 (#4) using 7378 atoms
average map value = 0.0001269, steps = 60
shifted from previous position = 1.78
rotated from previous position = 1.98 degrees
atoms outside contour = 7378, contour level = 0.022497
Position of 7btf.cif (#1) relative to emdb 30209 (#4) coordinates:
Matrix rotation and translation
0.46431014 0.83349215 -0.29951108 -105.86210178
0.85223467 -0.32841281 0.40723594 -52.65803244
0.24106461 -0.44433750 -0.86281630 211.55232008
Axis -0.84411459 -0.53584084 0.01857836
Axis point 0.00000000 40.82957480 102.61495734
Rotation angle (degrees) 149.70726375
Shift along axis 121.50636448
> hide #!1 models
> show #!2 models
> ui mousemode right translate
> ui mousemode right "move picked models"
> fitmap #2 inMap #4
Fit molecule AlphaFold Q13546 (#2) to map emdb 30209 (#4) using 5330 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 5330, contour level = 0.022497
Position of AlphaFold Q13546 (#2) relative to emdb 30209 (#4) coordinates:
Matrix rotation and translation
0.48878326 0.82700751 -0.27775791 -87.96621122
0.83486803 -0.35102425 0.42400163 -124.29752049
0.25315270 -0.43913609 -0.86201690 118.50303726
Axis -0.85174326 -0.52390195 0.00775675
Axis point 0.00000000 -16.34091027 66.90889906
Rotation angle (degrees) 149.55646953
Shift along axis 140.96353948
> show #!1 models
> hide #!4 models
> ui mousemode right select
Drag select of 7btf.cif_A SES surface, 2080 of 757870 triangles, 5 residues
> select up
101 atoms, 103 bonds, 13 residues, 2 models selected
> select up
7378 atoms, 7562 bonds, 917 residues, 2 models selected
> select up
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 4 models selected
> select up
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 4 models selected
> select up
12708 atoms, 13011 bonds, 9 pseudobonds, 1588 residues, 9 models selected
> select down
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 5 models selected
> ui mousemode right "move picked models"
> view matrix models
> #1,0.99948,0.02073,-0.024832,-5.6473,-0.021027,0.99971,-0.011754,-86.839,0.024581,0.01227,0.99962,-130.49
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.88665,0.28038,-0.36774,14.1,-0.077828,0.87436,0.47899,-119.74,0.45584,-0.39608,0.79708,-108.25
> ui mousemode right rotate
> select clear
> ui mousemode right rotate
> ui mousemode right select
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.13247,-0.98195,-0.13497,274.49,0.989,-0.1219,-0.083797,-59.448,0.065832,-0.14459,0.9873,-114.1
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.048907,-0.38211,-0.92282,265.21,0.97195,0.23102,-0.044148,-107.02,0.23006,-0.89477,0.38269,30.559
> view matrix models
> #1,-0.088813,-0.42896,-0.89895,285.43,0.98347,-0.18076,-0.010908,-59.544,-0.15782,-0.88505,0.43792,70.759
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.7872,-0.090861,-0.60997,295.2,0.12458,-0.99212,-0.012991,150.19,-0.60398,-0.086217,0.79232,-16.912
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.7872,-0.090861,-0.60997,203.16,0.12458,-0.99212,-0.012991,149.06,-0.60398,-0.086217,0.79232,54.989
> ui mousemode right translate
[Repeated 1 time(s)]
> select clear
> ui mousemode right select
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select #1/A:796@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
61 atoms, 61 bonds, 8 residues, 2 models selected
> select up
7378 atoms, 7562 bonds, 917 residues, 2 models selected
> select up
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.099734,-0.21152,-0.97227,150.73,-0.23259,0.94512,-0.22947,-30.136,0.96745,0.24902,0.045063,-96.138
> view matrix models
> #1,0.37089,0.35239,-0.85922,32.334,-0.56651,0.81898,0.091343,-9.4639,0.73587,0.45288,0.50338,-145.95
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> show sel surfaces
> ui mousemode right select
