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Opened 4 years ago
Closed 4 years ago
#6153 closed defect (duplicate)
Problem saving session: object of type 'SurfaceUpdaters' has no len()
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109160803 (2021-09-16 08:03:16 UTC)
Description
(Describe the actions that caused this problem to occur here) Problem saving sessions. Error: TypeError: object of type 'SurfaceUpdaters' has no len()
Log:
UCSF ChimeraX version: 1.3.dev202109160803 (2021-09-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/stutisharma/Documents/ATPsynthase/Manuscript/Figures_raw/Fig1-2/Fig1_cX.cxs
> format session
Opened halfVsum_-50_2.9A.mrc as #1, grid size 256,256,256, pixel 1, shown at
step 1, values float32
Log from Tue Nov 9 18:56:56 2021UCSF ChimeraX version: 1.3.dev202109160803
(2021-09-16)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/stutisharma/Documents/ATPsynthase/Manuscript/Figures_raw/halfVsum_-50_2.9A.mrc
Summary of feedback from opening
/Users/stutisharma/Documents/ATPsynthase/Manuscript/Figures_raw/halfVsum_-50_2.9A.mrc
---
notes | Unable to parse symmetry operators of halfVsum_-50_2.9A.mrc
b'\xc8d\xc6\xff\x923\x07\x08X4\x9f(\xe4X\x15(C\xec\x7f\xbf\xb0\n\xc9\xbc\x00\x00\x04\x00\x01\x00\x00\x00Xe\xc6\xff\x00\x00\x00\x00(e\xc6\xff\xb2\xf6\x05\x08X4\x9f(P\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00\x00\x1c-DT\xfb!\x99\xbf\x01\x00\x00\x00\x00\x00\x00\x00'
Opened halfVsum_-50_2.9A.mrc as #1, grid size 256,256,256, pixel 1, shown at
level 0.0402, step 1, values float32
> close #1
> open
> /Users/stutisharma/Documents/ATPsynthase/Manuscript/Figures_raw/halfVsum_-50_2.9A.mrc
> format mrc
Summary of feedback from opening
/Users/stutisharma/Documents/ATPsynthase/Manuscript/Figures_raw/halfVsum_-50_2.9A.mrc
---
notes | Unable to parse symmetry operators of halfVsum_-50_2.9A.mrc
b'\xc8d\xc6\xff\x923\x07\x08X4\x9f(\xe4X\x15(C\xec\x7f\xbf\xb0\n\xc9\xbc\x00\x00\x04\x00\x01\x00\x00\x00Xe\xc6\xff\x00\x00\x00\x00(e\xc6\xff\xb2\xf6\x05\x08X4\x9f(P\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00\x00\x1c-DT\xfb!\x99\xbf\x01\x00\x00\x00\x00\x00\x00\x00'
Opened halfVsum_-50_2.9A.mrc as #1, grid size 256,256,256, pixel 1, shown at
level 0.0402, step 1, values float32
No atomic structure models chosen
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> select #1
2 models selected
> ~select #1
Nothing selected
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/210913_pH6/6cp6_pH8.pdb
6cp6_pH8.pdb title:
Monomer yeast atp synthase (F1FO) reconstituted In nanodisc. [more info...]
Chain information for 6cp6_pH8.pdb #2
---
Chain | Description | UniProt
6 | atp synthase subunit H, mitochondrial | ATP14_YEAST
7 | atp synthase subunit D, mitochondrial | ATP7_YEAST
8 | atp synthase protein 8 | ATP8_YEAST
A | atp synthase subunit α, mitochondrial | ATPA_YEAST
B | atp synthase subunit α, mitochondrial | ATPA_YEAST
C | atp synthase subunit α, mitochondrial | ATPA_YEAST
D | atp synthase subunit β, mitochondrial | ATPB_YEAST
E | atp synthase subunit β, mitochondrial | ATPB_YEAST
F | atp synthase subunit β, mitochondrial | ATPB_YEAST
G | F-atpase γ subunit | ATPG_YEAST
H | F-atpase δ subunit | ATPD_YEAST
I | atpase subunit ε | ATP5E_YEAST
J | atpase synthase I subunit | ATP18_YEAST
K L N O P Q S T | atp synthase subunit 9, mitochondrial | ATP9_YEAST
M R | atp synthase subunit 9, mitochondrial | ATP9_YEAST
U | atp synthase subunit F, mitochondrial | ATPK_YEAST
X | F-atpase protein 6 | ATP6_YEAST
Y | atp synthase subunit 5, mitochondrial | ATPO_YEAST
Z | atp synthase subunit 4, mitochondrial | ATPF_YEAST
Non-standard residues in 6cp6_pH8.pdb #2
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
> hide #!1 models
> color bychain
[Repeated 1 time(s)]
> select #2
38814 atoms, 39444 bonds, 1 pseudobond, 5109 residues, 2 models selected
> color sel bychain
> rainbow sel
> show sel surfaces
> ~select #2
27 models selected
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
[Repeated 1 time(s)]
> view
[Repeated 1 time(s)]
> lighting simple
> show target m
[Repeated 1 time(s)]
> hide target m
[Repeated 1 time(s)]
> show #!2 models
> view #2 clip false
> log metadata #2
Metadata for 6cp6_pH8.pdb #2
---
Title | Monomer yeast atp synthase (F1FO) reconstituted In nanodisc.
Citation | High-resolution cryo-em analysis of the yeast atp synthasein A
lipid membrane. PMID: 29650704
Non-standard residues | ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288C)
(baker's yeast)
Experimental method | Electron microscopy
Resolution | 3.60Å
> log chains #2
Chain information for 6cp6_pH8.pdb #2
---
Chain | Description | UniProt
6 | atp synthase subunit H, mitochondrial | ATP14_YEAST
7 | atp synthase subunit D, mitochondrial | ATP7_YEAST
8 | atp synthase protein 8 | ATP8_YEAST
A | atp synthase subunit α, mitochondrial | ATPA_YEAST
B | atp synthase subunit α, mitochondrial | ATPA_YEAST
C | atp synthase subunit α, mitochondrial | ATPA_YEAST
D | atp synthase subunit β, mitochondrial | ATPB_YEAST
E | atp synthase subunit β, mitochondrial | ATPB_YEAST
F | atp synthase subunit β, mitochondrial | ATPB_YEAST
G | F-atpase γ subunit | ATPG_YEAST
H | F-atpase δ subunit | ATPD_YEAST
I | atpase subunit ε | ATP5E_YEAST
J | atpase synthase I subunit | ATP18_YEAST
K L N O P Q S T | atp synthase subunit 9, mitochondrial | ATP9_YEAST
M R | atp synthase subunit 9, mitochondrial | ATP9_YEAST
U | atp synthase subunit F, mitochondrial | ATPK_YEAST
X | F-atpase protein 6 | ATP6_YEAST
Y | atp synthase subunit 5, mitochondrial | ATPO_YEAST
Z | atp synthase subunit 4, mitochondrial | ATPF_YEAST
> ui tool show "Selection Inspector"
> color bychain
> lighting soft
> lighting full
> lighting flat
> lighting simple
> show surfaces
> select /C:195@CB
1 atom, 1 residue, 1 model selected
> color (#!2 & sel) red
> select /A/B/C
11641 atoms, 11820 bonds, 1521 residues, 1 model selected
> color (#!2 & sel) red
> select /D/E/F
10741 atoms, 10913 bonds, 1417 residues, 1 model selected
> color (#!2 & sel) yellow
> select clear
> select /G
2086 atoms, 2111 bonds, 1 pseudobond, 269 residues, 2 models selected
> color (#!2 & sel) forest green
> surface hidePatches (#!2 & sel)
> cartoon (#!2 & sel)
> hide (#!2 & sel) target a
> cartoon style (#!2 & sel) xsection oval modeHelix default
> cartoon style (#!2 & sel & coil) xsection oval
> cartoon style (#!2 & sel) xsection barbell modeHelix default
> cartoon style (#!2 & sel) modeHelix tube sides 20
> cartoon style (#!2 & sel) xsection oval modeHelix default
> view sel
> ui tool show "Model Panel"
> ui tool show "Side View"
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes true
> lighting soft
> select /G:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting full
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> select /X
1772 atoms, 1820 bonds, 224 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select /Z
1232 atoms, 1246 bonds, 155 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> cartoon (#!2 & sel)
> hide (#!2 & sel) target a
> select /Y
1254 atoms, 1272 bonds, 166 residues, 1 model selected
> select clear
> select /7
1363 atoms, 1382 bonds, 171 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> cartoon (#!2 & sel)
> hide (#!2 & sel) target a
> select /8
364 atoms, 374 bonds, 42 residues, 1 model selected
> select clear
> select /6
710 atoms, 725 bonds, 89 residues, 1 model selected
> cartoon (#!2 & sel)
> hide (#!2 & sel) target a
> surface hidePatches (#!2 & sel)
> select /U
639 atoms, 659 bonds, 85 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> hide (#!2 & sel) target a
> cartoon (#!2 & sel)
> cartoon hide (#!2 & sel)
Drag select of 18 residues
> cartoon hide (#!2 & sel)
Drag select of 11 residues
> cartoon hide (#!2 & sel)
> select /Z
1232 atoms, 1246 bonds, 155 residues, 1 model selected
> color (#!2 & sel) dim gray
> select /7
1363 atoms, 1382 bonds, 171 residues, 1 model selected
> color (#!2 & sel) dim gray
> select /G
2086 atoms, 2111 bonds, 1 pseudobond, 269 residues, 2 models selected
> cartoon style (#!2 & sel) modeHelix tube sides 20
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> cartoon style (#!2 & sel) xsection oval modeHelix default
> select /G:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /G:88
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add /F:394@O
11 atoms, 10 bonds, 2 residues, 2 models selected
