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Opened 3 years ago
Closed 3 years ago
#8107 closed defect (fixed)
Map→Style→Transparent surface not toggling transparency
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
Transparency toggle in "style" menu does not toggle properly - after selecting (and changing transparency to 50%), select it again does not return transparency to 100%
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/20221108-reaction-session.cxs"
Opened cryosparc_P37_J366_005_volume_map.mrc as #1.1, grid size 224,224,224,
pixel 1.65, shown at level 1.34, step 1, values float32
Opened cryosparc_P37_J368_005_volume_map.mrc as #1.3, grid size 224,224,224,
pixel 1.65, shown at level 0.811, step 1, values float32
Opened cryosparc_P37_J369_006_volume_map.mrc as #1.4, grid size 224,224,224,
pixel 1.65, shown at level 0.955, step 1, values float32
Opened cryosparc_P37_J370_005_volume_map.mrc as #1.5, grid size 224,224,224,
pixel 1.65, shown at level 1.33, step 1, values float32
Opened J366_denmod_map.ccp4 as #3, grid size 93,101,127, pixel 1.65, shown at
level 0.697, step 1, values float32
Opened J368_denmod_map.ccp4 as #4, grid size 107,111,127, pixel 1.65, shown at
level 0.734, step 1, values float32
Opened J369_denmod_map.ccp4 as #5, grid size 105,113,129, pixel 1.65, shown at
level 0.804, step 1, values float32
Opened J370_denmod_map.ccp4 as #7, grid size 107,107,129, pixel 1.65, shown at
level 0.835, step 1, values float32
Opened cryosparc_P37_J397_006_volume_map.mrc as #6.1, grid size 448,448,448,
pixel 0.826, shown at level 0.19, step 1, values float32
Opened cryosparc_P37_J398_006_volume_map.mrc as #6.2, grid size 448,448,448,
pixel 0.826, shown at level 0.164, step 1, values float32
Opened cryosparc_P37_J399_006_volume_map.mrc as #6.3, grid size 448,448,448,
pixel 0.826, shown at level 0.159, step 1, values float32
Opened cryosparc_P37_J400_005_volume_map.mrc as #6.4, grid size 448,448,448,
pixel 0.826, shown at level 0.176, step 1, values float32
Log from Thu Dec 1 10:44:18 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P3_J558_006_volume_map.mrc" format mrc
Opened cryosparc_P3_J558_006_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.826, shown at level 0.0443, step 2, values float32
> volume #1 step 1
> volume #1 level 0.06117
> ui mousemode right zoom
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J352_map_sharp.mrc"
Opened cryosparc_P37_J352_map_sharp.mrc as #2, grid size 224,224,224, pixel
1.65, shown at level 0.856, step 1, values float32
> hide #!1 models
> volume #2 step 2
> volume #2 step 1
> volume #2 level 2.977
> volume #2 level 1.94
> volume #2 level 1.658
> ui tool show "Side View"
> volume #2 level 1.375
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> surface dust #2 size 16.5
> volume #2 level 0.9506
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!2 target m
[Repeated 1 time(s)]
> view #2 clip false
> volume #2 level 0.715
> show #!1 models
> hide #!2 models
> close #1
> show #!2 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J353_005_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J356_005_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J357_005_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J358_006_volume_map.mrc"
Opened cryosparc_P37_J353_005_volume_map.mrc as #1.1, grid size 224,224,224,
pixel 1.65, shown at level 0.827, step 1, values float32
Opened cryosparc_P37_J356_005_volume_map.mrc as #1.2, grid size 224,224,224,
pixel 1.65, shown at level 0.83, step 1, values float32
Opened cryosparc_P37_J357_005_volume_map.mrc as #1.3, grid size 224,224,224,
pixel 1.65, shown at level 0.718, step 1, values float32
Opened cryosparc_P37_J358_006_volume_map.mrc as #1.4, grid size 224,224,224,
pixel 1.65, shown at level 0.811, step 1, values float32
> undo
[Repeated 1 time(s)]
> hide #!2 models
> close #1#1.1-4
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J353_005_volume_map.mrc"
Opened cryosparc_P37_J353_005_volume_map.mrc as #1, grid size 224,224,224,
pixel 1.65, shown at level 0.827, step 1, values float32
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J356_005_volume_map.mrc"
Opened cryosparc_P37_J356_005_volume_map.mrc as #3, grid size 224,224,224,
pixel 1.65, shown at level 0.83, step 1, values float32
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J357_005_volume_map.mrc"
Opened cryosparc_P37_J357_005_volume_map.mrc as #4, grid size 224,224,224,
pixel 1.65, shown at level 0.718, step 1, values float32
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J358_006_volume_map.mrc"
Opened cryosparc_P37_J358_006_volume_map.mrc as #5, grid size 224,224,224,
pixel 1.65, shown at level 0.811, step 1, values float32
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> volume #3 level 0.7555
> volume #3 level 2.526
> volume #3 level 1.296
> lighting soft
> graphics silhouettes true
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> volume #3 level 0.9978
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!1 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J447-MCM-channel-mask.mrc"
Opened J447-MCM-channel-mask.mrc as #6, grid size 192,192,192, pixel 1.65,
shown at level 0.0149, step 1, values float32
> close #6
> hide #!1 models
> ui tool show "Segment Map"
Segmenting cryosparc_P37_J356_005_volume_map.mrc, density threshold 0.997776
Showing 40 region surfaces
3797 watershed regions, grouped to 40 regions
Showing cryosparc_P37_J356_005_volume_map.seg - 40 regions, 40 surfaces
> hide #!3 models
Deleted 26 regions
Deleted 1 regions
Drag select of 5126, 5093, 5123, 5133, 5134, 5094, 5048, 5042, 5097, 5044,
5101, 4763, 5055
Grouped 13 regions
Saving 1 regions to mrc file...
Opened J356-dsDNA-CT-mask.mrc as #7, grid size 77,77,68, pixel 1.65, shown at
step 1, values float32
Wrote J356-dsDNA-CT-mask.mrc
> vop resample #7 ongrid #6
Map cryosparc_P37_J356_005_volume_map.mrc is now associated with
cryosparc_P37_J356_005_volume_map.seg
> vop resample #7 ongrid #6
> select add #6
2 models selected
> select subtract #6
Nothing selected
> vop resample #7 ongrid #6
> volume #7 level 2.752
> hide #!6 models
> volume #7 level 0.9103
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J356-dsDNA-CT-mask.mrc" models #3
> mask #7 #6
Unknown command: mask #7 #6
> show #!7 models
> hide #!6 models
> vop resample #7 ongrid #5
Opened J356-dsDNA-CT-mask.mrc resampled as #8, grid size 224,224,224, pixel
1.65, shown at step 1, values float32
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J356-dsDNA-CT-mask.mrc" models #8
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J356-dsDNA-CT-mask-2.mrc" models #8
> close #1-7
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J366_005_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J367_006_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J368_005_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J369_006_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J370_005_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J371_005_volume_map.mrc"
Opened cryosparc_P37_J366_005_volume_map.mrc as #1.1, grid size 224,224,224,
pixel 1.65, shown at level 0.707, step 1, values float32
Opened cryosparc_P37_J367_006_volume_map.mrc as #1.2, grid size 224,224,224,
pixel 1.65, shown at level 0.755, step 1, values float32
Opened cryosparc_P37_J368_005_volume_map.mrc as #1.3, grid size 224,224,224,
pixel 1.65, shown at level 0.866, step 1, values float32
Opened cryosparc_P37_J369_006_volume_map.mrc as #1.4, grid size 224,224,224,
pixel 1.65, shown at level 0.9, step 1, values float32
Opened cryosparc_P37_J370_005_volume_map.mrc as #1.5, grid size 224,224,224,
pixel 1.65, shown at level 0.867, step 1, values float32
Opened cryosparc_P37_J371_005_volume_map.mrc as #1.6, grid size 224,224,224,
pixel 1.65, shown at level 0.853, step 1, values float32
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!8 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.2 models
> close #1.2
> show #!1.3 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> show #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> show #!1.6 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.6 models
> show #!1.5 models
> show #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> show #!1.6 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> volume #1.6 level 0.6226
> close #1.6
> show #!1.5 models
> show #!1.4 models
> volume #1.5 level 0.9941
> hide #!1.5 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.3 models
> hide #!1.4 models
> volume #1.3 level 1.005
> fitmap #1.3 inMap #1.4
Fit map cryosparc_P37_J368_005_volume_map.mrc in map
cryosparc_P37_J369_006_volume_map.mrc using 90378 points
correlation = 0.9534, correlation about mean = 0.7682, overlap = 3.015e+05
steps = 64, shift = 0.253, angle = 0.503 degrees
Position of cryosparc_P37_J368_005_volume_map.mrc (#1.3) relative to
cryosparc_P37_J369_006_volume_map.mrc (#1.4) coordinates:
Matrix rotation and translation
0.99996165 0.00653793 0.00582654 -2.41275974
-0.00654069 0.99997851 0.00045457 1.38326309
-0.00582344 -0.00049266 0.99998292 1.27274191
Axis -0.05400249 0.66417560 -0.74562357
Axis point 200.11353147 369.38768566 0.00000000
Rotation angle (degrees) 0.50250517
Shift along axis 0.10003825
> fitmap #1.1 inMap #1.3
Fit map cryosparc_P37_J366_005_volume_map.mrc in map
cryosparc_P37_J368_005_volume_map.mrc using 112307 points
correlation = 0.8551, correlation about mean = 0.5059, overlap = 2.893e+05
steps = 72, shift = 0.564, angle = 0.874 degrees
Position of cryosparc_P37_J366_005_volume_map.mrc (#1.1) relative to
cryosparc_P37_J368_005_volume_map.mrc (#1.3) coordinates:
Matrix rotation and translation
0.99997842 0.00381380 0.00534924 -1.79337751
-0.00380696 0.99999192 -0.00128837 1.13918179
-0.00535411 0.00126798 0.99998486 0.86304486
Axis 0.19097849 0.79962054 -0.56932786
Axis point 168.42963016 0.00000000 338.68899536
Rotation angle (degrees) 0.38347036
Shift along axis 0.07706113
> volume #1.1 level 0.9686
> surface dust #1.1 size 16.5
> surface dust #1.3 size 16.5
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> volume #1.3 level 1.132
> volume #1.3 level 1.195
> volume #1.1 level 1.199
> hide #!1.1 models
> show #!1.1 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.1 models
> volume #1.4 level 1.204
> show #!1.1 models
> show #!1.3 models
> hide #!1.1 models
> surface dust #1.3 size 16.5
> surface dust #1.4 size 16.5
> volume #1.4 level 0.9553
> hide #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.3 models
> show #!1.3 models
> show #!1.4 models
> open 6skl
6skl title:
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
Conformation 1 [more info...]