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.0043797,-0.34998,-0.93675,177.21,-0.86926,0.46441,-0.16945,102.88,0.49433,0.81354,-0.30626,-70.091
> view matrix models
> #1,-0.31275,-0.23232,-0.92098,198.31,-0.40102,0.91127,-0.093693,-20.551,0.86103,0.34003,-0.37817,-46.451
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.31275,-0.23232,-0.92098,170.78,-0.40102,0.91127,-0.093693,-29.793,0.86103,0.34003,-0.37817,-68.034
> view matrix models
> #1,-0.31275,-0.23232,-0.92098,150.44,-0.40102,0.91127,-0.093693,-34.879,0.86103,0.34003,-0.37817,-74.414
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> hide sel surfaces
> hide #!1 models
> ~select #2
1 model selected
> select #2 :321
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) lime
> show sel surfaces
> select up
129 atoms, 129 bonds, 18 residues, 2 models selected
> select up
5330 atoms, 5449 bonds, 671 residues, 2 models selected
> show sel surfaces
> select #2 :321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2 :321
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) lime
> select #2 :334
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) lime
> select #2 :336
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!2 & sel) lime
> select ::name="SER"
648 atoms, 552 bonds, 108 residues, 2 models selected
> color (#!2 & sel) lime
> color (#!2 & sel) cornflower blue
> select #2 :320
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!2 & sel) lime
> color (#!2 & sel) orange
> view matrix models
> #2,1,0.00032903,0.0018048,0.016642,-0.0003277,1,-0.00073745,-0.0024547,-0.0018051,0.00073686,1,0.023867
> select #2 :331
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2 :331-333
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #2 :331-332
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2 :331, 333
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #2 :331, 333, 335
18 atoms, 15 bonds, 3 residues, 1 model selected
> color (#!2 & sel) lime
> color (#!2 & sel) orange
> undo
[Repeated 1 time(s)]
> redo
> select #2 :332, 334, 336
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!2 & sel) orange
> ui tool show "Color Actions"
> show #!1 models
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.24863,0.45828,-0.85333,46.486,-0.4457,-0.83631,-0.31928,219.89,-0.85996,0.30095,0.41218,52.321
> view matrix models
> #1,-0.65973,0.34679,-0.66671,90.076,0.3323,-0.66111,-0.67269,142.01,-0.67404,-0.66534,0.32091,163.46
> view matrix models
> #1,-0.63679,0.34018,-0.69194,90.973,0.35633,-0.66598,-0.65536,137.7,-0.68376,-0.66389,0.30287,166.52
> view matrix models
> #1,-0.43563,-0.35278,-0.82811,170.38,0.18646,0.86467,-0.46645,-58.74,0.8806,-0.35761,-0.3109,4.7583
> select #2 :1-303
2415 atoms, 2462 bonds, 303 residues, 1 model selected
> color (#!2 & sel) hot pink
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.65231,0.62677,-0.42621,25.938,0.37458,0.75542,0.53761,-182.34,0.65892,0.19104,-0.72755,9.3349
> view matrix models
> #1,-0.82544,0.35865,-0.43591,82.651,0.043075,0.80999,0.58486,-153.91,0.56284,0.46399,-0.68405,-18.716
> view matrix models
> #1,-0.51375,0.69624,-0.50131,8.5555,0.029271,0.5982,0.80081,-149.72,0.85744,0.39674,-0.3277,-86.979
> view matrix models
> #1,0.18956,0.79083,-0.58194,-80.913,0.40783,0.47573,0.77933,-178.2,0.89317,-0.38506,-0.23234,-2.2284
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.18956,0.79083,-0.58194,-49.524,0.40783,0.47573,0.77933,-159.16,0.89317,-0.38506,-0.23234,-1.3722
> view matrix models
> #1,0.18956,0.79083,-0.58194,-44.11,0.40783,0.47573,0.77933,-174.5,0.89317,-0.38506,-0.23234,-6.2361
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.088298,0.74585,-0.66023,4.7622,0.51529,0.60145,0.61053,-184.57,0.85246,-0.2863,-0.43743,9.512
> view matrix models
> #1,-0.50019,0.64423,-0.5786,59.152,0.20745,0.73789,0.64225,-167.75,0.8407,0.20121,-0.50273,-43.966