> select subtract /F:394@O
10 atoms, 10 bonds, 1 residue, 3 models selected
> select add /G:89
16 atoms, 15 bonds, 2 residues, 2 models selected
> select add /G:87
24 atoms, 22 bonds, 3 residues, 2 models selected
> select add /G:85
28 atoms, 25 bonds, 4 residues, 2 models selected
> select add /G:84
34 atoms, 30 bonds, 5 residues, 2 models selected
> select add /D:390@CG2
35 atoms, 30 bonds, 6 residues, 2 models selected
> select subtract /D:390@CG2
34 atoms, 30 bonds, 5 residues, 3 models selected
> select add /G:113
43 atoms, 38 bonds, 6 residues, 2 models selected
> select add /G:116
51 atoms, 45 bonds, 7 residues, 2 models selected
> cartoon hide (#!2 & sel)
> select /G:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /G:83
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add /G:82
21 atoms, 18 bonds, 3 residues, 2 models selected
> select add /G:81
30 atoms, 26 bonds, 4 residues, 2 models selected
> select add /F:394@CA
31 atoms, 26 bonds, 5 residues, 2 models selected
> select subtract /F:394@CA
30 atoms, 26 bonds, 4 residues, 3 models selected
> select add /F:394@CG
31 atoms, 26 bonds, 5 residues, 2 models selected
> select add /G:86
37 atoms, 31 bonds, 6 residues, 3 models selected
> select subtract /F:394@CG
36 atoms, 31 bonds, 5 residues, 3 models selected
> select add /G:90
45 atoms, 39 bonds, 6 residues, 2 models selected
> cartoon hide (#!2 & sel)
> select clear
> select /G:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /G:172
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add /G:174
20 atoms, 17 bonds, 3 residues, 2 models selected
> cartoon hide (#!2 & sel)
> select /G:120
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /G:112
19 atoms, 17 bonds, 2 residues, 2 models selected
> select add /G:135
28 atoms, 25 bonds, 3 residues, 2 models selected
> cartoon hide (#!2 & sel)
> select /C:361@NZ
1 atom, 1 residue, 1 model selected
> select add /G:121
8 atoms, 6 bonds, 2 residues, 2 models selected
> select subtract /C:361@NZ
7 atoms, 6 bonds, 1 residue, 3 models selected
> select add /G:119
15 atoms, 13 bonds, 2 residues, 2 models selected
> cartoon hide (#!2 & sel)
Drag select of 5 residues
> select add /6:55
52 atoms, 8 bonds, 6 residues, 2 models selected
Drag select of 5 residues
> select add /6:55
84 atoms, 8 bonds, 10 residues, 3 models selected
> cartoon hide (#!2 & sel)
> save
> /Users/stutisharma/Documents/ATPsynthase/Manuscript/Figures_raw/Fig1/Fig1_cX.cxs
> includeMaps true
——— End of log from Tue Nov 9 18:56:56 2021 ———
opened ChimeraX session
> ui tool show "Side View"
> cartoon sel
> surface hidePatches sel
[Repeated 1 time(s)]
> select #2
38814 atoms, 39444 bonds, 1 pseudobond, 5109 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> hide (#!2 & sel) target a
> cartoon (#!2 & sel)
> select clear
> select ::name="ADP"::name="ATP"::name="FME"
227 atoms, 227 bonds, 15 residues, 1 model selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byhetero
> select clear
> select #2/Y,6,Z,7,8,J
5215 atoms, 5301 bonds, 660 residues, 1 model selected
> color (#!2 & sel) dim gray
> select #2/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> color (#!2 & sel) cornflower blue
> hide (#!2 & sel) target a
> select #2/X
1772 atoms, 1820 bonds, 224 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select #2/H
990 atoms, 1004 bonds, 132 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #2/I
392 atoms, 398 bonds, 59 residues, 1 model selected
> color (#!2 & sel) hot pink
> select clear
> graphics silhouettes true
> show #!1 models
> volume #1 level 0.02949
> volume #1 level 0.03447
> hide #!1 models
> show #!1 models
> close #1
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/210913_pH6/F1_halfsum-80_3-0_0.mrc
Opened F1_halfsum-80_3-0_0.mrc as #1, grid size 256,256,256, pixel 1, shown at
level 0.0434, step 1, values float32
> fitmap #2 inMap #1
Fit molecule 6cp6_pH8.pdb (#2) to map F1_halfsum-80_3-0_0.mrc (#1) using 38814
atoms
average map value = 0.03738, steps = 264
shifted from previous position = 6.9
rotated from previous position = 6.58 degrees
atoms outside contour = 25919, contour level = 0.043427
Position of 6cp6_pH8.pdb (#2) relative to F1_halfsum-80_3-0_0.mrc (#1)
coordinates:
Matrix rotation and translation
0.99350269 -0.11380032 0.00137676 18.54369238
0.11377193 0.99341677 0.01338165 -10.22337161
-0.00289053 -0.01313807 0.99990951 4.99193014
Axis -0.11572984 0.01862212 0.99310615
Axis point 99.54167296 159.93167641 0.00000000
Rotation angle (degrees) 6.57916983
Shift along axis 2.62107711
> volume #1 level 0.0485
> volume #1 level 0.06269
> close #1
> open /Users/stutisharma/Documents/ATPsynthase/Model_Building/210622_Fo-maps-
> models/C5-MB002-halfVsum_-120_3.5A_0.mrc
Opened C5-MB002-halfVsum_-120_3.5A_0.mrc as #1, grid size 256,256,256, pixel
1, shown at level 0.0384, step 1, values float32
> volume #1 level 0.1243
> fitmap #2 inMap #1
Fit molecule 6cp6_pH8.pdb (#2) to map C5-MB002-halfVsum_-120_3.5A_0.mrc (#1)
using 38814 atoms
average map value = 0.01686, steps = 2000
shifted from previous position = 2.85
rotated from previous position = 5.09 degrees
atoms outside contour = 36495, contour level = 0.12426
Position of 6cp6_pH8.pdb (#2) relative to C5-MB002-halfVsum_-120_3.5A_0.mrc
(#1) coordinates:
Matrix rotation and translation
0.98807003 -0.13541451 -0.07335201 32.47146532
0.13956804 0.98869525 0.05479484 -21.62969592
0.06510277 -0.06437873 0.99579968 2.50366272
Axis -0.36098709 -0.41939156 0.83294600
Axis point 174.72788694 222.89332689 0.00000000
Rotation angle (degrees) 9.50108321
Shift along axis -0.56505208
> surface dust #1 size 10
> volume #1 level 0.1031
> volume #1 level 0.09469
> open
> /Users/stutisharma/Documents/ATPsynthase/MAPS_final/Conf0_F1_-50_2-9A.mrc
Opened Conf0_F1_-50_2-9A.mrc as #3, grid size 256,256,256, pixel 1, shown at
level 0.0402, step 1, values float32
> hide #!1 models
> surface dust #3 size 10
> show #!1 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> hide #!3 models
> show #!3 models
> hide #!3 models
> color zone #1 near #2 distance 6
> hide #!1 models
> show #!3 models
> color zone #3 near #2 distance 6
> show #!1 models
> volume #1 level 0.106
> hide #!2 models
> volume #3 level 0.04585
> volume #3 level 0.04371
> hide #!3 models
> surface dust #1 size 10
> show #!3 models
> volume #1 level 0.1074
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf0_comp-
> map.png width 1000 height 898 supersample 3 transparentBackground true
> volume #1 level 0.1031
> volume #3 level 0.04585
> volume #3 level 0.04229
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> select #3
2 models selected
> transparency sel 70 target s
> select clear
> hide #!3 models
> show #!1 models
> select #1
2 models selected
> ~select #1
Nothing selected
> hide #!1 models
> show #!1 models
> select #1
2 models selected
> transparency sel 80 target s
> select #1
3 models selected
> ~select #1
Nothing selected
> ui mousemode right clip
> ui mousemode right "mark surface"
[Repeated 1 time(s)]
> surface cap false
> hide #!1 models
> select /X:176
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (#!2 & sel) target ab
> style (#!2 & sel) stick
Changed 11 atom styles
> color (#!2 & sel) byhetero
> select clear
> select /S:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /R:59
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add /Q:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> show (#!2 & sel) target ab
> style (#!2 & sel) stick
Changed 27 atom styles
> color (#!2 & sel) byhetero
> select /P:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /O:59
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add /N:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> show (#!2 & sel) target ab
> style (#!2 & sel) stick
Changed 27 atom styles
> color (#!2 & sel) byhetero
> select /M:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /L:59
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add /K:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> select add /T:59
36 atoms, 32 bonds, 4 residues, 4 models selected
> select add /S:59
45 atoms, 40 bonds, 5 residues, 5 models selected
> show (#!2 & sel) target ab
> style (#!2 & sel) stick
Changed 45 atom styles
> color (#!2 & sel) byhetero
> select clear
> show #!3 models
> hide #!3 models
> show #!1 models
> graphics silhouettes false
> volume #1 level 0.106
> volume #1 level 0.09734