Chain information for 6skl #2
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST
3 | DNA replication licensing factor MCM3 | MCM3_YEAST
4 | DNA replication licensing factor MCM4 | MCM4_YEAST
5 | Minichromosome maintenance protein 5 | MCM5_YEAST
6 | DNA replication licensing factor MCM6 | MCM6_YEAST
7 | DNA replication licensing factor MCM7 | MCM7_YEAST
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST
B | DNA replication complex GINS protein PSF2 | PSF2_YEAST
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST
E | Cell division control protein 45 | CDC45_YEAST
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST
I | DNA fork, leading-strand template |
J | DNA fork, lagging-strand template |
X | Topoisomerase 1-associated factor 1 | TOF1_YEAST
Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST
Non-standard residues in 6skl #2
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
ZN — zinc ion
> hide atoms
> hide cartoons
> hide surfaces
[Repeated 1 time(s)]
> show cartoons
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.1 models
> hide #!1 models
> show #!1.5 models
> select add #2
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.027113,0.28509,-0.95812,323.31,0.98145,0.18955,0.028629,-45.031,0.18978,-0.93957,-0.28494,375.3
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.027113,0.28509,-0.95812,336.34,0.98145,0.18955,0.028629,-33.718,0.18978,-0.93957,-0.28494,380.13
> view matrix models
> #2,-0.027113,0.28509,-0.95812,336.31,0.98145,0.18955,0.028629,-33.6,0.18978,-0.93957,-0.28494,380.04
> view matrix models
> #2,-0.027113,0.28509,-0.95812,329.17,0.98145,0.18955,0.028629,-20.481,0.18978,-0.93957,-0.28494,377.11
> fitmap #2 inMap #1.5
Fit molecule 6skl (#2) to map cryosparc_P37_J370_005_volume_map.mrc (#1.5)
using 118220 atoms
average map value = 1.108, steps = 140
shifted from previous position = 10.1
rotated from previous position = 15.9 degrees
atoms outside contour = 62083, contour level = 0.99409
Position of 6skl (#2) relative to cryosparc_P37_J370_005_volume_map.mrc (#1.5)
coordinates:
Matrix rotation and translation
0.10194859 0.18194023 -0.97801034 328.45022492
0.91248129 0.37446680 0.16478021 -75.14550271
0.39621255 -0.90921525 -0.12784070 307.37059490
Axis -0.56796980 -0.72674153 0.38633800
Axis point 40.27211923 0.00000000 291.19584306
Rotation angle (degrees) 109.00875683
Shift along axis -13.18951113
> select clear
[Repeated 1 time(s)]
> select /G:841
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
393 atoms, 394 bonds, 25 residues, 1 model selected
> select up
1707 atoms, 1714 bonds, 111 residues, 1 model selected
> select up
6693 atoms, 6778 bonds, 422 residues, 1 model selected
> select up
118220 atoms, 119405 bonds, 7321 residues, 1 model selected
> select down
6693 atoms, 6778 bonds, 422 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /H:567
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
79 atoms, 80 bonds, 4 residues, 1 model selected
> select up
3082 atoms, 3129 bonds, 193 residues, 1 model selected
> select up
3104 atoms, 3150 bonds, 194 residues, 1 model selected
> select up
5034 atoms, 5112 bonds, 314 residues, 1 model selected
> select up
6769 atoms, 6854 bonds, 425 residues, 1 model selected
> select up
111527 atoms, 112627 bonds, 6899 residues, 1 model selected
> select down
6769 atoms, 6854 bonds, 425 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /F:921
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
286 atoms, 287 bonds, 17 residues, 1 model selected
> select up
1710 atoms, 1717 bonds, 110 residues, 1 model selected
> select up
6759 atoms, 6844 bonds, 424 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /D:13
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
159 atoms, 158 bonds, 10 residues, 1 model selected
> select up
219 atoms, 218 bonds, 14 residues, 1 model selected
> select up
235 atoms, 233 bonds, 15 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right zoom
> show #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.4 models
> select ::name="DA"::name="DC"::name="DG"::name="DT"
1878 atoms, 2015 bonds, 50 pseudobonds, 59 residues, 2 models selected
> hide #!1.5 models
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1878 atom styles
> nucleotides sel tube/slab shape muffler
> nucleotides sel slab
> style nucleic & sel stick
Changed 1878 atom styles
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> color sel bynucleotide
> select add #2
97764 atoms, 98695 bonds, 123 pseudobonds, 6035 residues, 4 models selected
> select subtract #2
Nothing selected
> show #!1.5 models
> volume #1.5 level 1.645
> volume #1.5 color #e5bf9952
> volume #1.5 level 0.8512
> volume #1.5 level 1.328
> volume #1.5 level 0.9782
> volume #1.5 level 1.312
> hide #!2 models
> show #!2 models
> select ::name="ANP"
132 atoms, 138 bonds, 3 residues, 1 model selected
> color sel byhetero
> style sel sphere
Changed 132 atom styles
> hide #!1.5 models
> select /A
3227 atoms, 3247 bonds, 1 pseudobond, 197 residues, 2 models selected
> select nucleic-acid
1878 atoms, 2015 bonds, 50 pseudobonds, 59 residues, 2 models selected
> color sel bychain
[Repeated 1 time(s)]
> color sel bynucleotide
> color sel bychain
> color sel byhetero
[Repeated 1 time(s)]
> color sel bypolymer
> rainbow sel
> color sel bynucleotide
> coulombic sel
Treating 5' terminal nucleic acids with phosphates as non-standard
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue DC (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Users/ben/Desktop/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/2q/dlfqyp9j6_l3r13l_xydx4780000gn/T/tmpbd35on9h/ante.in.mol2 -fi
mol2 -o
/var/folders/2q/dlfqyp9j6_l3r13l_xydx4780000gn/T/tmpbd35on9h/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(DC) ``
(DC) `Welcome to antechamber 20.0: molecular input file processor.`
(DC) ``
(DC) `Info: Finished reading file
(/var/folders/2q/dlfqyp9j6_l3r13l_xydx4780000gn/T/tmpbd35on9h/ante.in.mol2);
atoms read (37), bonds read (38).`
(DC) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(DC) `Running:
/Users/ben/Desktop/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(DC) ``
(DC) ``
(DC) `Running:
/Users/ben/Desktop/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(DC) `Info: Total number of electrons: 192; net charge: -3`
(DC) ``
(DC) `Running:
/Users/ben/Desktop/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out`
(DC)
`/Users/ben/Desktop/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(DC) `Cannot properly run
"/Users/ben/Desktop/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out".`
Failure running ANTECHAMBER for residue DC Check reply log for details
> color sel bychain
> select /J
686 atoms, 736 bonds, 22 residues, 1 model selected
> color sel yellow
> select /J
686 atoms, 736 bonds, 22 residues, 1 model selected
> color sel red
> select /I
1192 atoms, 1279 bonds, 37 residues, 1 model selected
> color sel cyan
[Repeated 1 time(s)]
> color sel white
> select /J
686 atoms, 736 bonds, 22 residues, 1 model selected
> color sel orange red
> color sel forest green
> select clear
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.3 models
> show #!1.4 models
> select /J
686 atoms, 736 bonds, 22 residues, 1 model selected
> hide #!1.4 models
> color sel orange
> select clear
> show #!1.5 models
> color #1.5 #e5bf99 models transparency 0
> show #!1.1 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.5 models
> hide #!2 models
> volume #1.3 level 0.9317
> hide #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.4 models
> hide #!1.3 models
> show #!1.5 models
> hide #!1.4 models
> show #!1.4 models
> lighting soft
> volume #1.5 level 0.9591
> surface dust #1.5 size 16.5
> show #!2 models
> hide #!1.4 models
> show #!1.5 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.5 models
> show #!1.4 models
> color #1.4 #b2ffb26a models
> color #1.4 #b2ffb2a0 models
> color #1.4 #82ae85a0 models
> color #1.4 #82ae859d models
> color #1.4 #82ae859e models
> color #1.4 #82ae85 models transparency 0
> color #1.4 #618263 models transparency 0
> color #1.4 #618263c2 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
Traceback (most recent call last):
File
"/Users/ben/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback
_color_callback(*args)
File
"/Users/ben/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 134, in _color_changed_cb
self.color_changed.emit(self._color)
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted
Populating font family aliases took 340 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted
File
"/Users/ben/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 134, in _color_changed_cb
self.color_changed.emit(self._color)
See log for complete Python traceback.