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.50019,0.64423,-0.5786,35.888,0.20745,0.73789,0.64225,-263.71,0.8407,0.20121,-0.50273,-147.33
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.63552,0.74929,0.18622,-48.058,0.76581,0.64243,0.028533,-250.28,-0.098255,0.16074,-0.98209,28.037
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.63552,0.74929,0.18622,26.797,0.76581,0.64243,0.028533,-228.78,-0.098255,0.16074,-0.98209,83.693
> view matrix models
> #1,-0.63552,0.74929,0.18622,-14.404,0.76581,0.64243,0.028533,-148.57,-0.098255,0.16074,-0.98209,103.14
> view matrix models
> #1,-0.63552,0.74929,0.18622,-3.2761,0.76581,0.64243,0.028533,-121.41,-0.098255,0.16074,-0.98209,105.44
> view matrix models
> #1,-0.63552,0.74929,0.18622,-7.8055,0.76581,0.64243,0.028533,-122.55,-0.098255,0.16074,-0.98209,113.22
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.36752,0.92242,0.11863,-145.7,0.85546,-0.28525,-0.43222,37.602,-0.36485,0.26033,-0.89393,123.25
> view matrix models
> #1,0.36737,0.87401,-0.31803,-89.722,0.90419,-0.41573,-0.098047,10.213,-0.21791,-0.25154,-0.943,176.24
> view matrix models
> #1,0.40747,0.85306,-0.32597,-91.072,0.90178,-0.43217,-0.0037386,1.8657,-0.14407,-0.29243,-0.94537,172.65
> view matrix models
> #1,0.34782,0.88393,-0.31256,-89.208,0.90242,-0.40605,-0.14409,14.44,-0.25428,-0.23194,-0.9389,177.74
> view matrix models
> #1,0.37534,0.86991,-0.31995,-89.959,0.90435,-0.41936,-0.079284,8.5195,-0.20315,-0.25959,-0.94411,175.58
> view matrix models
> #1,0.3953,0.8743,-0.28165,-97.343,0.90396,-0.42472,-0.0497,5.8823,-0.16308,-0.23496,-0.95823,169.1
> view matrix models
> #1,-0.074083,0.98093,-0.17969,-64.835,0.99441,0.059067,-0.08753,-62.828,-0.075247,-0.18517,-0.97982,154.38
> view matrix models
> #1,-0.73227,0.27155,-0.62454,157.61,0.40849,0.90891,-0.083756,-99.867,0.54491,-0.31645,-0.77649,71.683
> view matrix models
> #1,-0.33243,-0.29097,-0.89712,211.43,-0.53584,0.84105,-0.074225,23.949,0.77612,0.45604,-0.4355,-94.455
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.33243,-0.29097,-0.89712,207.41,-0.53584,0.84105,-0.074225,-27.188,0.77612,0.45604,-0.4355,-124
> view matrix models
> #1,-0.33243,-0.29097,-0.89712,178.2,-0.53584,0.84105,-0.074225,-26.487,0.77612,0.45604,-0.4355,-87.454
> view matrix models
> #1,-0.33243,-0.29097,-0.89712,165.05,-0.53584,0.84105,-0.074225,-27.903,0.77612,0.45604,-0.4355,-73.311
> ui mousemode right "contour level"
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.33243,-0.29097,-0.89712,154.46,-0.53584,0.84105,-0.074225,-28.224,0.77612,0.45604,-0.4355,-68.648
> view matrix models
> #1,-0.33243,-0.29097,-0.89712,148.64,-0.53584,0.84105,-0.074225,-34.976,0.77612,0.45604,-0.4355,-46.722
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.56906,-0.29084,-0.76915,163.16,-0.49111,0.87043,0.034211,-56.597,0.65953,0.3972,-0.63816,-1.7521
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.56906,-0.29084,-0.76915,183.98,-0.49111,0.87043,0.034211,-54.015,0.65953,0.3972,-0.63816,-9.2151
> view matrix models
> #1,-0.56906,-0.29084,-0.76915,175.94,-0.49111,0.87043,0.034211,-51.432,0.65953,0.3972,-0.63816,-23.426
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.45626,0.10581,-0.88353,124.35,-0.42511,0.84636,0.32089,-89.145,0.78174,0.522,-0.34118,-88.275
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.45626,0.10581,-0.88353,122.85,-0.42511,0.84636,0.32089,-87.259,0.78174,0.522,-0.34118,-81.264
> view matrix models
> #1,-0.45626,0.10581,-0.88353,122.81,-0.42511,0.84636,0.32089,-79.214,0.78174,0.522,-0.34118,-84.872
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.5123,0.051032,-0.85729,133.72,-0.46708,0.82113,0.32799,-71.632,0.72069,0.56845,-0.39683,-76.96
> view matrix models
> #1,-0.51932,0.044467,-0.85342,134.99,-0.46071,0.82653,0.32341,-72.584,0.71976,0.56113,-0.40875,-74.551
> view matrix models
> #1,-0.50715,-0.013575,-0.86175,141.86,-0.60139,0.7218,0.34255,-44.053,0.61736,0.69197,-0.37422,-82.621