> undo
> show #!1 models
> color zone #1 near #2 distance 6
> select #1
2 models selected
> transparency sel 80 target s
> select clear
> hide #1#2.2-28#!2 target a
> color zone #1 near #2 distance 6
> ui tool show "Color Actions"
> select #1
2 models selected
> transparency sel 80 target s
> volume #1 color #d6d6d6
> transparency sel 80 target s
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting soft
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> select clear
> hide #!1 models
> select /X:176
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /T:59
20 atoms, 18 bonds, 2 residues, 2 models selected
> select add /S:59
29 atoms, 26 bonds, 3 residues, 3 models selected
> select add /R:59
38 atoms, 34 bonds, 4 residues, 4 models selected
> select add /Q:59
47 atoms, 42 bonds, 5 residues, 5 models selected
> select add /P:59
56 atoms, 50 bonds, 6 residues, 6 models selected
> select add /O:59
65 atoms, 58 bonds, 7 residues, 7 models selected
> select add /N:59
74 atoms, 66 bonds, 8 residues, 8 models selected
> select add /M:59
83 atoms, 74 bonds, 9 residues, 9 models selected
> select add /L:59
92 atoms, 82 bonds, 10 residues, 10 models selected
> select add /K:59
101 atoms, 90 bonds, 11 residues, 11 models selected
> show (#!2 & sel) target ab
> select /X:234
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add /X:230
23 atoms, 23 bonds, 2 residues, 2 models selected
> select clear
> show #!1 models
> graphics silhouettes true
> graphics silhouettes false
Drag select of 21 residues, 1 C5-MB002-halfVsum_-120_3.5A_0.mrc
> ~select #1
164 atoms, 21 residues, 4 models selected
> hide #!1 models
> cartoon hide (#!2 & sel)
Drag select of 1 residues
Drag select of 7 residues
> select subtract /X:184
52 atoms, 7 residues, 3 models selected
> cartoon hide (#!2 & sel)
> select /X:234
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add /X:231
18 atoms, 18 bonds, 2 residues, 2 models selected
> select add /X:230
27 atoms, 26 bonds, 3 residues, 2 models selected
> select add /X:228
35 atoms, 33 bonds, 4 residues, 2 models selected
Drag select of 3 residues
Drag select of 14 residues
> cartoon hide (#!2 & sel)
> select #1
2 models selected
> show #!1 models
> ~select #1
Nothing selected
> hide #!1 models
> cartoon style #2.2-28#!2 modeHelix tube sides 20
> cartoon style #2.2-28#!2 xsection oval modeHelix default
> show #!1 models
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes true
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes width 0.5
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> graphics silhouettes width 0.5
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 4
> graphics silhouettes true width 1
> graphics silhouettes true width 0.8
> graphics silhouettes true width 1
> lighting simple
> graphics silhouettes true width 0.9
> graphics silhouettes true width 1
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf0_Fo-
> slice.png width 1000 height 898 supersample 3
> hide #!1 models
> select clear
Drag select of 13 residues
Drag select of 2 residues
> select clear
> show #!1 models
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf0_Fo-
> slice.png width 1000 height 898 supersample 3 transparentBackground true
> graphics silhouettes true
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf0_Fo-
> slice.png width 1000 height 898 supersample 3 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true width 0.8
> graphics silhouettes true depthJump 0.1
> graphics silhouettes false
> graphics silhouettes true width 1 depthJump 0.1
> graphics silhouettes true width 1 depthJump 0.2
> graphics silhouettes true width 1 depthJump 0.3
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf0_Fo-
> slice.png width 1000 height 898 supersample 3
> select #2/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> hide #!1 models
> save /Users/stutisharma/Documents/ATPsynthase/Model_Building/c-ring_6cp6.pdb
> selectedOnly true relModel #1
> hide #!2 models
> show #!2 models
> select clear
> open /Users/stutisharma/Documents/ATPsynthase/Models/CONF1_F1Fo-RSR23_re-
> chainID.pdb
Chain information for CONF1_F1Fo-RSR23_re-chainID.pdb #4
---
Chain | Description
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K P | No description available
L M N O Q R S T | No description available
U | No description available
X | No description available
Y | No description available
Z | No description available
> hide #4#2.2-28#!2 target a
> cartoon #4#2.2-28#!2
> dssp
> hide #!2 models
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/211017_pH6/F1_conf1_halfsum_-80_2.7A_0.mrc
Opened F1_conf1_halfsum_-80_2.7A_0.mrc as #5, grid size 256,256,256, pixel 1,
shown at level 0.0383, step 1, values float32
> open /Users/stutisharma/Documents/ATPsynthase/Model_Building/210622_Fo-maps-
> models/C4-MB001-halfsum_-130-3-3A_0.mrc
Opened C4-MB001-halfsum_-130-3-3A_0.mrc as #6, grid size 256,256,256, pixel 1,
shown at level 0.0296, step 1, values float32
> volume #6 level 0.1184
> surface dust #6 size 10
> surface dust #5 size 10
> volume #5 level 0.02372
> volume #5 level 0.03269
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!6 models
> hide #!6 models
> fitmap #4 inMap #5
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) using 38735 atoms
average map value = 0.06929, steps = 116
shifted from previous position = 2.81
rotated from previous position = 3.79 degrees
atoms outside contour = 17626, contour level = 0.032693
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) coordinates:
Matrix rotation and translation
0.99790479 -0.01671707 0.06250262 -7.69123572
0.01585035 0.99977158 0.01433708 -4.93854004
-0.06272801 -0.01331635 0.99794182 7.51147734
Axis -0.20899216 0.94643666 0.24612988
Axis point 120.22175634 0.00000000 131.15672473
Rotation angle (degrees) 3.79340289
Shift along axis -1.21780834
> hide #!5 models
> show #!6 models
> volume #6 level 0.07524
> fitmap #4 inMap #6
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) using 38735 atoms
average map value = 0.009258, steps = 136
shifted from previous position = 2.94
rotated from previous position = 4.01 degrees
atoms outside contour = 36344, contour level = 0.075239
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) coordinates:
Matrix rotation and translation
0.99984073 0.01774363 0.00191791 -2.55824391
-0.01775935 0.99980606 0.00851127 1.53752056
-0.00176651 -0.00854398 0.99996194 -3.96550201
Axis -0.43113407 0.09313722 -0.89746803
Axis point 61.07014588 27.97321283 0.00000000
Rotation angle (degrees) 1.13335709
Shift along axis 4.80505779
> volume #6 level 0.07031
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> fitmap #4 inMap #6
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) using 38735 atoms
average map value = 0.009257, steps = 80
shifted from previous position = 0.00884
rotated from previous position = 0.00647 degrees
atoms outside contour = 36197, contour level = 0.070309
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) coordinates:
Matrix rotation and translation
0.99983904 0.01783375 0.00196005 -2.57319780
-0.01784972 0.99980491 0.00845773 1.54965455
-0.00180883 -0.00849136 0.99996231 -3.96676355
Axis -0.42710594 0.09497321 -0.89919998
Axis point 60.88438173 29.56677568 0.00000000
Rotation angle (degrees) 1.13692519
Shift along axis 4.81311744
> fitmap #4 inMap #6
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) using 38735 atoms
average map value = 0.009255, steps = 124
shifted from previous position = 0.0164
rotated from previous position = 0.0053 degrees
atoms outside contour = 36191, contour level = 0.070309
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) coordinates:
Matrix rotation and translation
0.99983975 0.01780348 0.00187351 -2.55022901
-0.01781874 0.99980536 0.00846973 1.53458061
-0.00172236 -0.00850176 0.99996238 -3.98912311
Axis -0.42833485 0.09075440 -0.89905111
Axis point 61.27793144 27.87719480 0.00000000
Rotation angle (degrees) 1.13516157
Shift along axis 4.81804746
> fitmap #4 inMap #5
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) using 38735 atoms
average map value = 0.06929, steps = 108
shifted from previous position = 2.94
rotated from previous position = 4.01 degrees
atoms outside contour = 17628, contour level = 0.032693
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) coordinates:
Matrix rotation and translation