> color #1.4 #618263 models transparency 0
> hide #!2 models
> color #1.4 #c8ffcf models transparency 0
> color #1.4 #a7d5ad models transparency 0
> color #1.5 #baa086 models transparency 0
> hide #!1.4 models
> show #!2 models
> ui tool show "Side View"
> volume #!1.5 style image
[Repeated 1 time(s)]
> volume #!1.5 style surface
> transparency #1.5.1 50
> transparency #1.5.1 0
> transparency #1.5.1 50
> transparency #1.5.1 0
> transparency #1.5.1 50
> transparency #1.5.1 0
> transparency #1.5.1 50
> transparency #1.5.1 0
> transparency #1.5.1 50
> hide #!2 models
> show #!2 models
> hide #!2 models
> transparency #1.5.1 0
> hide #!1.5 models
> show #!2 models
> show #!1.5 models
> hide #!2 models
> show #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!2 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!2 models
> hide #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> show #!1.1 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.1 models
> show #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!2 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> lighting soft
[Repeated 1 time(s)]
> hide #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.3 models
> show #!1.1 models
> hide #!2 models
> show #!1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> volume #1.3 level 0.6332
> volume #1.3 level 0.7034
> show #!2 models
> volume #1.3 level 0.9492
> show #!1.4 models
> hide #!1.4 models
> hide #!2 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> volume #1.3 level 0.721
> show #!2 models
> hide #!1.3 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Density Modification/J366/J366_denmod_map.ccp4"
Opened J366_denmod_map.ccp4 as #3, grid size 93,101,127, pixel 1.65, shown at
level 4.57, step 1, values float32
> hide #!2 models
> volume #3 level 4.336
> volume #3 level 1.43
> volume #3 level 0.5327
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Density Modification/J368/J368_denmod_map.ccp4"
Opened J368_denmod_map.ccp4 as #4, grid size 107,111,127, pixel 1.65, shown at
level 4.47, step 1, values float32
> hide #!3 models
> volume #4 level 0.9804
> show #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> volume #4 level 0.6943
> hide #!4 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Density Modification/J369/J369_denmod_map.ccp4"
Opened J369_denmod_map.ccp4 as #5, grid size 105,113,129, pixel 1.65, shown at
level 4.5, step 1, values float32
> volume #5 level 0.6988
> hide #!5 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.3 models
> show #!3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> volume #3 level 0.4899
> surface dust #3 size 16.5
> volume #3 level 0.4899
> volume #4 level 0.4655
> surface dust #4 size 16.5
> volume #5 level 0.4876
> surface dust #4 size 16.5
> surface dust #5 size 16.5
> show #!2 models
> volume #5 step 2
> volume #5 step 4
> volume #5 step 16
> volume #5 step 1
> volume #3 color #cccc99d9
> volume #3 color #99997bd9
[Repeated 1 time(s)]
> volume #3 color #99997ba7
> volume #3 color #b0b08ea7
> volume #5 level 0.3821
> volume #3 level 0.2336
> volume #3 level 0.4472
> hide #!2 models
> transparency #3.1 0
> transparency #3.1 50
> transparency #3.1 0
> show #!2 models
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Density Modification/J369/6SKL-aligned-J366.pdb" relModel #3
> save "/Users/ben/Google Drive/My Drive/Grad School/Thesis Work/EM Data
> Processing/20221108-CMG-reaction/Density Modification/J366/6SKL-
> aligned-J366.pdb" relModel #3
> volume #3 level 1.131
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!5 models
> hide #!3 models
> show #!3 models
> color #3 #be5752 models transparency 0
> color #3 #be7862 models transparency 0
> color #3 #be7771 models transparency 0
> color #5 #d0ce9c models transparency 0
> show #!4 models
> show #!2 models
> hide #!5 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #5 level 1.068
> volume #4 level 1.07
> volume #4 level 0.4979
> hide #!3 models
> show #!1.1 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> color #1.5 #5aa5c7 models transparency 0
> color #1.5 #67bce2 models transparency 0
> color #1.3 #ff9faf models transparency 0
> color #1.3 #ffa0b4 models transparency 0
> hide #!1 models
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.1 models
> save /Users/ben/Desktop/image7.png supersample 3
> hide #!1.1 models
> show #!1.3 models
> volume #1.1 level 0.9775
> volume #1.3 level 0.9533
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.1 models
> volume #1.1 level 0.917
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.5 models
> show #!1.4 models
> hide #!1.3 models
> hide #!1.1 models
> hide #!1.4 models
> set bgColor white
> hide #!1.5 models
> show #!1.1 models
> save /Users/ben/Desktop/image8.png supersample 3
> hide #!1.1 models
> show #!1.3 models
> save /Users/ben/Desktop/image9.png supersample 3
> hide #!1.3 models
> show #!1.4 models
> save /Users/ben/Desktop/image10.png supersample 3
> hide #!1.4 models
> show #!1.5 models
> save /Users/ben/Desktop/image11.png supersample 3
> hide #!1.5 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> save /Users/ben/Desktop/image12.png supersample 3
> hide #!1.3 models
> show #!1.1 models
> save /Users/ben/Desktop/image13.png supersample 3
> hide #!1.1 models
> show #!1.4 models
> save /Users/ben/Desktop/image14.png supersample 3
> show #!1.5 models
> hide #!1.4 models
> save /Users/ben/Desktop/image15.png supersample 3
> show #!1.1 models
> hide #!1.5 models
> hide #!1.1 models
> show #!3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> volume #1.1 level 0.9573
> volume #1.1 level 0.917
> save /Users/ben/Desktop/image16.png supersample 3
> hide #!1.1 models
> show #!1.3 models
> save /Users/ben/Desktop/image17.png supersample 3
> save /Users/ben/Desktop/image18.png supersample 3
> show #!1.1 models
> hide #!1.3 models
> save /Users/ben/Desktop/image19.png supersample 3
> hide #!1.1 models
> show #!1.4 models
> save /Users/ben/Desktop/image20.png supersample 3
> hide #!1.4 models
> show #!1.5 models
> save /Users/ben/Desktop/image21.png supersample 3
> hide #!1.5 models
> show #!1.1 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ben/Desktop/movie6.mp4
Movie saved to /Users/ben/Desktop/movie6.mp4
> hide #!1.1 models
> show #!1.3 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ben/Desktop/movie7.mp4
Movie saved to /Users/ben/Desktop/movie7.mp4
> hide #!1.3 models
> show #!1.4 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ben/Desktop/movie8.mp4
Movie saved to /Users/ben/Desktop/movie8.mp4
> hide #!1.4 models
> show #!1.5 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ben/Desktop/movie9.mp4
Movie saved to /Users/ben/Desktop/movie9.mp4
> hide #!1.5 models
> show #!5 models
> volume #4 level 1.07
> volume #4 level 0.8412
> volume #5 level 0.8043
> hide #!5 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.5 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.4 models
> show #!1.3 models
> hide #!1 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1.3 models
> volume #4 level 0.4407
> volume #4 level 0.784
> volume #4 level 0.5551
> hide #!4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.3 models
> ui tool show "Segment Map"
Segmenting cryosparc_P37_J368_005_volume_map.mrc, density threshold 0.953270
Showing 40 region surfaces
3733 watershed regions, grouped to 40 regions
Showing cryosparc_P37_J368_005_volume_map.seg - 40 regions, 40 surfaces
> hide #!1.3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
Grouped 7 regions
Deleted 33 regions
> vop resample #6 ongrid #1.3
> hide #!6 models
> show #!6 models
> hide #!5 models
Saving 1 regions to mrc file...
Opened J368-C-tier-mask.mrc as #7, grid size 58,84,82, pixel 1.65, shown at
step 1, values float32
Wrote J368-C-tier-mask.mrc
> hide #!6 models
> vop resample #7 ongrid #1.3
Opened J368-C-tier-mask.mrc resampled as #9, grid size 224,224,224, pixel
1.65, shown at step 1, values float32
> close #7
> volume #9 level 0.9694
> volume #9 level 0.9311
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> volume #9 level 0.7433
> volume #9 level 0.9349
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J368-C-tier-mask.mrc" models #9
> hide #!9 models
> show #!1.1 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.4 models
> hide #!1.1 models
> set bgColor black
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!2 models
> hide #!2 models
> show #!1.4 models
> show #!1.5 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.1 models
> show #!1.3 models
> hide #!1.1 models
> hide #!1.3 models
> show #!1.3 models
> volume #1.3 level 0.7719
> hide #!1.3 models
> hide #!1 models
> show #!9 models
> show #!1.3 models
> volume #1.1 level 0.9642
> volume #9 level 0.9004
> hide #!1.3 models
> hide #!9 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.3 models
> hide #!1.1 models
> show #!2 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> volume #1.4 level 1.125
> hide #!2 models
> volume #1.4 level 0.9694
> show #!2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.4 models
> show #!1.3 models
> hide #!1.1 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> hide #!2 models
> hide #!1.5 models
> show #!1.1 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.1 models
> show #!2 models
> hide #!2 models
> show #!1.1 models
> hide #!1.3 models
> show #!2 models
> hide #!1.1 models
> show #!1.3 models
> hide #!2 models
> volume #1.3 level 0.9403
> show #!2 models
> hide #!1.3 models
> show #!1.4 models
> hide #!2 models
> show #!1.5 models
> hide #!1.4 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.1 models
> show #!1.4 models
> hide #!1.1 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> show #!1.1 models
> show #!1.3 models
> hide #!1.1 models
> hide #!1.3 models
> show #!2 models
> hide #!1.4 models
> show #!8 models
> hide #!2 models
> show #!6 models
> show #!5 models
> select add #6
2 models selected
> select subtract #6
Nothing selected
> hide #!6 models
> hide #!8 models
> show #!4 models
> show #!3 models
> hide #!5 models
> hide #!4 models
> volume #3 level 0.3302
> volume #3 level 0.3969
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!1.5 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/Density Modification/J370/J370_denmod_map.ccp4"
Opened J370_denmod_map.ccp4 as #7, grid size 107,107,129, pixel 1.65, shown at
level 4.69, step 1, values float32
> volume #7 level 0.9755
> hide #!5 models
> hide #!1.5 models
> volume #7 level 0.66
> surface dust #7 size 16.5
> show #!2 models
> show #!1.5 models
> hide #!7 models
> show #!7 models
> hide #!1.5 models
> volume #7 level 0.8353
> hide #!2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!7 models
> set bgColor white
> save /Users/ben/Desktop/image22.png supersample 3
> hide #!1.1 models
> show #!1.3 models
> save /Users/ben/Desktop/image23.png supersample 3
> hide #!1.3 models
> show #!1.4 models
> save /Users/ben/Desktop/image24.png supersample 3
> hide #!1.4 models
> show #!1.5 models
> save /Users/ben/Desktop/image25.png supersample 3
> show #!1.1 models
> hide #!1.5 models
> hide #!1.1 models
> show #!2 models
> hide #!2 models
> show #!1.1 models
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!2 models
> open 6sko
Summary of feedback from opening 6sko fetched from pdb
---
note | Fetching compressed mmCIF 6sko from
http://files.rcsb.org/download/6sko.cif
6sko title:
Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication
Fork - conformation 2 MCM CTD:ssDNA [more info...]