> view matrix models
> #1,0.15344,-0.35303,-0.92294,110.96,-0.67187,0.64762,-0.35942,54.106,0.72461,0.67524,-0.13782,-120.62
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.15344,-0.35303,-0.92294,123.33,-0.67187,0.64762,-0.35942,54.138,0.72461,0.67524,-0.13782,-122.63
> view matrix models
> #1,0.15344,-0.35303,-0.92294,120.09,-0.67187,0.64762,-0.35942,56.133,0.72461,0.67524,-0.13782,-109.45
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.14837,-0.27491,-0.94995,113.8,-0.32268,0.89455,-0.30928,-24.144,0.93481,0.35242,0.044015,-114.75
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.19335,-0.24227,-0.95075,104.18,-0.33411,0.89485,-0.29598,-24.292,0.92249,0.37489,0.092075,-121.58
> view matrix models
> #1,-0.044367,0.19651,-0.9795,80.576,0.14726,0.97104,0.18815,-148.45,0.9881,-0.13589,-0.07202,-45.614
> view matrix models
> #1,-0.39532,0.31587,-0.86252,95.169,-0.081975,0.92313,0.37564,-135.48,0.91488,0.21921,-0.33904,-51.599
> view matrix models
> #1,-0.48234,0.30109,-0.82261,103.22,0.13386,0.95338,0.27047,-153.93,0.8657,0.02034,-0.50015,-1.7454
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.48234,0.30109,-0.82261,108.18,0.13386,0.95338,0.27047,-155.32,0.8657,0.02034,-0.50015,-16.401
> view matrix models
> #1,-0.48234,0.30109,-0.82261,108.11,0.13386,0.95338,0.27047,-144.22,0.8657,0.02034,-0.50015,-22.794
> view matrix models
> #1,-0.48234,0.30109,-0.82261,105.8,0.13386,0.95338,0.27047,-143.24,0.8657,0.02034,-0.50015,-22.489
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.49708,0.65089,-0.57381,34.508,0.30486,0.75014,0.58682,-174.34,0.81239,0.11676,-0.57131,-20.154
> view matrix models
> #1,-0.69269,0.49708,-0.52258,72.421,0.1942,0.82635,0.52862,-163.83,0.6946,0.26468,-0.66893,-13.456
> view matrix models
> #1,-0.70375,0.53655,-0.46568,62.249,0.15263,0.75435,0.63849,-162.03,0.69386,0.37826,-0.61276,-34.295
> view matrix models
> #1,-0.66727,0.72928,-0.15135,-2.7169,0.26276,0.42063,0.86835,-159.09,0.69693,0.53965,-0.4723,-71.327
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.66727,0.72928,-0.15135,-5.5735,0.26276,0.42063,0.86835,-158.37,0.69693,0.53965,-0.4723,-66.676
> view matrix models
> #1,-0.66727,0.72928,-0.15135,-6.7295,0.26276,0.42063,0.86835,-157.61,0.69693,0.53965,-0.4723,-63.713
> view matrix models
> #1,-0.66727,0.72928,-0.15135,1.3921,0.26276,0.42063,0.86835,-164.99,0.69693,0.53965,-0.4723,-65.516
> view matrix models
> #1,-0.66727,0.72928,-0.15135,0.4755,0.26276,0.42063,0.86835,-162.68,0.69693,0.53965,-0.4723,-66.473
> view matrix models
> #1,-0.66727,0.72928,-0.15135,-0.22464,0.26276,0.42063,0.86835,-160.15,0.69693,0.53965,-0.4723,-67.047
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.66727,0.72928,-0.15135,4.9791,0.26276,0.42063,0.86835,-164.48,0.69693,0.53965,-0.4723,-68.36
> view matrix models
> #1,-0.66727,0.72928,-0.15135,0.077862,0.26276,0.42063,0.86835,-148.45,0.69693,0.53965,-0.4723,-66.418
> view matrix models
> #1,-0.66727,0.72928,-0.15135,2.6684,0.26276,0.42063,0.86835,-155.09,0.69693,0.53965,-0.4723,-62.312
> view matrix models
> #1,-0.66727,0.72928,-0.15135,1.2267,0.26276,0.42063,0.86835,-154.43,0.69693,0.53965,-0.4723,-60.553
> view matrix models
> #1,-0.66727,0.72928,-0.15135,1.7978,0.26276,0.42063,0.86835,-159.21,0.69693,0.53965,-0.4723,-61.439
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.68645,0.70135,-0.19209,12.373,0.19888,0.43515,0.87812,-154.32,0.69945,0.56458,-0.43819,-68.826
> view matrix models
> #1,0.038966,0.35612,-0.93363,51.766,0.5579,0.76739,0.316,-176.95,0.82899,-0.53319,-0.16878,24.964
> view matrix models
> #1,-0.64096,0.31549,-0.69974,113.99,-0.28745,0.74663,0.59993,-102.61,0.71172,0.58567,-0.38788,-78.768
> view matrix models
> #1,-0.63148,0.54562,-0.55093,66.424,0.081007,0.75306,0.65295,-154.82,0.77115,0.3677,-0.51974,-43.17