0.99790282 -0.01673568 0.06252910 -7.69487103
0.01586862 0.99977129 0.01433746 -4.93462150
-0.06275475 -0.01331514 0.99794015 7.51924188
Axis -0.20889234 0.94641490 0.24629824
Axis point 120.26721810 0.00000000 131.13934899
Rotation angle (degrees) 3.79510461
Shift along axis -1.21082373
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> open
> /Users/stutisharma/Documents/ATPsynthase/Maps_concensusREF/CONF1_relion_class001.mrc
Opened CONF1_relion_class001.mrc as #7, grid size 256,256,256, pixel 1, shown
at level 0.0168, step 1, values float32
> volume #7 level 0.01178
> hide #!4 models
> fitmap #5 inMap #7
Fit map F1_conf1_halfsum_-80_2.7A_0.mrc in map CONF1_relion_class001.mrc using
196131 points
correlation = 0.9109, correlation about mean = 0.6407, overlap = 415.9
steps = 84, shift = 3.21, angle = 2.51 degrees
Position of F1_conf1_halfsum_-80_2.7A_0.mrc (#5) relative to
CONF1_relion_class001.mrc (#7) coordinates:
Matrix rotation and translation
0.99912299 0.01178384 -0.04017961 4.59919402
-0.01229427 0.99984654 -0.01248024 4.05659539
0.04002637 0.01296328 0.99911453 -3.92149058
Axis 0.29070949 -0.91640774 -0.27510878
Axis point 109.60665691 0.00000000 121.49107406
Rotation angle (degrees) 2.50812600
Shift along axis -1.30162959
> hide #!5 models
> show #!6 models
> fitmap #6 inMap #7
Fit map C4-MB001-halfsum_-130-3-3A_0.mrc in map CONF1_relion_class001.mrc
using 50429 points
correlation = 0.9273, correlation about mean = 0.2841, overlap = 68.78
steps = 84, shift = 0.569, angle = 0.631 degrees
Position of C4-MB001-halfsum_-130-3-3A_0.mrc (#6) relative to
CONF1_relion_class001.mrc (#7) coordinates:
Matrix rotation and translation
0.99999257 0.00104466 -0.00371182 -0.40285837
-0.00108286 0.99994632 -0.01030493 1.03466891
0.00370085 0.01030888 0.99994001 -1.94415534
Axis 0.93660135 -0.33679922 -0.09666544
Axis point 0.00000000 194.10998428 81.81492692
Rotation angle (degrees) 0.63052870
Shift along axis -0.53786073
> hide #!6 models
> show #!4 models
> fitmap #4 inMap #7
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
CONF1_relion_class001.mrc (#7) using 38735 atoms
average map value = 0.01772, steps = 112
shifted from previous position = 2.88
rotated from previous position = 2.75 degrees
atoms outside contour = 13609, contour level = 0.011776
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
CONF1_relion_class001.mrc (#7) coordinates:
Matrix rotation and translation
0.99982747 -0.00360747 0.01822106 -2.68046663
0.00358999 0.99999306 0.00099188 -0.74649577
-0.01822452 -0.00092629 0.99983349 2.63527580
Axis -0.05156502 0.97974709 0.19348565
Axis point 144.12597372 0.00000000 148.70842988
Rotation angle (degrees) 1.06573339
Shift along axis -0.08327071
> show #!5 models
> show #!6 models
> hide #!7 models
> volume #5 level 0.04078
> hide #!5 models
> hide #!6 models
> select #4/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> color sel cornflower blue
> select #4/A-C
11602 atoms, 11779 bonds, 1520 residues, 1 model selected
> color sel red
> select #4/D-F
10768 atoms, 10939 bonds, 1420 residues, 1 model selected
> color sel yellow
> select #4/G
2024 atoms, 2049 bonds, 1 pseudobond, 260 residues, 2 models selected
> color (#!4 & sel) forest green
> ui tool show "Color Actions"
> color sel medium purple
> color sel forest green
> select #4/H
990 atoms, 1004 bonds, 132 residues, 1 model selected
> color sel medium purple
> select #4/I
392 atoms, 398 bonds, 59 residues, 1 model selected
> color sel hot pink
> select #4/Y,6,Z,7,8,J
5207 atoms, 5293 bonds, 659 residues, 1 model selected
> select #4/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> color sel dim gray
> select clear
> show #!6 models
> show #!5 models
> volume #6 level 0.07539
> volume #5 level 0.03616
> hide #!6 models
> color zone #5 near #4 distance 6
> hide #!5 models
> show #!6 models
> color zone #6 near #4 distance 6
> select #4/X
1772 atoms, 1820 bonds, 224 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> color zone #6 near #4 distance 6
> show #!5 models
> hide #!4 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 1 depthJump 0.3
> graphics silhouettes true width 3depthJump 0.3
Invalid "width" argument: Expected a number
> graphics silhouettes true width 3 depthJump 0.3
> graphics silhouettes true width 1 depthJump 0.1
> lighting soft
> volume #6 level 0.07539
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf1_composite-
> map.png width 1200 height 1078 supersample 3 transparentBackground true
> hide #!5 models
> hide #!6 models
> show #!4 models
> show #!7 models
> volume #7 level 0.01212
> volume #7 level 0.01247
> surface dust #7 size 10
> volume #7 level 0.0116
> color zone #7 near #4 distance 6
> hide #!4 models
> show #!4 models
> volume #7 level 0.009864
> volume #7 color #ebebeb
> color zone #7 near #4 distance 6
> volume #7 level 0.01091
> volume #7 level 0.01108
> hide #!4 models
> hide #!7 models
> show #!5 models
> show #!6 models
> volume #5 level 0.02807
> volume #5 level 0.03385
> volume #5 level 0.03847
> volume #5 level 0.03616
> volume #5 level 0.03154
> volume #5 level 0.03385
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf1_composite-
> map2.png width 1000 height 898 supersample 3 transparentBackground true
> volume #7 level 0.01282
> volume #7 level 0.01264
> volume #7 level 0.0123
> volume #7 level 0.01212
> volume #7 level 0.01195
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> show #!4 models
> select #7
2 models selected
> transparency sel 80 target s
> select clear
> select ::name="ADP"::name="ATP"::name="FME"::name="MG"
422 atoms, 417 bonds, 32 residues, 2 models selected
> select ::name="ADP"
135 atoms, 145 bonds, 5 residues, 2 models selected
> select ::name="ADP"::name="ATP"::name="FME"::name="MG"
422 atoms, 417 bonds, 32 residues, 2 models selected
> show (#!4 & sel) target ab
> style (#!4 & sel) ball
Changed 195 atom styles
> color (#!4 & sel) byhetero
> hide #!7 models
Drag select of 60 atoms, 67 residues, 50 bonds
Drag select of 60 atoms, 97 residues, 50 bonds
> select clear
Drag select of 60 atoms, 233 residues, 50 bonds
> hide sel target a
> select clear
> show #!7 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 2 depthJump 0.1
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf1_model1.png
> width 1200 height 1078 supersample 3 transparentBackground true
> lighting simple
> lighting full
> graphics silhouettes true width 1 depthJump 0.1
> lighting full
> lighting simple
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf1_model1.png
> width 1200 height 1078 supersample 3 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> graphics silhouettes true width 3 depthJump 0.1
> graphics silhouettes true width 2 depthJump 0.1
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf1_model1.png
> width 1200 height 1078 supersample 3 transparentBackground true
> hide #!7 models
> graphics silhouettes true width 1 depthJump 0.1
> graphics silhouettes true width 2 depthJump 0.1
> graphics silhouettes true width 2 depthJump 0.3
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes true width 2 depthJump 0.1
> graphics silhouettes true width 1 depthJump 0.1
> graphics silhouettes true width 2 depthJump 0.1
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf1_model1.png
> width 1200 height 1078 supersample 3 transparentBackground true
> show #!5 models
> show #!6 models
> volume #5 level 0.03269
> volume #5 level 0.03616
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!6 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select #2/U
639 atoms, 659 bonds, 85 residues, 1 model selected
> color (#!2 & sel) dim gray
> select clear
> show #!4 models
> ui tool show Matchmaker
> matchmaker #!4 to #2
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 6cp6_pH8.pdb, chain C (#2) with CONF1_F1Fo-RSR23_re-chainID.pdb,
chain C (#4), sequence alignment score = 2447.4
RMSD between 483 pruned atom pairs is 0.893 angstroms; (across all 505 pairs:
1.091)
> morph #2,4
Computed 51 frame morph #8
> coordset #8 1,51
> show #!5 models
> select #5
2 models selected
> transparency sel 90 target s
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 2 depthJump 0.1
> select clear
> fitmap #8 inMap #5
Fit molecule Morph - 6cp6_pH8.pdb (#8) to map F1_conf1_halfsum_-80_2.7A_0.mrc
(#5) using 38583 atoms
average map value = 0.03844, steps = 168
shifted from previous position = 2.6