Chain information for 6sko #10
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST
3 | DNA replication licensing factor MCM3 | MCM3_YEAST
4 | DNA replication licensing factor MCM4 | MCM4_YEAST
5 | Minichromosome maintenance protein 5 | MCM5_YEAST
6 | DNA replication licensing factor MCM6 | MCM6_YEAST
7 | DNA replication licensing factor MCM7 | MCM7_YEAST
I | ssDNA, leading-strand template |
Non-standard residues in 6sko #10
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
> hide #!10 atoms
> hide #!10 cartoons
> hide #!10 surfaces
> show #!10 cartoons
> align #10 toAtoms #2
Unequal number of atoms to pair, 31618 and 97764
> hide #!1.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #10
31618 atoms, 31846 bonds, 34 pseudobonds, 1981 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.77499,-0.089743,-0.62557,185.47,0.39206,-0.70808,0.58728,129.78,-0.49566,-0.7004,-0.51357,530.68
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.77499,-0.089743,-0.62557,206.58,0.39206,-0.70808,0.58728,136.38,-0.49566,-0.7004,-0.51357,471.24
> view matrix models
> #10,0.77499,-0.089743,-0.62557,225.59,0.39206,-0.70808,0.58728,27.397,-0.49566,-0.7004,-0.51357,452.98
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.55777,-0.22495,-0.79893,321.38,0.77704,0.47984,0.40739,-213.63,0.29172,-0.84803,0.44243,153.62
> view matrix models
> #10,0.62611,0.30536,-0.71745,195.15,0.46717,0.58978,0.65872,-239.86,0.62429,-0.7476,0.22661,129.78
> view matrix models
> #10,0.63259,0.35525,-0.68821,178.65,0.57098,0.38645,0.72432,-232.33,0.52327,-0.85115,0.041628,204.22
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.63259,0.35525,-0.68821,155.21,0.57098,0.38645,0.72432,-129.43,0.52327,-0.85115,0.041628,247.91
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.67637,0.43612,-0.59357,113.18,0.70147,-0.1356,0.69969,-47.685,0.22466,-0.88961,-0.39764,395.37
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.67637,0.43612,-0.59357,117.34,0.70147,-0.1356,0.69969,-61.37,0.22466,-0.88961,-0.39764,384.56
> align #10 toAtoms #2
Unequal number of atoms to pair, 31618 and 97764
> view matrix models
> #10,0.67637,0.43612,-0.59357,117.39,0.70147,-0.1356,0.69969,-60.557,0.22466,-0.88961,-0.39764,381.59
> view matrix models
> #10,0.67637,0.43612,-0.59357,118.23,0.70147,-0.1356,0.69969,-59.272,0.22466,-0.88961,-0.39764,378.44
> set bgColor black
> view matrix models
> #10,0.67637,0.43612,-0.59357,116.3,0.70147,-0.1356,0.69969,-64.677,0.22466,-0.88961,-0.39764,376.23
> view matrix models
> #10,0.67637,0.43612,-0.59357,117.98,0.70147,-0.1356,0.69969,-60.675,0.22466,-0.88961,-0.39764,386.3
> view matrix models
> #10,0.67637,0.43612,-0.59357,118.39,0.70147,-0.1356,0.69969,-59.75,0.22466,-0.88961,-0.39764,386.81
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.64778,0.51059,-0.5654,102.99,0.64417,0.029118,0.76433,-95.229,0.40672,-0.85933,-0.31004,334.25
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.64778,0.51059,-0.5654,105.92,0.64417,0.029118,0.76433,-88.804,0.40672,-0.85933,-0.31004,333.97
> view matrix models
> #10,0.64778,0.51059,-0.5654,103.74,0.64417,0.029118,0.76433,-92.576,0.40672,-0.85933,-0.31004,335.47
> view matrix models
> #10,0.64778,0.51059,-0.5654,104.35,0.64417,0.029118,0.76433,-94.445,0.40672,-0.85933,-0.31004,337.47
> view matrix models
> #10,0.64778,0.51059,-0.5654,105.03,0.64417,0.029118,0.76433,-90.532,0.40672,-0.85933,-0.31004,335.52
> view matrix models
> #10,0.64778,0.51059,-0.5654,98.881,0.64417,0.029118,0.76433,-89.033,0.40672,-0.85933,-0.31004,382.7
> view matrix models
> #10,0.64778,0.51059,-0.5654,71.789,0.64417,0.029118,0.76433,-88.344,0.40672,-0.85933,-0.31004,350.21
> view matrix models
> #10,0.64778,0.51059,-0.5654,74.558,0.64417,0.029118,0.76433,-91.863,0.40672,-0.85933,-0.31004,333.5
> view matrix models
> #10,0.64778,0.51059,-0.5654,74.288,0.64417,0.029118,0.76433,-94.033,0.40672,-0.85933,-0.31004,340.46
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.65592,0.46877,-0.59163,86.394,0.61394,0.12468,0.77944,-110.29,0.43914,-0.87448,-0.20601,315.96
> view matrix models
> #10,0.79702,-0.16942,-0.57971,180.17,0.55999,-0.15223,0.8144,-58.146,-0.22622,-0.97372,-0.026462,398.87
> view matrix models
> #10,0.62709,0.06711,-0.77605,204.74,0.76892,0.10598,0.6305,-98.907,0.12456,-0.9921,0.014859,339.12
> view matrix models
> #10,0.26239,0.040302,-0.96412,306.45,0.94934,0.16826,0.26541,-60.153,0.17292,-0.98492,0.0058905,332.23
> view matrix models
> #10,0.36107,0.084866,-0.92867,275.33,0.85103,0.37717,0.36535,-105.03,0.38128,-0.92225,0.063962,275.93
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.36107,0.084866,-0.92867,286.15,0.85103,0.37717,0.36535,-105.98,0.38128,-0.92225,0.063962,271.71
> view matrix models
> #10,0.36107,0.084866,-0.92867,288.44,0.85103,0.37717,0.36535,-105.99,0.38128,-0.92225,0.063962,272.03
> view matrix models
> #10,0.36107,0.084866,-0.92867,288.37,0.85103,0.37717,0.36535,-106.81,0.38128,-0.92225,0.063962,270.87
> hide #!2 models
> select subtract #10
Nothing selected
> ui mousemode right zoom
> show #!1.3 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #!10 models
> show #!1.5 models
> show #!1.1 models
> hide #!1.5 models
> volume #1.1 level 0.8068
> show #!3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!3 models
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> save /Users/ben/Desktop/image26.png supersample 3
> set bgColor white
> save /Users/ben/Desktop/image27.png supersample 3
> hide #!2 models
> save /Users/ben/Desktop/image28.png supersample 3
> set bgColor black
> save /Users/ben/Desktop/image29.png supersample 3
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!2 models
> hide #!1.1 models
> show #!1.3 models
> show #!2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save /Users/ben/Desktop/image30.png supersample 3
> show #!2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!2 models
> save /Users/ben/Desktop/image31.png supersample 3
> show #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.4 models
> hide #!1.3 models
> show #!1.4 models
> show #!1.3 models
> hide #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.4 models
> volume #1.4 level 0.9269
> volume #1.1 level 0.9485
> volume #1.5 change image level -0.1838,0 level 0.8665,0.8 level 7.054,1
> volume #1.5 level 0.9429
> hide #!1.4 models
> hide #!1.1 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> save /Users/ben/Desktop/image32.png supersample 3
> show #!1.4 models
> show #!1.5 models
> show #!1.1 models
> save /Users/ben/Desktop/image33.png supersample 3
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.5 models
> show #!1.4 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.5 models
> save /Users/ben/Desktop/image34.png supersample 3
> show #!1.4 models
> hide #!1.5 models
> hide #!1.3 models
> show #!1.1 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> save /Users/ben/Desktop/image35.png supersample 3
> show #!10 models
> hide #!1.1 models
> volume #1.4 color #a7d5ad62
> volume #1.4 color #a7d5ad63
> select add #10
31618 atoms, 31846 bonds, 34 pseudobonds, 1981 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.36107,0.084866,-0.92867,288.71,0.85103,0.37717,0.36535,-107.86,0.38128,-0.92225,0.063962,271.28
> view matrix models
> #10,0.36107,0.084866,-0.92867,288.19,0.85103,0.37717,0.36535,-107.48,0.38128,-0.92225,0.063962,270.61
> fitmap #10 inMap #1.4
Fit molecule 6sko (#10) to map cryosparc_P37_J369_006_volume_map.mrc (#1.4)
using 31618 atoms
average map value = 0.8968, steps = 108
shifted from previous position = 0.799
rotated from previous position = 9.12 degrees
atoms outside contour = 16798, contour level = 0.92695
Position of 6sko (#10) relative to cryosparc_P37_J369_006_volume_map.mrc
(#1.4) coordinates:
Matrix rotation and translation
0.28240223 0.21349811 -0.93523664 277.05579112
0.87834312 0.33443215 0.34156776 -98.46488137
0.38569726 -0.91791815 -0.09308021 303.55524629
Axis -0.64839398 -0.68002793 0.34226783
Axis point 8.65378388 0.00000000 283.51066315
Rotation angle (degrees) 103.77577981
Shift along axis -8.78524458
> select subtract #10
Nothing selected
> undo
> select subtract #10
Nothing selected
> select add #10
31618 atoms, 31846 bonds, 34 pseudobonds, 1981 residues, 3 models selected
> select subtract #10
Nothing selected
> ui mousemode right zoom
> save /Users/ben/Desktop/image36.png supersample 3
> show #!1.5 models
> hide #!1.4 models
> hide #!10 models
> show #!2 models
> hide #!1.5 models
> hide #!2 models
> show #!1.1 models
> show #!2 models
> hide #!1.1 models
> select ::name="ANP"
352 atoms, 368 bonds, 8 residues, 2 models selected
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 132 atom styles
> show #!1.1 models
> transparency #1.1.1 50
> volume #1.1 level 1.185
> volume #1.3 level 1.173
> volume #1.4 level 1.182
> volume #1.5 level 1.17
> volume #1.4 color #a7d5ad
> transparency #1.1.1#1.3.1#1.4.1#1.5.1 0
> transparency #1.1.1#1.3.1#1.4.1#1.5.1 50
> hide #!1 models
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!2 models
> show #!2 models
> hide sel & #!2 cartoons
> select add #2
97984 atoms, 98925 bonds, 123 pseudobonds, 6040 residues, 5 models selected
> select subtract #2
220 atoms, 230 bonds, 5 residues, 1 model selected
> select add #2
97984 atoms, 98925 bonds, 123 pseudobonds, 6040 residues, 5 models selected
> hide sel & #!2 cartoons
[Repeated 2 time(s)]
> select subtract #2
220 atoms, 230 bonds, 5 residues, 1 model selected
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> volume #1.3 level 0.9792
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> show #!1.3 models
> hide #!1.5 models
> show #!1.1 models
> show #!1.4 models
> show #!1.5 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!2 models
> show #!1.1 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> transparency #1.1.1#1.3.1#1.4.1#1.5.1 0
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!2 cartoons
> show #!1.1 models
> hide #!1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!2 models
> show #!1.4 models
> show #!1.5 models
> show #!2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.3 models
> volume #1.5 level 0.8453
> hide #!1.4 models
> show #!1.3 models
> hide #!1.5 models
> hide #!2 models
> volume #1.3 level 1.277
> volume #1.3 level 0.9921
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> volume #1.3 level 0.746
> volume #1.3 level 0.8237
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1.3 models
> show #!10 models
> hide #!2 models
> show #!2 models
> hide #!10 models
> show #!10 models
> show #!1.1 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #!10 models
> show #!10 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.4 models
> hide #!2 models
> hide #!1.1 models
> hide #!1.4 models
> hide #!10 models
> show #!2 models
> hide #!2 cartoons
> show #!1.1 models
> transparency #1.1.1 50
> volume #1.1 level 2.349
> transparency #1.1.1 0
> show #!1.4 models
> hide #!1.1 models
> transparency #1.4.1 50
> show #!1.5 models
> hide #!1.4 models
> transparency #1.5.1 50
> volume #1.5 level 1.593
> show #!2 cartoons
> volume #1.5 level 1.333
> save /Users/ben/Desktop/image37.png supersample 3
> hide #!1.5 models
> save /Users/ben/Desktop/image38.png supersample 3
> show #!1.5 models
> save /Users/ben/Desktop/image39.png supersample 3
> show #!1.1 models
> transparency #1.1.1#1.5.1 0
> transparency #1.1.1#1.5.1 50
> hide #!1.1 models
> hide #!1.5 models
> show #!1.1 models
> volume #1.1 level 1.547
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> transparency #1.1.1 0
> transparency #1.1.1 50
> save /Users/ben/Desktop/image40.png supersample 3
> show #!1.5 models
> hide #!1.1 models
> save /Users/ben/Desktop/image41.png supersample 3
> show #!1.4 models
> hide #!1.5 models
> hide #!2 models
> volume #1.4 level 0.9553
> show #!2 models
> hide #!1.4 models
> show #!5 models
> transparency #5.1 50
> open 6skl
6skl title:
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
Conformation 1 [more info...]