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.63148,0.54562,-0.55093,65.267,0.081007,0.75306,0.65295,-154.53,0.77115,0.3677,-0.51974,-40.051
> view matrix models
> #1,-0.63148,0.54562,-0.55093,63.467,0.081007,0.75306,0.65295,-164.98,0.77115,0.3677,-0.51974,-41.726
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.40315,0.50437,-0.76359,64.878,0.12159,0.85653,0.50157,-165.96,0.90702,0.10936,-0.40664,-38.289
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.40315,0.50437,-0.76359,70.398,0.12159,0.85653,0.50157,-159.45,0.90702,0.10936,-0.40664,-38.994
> view matrix models
> #1,-0.40315,0.50437,-0.76359,73.454,0.12159,0.85653,0.50157,-158.54,0.90702,0.10936,-0.40664,-44.43
> save /Users/courtneykarl/Desktop/yeet.cxs
——— End of log from Wed Nov 3 02:36:28 2021 ———
opened ChimeraX session
> save /Users/courtneykarl/Desktop/colors.cxs
——— End of log from Wed Nov 3 02:36:47 2021 ———
opened ChimeraX session
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui mousemode right pivot
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> style sel sphere
Changed 7378 atom styles
> hide sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7btf.cif_A SES surface #1.4: minimum, -21.54, mean -1.65,
maximum 15.70
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 7btf.cif_A SES surface #1.4: minimum, -21.54, mean -1.65,
maximum 15.70
To also show corresponding color key, enter the above coulombic command and
add key true
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AlphaFold Q13546_A SES surface #2.1: minimum, -17.19,
mean -1.90, maximum 13.10
To also show corresponding color key, enter the above coulombic command and
add key true
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> show sel atoms
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> show sel atoms
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.40315,0.50437,-0.76359,75.012,0.12159,0.85653,0.50157,-150.13,0.90702,0.10936,-0.40664,-26.478
> select #1 :323
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> view matrix models
> #1,-0.40315,0.50437,-0.76359,63.189,0.12159,0.85653,0.50157,-171.51,0.90702,0.10936,-0.40664,-40.461
> view matrix models
> #1,-0.40315,0.50437,-0.76359,61.1,0.12159,0.85653,0.50157,-169.01,0.90702,0.10936,-0.40664,-33.34
> view matrix models
> #1,-0.40315,0.50437,-0.76359,70.749,0.12159,0.85653,0.50157,-179.47,0.90702,0.10936,-0.40664,-42.952
> view matrix models
> #1,-0.6625,-0.47198,-0.58166,206.83,-0.45434,0.87057,-0.18892,-31.701,0.59553,0.13911,-0.79119,35.399
> view matrix models
> #1,-0.6625,-0.47198,-0.58166,199.86,-0.45434,0.87057,-0.18892,-34.477,0.59553,0.13911,-0.79119,50.073
> view matrix models
> #1,-0.6625,-0.47198,-0.58166,183.01,-0.45434,0.87057,-0.18892,-37.479,0.59553,0.13911,-0.79119,29.148
> view matrix models
> #1,-0.6625,-0.47198,-0.58166,194.64,-0.45434,0.87057,-0.18892,-32.967,0.59553,0.13911,-0.79119,36.588
> view matrix models
> #1,-0.6625,-0.47198,-0.58166,189.48,-0.45434,0.87057,-0.18892,-36.726,0.59553,0.13911,-0.79119,42.59
> undo
> redo
> view matrix models
> #1,-0.25806,-0.7259,-0.63755,178.56,-0.96283,0.24771,0.10768,71.732,0.07976,0.64164,-0.76285,38.548
> view matrix models
> #1,-0.63556,-0.4794,-0.60518,189.8,-0.60298,0.79776,0.0012929,-30.795,0.48217,0.36573,-0.79609,28.109
> view matrix models
> #1,-0.63556,-0.4794,-0.60518,173.68,-0.60298,0.79776,0.0012929,-27.189,0.48217,0.36573,-0.79609,39.288
> view matrix models
> #1,-0.6869,-0.3667,-0.62745,168.12,-0.39754,0.91234,-0.09799,-55.815,0.60838,0.18213,-0.77246,44.551
> view matrix models
> #1,-0.6869,-0.3667,-0.62745,185.78,-0.39754,0.91234,-0.09799,-47.041,0.60838,0.18213,-0.77246,37.438
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> open /Users/courtneykarl/Desktop/4ith.pdb
4ith.pdb title:
Crystal structure of RIP1 kinase In complex with necrostatin-1 analog [more
info...]