rotated from previous position = 6.24 degrees
atoms outside contour = 26330, contour level = 0.036158
Position of Morph - 6cp6_pH8.pdb (#8) relative to
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) coordinates:
Matrix rotation and translation
0.98898148 -0.13234002 0.06634569 10.98821730
0.13069604 0.99101119 0.02855469 -15.03049110
-0.06952825 -0.01956894 0.99738803 11.85222909
Axis -0.16044275 0.45299979 0.87695457
Axis point 126.45716469 74.71047504 0.00000000
Rotation angle (degrees) 8.62526405
Shift along axis 1.82207730
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!8 models
> fitmap #4 inMap #5
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) using 38735 atoms
average map value = 0.06929, steps = 248
shifted from previous position = 2.56
rotated from previous position = 7.21 degrees
atoms outside contour = 18420, contour level = 0.036158
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
F1_conf1_halfsum_-80_2.7A_0.mrc (#5) coordinates:
Matrix rotation and translation
0.99790363 -0.01673315 0.06251670 -7.68956633
0.01586496 0.99977105 0.01435803 -4.94410013
-0.06274264 -0.01333610 0.99794063 7.52531563
Axis -0.20923142 0.94634440 0.24628132
Axis point 120.41147424 0.00000000 131.10960219
Rotation angle (degrees) 3.79464410
Shift along axis -1.21657787
> volume #5 level 0.1001
> volume #5 color #d6d6d6
> select #5
2 models selected
> transparency sel 90 target s
> select clear
> style #4-5 stick
Changed 38735 atom styles
> volume #5 level 0.1167
> graphics silhouettes true width 3 depthJump 0.1
> rock y 3 136 cycle 68
> rock y 10 136 cycle 68
> rock y 20 136 cycle 68
> movie record
> wait 20
> rock y 20 136 cycle 68
> wait
> movie record
Already recording a movie
> abort
Unknown command: abort
> movie abort
Not currently encoding
> movie record abort
Expected a keyword
> stop
> movie record
Already recording a movie
> stop
> stop recording
Expected fewer arguments
> stop
> movie record
Already recording a movie
> movie reset
> graphics silhouettes true width 4 depthJump 0.1
> movie record
> wait 20
> rock y 20 136 cycle 68
> wait
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> select #4/C:375
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #4/D:164
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select clear
> movie record
> wait 20
> rock y 20 136 cycle 68
> wait
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> volume #5 level 0.08346
> volume #5 level 0.08601
> select #4/F:164
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select clear
> select #4/B:375
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #4/F:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #4/F:164
7 atoms, 6 bonds, 1 residue, 1 model selected
> cartoon hide sel
> hide sel target a
> select #4/F:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4/F:166
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #4/F:163
27 atoms, 25 bonds, 3 residues, 1 model selected
> cartoon hide sel
> cartoon sel
> select clear
> select #4/F:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/ADP-
> Mg.png width 1200 height 1016 supersample 3 transparentBackground true
> lighting soft
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 4 depthJump 0.1
> select #4/F:424
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/ADP-
> Mg2.png width 1200 height 1016 supersample 3 transparentBackground true
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!6 models
> color #6 #d6d6d6 models
> select #6
2 models selected
> select up
116132 atoms, 118005 bonds, 15305 residues, 13 models selected
> select up
116132 atoms, 118005 bonds, 1 pseudobond, 15305 residues, 41 models selected
> select down
116132 atoms, 118005 bonds, 15305 residues, 40 models selected
> select down
29 models selected
> transparency sel 90 target s
> select clear
> hide #!6 models
> select #4/X:176
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #4/R:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #4/P:59
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #4/O:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select add #4/N:56
41 atoms, 36 bonds, 5 residues, 1 model selected
> select subtract #4/N:56
36 atoms, 32 bonds, 4 residues, 1 model selected
> select add #4/N:59
45 atoms, 40 bonds, 5 residues, 1 model selected
> select add #4/M:59
54 atoms, 48 bonds, 6 residues, 1 model selected
> show sel target ab
> color sel byhetero
> select #4/L:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/K:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #4/T:59
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #4/S:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel target ab
> color sel byhetero
> select clear
> select #4
38735 atoms, 39359 bonds, 1 pseudobond, 5104 residues, 2 models selected
> ~select #4
Nothing selected
> show #!6 models
> volume #6 level 0.07539
> fitmap #4 inMap #6
Fit molecule CONF1_F1Fo-RSR23_re-chainID.pdb (#4) to map
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) using 38735 atoms
average map value = 0.01871, steps = 2000
shifted from previous position = 0.974
rotated from previous position = 1.18 degrees
atoms outside contour = 34471, contour level = 0.075385
Position of CONF1_F1Fo-RSR23_re-chainID.pdb (#4) relative to
C4-MB001-halfsum_-130-3-3A_0.mrc (#6) coordinates:
Matrix rotation and translation
0.99993512 0.00524876 0.01010922 -1.19805315
-0.00529281 0.99997659 0.00433553 -0.01312716
-0.01008623 -0.00438875 0.99993950 2.07173564
Axis -0.35763227 0.82786738 -0.43212817
Axis point 184.11847782 0.00000000 136.59056109
Rotation angle (degrees) 0.69886984
Shift along axis -0.47766042
Drag select of 17 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> select clear
Drag select of 16 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> cartoon hide (#!4 & sel)
Drag select of 5 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> select clear
Drag select of 6 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> cartoon hide (#!4 & sel)
> select clear
Drag select of 13 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> cartoon hide (#!4 & sel)
> select clear
> graphics silhouettes true width 1 depthJump 0.1
> graphics silhouettes true width 2 depthJump 0.1
Drag select of 24 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> cartoon hide (#!4 & sel)
Drag select of 8 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> select clear
Drag select of 4 residues, 6 C4-MB001-halfsum_-130-3-3A_0.mrc
> cartoon hide (#!4 & sel)
> select clear
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Fo-
> slice_conf1.png width 1200 height 1016 supersample 3 transparentBackground
> true
> style #4 sphere
Changed 38735 atom styles
> hide #!4 models
> show #!8 models
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> select ::name="ADP"::name="ATP"::name="FME"::name="MG"
496 atoms, 481 bonds, 42 residues, 3 models selected
> show (#!8 & sel) target ab
> hide (#!8 & sel) target a
> select clear
> movie record
> coordset #8 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> select #8
38583 atoms, 39202 bonds, 2 pseudobonds, 5092 residues, 2 models selected
> surface (#!8 & sel)
> select #8/A-C
11548 atoms, 11721 bonds, 1518 residues, 1 model selected
> color (#!8 & sel) red
> select #8/D-F
10687 atoms, 10855 bonds, 1415 residues, 1 model selected
> color (#!8 & sel) yellow
> select #8/G
2024 atoms, 2048 bonds, 2 pseudobonds, 260 residues, 2 models selected
> color (#!8 & sel) forest green
> select #8/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> color (#!8 & sel) dim gray
> select clear
> select #8/G
2024 atoms, 2048 bonds, 2 pseudobonds, 260 residues, 2 models selected
> surface hidePatches (#!8 & sel)
> select clear
Drag select of Morph - 6cp6_pH8.pdb_6 SES surface, 35985 of 120424 triangles,
Morph - 6cp6_pH8.pdb_7 SES surface, 85298 of 241148 triangles, Morph -
6cp6_pH8.pdb_B SES surface, 6584 of 408746 triangles, Morph - 6cp6_pH8.pdb_U
SES surface, 14085 of 117458 triangles, Morph - 6cp6_pH8.pdb_Z SES surface,
44514 of 208752 triangles, 155 residues
> cartoon hide (#!8 & sel)
> cartoon (#!8 & sel)
> select #8/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> surface hidePatches (#!8 & sel)
Drag select of Morph - 6cp6_pH8.pdb_B SES surface, 35134 of 408746 triangles,
Morph - 6cp6_pH8.pdb_C SES surface, 668 of 379318 triangles, Morph -