Chain information for 6skl #11
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST
3 | DNA replication licensing factor MCM3 | MCM3_YEAST
4 | DNA replication licensing factor MCM4 | MCM4_YEAST
5 | Minichromosome maintenance protein 5 | MCM5_YEAST
6 | DNA replication licensing factor MCM6 | MCM6_YEAST
7 | DNA replication licensing factor MCM7 | MCM7_YEAST
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST
B | DNA replication complex GINS protein PSF2 | PSF2_YEAST
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST
E | Cell division control protein 45 | CDC45_YEAST
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST
I | DNA fork, leading-strand template |
J | DNA fork, lagging-strand template |
X | Topoisomerase 1-associated factor 1 | TOF1_YEAST
Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST
Non-standard residues in 6skl #11
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
ZN — zinc ion
> hide #!2,11 atoms
> show #!2,11 cartoons
> hide #!5 models
> hide #!2 models
> select add #11
118440 atoms, 119635 bonds, 130 pseudobonds, 7326 residues, 5 models selected
> select subtract #11
220 atoms, 230 bonds, 5 residues, 1 model selected
> select add #10
31618 atoms, 31846 bonds, 34 pseudobonds, 1981 residues, 3 models selected
> select subtract #10
Nothing selected
> select add #11
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> select clear
> select #11/C:119
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #11/G:568
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/E:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
325 atoms, 328 bonds, 18 residues, 1 model selected
> select up
3488 atoms, 3524 bonds, 214 residues, 1 model selected
> select up
3514 atoms, 3548 bonds, 216 residues, 1 model selected
> select up
6556 atoms, 6620 bonds, 403 residues, 1 model selected
> select up
6745 atoms, 6809 bonds, 415 residues, 1 model selected
> select up
9129 atoms, 9213 bonds, 564 residues, 1 model selected
> select up
118220 atoms, 119405 bonds, 7321 residues, 1 model selected
> select down
9129 atoms, 9213 bonds, 564 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/D:92
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #11/F:599
22 atoms, 20 bonds, 2 residues, 1 model selected
> select up
549 atoms, 553 bonds, 32 residues, 1 model selected
> select up
3960 atoms, 4016 bonds, 246 residues, 1 model selected
> select up
4037 atoms, 4090 bonds, 251 residues, 1 model selected
> select up
9057 atoms, 9171 bonds, 557 residues, 1 model selected
> select up
10767 atoms, 10888 bonds, 667 residues, 1 model selected
> select up
109091 atoms, 110192 bonds, 6757 residues, 1 model selected
> select down
10767 atoms, 10888 bonds, 667 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/H:912
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
296 atoms, 297 bonds, 17 residues, 1 model selected
> select up
1735 atoms, 1742 bonds, 111 residues, 1 model selected
> select up
6769 atoms, 6854 bonds, 425 residues, 1 model selected
> select up
98324 atoms, 99304 bonds, 6090 residues, 1 model selected
> select down
6769 atoms, 6854 bonds, 425 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/G:628
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
104 atoms, 105 bonds, 6 residues, 1 model selected
> select up
3027 atoms, 3074 bonds, 190 residues, 1 model selected
> select up
3049 atoms, 3095 bonds, 191 residues, 1 model selected
> select up
4986 atoms, 5064 bonds, 311 residues, 1 model selected
> select up
6693 atoms, 6778 bonds, 422 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/C:73
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #11/A:54
34 atoms, 32 bonds, 2 residues, 1 model selected
> select up
548 atoms, 548 bonds, 32 residues, 1 model selected
> select up
3023 atoms, 3048 bonds, 184 residues, 1 model selected
> select up
3072 atoms, 3095 bonds, 188 residues, 1 model selected
> select #11/B:163
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #11/C:107
38 atoms, 36 bonds, 2 residues, 1 model selected
> select add #11/A:67
54 atoms, 51 bonds, 3 residues, 1 model selected
> select up
1006 atoms, 1015 bonds, 58 residues, 1 model selected
> select up
5663 atoms, 5714 bonds, 339 residues, 1 model selected
> select up
5889 atoms, 5937 bonds, 352 residues, 1 model selected
> select up
7940 atoms, 8017 bonds, 477 residues, 1 model selected
> select up
9377 atoms, 9464 bonds, 567 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> hide #!11 models
> show #!11 models
> select #11/6:160
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #11/4:228
39 atoms, 37 bonds, 2 residues, 1 model selected
> select add #11/7:354
58 atoms, 55 bonds, 3 residues, 1 model selected
> select add #11/5:62
72 atoms, 68 bonds, 4 residues, 1 model selected
> select add #11/2:250
82 atoms, 77 bonds, 5 residues, 1 model selected
> select up
703 atoms, 706 bonds, 42 residues, 1 model selected
> select up
18986 atoms, 19150 bonds, 1199 residues, 1 model selected
> select down
703 atoms, 706 bonds, 42 residues, 1 model selected
> select clear
> select #11/7:349
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
156 atoms, 157 bonds, 10 residues, 1 model selected
> select up
2563 atoms, 2586 bonds, 167 residues, 1 model selected
> select up
2650 atoms, 2672 bonds, 173 residues, 1 model selected
> select down
2563 atoms, 2586 bonds, 167 residues, 1 model selected
> select up
2650 atoms, 2672 bonds, 173 residues, 1 model selected
> select up
3698 atoms, 3730 bonds, 236 residues, 1 model selected
> select down
2650 atoms, 2672 bonds, 173 residues, 1 model selected
> select down
2563 atoms, 2586 bonds, 167 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/4:328
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
189 atoms, 188 bonds, 11 residues, 1 model selected
> select up
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/6:165
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
118 atoms, 117 bonds, 9 residues, 1 model selected
> select up
1807 atoms, 1824 bonds, 110 residues, 1 model selected
> select up
1953 atoms, 1971 bonds, 119 residues, 1 model selected
> select up
4406 atoms, 4450 bonds, 275 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/X:337
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #11/Y:83
36 atoms, 34 bonds, 2 residues, 1 model selected
> select up
759 atoms, 767 bonds, 45 residues, 1 model selected
> select up
2892 atoms, 2915 bonds, 171 residues, 1 model selected
> select up
3202 atoms, 3227 bonds, 191 residues, 1 model selected
> select up
5597 atoms, 5649 bonds, 336 residues, 1 model selected
> select up
5627 atoms, 5678 bonds, 338 residues, 1 model selected
> select up
8187 atoms, 8258 bonds, 494 residues, 1 model selected
> select up
12606 atoms, 12724 bonds, 759 residues, 1 model selected
> select up
63723 atoms, 64338 bonds, 3938 residues, 1 model selected
> select down
12606 atoms, 12724 bonds, 759 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/5:34
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
299 atoms, 301 bonds, 18 residues, 1 model selected
> select up
1464 atoms, 1475 bonds, 88 residues, 1 model selected
> select up
1542 atoms, 1554 bonds, 93 residues, 1 model selected
> select up
2534 atoms, 2551 bonds, 156 residues, 1 model selected
> select up
2742 atoms, 2760 bonds, 171 residues, 1 model selected
> select up
3816 atoms, 3845 bonds, 236 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/3:109
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
163 atoms, 165 bonds, 10 residues, 1 model selected
> select up
3797 atoms, 3843 bonds, 243 residues, 1 model selected
> select up
3915 atoms, 3960 bonds, 250 residues, 1 model selected
> select up
8254 atoms, 8332 bonds, 529 residues, 1 model selected
> select down
3915 atoms, 3960 bonds, 250 residues, 1 model selected
> select down
3797 atoms, 3843 bonds, 243 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/7:104
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
104 atoms, 103 bonds, 7 residues, 1 model selected
> select up
1527 atoms, 1536 bonds, 98 residues, 1 model selected
> select up
1573 atoms, 1582 bonds, 101 residues, 1 model selected
> select up
1894 atoms, 1910 bonds, 119 residues, 1 model selected
> select up
1906 atoms, 1921 bonds, 120 residues, 1 model selected
> select down
1894 atoms, 1910 bonds, 119 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/3:51
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
304 atoms, 305 bonds, 20 residues, 1 model selected
> select up
627 atoms, 633 bonds, 39 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/7:24
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
258 atoms, 261 bonds, 16 residues, 1 model selected
> select up
485 atoms, 490 bonds, 31 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/6:461
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
196 atoms, 198 bonds, 12 residues, 1 model selected
> select up
456 atoms, 458 bonds, 30 residues, 1 model selected
> select up
502 atoms, 503 bonds, 33 residues, 1 model selected
> select up
2256 atoms, 2270 bonds, 149 residues, 1 model selected
> select down
502 atoms, 503 bonds, 33 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/2:431
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
173 atoms, 173 bonds, 11 residues, 1 model selected
> select up
8359 atoms, 8431 bonds, 538 residues, 1 model selected
> select down
173 atoms, 173 bonds, 11 residues, 1 model selected
> select #11/2:458
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #11/2:173
36 atoms, 34 bonds, 2 residues, 1 model selected
> select up
326 atoms, 325 bonds, 20 residues, 1 model selected
> select up
8359 atoms, 8431 bonds, 538 residues, 1 model selected
> select down
326 atoms, 325 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/2:425
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
173 atoms, 173 bonds, 11 residues, 1 model selected
> select up
4207 atoms, 4250 bonds, 266 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/5:345
11 atoms, 10 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/5:334
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
182 atoms, 183 bonds, 11 residues, 1 model selected
> select up
394 atoms, 397 bonds, 25 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.1 models
> hide #!1.1 models
> show #!2 models
> select add #11
35058 atoms, 35402 bonds, 73 pseudobonds, 2166 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-10.789,0,1,0,6.0502,0,0,1,-107.23
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.64302,0.74421,0.18078,-138.12,-0.63074,0.6485,-0.42616,260.9,-0.43439,0.16,0.8864,-47.495
> view matrix models
> #11,0.62509,0.56695,-0.53649,44.987,-0.77015,0.33614,-0.54211,367.93,-0.12701,0.75205,0.64676,-164.07
> view matrix models
> #11,0.1271,0.051383,-0.99056,316.99,0.93978,0.31321,0.13683,-33.917,0.31728,-0.94829,-0.008479,234.29
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.1271,0.051383,-0.99056,357.85,0.93978,0.31321,0.13683,-57.344,0.31728,-0.94829,-0.008479,296.84
> align #11 toAtoms #2
Unequal number of atoms to pair, 35058 and 97764
> show #!1.1 models
> align #11 toAtoms #1.1
Unequal number of atoms to pair, 35058 and 0
> fitmap #11 inMap #1.1
Fit molecule 6skl (#11) to map cryosparc_P37_J366_005_volume_map.mrc (#1.1)
using 35058 atoms
average map value = 1.305, steps = 108
shifted from previous position = 9.37
rotated from previous position = 8.22 degrees
atoms outside contour = 22534, contour level = 1.5465
Position of 6skl (#11) relative to cryosparc_P37_J366_005_volume_map.mrc
(#1.1) coordinates:
Matrix rotation and translation
0.10985538 0.17936473 -0.97762986 327.21113039
0.90936527 0.37891027 0.17170282 -76.86985105
0.40123141 -0.90788510 -0.12148272 304.85372341
Axis -0.56901893 -0.72675708 0.38476175
Axis point 40.06628381 0.00000000 290.63496259
Rotation angle (degrees) 108.44284659
Shift along axis -13.02756856
> hide #!2 models
> show #!2 models
> hide #!1.1 models
> select subtract #11
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1.4 models