Chain information for 4ith.pdb #5
---
Chain | Description | UniProt
A | receptor-interacting serine/threonine-protein kinase 1 | RIPK1_HUMAN
B | receptor-interacting serine/threonine-protein kinase 1 | RIPK1_HUMAN
Non-standard residues in 4ith.pdb #5
---
IOD — iodide ion
NA — sodium ion
RCM — (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione
> select #5
4220 atoms, 4160 bonds, 5 pseudobonds, 663 residues, 2 models selected
> color (#!5 & sel) cyan
> show sel surfaces
> hide #!1 models
> select #5, 2
9550 atoms, 9609 bonds, 5 pseudobonds, 1334 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!2 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 4ith.pdb, chain B (#5) with AlphaFold Q13546, chain A (#2),
sequence alignment score = 1237.6
RMSD between 234 pruned atom pairs is 0.745 angstroms; (across all 270 pairs:
2.083)
> select #5 :1 \- 50
Expected a keyword
> select #5 :1-50
495 atoms, 498 bonds, 2 pseudobonds, 66 residues, 2 models selected
> select #5/A
2035 atoms, 2003 bonds, 3 pseudobonds, 320 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
Drag select of AlphaFold Q13546_A SES surface, 8471 of 811362 triangles,
4ith.pdb_B SES surface, 6283 of 229544 triangles, 65 atoms, 31 residues, 56
bonds
> hide #!2 models
> show #!1 models
> select #5 :320
Nothing selected
> select #5
2185 atoms, 2157 bonds, 2 pseudobonds, 343 residues, 2 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
4ith.pdb #5/B LEU 7
4ith.pdb #5/B GLU 19
4ith.pdb #5/B GLU 22
4ith.pdb #5/B LEU 23
4ith.pdb #5/B LYS 30
4ith.pdb #5/B GLU 58
4ith.pdb #5/B GLU 85
4ith.pdb #5/B GLU 107
4ith.pdb #5/B MET 108
4ith.pdb #5/B GLU 142
4ith.pdb #5/B LYS 167
4ith.pdb #5/B GLU 171
4ith.pdb #5/B GLU 172
4ith.pdb #5/B HIS 173
4ith.pdb #5/B ASN 174
4ith.pdb #5/B GLU 175
4ith.pdb #5/B LYS 204
4ith.pdb #5/B ARG 258
4ith.pdb #5/B LYS 284
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/7j/l1kb87vd0rl06pk011gg22300000gn/T/tmp9meias1r/ante.in.mol2 -fi
mol2 -o
/var/folders/7j/l1kb87vd0rl06pk011gg22300000gn/T/tmp9meias1r/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/7j/l1kb87vd0rl06pk011gg22300000gn/T/tmp9meias1r/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HIS) ``
Charges for residue HIS determined
Coulombic values for 4ith.pdb_B SES surface #5.3: minimum, -20.36, mean -2.41,
maximum 16.07
To also show corresponding color key, enter the above coulombic command and
add key true
> show sel cartoons
> show sel atoms
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> hide sel atoms
> select clear
> select #5
2185 atoms, 2157 bonds, 2 pseudobonds, 343 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,41.719,0,1,0,4.1922,0,0,1,1.1223
> view matrix models #5,1,0,0,13.397,0,1,0,19.708,0,0,1,-19.135
> view matrix models
> #5,0.69699,-0.66039,-0.27946,-20.902,0.70132,0.54651,0.4577,-10.067,-0.14953,-0.515,0.84405,-46.476
> view matrix models
> #5,0.69699,-0.66039,-0.27946,-20.956,0.70132,0.54651,0.4577,-7.4744,-0.14953,-0.515,0.84405,-47.253
> view matrix models
> #5,0.19247,-0.93731,-0.29052,-40.728,0.98085,0.17476,0.086003,-18.492,-0.029841,-0.30151,0.953,-36.379
> view matrix models
> #5,0.19247,-0.93731,-0.29052,-17.368,0.98085,0.17476,0.086003,22.081,-0.029841,-0.30151,0.953,-16.89
> view matrix models
> #5,-0.0094153,-0.96323,-0.26851,-20.994,0.99738,-0.028315,0.0666,11.035,-0.071754,-0.26718,0.96097,-15.447
> view matrix models
> #5,-0.0094153,-0.96323,-0.26851,-28.564,0.99738,-0.028315,0.0666,4.1401,-0.071754,-0.26718,0.96097,-18.168
> view matrix models
> #5,-0.67399,-0.50385,-0.54026,-4.1601,0.72975,-0.34034,-0.59298,0.86806,0.11491,-0.79392,0.59707,-45.315
> view matrix models
> #5,-0.099129,-0.66618,-0.73917,-4.4302,0.98357,-0.17821,0.028708,-0.95421,-0.15085,-0.72418,0.67291,-45.151
> view matrix models
> #5,-0.057041,-0.78869,-0.61214,-13.77,0.9315,-0.26267,0.25163,-10.939,-0.35925,-0.55586,0.74964,-38.9
> view matrix models
> #5,-0.057041,-0.78869,-0.61214,-9.6364,0.9315,-0.26267,0.25163,-8.7571,-0.35925,-0.55586,0.74964,-24.23
> view matrix models
> #5,-0.24902,-0.80941,-0.53182,-13.801,0.6522,-0.5461,0.52575,-33.193,-0.71598,-0.21593,0.66389,-6.3473