6cp6_pH8.pdb_F SES surface, 62866 of 355196 triangles, Morph - 6cp6_pH8.pdb_I
SES surface, 59 of 68180 triangles, 178 residues
> cartoon hide (#!8 & sel)
Drag select of Morph - 6cp6_pH8.pdb_B SES surface, 17591 of 408746 triangles,
Morph - 6cp6_pH8.pdb_C SES surface, 59882 of 379318 triangles, Morph -
6cp6_pH8.pdb_D SES surface, 4122 of 369716 triangles, Morph - 6cp6_pH8.pdb_F
SES surface, 68624 of 355196 triangles, Morph - 6cp6_pH8.pdb_I SES surface, 89
of 68180 triangles, 110 residues
> cartoon hide (#!8 & sel)
> select clear
Drag select of Morph - 6cp6_pH8.pdb_B SES surface, 10047 of 408746 triangles,
Morph - 6cp6_pH8.pdb_F SES surface, 1665 of 355196 triangles, 12 residues
> select #8/A-F
22235 atoms, 22576 bonds, 2933 residues, 1 model selected
> cartoon hide (#!8 & sel)
> select clear
> select #8/I
392 atoms, 398 bonds, 59 residues, 1 model selected
> surface hidePatches (#!8 & sel)
Drag select of Morph - 6cp6_pH8.pdb_A SES surface, 2691 of 383766 triangles,
Morph - 6cp6_pH8.pdb_B SES surface, 23223 of 408746 triangles, Morph -
6cp6_pH8.pdb_E SES surface, 115 of 430278 triangles, Morph - 6cp6_pH8.pdb_F
SES surface, 2554 of 355196 triangles, 18 residues
> cartoon hide (#!8 & sel)
Drag select of Morph - 6cp6_pH8.pdb_C SES surface, 3645 of 379318 triangles,
Morph - 6cp6_pH8.pdb_F SES surface, 8228 of 355196 triangles, 2 residues
> cartoon hide (#!8 & sel)
Drag select of Morph - 6cp6_pH8.pdb_A SES surface, 15220 of 383766 triangles,
4 residues
> cartoon hide (#!8 & sel)
Drag select of Morph - 6cp6_pH8.pdb_F SES surface, 1055 of 407276 triangles, 1
residues
> cartoon hide (#!8 & sel)
> graphics silhouettes false
Drag select of Morph - 6cp6_pH8.pdb_A SES surface, 6889 of 430096 triangles,
Morph - 6cp6_pH8.pdb_C SES surface, 7686 of 442856 triangles, Morph -
6cp6_pH8.pdb_D SES surface, 23729 of 401516 triangles, Morph - 6cp6_pH8.pdb_F
SES surface, 1130 of 407276 triangles, 6 residues
> cartoon hide (#!8 & sel)
> graphics silhouettes true
Drag select of Morph - 6cp6_pH8.pdb_C SES surface, 74800 of 442856 triangles,
Morph - 6cp6_pH8.pdb_D SES surface, 21551 of 401516 triangles, Morph -
6cp6_pH8.pdb_F SES surface, 16946 of 407276 triangles, 3 residues
> cartoon hide (#!8 & sel)
> movie record
> coordset #8 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> hide #!8 models
> show #!4 models
> show #!2 models
> show #!3 models
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/1.cxs
Traceback (most recent call last):
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
> hide #!2 models
> hide #!3 models
> hide #!4 models
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/211017_pH6/F1_conf2_halfsum_-50_2.8A_0.mrc
Opened F1_conf2_halfsum_-50_2.8A_0.mrc as #9, grid size 256,256,256, pixel 1,
shown at level 0.0383, step 1, values float32
> volume #9 level 0.03653
> open /Users/stutisharma/Documents/ATPsynthase/MAPS_final/Conf2_Fo-
> CR_halfVsum_-50_3.7A.mrc
Summary of feedback from opening
/Users/stutisharma/Documents/ATPsynthase/MAPS_final/Conf2_Fo-
CR_halfVsum_-50_3.7A.mrc
---
notes | Unable to parse symmetry operators of Conf2_Fo-
CR_halfVsum_-50_3.7A.mrc
b'\xa8k\x84\xff\x923\x07\x08X\xb4C(\xe4\xd8\x11(\xe9\xdc\x7f\xbfr\x04\x06\xbd\x00@\x02\x00\x01\x00\x00\x008l\x84\xff\x00\x00\x00\x00\x08l\x84\xff\xb2\xf6\x05\x08X\xb4C(P\x01\xb0\x01\x00\x00\x00\x00\x00\x00\x00\x00hs-8R\xc1\xa0\xbf\x01\x00\x00\x00\x00\x00\x00\x00'
Opened Conf2_Fo-CR_halfVsum_-50_3.7A.mrc as #10, grid size 192,192,192, pixel
1, shown at level 0.0429, step 1, values float32
> close #10
> open /Users/stutisharma/Documents/ATPsynthase/MAPS_final/Conf2_Fo-
> CR_halfVsum_-50_3.7A_0.mrc
Opened Conf2_Fo-CR_halfVsum_-50_3.7A_0.mrc as #10, grid size 192,192,192,
pixel 1, shown at level 0.0429, step 1, values float32
> open
> /Users/stutisharma/Documents/ATPsynthase/Maps_concensusREF/CONF2_noMSK_relion_class001.mrc
Opened CONF2_noMSK_relion_class001.mrc as #11, grid size 256,256,256, pixel 1,
shown at level 0.0171, step 1, values float32
> hide #!9 models
> volume #11 level 0.01003
> fitmap #10 inMap #11
Fit map Conf2_Fo-CR_halfVsum_-50_3.7A_0.mrc in map
CONF2_noMSK_relion_class001.mrc using 70775 points
correlation = 0.8903, correlation about mean = 0.0882, overlap = 45.98
steps = 276, shift = 44.9, angle = 2.68 degrees
Position of Conf2_Fo-CR_halfVsum_-50_3.7A_0.mrc (#10) relative to
CONF2_noMSK_relion_class001.mrc (#11) coordinates:
Matrix rotation and translation
0.99891319 -0.04516824 0.01150075 26.18730456
0.04520163 0.99897434 -0.00266041 31.28559572
-0.01136879 0.00317737 0.99993033 -14.76936616
Axis 0.06250213 0.24485242 0.96754368
Axis point -705.48275181 603.65641344 0.00000000
Rotation angle (degrees) 2.67672464
Shift along axis -4.99289101
> hide #!11 models
> show #!9 models
> volume #9 level 0.03387
> volume #9 level 0.04539
> volume #10 level 0.04716
> hide #!9 models
> surface dust #10 size 10
> show #!9 models
> hide #!10 models
> surface dust #9 size 10
> show #!10 models
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/211017_pH6/CONF-2_Rsr23_fit-F1_conf2-coot-5_real_space_refined_030.pdb
Chain information for
CONF-2_Rsr23_fit-F1_conf2-coot-5_real_space_refined_030.pdb #12
---
Chain | Description
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K L N O P Q S T | No description available
M R | No description available
U | No description available
X | No description available
Y | No description available
Z | No description available
> select #12
38760 atoms, 39385 bonds, 1 pseudobond, 5107 residues, 2 models selected
> cartoon (#!12 & sel)
> hide (#!12 & sel) target a
> select clear
> hide #!12 models
> hide #!10 models
> hide #!9 models
> show #!12 models
> select #12/A-C
11629 atoms, 11808 bonds, 1521 residues, 1 model selected
> color sel red
> select #12/D-F
10764 atoms, 10936 bonds, 1420 residues, 1 model selected
> color sel yellow
> select #12/G
2024 atoms, 2049 bonds, 1 pseudobond, 260 residues, 2 models selected
> color (#!12 & sel) forest green
> select #12/H
392 atoms, 398 bonds, 59 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #12/I
990 atoms, 1004 bonds, 132 residues, 1 model selected
> color sel hot pink
> dssp
[Repeated 1 time(s)]
> select #12/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> color sel cornflower blue
> select #12/X
1772 atoms, 1820 bonds, 224 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select #12/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> color sel dim gray
> select clear
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!11 models
> fitmap #12 inMap #11
Fit molecule CONF-2_Rsr23_fit-F1_conf2-coot-5_real_space_refined_030.pdb (#12)
to map CONF2_noMSK_relion_class001.mrc (#11) using 38760 atoms
average map value = 0.01954, steps = 124
shifted from previous position = 0.141
rotated from previous position = 0.236 degrees
atoms outside contour = 13172, contour level = 0.010028
Position of CONF-2_Rsr23_fit-F1_conf2-coot-5_real_space_refined_030.pdb (#12)
relative to CONF2_noMSK_relion_class001.mrc (#11) coordinates:
Matrix rotation and translation
0.99999366 -0.00350870 -0.00060726 0.42789476
0.00350744 0.99999170 -0.00207398 -0.11995230
0.00061453 0.00207184 0.99999766 -0.40685832
Axis 0.50309949 -0.14826554 0.85141543
Axis point 39.31772761 138.13368012 0.00000000
Rotation angle (degrees) 0.23607544
Shift along axis -0.11334702
> fitmap #12 inMap #11
Fit molecule CONF-2_Rsr23_fit-F1_conf2-coot-5_real_space_refined_030.pdb (#12)
to map CONF2_noMSK_relion_class001.mrc (#11) using 38760 atoms
average map value = 0.01954, steps = 104
shifted from previous position = 0.0151
rotated from previous position = 0.00664 degrees
atoms outside contour = 13183, contour level = 0.010028
Position of CONF-2_Rsr23_fit-F1_conf2-coot-5_real_space_refined_030.pdb (#12)
relative to CONF2_noMSK_relion_class001.mrc (#11) coordinates:
Matrix rotation and translation
0.99999372 -0.00350557 -0.00051560 0.41133083
0.00350446 0.99999156 -0.00214497 -0.11117271
0.00052312 0.00214315 0.99999757 -0.38965083
Axis 0.51770325 -0.12540413 0.84631977
Axis point 35.72379993 132.46579582 0.00000000
Rotation angle (degrees) 0.23728977
Shift along axis -0.10288037
> hide #!11 models
> show #!9 models
> show #!10 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> hide #!10 models
> color zone #9 near #12 distance 6
> hide #!9 models
> show #!10 models
> color zone #10 near #12 distance 6
> show #!9 models