> transparency #1.4.1 0
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> transparency #1.4.1 50
> fitmap #11 inMap #1.4
Fit molecule 6skl (#11) to map cryosparc_P37_J369_006_volume_map.mrc (#1.4)
using 35058 atoms
average map value = 0.8499, steps = 56
shifted from previous position = 4.92
rotated from previous position = 3.8 degrees
atoms outside contour = 20689, contour level = 0.95527
Position of 6skl (#11) relative to cryosparc_P37_J369_006_volume_map.mrc
(#1.4) coordinates:
Matrix rotation and translation
0.06544990 0.19887909 -0.97783611 330.29180323
0.90433084 0.40238840 0.14237048 -77.21612952
0.42178440 -0.89360547 -0.15351621 303.98250823
Axis -0.55140639 -0.74495909 0.37548228
Axis point 49.15018156 -0.00000000 284.90421249
Rotation angle (degrees) 110.04993331
Shift along axis -10.46211042
> hide #!1.4 models
> show #!1.4 models
> transparency #1.4.1 0
> show #!2 models
> hide #!2 models
> ui mousemode right zoom
> show #!1.5 models
> hide #!1.4 models
> transparency #1.5.1 0
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!1.5 models
> show #!1.3 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!1.3 models
> fitmap #11 inMap #4
Fit molecule 6skl (#11) to map J368_denmod_map.ccp4 (#4) using 35058 atoms
average map value = 0.2095, steps = 64
shifted from previous position = 1.68
rotated from previous position = 0.694 degrees
atoms outside contour = 27605, contour level = 0.55513
Position of 6skl (#11) relative to J368_denmod_map.ccp4 (#4) coordinates:
Matrix rotation and translation
0.07407024 0.19637091 -0.97772803 328.80850021
0.90040494 0.40829649 0.15021638 -78.28731996
0.42870104 -0.89147770 -0.14657072 302.04739361
Axis -0.55218726 -0.74552810 0.37319845
Axis point 48.10113405 0.00000000 284.82987996
Rotation angle (degrees) 109.39640721
Shift along axis -10.47484648
> transparency #4.1 50
> volume #4 level 0.5998
> select add #11
35058 atoms, 35402 bonds, 73 pseudobonds, 2166 residues, 4 models selected
> select ::name="ANP"
484 atoms, 506 bonds, 11 residues, 3 models selected
> show sel & #!11 atoms
> style sel & #!11 stick
Changed 132 atom styles
> style sel & #!11 ball
Changed 132 atom styles
> style sel & #!11 stick
Changed 132 atom styles
> select add #11
35410 atoms, 35770 bonds, 73 pseudobonds, 2174 residues, 6 models selected
> hide sel & #!11 cartoons
> save "/Users/ben/Google Drive/My Drive/Grad School/Thesis Work/EM Data
> Processing/20221108-CMG-reaction/6SKL-C-tier-model.pdb" models #11 relModel
> #4
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/6SKL-
> C-tier-model.pdb"
Chain information for 6SKL-C-tier-model.pdb #12
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
I | No description available
J | No description available
> style sel & #!11 stick
Changed 35058 atom styles
> hide sel & #!11 atoms
> show sel & #!11 cartoons
> select subtract #11
352 atoms, 368 bonds, 8 residues, 2 models selected
> select add #12
35410 atoms, 35770 bonds, 23 pseudobonds, 2174 residues, 5 models selected
> select add #10
66808 atoms, 67386 bonds, 57 pseudobonds, 4150 residues, 7 models selected
> select subtract #10
35190 atoms, 35540 bonds, 23 pseudobonds, 2169 residues, 4 models selected
> style sel & #!12 stick
Changed 35058 atom styles
> hide sel & #!12 atoms
> show sel & #!12 cartoons
> select ::name="ANP"
616 atoms, 644 bonds, 14 residues, 4 models selected
> show sel & #!11-12 atoms
> select add #12
35542 atoms, 35908 bonds, 23 pseudobonds, 2177 residues, 6 models selected
> select add #11
70468 atoms, 71172 bonds, 96 pseudobonds, 4340 residues, 9 models selected
> select subtract #11
35410 atoms, 35770 bonds, 23 pseudobonds, 2174 residues, 5 models selected
> hide sel & #!12 cartoons
> hide #!11 models
> show #!11 models
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> close #11
> show #!10 models
> hide #!10 models
> select add #10
66808 atoms, 67386 bonds, 57 pseudobonds, 4150 residues, 7 models selected
> select subtract #10
35190 atoms, 35540 bonds, 23 pseudobonds, 2169 residues, 4 models selected
> hide #!4 models
> show #!4 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> volume #4 level 0.4658
> show sel & #!12 cartoons
> select subtract #12
132 atoms, 138 bonds, 3 residues, 1 model selected
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #4 level 0.8678
> volume #4 level 0.5551
> hide #!4 models
> show #!1.3 models
> volume #1.3 level 0.8756
> select add #2
97764 atoms, 98695 bonds, 123 pseudobonds, 6035 residues, 4 models selected
> select subtract #2
Nothing selected
> show #!2 models
> hide #!2 models
> volume #1.3 level 0.7719
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> transparency #1.3.1 50
> volume #1.3 level 0.8108
> hide #!1.3 models
> hide #!12 models
> show #!2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!2 models
> transparency #1.3.1 0
> volume #!1.3 style image
> show #!2 models
> hide #!2 models
> volume #!1.3 style image
> volume #!1.3 style surface
> volume #!1.3 style mesh
> volume #!1.3 style surface
> volume #!1.3 showOutlineBox true
> volume #!1.3 showOutlineBox false
> volume #!1.3 step 2
> volume #!1.3 step 1
> volume #!1.3 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 189.2 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 189.2 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 187.5 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #9 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #7 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 187.5 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.3 tiltedSlabAxis 0.0478,0.06322,-0.9969 tiltedSlabOffset -187.6
> volume #1.3 tiltedSlabAxis -0.7657,0.6296,-0.1316 tiltedSlabOffset -118.3
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> volume #!1.3 region all imageMode "full region"
> volume unzone #!1.3
> mousemode rightMode "crop volume"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 189.2 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 189.2 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 187.5 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #9 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #7 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 187.5 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #!1.3 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #!1.3 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #!1.3 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #!1.3 style surface
> transparency #1.3.1 50
> volume #!1.3 style surface
> volume #!1.3 region all imageMode "full region"
> volume unzone #!1.3
> mousemode rightMode "crop volume"
> volume #!1.3 showOutlineBox false
> volume #!1.3 style surface
> transparency #1.3.1 0
> volume #8 orthoplanes xyz positionPlanes 112,112,112 style image region all
> mousemode rightMode "move planes"
> volume #1.1 orthoplanes xyz positionPlanes 112,112,112 style image region
> all
> mousemode rightMode "move planes"
> volume #1.3 orthoplanes xyz positionPlanes 112,112,112 style image region
> all
> mousemode rightMode "move planes"
> volume #1.4 orthoplanes xyz positionPlanes 112,112,112 style image region
> all
> mousemode rightMode "move planes"
> volume #1.5 orthoplanes xyz positionPlanes 112,112,112 style image region
> all
> mousemode rightMode "move planes"
> volume #3 orthoplanes xyz positionPlanes 46,50,63 style image region all
> mousemode rightMode "move planes"
> volume #4 orthoplanes xyz positionPlanes 53,55,63 style image region all
> mousemode rightMode "move planes"
> volume #5 orthoplanes xyz positionPlanes 52,56,64 style image region all
> mousemode rightMode "move planes"
> volume #9 orthoplanes xyz positionPlanes 112,112,112 style image region all
> mousemode rightMode "move planes"
> volume #7 orthoplanes xyz positionPlanes 53,53,64 style image region all
> mousemode rightMode "move planes"
> volume #!1.3 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 189.2 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 189.2 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 187.5 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #9 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 185 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #7 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 187.5 tiltedSlabSpacing 1.652 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.3 tiltedSlabAxis -0.4061,-0.913,-0.03781 tiltedSlabOffset -257.7
> volume #!1.3 region all imageMode "full region"
> volume unzone #!1.3
> mousemode rightMode "crop volume"
> volume #!1.3 style surface
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> volume #!1.3 showOutlineBox false
> transparency #1.3.1 50
> volume #1.3 region 21,0,0,223,223,223
> ui mousemode right zoom
> volume #!1.3 appearance chest
> show #!2 models
> show #!3 models
> hide #!1.3 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!7 models
> hide #!5 models
> hide #!7 models
> show #!2-10,12#!1.1,3-5 target m
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume showOutlineBox false
> hide #!1-10,12#!1.1,3-5 target m
> show #!1.1 models
> volume #!1.1 region all imageMode "full region"
> volume unzone #!1.1
> mousemode rightMode "crop volume"
> volume #!1.1 style surface
> transparency #1.1.1 0
> show #!1.3 models
> hide #!1.1 models
> transparency #1.3.1 0
> show #!1.4 models
> hide #!1.3 models
> volume #!1.4 style surface
> show #!1.5 models
> hide #!1.4 models
> volume #!1.5 style surface
> show #!2 models
> hide #!1.5 models
> hide #!2 models
> show #!3 models
> volume #!3 style surface
> volume #3 change image level -0.5028,0 level 4.567,0.8 level 13.22,1
> volume #3 level 0.6972
> hide #!3 models
> show #!4 models
> volume #!4 style surface
> transparency #4.1 0
> volume #4 change image level -0.419,0 level 4.469,0.8 level 15.97,1
> volume #4 level 0.7338
> show #!5 models
> hide #!4 models
> volume #!5 style surface
> transparency #5.1 0
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> volume #!7 style surface
> show #!8 models
> hide #!7 models
> volume #!8 style surface
> show #!9 models
> hide #!8 models
> volume #!9 style surface
> show #!10 models
> hide #!9 models
> show #!12 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!12 models
> show #!10 models
> show #!12 models
> hide #!12 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #!6 models
> show #!9 models
> hide #!6 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> transparency #9.1#1.3.1 50
> volume #!9#!1.3 style surface
> transparency #9.1#1.3.1 0
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> volume #1.3 region 55,0,0,223,223,223
> ui mousemode right zoom
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!9 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J375_mask.mrc"
Opened cryosparc_P37_J375_mask.mrc as #11, grid size 224,224,224, pixel 0.826,
shown at level 0.905, step 1, values float32
> hide #!1.3 models
> hide #!11 models
> show #!11 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!9 models
> hide #!1.3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!11 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> show #!11 models
> hide #!9 models
> hide #!1.3 models
> show #!9 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J345_012_volume_map.mrc"
Opened cryosparc_P37_J345_012_volume_map.mrc as #13, grid size 448,448,448,
pixel 0.826, shown at level 0.13, step 2, values float32
Window position QRect(1851,487 709x557) outside any known screen, using
primary screen
> ui tool show "Model Panel"
[Repeated 1 time(s)]
> volume #9 change image level 0,0 level 0.2587,0.8 level 2.587,1
> ui favorite true "Model Panel"
> hide #!11 models
> volume #13 step 1
> show #!13 target m
[Repeated 1 time(s)]
> view #13 clip false
> ui tool show "Segment Map"
> ui favorite true "Segment Map"
Window position QRect(1944,1088 331x152) outside any known screen, using
primary screen
Segmenting cryosparc_P37_J345_012_volume_map.mrc, density threshold 0.130206
Only showing 200 of 333 regions.