> view matrix models
> #5,-0.24902,-0.80941,-0.53182,-23.414,0.6522,-0.5461,0.52575,-39.553,-0.71598,-0.21593,0.66389,-14.564
> view matrix models
> #5,-0.052764,-0.89169,-0.44957,-28.225,0.80217,-0.30598,0.51274,-24.319,-0.59476,-0.33358,0.73143,-21.706
> view matrix models
> #5,-0.052764,-0.89169,-0.44957,-28.276,0.80217,-0.30598,0.51274,-24.334,-0.59476,-0.33358,0.73143,-16.093
> view matrix models
> #5,-0.052764,-0.89169,-0.44957,-27.941,0.80217,-0.30598,0.51274,-24.368,-0.59476,-0.33358,0.73143,-17.128
> view matrix models
> #5,-0.052764,-0.89169,-0.44957,-24.185,0.80217,-0.30598,0.51274,-21.331,-0.59476,-0.33358,0.73143,-11.64
> view matrix models
> #5,-0.0043063,-0.90634,-0.42253,-25.192,0.87241,-0.20992,0.44139,-13.748,-0.48875,-0.36672,0.7916,-13.928
> view matrix models
> #5,0.0037435,-0.85478,-0.51898,-20.135,0.77783,-0.32368,0.53872,-23.095,-0.62847,-0.40569,0.66366,-14.6
> view matrix models
> #5,-0.30521,-0.80904,-0.5023,-20.446,0.63842,-0.56521,0.52245,-37.7,-0.70659,-0.16122,0.68902,-1.8275
> view matrix models
> #5,-0.30521,-0.80904,-0.5023,-13.09,0.63842,-0.56521,0.52245,-41.106,-0.70659,-0.16122,0.68902,-10.089
> view matrix models
> #5,-0.1485,-0.7636,-0.62837,-6.5179,0.65436,-0.5523,0.51651,-40.11,-0.74146,-0.33448,0.58169,-17.995
> view matrix models
> #5,0.25455,-0.76168,-0.59586,-3.7469,0.7058,-0.27489,0.65291,-26.736,-0.6611,-0.58675,0.46762,-29.312
> view matrix models
> #5,0.16351,-0.80798,-0.56606,-7.7801,0.78289,-0.24287,0.5728,-22.567,-0.60029,-0.53682,0.59285,-28.612
> view matrix models
> #5,0.057669,-0.77213,-0.63284,-5.1957,0.51333,-0.52075,0.68214,-42.995,-0.85625,-0.3642,0.36633,-16.077
> view matrix models
> #5,0.12619,-0.64371,-0.75479,5.294,0.75863,-0.42764,0.49153,-31.595,-0.63919,-0.63463,0.43437,-31.159
> view matrix models
> #5,-0.026244,-0.69975,-0.7139,-0.041014,0.61477,-0.57443,0.54045,-42.211,-0.78827,-0.4247,0.44526,-20.642
> view matrix models
> #5,-0.023628,-0.75838,-0.65139,-4.6928,0.66786,-0.49682,0.55419,-37.629,-0.74391,-0.42194,0.51823,-21.664
> view matrix models
> #5,-0.037522,-0.80686,-0.58955,-8.8891,0.71719,-0.43257,0.54637,-33.384,-0.69586,-0.40232,0.59491,-21.77
> view matrix models
> #5,-0.037522,-0.80686,-0.58955,-10.398,0.71719,-0.43257,0.54637,-29.729,-0.69586,-0.40232,0.59491,-14.242
> view matrix models
> #5,0.23019,-0.86565,-0.4446,-14.604,0.965,0.14407,0.21912,12.201,-0.12563,-0.47948,0.86852,-19.713
> view matrix models
> #5,0.23019,-0.86565,-0.4446,-22.67,0.965,0.14407,0.21912,12.578,-0.12563,-0.47948,0.86852,-17.394
> view matrix models
> #5,0.23019,-0.86565,-0.4446,-24.022,0.965,0.14407,0.21912,12.658,-0.12563,-0.47948,0.86852,-19.182
> color #5 #fa807225
> color #5 #fa807226
> color #5 #fa8072a7
> show #!2 models
> view matrix models
> #5,-0.06112,-0.9336,-0.35307,-32.266,0.99592,-0.033518,-0.083774,9.2011,0.066377,-0.35675,0.93184,-11.922
> undo
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> view matrix models
> #2,-0.31345,-0.34911,-0.8831,-0.46385,-0.77026,-0.45043,0.45146,-48.95,-0.55538,0.82173,-0.12772,25.353
> view matrix models
> #2,-0.31345,-0.34911,-0.8831,34.384,-0.77026,-0.45043,0.45146,-38.096,-0.55538,0.82173,-0.12772,30.653
> view matrix models
> #2,0.024352,0.82098,0.57043,39.014,0.985,-0.11722,0.12665,-68.868,0.17085,0.55879,-0.81152,14.098
> undo
> color #2 hotpink
> color #2 #ff69b42a
> color #2 #ff69b429
> view matrix models
> #2,-0.31345,-0.34911,-0.8831,31.472,-0.77026,-0.45043,0.45146,-43.502,-0.55538,0.82173,-0.12772,24.769
> view matrix models
> #2,-0.28,-0.3566,-0.89131,30.923,-0.78315,-0.45213,0.42691,-43.547,-0.55522,0.81757,-0.15267,24.535
> view matrix models
> #2,-0.44777,-0.31671,-0.83618,34.119,-0.70779,-0.44591,0.54791,-43.612,-0.54639,0.83717,-0.024501,25.6
> view matrix models
> #2,0.093968,-0.42653,-0.89958,25.862,-0.86328,-0.48498,0.13978,-45.197,-0.4959,0.76345,-0.41379,21.274
> view matrix models
> #2,0.15259,-0.40572,-0.90117,24.887,-0.93927,-0.34314,-0.0045542,-46.083,-0.30738,0.84714,-0.43344,17.924
> view matrix models