> hide #!12 models
> volume #10 level 0.04291
> volume #10 color #ebebeb
> volume #10 level 0.04291
> hide #!9 models
> show #!12 models
> color zone #10 near #12 distance 6
> show #!9 models
> hide #!12 models
> hide #!10 models
> show #!10 models
> show #!12 models
> hide #!9 models
> hide #!10 models
> select #12/H
392 atoms, 398 bonds, 59 residues, 1 model selected
> color sel hot pink
> select #12/I
990 atoms, 1004 bonds, 132 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> ui tool show "Build Structure"
> select clear
> show #!11 models
> hide #!11 models
> show #!10 models
> color zone #10 near #12 distance 6
> hide #!12 models
> show #!9 models
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf2_comp-
> map.png width 1200 height 903 supersample 3 transparentBackground true
> volume #9 level 0.05338
> hide #!10 models
> hide #!9 models
> show #!12 models
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/stutisharma/Documents/Application_material/Stony_Brook/Interview/Job_talk/Conf2_model.png
> width 1200 height 903 supersample 3 transparentBackground true
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting soft
> show #!4 models
> close #12
> hide #4 target a
> open /Users/stutisharma/Documents/ATPsynthase/Models/CONF2_RSR30_chain-ID-
> renumber.pdb
Chain information for CONF2_RSR30_chain-ID-renumber.pdb #12
---
Chain | Description
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K L N O P Q S T | No description available
M R | No description available
U | No description available
X | No description available
Y | No description available
Z | No description available
> hide #!4 models
> cartoon #12
> hide #12 target a
> dssp
> show #!4 models
> ui tool show Matchmaker
> matchmaker #!12 to #4
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 CONF1_F1Fo-RSR23_re-chainID.pdb, chain C (#4) with
CONF2_RSR30_chain-ID-renumber.pdb, chain C (#12), sequence alignment score =
2455.2
RMSD between 499 pruned atom pairs is 0.460 angstroms; (across all 505 pairs:
0.580)
> matchmaker #!12 to #4
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 CONF1_F1Fo-RSR23_re-chainID.pdb, chain C (#4) with
CONF2_RSR30_chain-ID-renumber.pdb, chain C (#12), sequence alignment score =
2455.2
RMSD between 499 pruned atom pairs is 0.460 angstroms; (across all 505 pairs:
0.580)
> hide #!4 models
> select #12/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> color sel dim gray
> select #12/I
392 atoms, 398 bonds, 59 residues, 1 model selected
> color sel hot pink
> select #12/H
990 atoms, 1004 bonds, 132 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #12/X
1772 atoms, 1820 bonds, 224 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select #12/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> color sel cornflower blue
> select #12/A-C
11629 atoms, 11808 bonds, 1521 residues, 1 model selected
> color sel red
> select #12/D-F
10764 atoms, 10936 bonds, 1420 residues, 1 model selected
> color sel yellow
> select clear
> select #12/G
2024 atoms, 2049 bonds, 1 pseudobond, 260 residues, 2 models selected
> color (#!12 & sel) forest green
> select clear
> show #!4 models
> morph #4,12
Computed 51 frame morph #13
> coordset #13 1,51
> hide #!13 models
> show #!13 models
> movie record
> movie encode /Users/stutisharma/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> close #13
> show #!12 models
> close #12
> open /Users/stutisharma/Documents/ATPsynthase/Models/CONF2_RSR30_chain-ID-
> renumber.pdb
Chain information for CONF2_RSR30_chain-ID-renumber.pdb #12
---
Chain | Description
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K L N O P Q S T | No description available
M R | No description available
U | No description available
X | No description available
Y | No description available
Z | No description available
> cartoon #12
> hide #12 target a
> show #!4 models
> close #12
> show #!11 models
> hide #!11 models
> open /Users/stutisharma/Documents/ATPsynthase/Models/CONF2_RSR30_chain-ID-
> renumber2.pdb
Chain information for CONF2_RSR30_chain-ID-renumber2.pdb #12
---
Chain | Description
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K P | No description available
L M N O Q R S T | No description available
U | No description available
X | No description available
Y | No description available
Z | No description available
> hide #!4 models
> hide #12 target a
> cartoon #12
> show #!4 models
> hide #!4 models
> select #12/A-C
11629 atoms, 11808 bonds, 1521 residues, 1 model selected
> color sel red
> select #12/D-F
10764 atoms, 10936 bonds, 1420 residues, 1 model selected
> color sel yellow
> select #12/G
2024 atoms, 2049 bonds, 1 pseudobond, 260 residues, 2 models selected
> color (#!12 & sel) forest green
> select #12/H
990 atoms, 1004 bonds, 132 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #12/I
392 atoms, 398 bonds, 59 residues, 1 model selected
> color sel hot pink
> select #12/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> color sel cornflower blue
> select #12/X
1772 atoms, 1820 bonds, 224 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select #12/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> color sel dim gray
> select clear
> show #!4 models
> hide #!12 models
> show #!12 models
> ui tool show Matchmaker
> matchmaker #!12 to #4
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 CONF1_F1Fo-RSR23_re-chainID.pdb, chain C (#4) with
CONF2_RSR30_chain-ID-renumber2.pdb, chain C (#12), sequence alignment score =
2455.2
RMSD between 499 pruned atom pairs is 0.460 angstroms; (across all 505 pairs:
0.580)
> matchmaker #!12 to #4
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 CONF1_F1Fo-RSR23_re-chainID.pdb, chain C (#4) with
CONF2_RSR30_chain-ID-renumber2.pdb, chain C (#12), sequence alignment score =
2455.2
RMSD between 499 pruned atom pairs is 0.460 angstroms; (across all 505 pairs:
0.580)
> morph #4,12
Computed 51 frame morph #13
> coordset #13 1,51
> movie record
> stop
> morph stop
Missing or invalid "structures" argument: invalid structures specifier
> movie encode /Users/stutisharma/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> wait 20
> coordset #13 1,51
> 123angle wait 60; turn y 180; coordset #13 1,51; wait 70
123angle is provided by the uninstalled bundle SEQCROW versions 0.13 – 0.15
> wait 20
> coordset #13 1,51
> 123angle wait 60; turn y 1 180; coordset #13 1,51; wait 70
123angle is provided by the uninstalled bundle SEQCROW versions 0.13 – 0.15
> movie record
> movie encode /Users/stutisharma/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> wait 20
> coordset #13 1,51
> wait 60
> turn y 180
> coordset #13 1,51
> wait 70
> turn y 180
> movie record
> wait 20
> coordset #13 1,51
> wait 70
> turn y 180
> coordset #13 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> turn y 180
> savepos p1
Unknown command: savepos p1
> save position p1
Cannot determine format for 'position'
> save view p1
Cannot determine format for 'view'
> view p1
Expected an objects specifier or a view name or a keyword
> view name p1
> fly 80 p1
> fly p1 80
> view name p1
> fly p1
[Repeated 1 time(s)]
> savepos
Unknown command: savepos
> ~savepos
Unknown command: ~savepos
> view name p1 clip true
Expected fewer arguments
> view name p1
> fly 100 p1
> fly 200 p1
> view name p1
> view #13 p1 clip true
Expected an integer >= 1 or a keyword
> select #13/A-C
11548 atoms, 11721 bonds, 1518 residues, 1 model selected
> surface sel
> color (#!13 & sel) red
> select #13/D-F
10710 atoms, 10877 bonds, 1418 residues, 1 model selected
> surface sel
> color (#!13 & sel) yellow
> select clear
Drag select of Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_B SES surface, 50280 of
406762 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_C SES surface, 396
of 378524 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_F SES surface,
41616 of 356422 triangles, 170 residues
> cartoon hide (#!13 & sel)
Drag select of Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_C SES surface, 15151 of
378524 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_F SES surface, 5814
of 356422 triangles, 27 residues
> cartoon hide (#!13 & sel)
Drag select of Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_A SES surface, 9394 of
384758 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_B SES surface, 11084
of 406762 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_E SES surface,