Showing 200 of 333 region surfaces
5760 watershed regions, grouped to 333 regions
Showing cryosparc_P37_J345_012_volume_map.seg - 333 regions, 200 surfaces
Window position QRect(1903,567 258x470) outside any known screen, using
primary screen
Deleted 71 regions
> hide #!13 models
Deleted 38 regions
Deleted 16 regions
Deleted 3 regions
Deleted 2 regions
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
Drag select of 8378, 8472, 8383, 8453, 8409, 8449, 8359, 8381, 8425, 8414,
8405, 8439, 8393, 8441, 8379, 8371, 8389, 8346, 8076, 8417, 8450, 7961, 8310,
8388, 8355, 8407, 8426, 8464, 8418, 8478, 8488, 8463, 8386, 8462, 8474, 8036,
8164, 8313, 8437, 7993, 8433, 8114, 8408, 7960, 8139, 8146, 8074, 8415, 8429,
8447, 8375, 8468, 8484, 8442, 8078, 8274, 5809, 8207, 8461, 8322, 8073, 8133,
7971, 8193, 8213, 8220, 8451, 8149, 8351, 8432
Grouped 70 regions
Window position QRect(1853,1062 279x188) outside any known screen, using
primary screen
> hide #!6 models
> show #!6 models
> volume mask #13 surfaces #6 modelID #14
Expected a keyword
> volume mask #13 surfaces #6
Opened cryosparc_P37_J345_012_volume_map.mrc masked as #14, grid size
106,161,158, pixel 0.826, shown at step 1, values float32
> hide #!6 models
> vop resample #14 ongrid #13
Opened cryosparc_P37_J345_012_volume_map.mrc masked resampled as #15, grid
size 448,448,448, pixel 0.826, shown at step 1, values float32
> close #14
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J345-C-tier-mask.mrc" models #15
> show #!9 models
> hide #!15 models
Window position QRect(1851,872 709x246) outside any known screen, using
primary screen
> ui autostart true "Side View"
> ui autostart true "Volume Viewer"
Window position QRect(1851,113 709x1189) outside any known screen, using
primary screen
[Repeated 3 time(s)]
Window position QRect(1851,113 709x101) outside any known screen, using
primary screen
Window position QRect(1851,113 709x123) outside any known screen, using
primary screen
Window position QRect(1851,113 709x1189) outside any known screen, using
primary screen
Window position QRect(1851,113 709x101) outside any known screen, using
primary screen
> close #9
> show #!15 models
> close #15
> show #!12 models
> hide #!12 models
> show #!13 models
> close #13
> show #!8 models
> close #8
> show #!10 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!10 models
> close #11
> show #!6 models
> close #6
> show #!1.1 models
> show #!1.3 models
> hide #!1.1 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J384_005_volume_map.mrc"
Opened cryosparc_P37_J384_005_volume_map.mrc as #6, grid size 224,224,224,
pixel 1.65, shown at level 0.78, step 1, values float32
> hide #!1.3 models
> volume #6 level 1.045
> volume #6 step 2
> volume #6 step 1
> volume #6 level 1.442
> volume #6 level 0.2719
> volume #6 level 1.067
> surface dust #6 size 16.5
> close #6
> show #!1.1 models
> show #!1.3 models
> hide #!1.1 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J397_006_volume_map.mrc"
Opened cryosparc_P37_J397_006_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.826, shown at level 0.126, step 2, values float32
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J398_006_volume_map.mrc"
Opened cryosparc_P37_J398_006_volume_map.mrc as #8, grid size 448,448,448,
pixel 0.826, shown at level 0.153, step 2, values float32
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J399_006_volume_map.mrc"
Opened cryosparc_P37_J399_006_volume_map.mrc as #9, grid size 448,448,448,
pixel 0.826, shown at level 0.159, step 2, values float32
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J400_005_volume_map.mrc"
Opened cryosparc_P37_J400_005_volume_map.mrc as #11, grid size 448,448,448,
pixel 0.826, shown at level 0.153, step 2, values float32
> volume #6 step 1
> hide #!1.3 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!11 models
> close #6
> close #8
> close #9
> close #11
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J397_006_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J398_006_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J399_006_volume_map.mrc"
> "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J400_005_volume_map.mrc"
Opened cryosparc_P37_J397_006_volume_map.mrc as #6.1, grid size 448,448,448,
pixel 0.826, shown at level 0.126, step 2, values float32
Opened cryosparc_P37_J398_006_volume_map.mrc as #6.2, grid size 448,448,448,
pixel 0.826, shown at level 0.153, step 2, values float32
Opened cryosparc_P37_J399_006_volume_map.mrc as #6.3, grid size 448,448,448,
pixel 0.826, shown at level 0.159, step 2, values float32
Opened cryosparc_P37_J400_005_volume_map.mrc as #6.4, grid size 448,448,448,
pixel 0.826, shown at level 0.153, step 2, values float32
> hide #!6.1 models
> hide #!6.2 models
> hide #!6.3 models
> hide #!6.4 models
> show #!6.1 models
> volume #6.1 step 1
> volume #6.1 level 0.1318
> volume #6.1 level 0.1441
> hide #!6.1 models
> show #!6.2 models
> volume #6.2 step 1
> volume #6.2 level 0.1681
> volume #6.2 level 0.2184
> volume #6.3 step 1
> show #!6.2 models
> hide #!6.2 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> show #!6.2 models
> hide #!6.3 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> volume #6.2 level 0.1707
> hide #!6.3 models
> show #!6.4 models
> volume #6.4 step 1
> color #6.4 #9fe3ea models transparency 0
> color #6.4 #66bce1 models transparency 0
> color #6.3 #a7d5ad models transparency 0
> color #6.2 #ffb2b2 models transparency 0
> color #6.2 #ffa0b4 models transparency 0
> color #6.1 #b2b2ff models transparency 0
> show #!6.1 models
> hide #!6.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!1.1 models
> hide #!6.1 models
> show #!1.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> volume #1.1 change image level -0.1507,0 level 0.7067,0.8 level 7.078,1
> volume #1.1 level 1.342
> volume #6.1 level 0.2951
> hide #!1.1 models
> volume #6.1 level 0.2735
> volume #6.1 level 0.2612
> hide #!6.1 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.4 models
> volume #6.4 level 0.1756
> show #!6.1 models
> hide #!6.4 models
> volume #6.1 level 0.1903
> show #!6.2 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.2 models
> show #!6.2 models
> show #!6.3 models
> hide #!6.2 models
> hide #!6.1 models
> show #!6.4 models
> hide #!6.3 models
> show #!6.2 models
> hide #!6.4 models
> volume #6.2 level 0.1411
> volume #6.2 level 0.1641
> ui mousemode right "mark point"
> marker #8 position 169.8,174.8,201.1 color yellow radius 1
> marker #8 position 181.1,185.9,198 color yellow radius 1
> marker #8 position 167.3,178.5,197.2 color yellow radius 1
> marker #8 position 184.9,180.5,199.8 color yellow radius 1
> marker #8 position 183.7,180.6,199.3 color yellow radius 1
> marker #8 position 183.1,180,199.3 color yellow radius 1
> ui tool show Distances
Exactly two atoms must be selected!
> select add #8/M:3@M
2 atoms, 2 residues, 1 model selected
> distance #8/M:6@M #8/M:3@M
Distance between markers #8/M mark 6 M and mark 3 M: 16.004Å
> select #8/M:1@M
1 atom, 1 residue, 1 model selected
> select add #8/M:2@M
2 atoms, 2 residues, 1 model selected
> distance #8/M:1@M #8/M:2@M
Distance between markers #8/M mark 1 M and mark 2 M: 16.111Å
> marker #8 position 176.2,191.7,199.7 color yellow radius 1
> marker #8 position 207.9,234.1,197.6 color yellow radius 1
> ui mousemode right "mark point"
> marker #8 position 238.7,198.5,136 color yellow radius 1
> marker #8 position 233.5,209.6,145 color yellow radius 1
> marker #8 position 235.4,207.3,145.1 color yellow radius 1
> marker #8 position 234.9,210.9,148.8 color yellow radius 1
> ui tool show Distances
> marker #8 position 240.5,197.8,137.9 color yellow radius 1
> select add #8/M:12@M
2 atoms, 2 residues, 1 model selected
> distance #8/M:13@M #8/M:12@M
Distance between markers #8/M mark 13 M and mark 12 M: 17.932Å
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/20221108-reaction-session.cxs" includeMaps true
——— End of log from Thu Dec 1 10:44:18 2022 ———
opened ChimeraX session
> ui mousemode right "delete markers"
> marker delete #8:9
> ui mousemode right "delete markers"
> ui mousemode right "move markers"
[Repeated 1 time(s)]
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "mark point"
> ui mousemode right "link markers"
> marker link #8:13,12 color #659cef radius 0.5
> ui mousemode right "move markers"
> marker change #8:13 position 239.3,195.8,137.8
> marker change #8:12 position 233.8,210.7,149.9
> ui mousemode right "mark plane"
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right zoom
> select add #8
12 atoms, 1 bond, 3 pseudobonds, 12 residues, 2 models selected
> select subtract #8
Nothing selected
> hide #!9 models
> hide #8 models
> hide #!6 models
> show #!1.1 models
> view #1.1 clip false
> show #!1.3 models
> hide #!1.1 models
> volume #1.3 level 1.07
> volume #1.3 level 1.784
> volume #1.3 level 0.9406
> show #!1.1 models
> hide #!1.1 models
> volume #1.3 level 0.973
> show #!1.5 models
> hide #!1.3 models
> volume #1.5 level 1.415
> show #!2 models
> volume #1.5 level 0.8241
> volume #1.5 level 1.659
> show #!1.4 models
> hide #!2 models
> hide #!1.4 models
> hide #!1.5 models
> show #!2 models
> show #!10 models
> hide #!2 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.1 models
> show #!2 models
> hide #!10 models
> transparency #1.1.1 50
> select ::name="ANP"
484 atoms, 506 bonds, 11 residues, 3 models selected
> style sel & #!2 stick
Changed 132 atom styles
> select add #2
98116 atoms, 99063 bonds, 123 pseudobonds, 6043 residues, 6 models selected
> hide sel & #!2 cartoons
> select ::name="ANP"
484 atoms, 506 bonds, 11 residues, 3 models selected
> style sel & #!2 stick
Changed 132 atom styles
> style sel & #!2 ball
Changed 132 atom styles
> show sel & #!2 atoms
> volume #1.1 level 2.623
> show #!1.5 models
> hide #!1.1 models
> transparency #1.5.1 50
> hide #!1.5 models
> show #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.4 models
> transparency #6.4.1 50
> volume #6.4 level 0.2999
> volume #6.4 level 0.2277
> volume #6.4 level 0.1836
> select add #2
98116 atoms, 99063 bonds, 123 pseudobonds, 6043 residues, 6 models selected
> select subtract #2
352 atoms, 368 bonds, 8 residues, 2 models selected
> select add #2
98116 atoms, 99063 bonds, 123 pseudobonds, 6043 residues, 6 models selected
> show sel & #!2 cartoons
> hide #!6.4 models
> show #!6.3 models
> show #!6.1 models
> hide #!6.3 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.4 models
> hide #!6.4 models
> show #!6.4 models
> show #!6.3 models
> hide #!6.4 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.2 models
> hide #!6.1 models
> select subtract #2
352 atoms, 368 bonds, 8 residues, 2 models selected
> hide #!2 models
> show #!6.3 models
> hide #!6.3 models
> hide #!6.2 models
> hide #!6 models
> open "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/cryosparc_P37_J345_012_volume_map.mrc"
Opened cryosparc_P37_J345_012_volume_map.mrc as #11, grid size 448,448,448,
pixel 0.826, shown at level 0.13, step 2, values float32
> volume #11 step 1
> ui tool show "Segment Map"
Segmenting cryosparc_P37_J345_012_volume_map.mrc, density threshold 0.130206
Only showing 200 of 333 regions.