> #2,0.15259,-0.40572,-0.90117,17.334,-0.93927,-0.34314,-0.0045542,-29.709,-0.30738,0.84714,-0.43344,46.089
> view matrix models
> #2,0.15259,-0.40572,-0.90117,65.484,-0.93927,-0.34314,-0.0045542,58.674,-0.30738,0.84714,-0.43344,42.925
> view matrix models
> #2,0.67658,0.45481,-0.57913,57.344,-0.64197,0.74956,-0.16133,48.194,0.36072,0.48094,0.79911,46.739
> view matrix models
> #2,0.67658,0.45481,-0.57913,39.878,-0.64197,0.74956,-0.16133,64.019,0.36072,0.48094,0.79911,18.287
> view matrix models
> #2,0.49187,0.33781,-0.80246,40.888,-0.05657,0.93211,0.35772,59.709,0.86883,-0.13056,0.47759,10.021
> view matrix models
> #2,0.22514,-0.9202,-0.32023,54.832,-0.42151,0.20433,-0.8835,55.781,0.87843,0.33389,-0.34187,-0.18748
> view matrix models
> #2,0.72982,-0.45545,-0.50984,43.498,-0.013833,0.73578,-0.67708,49.516,0.6835,0.5012,0.53068,10.724
> view matrix models
> #2,0.74853,-0.44525,-0.49138,43.361,-0.17789,0.57904,-0.79566,51.425,0.63879,0.68299,0.35422,8.887
> view matrix models
> #2,0.84425,-0.28154,-0.45605,41.614,-0.28595,0.48307,-0.82757,53.113,0.4533,0.82908,0.32733,10.785
> view matrix models
> #2,0.84425,-0.28154,-0.45605,13.916,-0.28595,0.48307,-0.82757,34.341,0.4533,0.82908,0.32733,31.261
> view matrix models
> #2,0.84425,-0.28154,-0.45605,14.169,-0.28595,0.48307,-0.82757,0.11229,0.4533,0.82908,0.32733,26.146
> select #1
7378 atoms, 7562 bonds, 9 pseudobonds, 917 residues, 3 models selected
> color #1 mediumblue
> select #1 :323
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
Window position QRect(631,-769 658x459) outside any known screen, using
primary screen
> save /Users/courtneykarl/Desktop/RIP.cxs
——— End of log from Wed Nov 3 04:32:36 2021 ———
opened ChimeraX session
> select #2
5330 atoms, 5449 bonds, 671 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/region_browser.py", line 1465, in _mouse_drag_cb
block = self.seq_canvas.bounded_by(canvas_x, canvas_y, self._start_x,
self._start_y,
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/seq_canvas.py", line 428, in bounded_by
return self.lead_block.bounded_by(x1, y1, x2, y2, exclude_headers)
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/seq_canvas.py", line 1738, in bounded_by
return self.next_block.bounded_by(x1, y1, x2, y2, exclude_headers)
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/seq_canvas.py", line 1738, in bounded_by
return self.next_block.bounded_by(x1, y1, x2, y2, exclude_headers)
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/seq_canvas.py", line 1738, in bounded_by
return self.next_block.bounded_by(x1, y1, x2, y2, exclude_headers)
[Previous line repeated 10 more times]
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/seq_canvas.py", line 1751, in bounded_by
if hi_row < num_headers:
TypeError: '<' not supported between instances of 'NoneType' and 'int'
TypeError: '
File
"/Applications/ChimeraX-1.3-rc2021.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/seq_canvas.py", line 1751, in bounded_by
if hi_row < num_headers:
See log for complete Python traceback.
> select #2/A:671
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:1-671
5330 atoms, 5449 bonds, 671 residues, 1 model selected
OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 4 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 11.6 (20G165)
Kernel Version: Darwin 20.6.0
Time since boot: 49 days 17:54
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
E2350:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Color LCD:
Resolution: 2560 x 1600
UI Looks like: 1280 x 800 @ 60.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.2
ChimeraX-AtomicLibrary: 4.1.5
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3rc202110301701
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.2
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.5
ChimeraX-ModelPanel: 1.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.21
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.4
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Region bound checking using None |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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