10833 of 432504 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_F SES
surface, 632 of 356422 triangles, 36 residues
> select clear
Drag select of Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_A SES surface, 2363 of
384758 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_E SES surface, 3137
of 432504 triangles, 7 residues
> cartoon hide (#!13 & sel)
Drag select of Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_A SES surface, 5471 of
384758 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_E SES surface, 22 of
432504 triangles, 15 residues
> cartoon hide (#!13 & sel)
Drag select of Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_B SES surface, 1295 of
406762 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_E SES surface, 18 of
432504 triangles, Morph - CONF1_F1Fo-RSR23_re-chainID.pdb_F SES surface, 884
of 356422 triangles, 2 residues
> cartoon hide sel
> select clear
> movie record
> coordset #13 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> select #13/D-F
10710 atoms, 10877 bonds, 1418 residues, 1 model selected
> surface hidePatches (#!13 & sel)
> cartoon hide (#!13 & sel)
> select #13/A-C
11548 atoms, 11721 bonds, 1518 residues, 1 model selected
> surface hidePatches (#!13 & sel)
> cartoon hide (#!13 & sel)
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select #13/Y,6,Z,7,8,J,U
5846 atoms, 5952 bonds, 744 residues, 1 model selected
> cartoon hide sel
> select #13/K-T
5338 atoms, 5418 bonds, 742 residues, 1 model selected
> cartoon hide sel
Drag select of 186 residues
> cartoon hide sel
> coordset #13 1,51
> movie record
> movie encode /Users/stutisharma/Desktop/movie.mp4 framerate 25.0
Movie encoding failed because no images were recorded.
> cartoon style sel modeHelix tube sides 20
> select #13/G:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> cartoon hide sel
> movie record
> movie encode /Users/stutisharma/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> movie record
> movie encode /Users/stutisharma/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> morph stop
Missing or invalid "structures" argument: invalid structures specifier
> morph #13 stop
Expected a keyword
> movie abort
No movie being recorded.
> wait 20
> coordset #13 1,51
> wait 70
> movie record
> wait 20
> coordset #13 1,51
> wait 60
> turn y 180
> coordset #13 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> cartoon style sel xsection oval modeHelix default
> movie record
> wait 20
> coordset #13 1,51
> wait 60
> turn y 180
> coordset #13 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> movie abort
No movie being recorded.
> movie record
> wait 20
> coordset #13 1,51
> wait 60
> turn y 180
> coordset #13 1,51
> wait 70
> movie encode
Movie saved to /Users/stutisharma/Desktop/movie.mp4
> select #13
38620 atoms, 39239 bonds, 1 pseudobond, 5097 residues, 2 models selected
> ~select #13
6 models selected
> hide #!13 models
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/Conf3_merged_5_fit_220120-map.pdb
Chain information for Conf3_merged_5_fit_220120-map.pdb #14
---
Chain | Description
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
K L N O P Q S T | No description available
M R | No description available
U | No description available
X | No description available
Y | No description available
Z | No description available
> cartoon #14
> hide #14 target a
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/Conf-3_220120/Fomap_fit-
> halfsum_4-2.mrc
Opened Fomap_fit-halfsum_4-2.mrc as #15, grid size 320,320,320, pixel 1, shown
at level 0.0106, step 2, values float32
> volume #15 step 1
> volume #15 level 0.02191
> open
> /Users/stutisharma/Documents/ATPsynthase/Model_Building/Conf-3_220120/F1Fo_halfsum-50_4-2_0_fit-
> whole.mrc
Opened F1Fo_halfsum-50_4-2_0_fit-whole.mrc as #16, grid size 320,320,320,
pixel 1, shown at level 0.0313, step 2, values float32
> volume #16 step 1
> fitmap #14 inMap #15
Fit molecule Conf3_merged_5_fit_220120-map.pdb (#14) to map Fomap_fit-
halfsum_4-2.mrc (#15) using 38248 atoms
average map value = 0.01033, steps = 2000
shifted from previous position = 3.9
rotated from previous position = 3.93 degrees
atoms outside contour = 33388, contour level = 0.021915
Position of Conf3_merged_5_fit_220120-map.pdb (#14) relative to Fomap_fit-
halfsum_4-2.mrc (#15) coordinates:
Matrix rotation and translation
0.99799985 0.05990451 0.02019303 -11.22049301
-0.05934799 0.99786897 -0.02711704 14.30371326
-0.02177443 0.02586438 0.99942829 -3.64219093
Axis 0.38651513 0.30616507 -0.86998219
Axis point 216.71966824 215.26065115 0.00000000
Rotation angle (degrees) 3.92998017
Shift along axis 3.21104823
> fitmap #14 inMap #16
Fit molecule Conf3_merged_5_fit_220120-map.pdb (#14) to map
F1Fo_halfsum-50_4-2_0_fit-whole.mrc (#16) using 38248 atoms
average map value = 0.03327, steps = 92
shifted from previous position = 3.9
rotated from previous position = 3.93 degrees
atoms outside contour = 18373, contour level = 0.031322
Position of Conf3_merged_5_fit_220120-map.pdb (#14) relative to
F1Fo_halfsum-50_4-2_0_fit-whole.mrc (#16) coordinates:
Matrix rotation and translation
1.00000000 -0.00003615 0.00003183 -0.00425126
0.00003614 1.00000000 0.00008927 -0.03619555
-0.00003184 -0.00008927 1.00000000 0.01689472
Axis -0.88007166 0.31385385 0.35632799
Axis point 0.00000000 195.61523085 399.84626729
Rotation angle (degrees) 0.00581183
Shift along axis -0.00159864
> volume #16 level 0.03747
> surface dust #16 size 10
> volume #16 level 0.03308
> hide #!16 models
> dssp
> save /Users/stutisharma/session_F1Fo.cxs includeMaps true
Traceback (most recent call last):
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
OpenGL version: 4.1 ATI-3.10.22
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro13,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 429.140.8.0.0
SMC Version (system): 2.38f12
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1323)
Kernel Version: Darwin 19.6.0
Time since boot: 23:13
Graphics/Displays:
Intel HD Graphics 530:
Chipset Model: Intel HD Graphics 530
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x191b
Revision ID: 0x0006
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal: Supported, feature set macOS GPUFamily2 v1
Radeon Pro 455:
Chipset Model: AMD Radeon Pro 455
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c7
ROM Revision: 113-C980AF-908
VBIOS Version: 113-C9801AP-028
EFI Driver Version: 01.A0.908
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
ASUS PB278:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: G6LMTF187547
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
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: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.29.1
ChimeraX-AtomicLibrary: 4.1.4
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: 2.5.3
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: 2.1
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: 1.3.dev202109160803
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
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: 2.1.1
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: 2.0.1
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
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: 2.6.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
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: 2.4.3
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: 1.12.1
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: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
distlib: 0.3.2
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
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: 4.7.1
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: 3.0.20
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: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.1
RandomWords: 0.3.0
requests: 2.25.1
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: 5.1.0
urllib3: 1.26.6
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
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem saving session: object of type 'SurfaceUpdaters' has no len() |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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This error saving sessions was fixed several months ago and is fixed in current ChimeraX 1.3. I suggest you update to the current release.