Showing 200 of 333 region surfaces
5760 watershed regions, grouped to 333 regions
Showing cryosparc_P37_J345_012_volume_map.seg - 333 regions, 200 surfaces
> hide #!11 models
> select add #10
31750 atoms, 31984 bonds, 34 pseudobonds, 1984 residues, 4 models selected
> select subtract #10
132 atoms, 138 bonds, 3 residues, 1 model selected
> select add #12
35058 atoms, 35402 bonds, 23 pseudobonds, 2166 residues, 3 models selected
> select subtract #12
Nothing selected
Drag select of 8424, 8361, 8434, 18510 of 19996 triangles, 8364, 14006 of
18064 triangles, 8452, 15390 of 15596 triangles, 8413, 15408 of 19240
triangles, 7993, 12491 of 17392 triangles, 8478, 8482, 981 of 19340 triangles,
8377, 14707 of 15700 triangles, 8463, 7760 of 12276 triangles, 8426, 13528 of
16608 triangles, 8302, 8328, 8462, 7973, 7062, 8484, 8354, 8445, 14065 of
14824 triangles, 8064, 10764 of 12240 triangles, 8401, 8369, 8028, 8062, 8414,
4960 of 14680 triangles, 7564, 9399 of 9848 triangles, 7365, 8100, 8433, 364
of 12752 triangles, 8453, 8420, 9966 of 11592 triangles, 7052, 8403, 1258 of
10612 triangles, 8490, 653 of 9516 triangles, 8387, 8473, 8282, 126 of 9556
triangles, 8339, 8232, 8427, 4880 of 8780 triangles, 8355, 8335, 7056, 8368,
8237, 4396 of 8192 triangles
> select #13.48
1 model selected
Drag select of 8424, 8361, 8434, 19970 of 19996 triangles, 8364, 17270 of
18064 triangles, 8452, 8413, 17986 of 19240 triangles, 8418, 191 of 13608
triangles, 7993, 15279 of 17392 triangles, 8478, 8482, 2887 of 19340
triangles, 8377, 8463, 9895 of 12276 triangles, 8426, 15004 of 16608
triangles, 8302, 8469, 172 of 16860 triangles, 8328, 8462, 7973, 7062, 8484,
8354, 8445, 8064, 12124 of 12240 triangles, 8401, 8369, 8028, 8062, 8414, 8289
of 14680 triangles, 7564, 7365, 8333, 289 of 12960 triangles, 8100, 8433, 2084
of 12752 triangles, 8453, 8420, 11447 of 11592 triangles, 7052, 8403, 3318 of
10612 triangles, 8490, 2475 of 9516 triangles, 8387, 8473, 8282, 1768 of 9556
triangles, 8339, 8232, 8427, 6699 of 8780 triangles, 8355, 8335, 7056, 8368,
8237, 6119 of 8192 triangles
> select subtract #13.129
47 models selected
> select add #13.153
48 models selected
> select add #13.128
49 models selected
> select add #13.174
50 models selected
> select add #13.108
51 models selected
> select add #13.146
52 models selected
Deleted 52 regions
> select #13.48
1 model selected
> select add #13.91
2 models selected
> select add #13.112
3 models selected
> select add #13.136
4 models selected
> select add #13.96
5 models selected
> select add #13.19
6 models selected
> select add #13.2
7 models selected
> select add #13.120
8 models selected
> select add #13.29
9 models selected
> select add #13.51
10 models selected
> select add #13.26
11 models selected
> select add #13.32
12 models selected
> select add #13.179
13 models selected
> select subtract #13.179
12 models selected
> select subtract #13.32
11 models selected
> select subtract #13.51
10 models selected
> select subtract #13.26
9 models selected
> select add #13.51
10 models selected
> select add #13.81
11 models selected
> select add #13.54
12 models selected
> select add #13.125
13 models selected
> select add #13.155
14 models selected
> select add #13.158
15 models selected
> select add #13.21
16 models selected
> select add #13.172
17 models selected
> select add #13.1
18 models selected
Drag select of 8375, 644 of 33340 triangles, 8367, 1031 of 29708 triangles,
8358, 1273 of 23416 triangles, 8382, 121 of 22748 triangles, 8442, 19053 of
23068 triangles, 8342, 15973 of 19704 triangles, 8345, 233 of 20472 triangles,
8392, 8441, 9731 of 19460 triangles, 8438, 2230 of 18316 triangles, 8461, 1522
of 21844 triangles, 7999, 12416 of 14544 triangles, 8352, 27 of 13136
triangles, 8457, 4632 of 12784 triangles, 8353, 13531 of 13744 triangles,
8008, 13445 of 14512 triangles, 8362, 8307, 8489 of 13204 triangles, 8467,
12024 of 12288 triangles, 8391, 3716 of 10168 triangles, 8428, 1129 of 9236
triangles, 8349, 8802 of 9240 triangles, 8336, 7646 of 8584 triangles, 8252,
2536 of 9864 triangles
Deleted 38 regions
> select #13.10
1 model selected
Deleted 1 regions
> select add #13.158
1 model selected
> select add #13.21
2 models selected
Deleted 2 regions
> select add #13.36
1 model selected
> select add #13.149
2 models selected
> select add #13.5
3 models selected
> select add #13.137
4 models selected
> select add #13.110
5 models selected
> select add #13.61
6 models selected
> select add #13.197
7 models selected
> select add #13.68
8 models selected
Drag select of 8488, 13 of 13152 triangles, 8022, 7 of 10400 triangles
> select add #13.199
11 models selected
Deleted 11 regions
> select add #13.24
1 model selected
> select add #13.31
2 models selected
> select add #13.66
3 models selected
> select add #13.130
4 models selected
> select add #13.160
5 models selected
> select add #13.45
6 models selected
> select add #13.72
7 models selected
> select add #13.46
8 models selected
> select add #13.18
9 models selected
> select add #13.23
10 models selected
> select add #13.191
11 models selected
> select add #13.159
12 models selected
> select add #13.14
13 models selected
> select add #13.41
14 models selected
> select add #13.106
15 models selected
> select add #13.139
16 models selected
> select add #13.148
17 models selected
> select add #13.67
18 models selected
> select add #13.184
19 models selected
> select add #13.90
20 models selected
> select add #13.52
21 models selected
> select add #13.129
22 models selected
> select add #13.35
23 models selected
> select add #13.16
24 models selected
> select add #13.74
25 models selected
> select add #13.95
26 models selected
> select add #13.65
27 models selected
> select add #13.47
28 models selected
Deleted 28 regions
> select add #13.173
1 model selected
> select add #13.131
2 models selected
> select add #13.101
3 models selected
> select add #13.11
4 models selected
> select add #13.185
5 models selected
> select add #13.167
6 models selected
> select add #13.26
7 models selected
> select add #13.32
8 models selected
> select add #13.179
9 models selected
> select add #13.124
10 models selected
> select add #13.190
11 models selected
> select add #13.59
12 models selected
> select add #13.79
13 models selected
> select add #13.63
14 models selected
> select add #13.189
15 models selected
> select add #13.143
16 models selected
> select add #13.33
17 models selected
> select subtract #13.33
16 models selected
> select add #13.33
17 models selected
> select add #13.144
18 models selected
> select add #13.156
19 models selected
> select clear
> select add #13.165
1 model selected
> select add #13.6
2 models selected
> select add #13.55
3 models selected
> select add #13.142
4 models selected
> select add #13.140
5 models selected
> select add #13.176
6 models selected
> select add #13.126
7 models selected
> select add #13.152
8 models selected
> select add #13.40
9 models selected
> select add #13.175
10 models selected
> select add #13.85
11 models selected
> select add #13.187
12 models selected
> select add #13.115
13 models selected
Deleted 13 regions
> select add #13.83
1 model selected
> select add #13.30
2 models selected
> select add #13.79
3 models selected
Deleted 3 regions
> select add #13.124
1 model selected
> select add #13.63
2 models selected
> select add #13.173
3 models selected
> select add #13.131
4 models selected
> select add #13.101
5 models selected
> select add #13.26
6 models selected
> select add #13.32
7 models selected
> select add #13.179
8 models selected
> select clear
> select #13.32
1 model selected
> select #13.173
1 model selected
> select add #13.131
2 models selected
> select add #13.26
3 models selected
> select subtract #13.26
2 models selected
Deleted 2 regions
> select add #13.162
1 model selected
> select add #13.28
2 models selected
> select subtract #13.28
1 model selected
> select add #13.180
2 models selected
Deleted 2 regions
> select add #13.93
1 model selected
> select add #13.57
2 models selected
> select add #13.75
3 models selected
> select add #13.102
4 models selected
Deleted 4 regions
> select #13.116
1 model selected
Deleted 1 regions
> select #13.43
1 model selected
Deleted 1 regions
> select #13.101
1 model selected
Deleted 1 regions
Drag select of 8444, 8412, 8407, 8376, 8430, 8389, 8018, 8385, 8431, 8351,
8455, 8450, 8343, 8053, 8454, 8464, 8485, 8447, 8460, 8425, 8451, 8397, 8077,
8429, 8378, 8381, 8370, 8388, 8360, 8449, 8486, 8432, 8094, 7957, 8439, 8422,
7964, 8060, 8386, 8474, 8402
Grouped 41 regions
Segmenting cryosparc_P37_J345_012_volume_map.mrc, density threshold 0.130206
Only showing 200 of 333 regions.
Showing 200 of 333 region surfaces
5760 watershed regions, grouped to 333 regions
Showing cryosparc_P37_J345_012_volume_map.seg - 333 regions, 200 surfaces
> undo
[Repeated 1 time(s)]
> redo
> undo
> redo
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]Drag select of 8343, 8385, 8429, 8427, 4406 of 18064
triangles, 8344, 8461, 8349, 7910 of 13608 triangles, 8313, 985 of 17392
triangles, 8445, 15477 of 15996 triangles, 8487, 5295 of 19340 triangles,
8438, 9806 of 15700 triangles, 8413, 8458, 7957, 8453, 5177 of 16860
triangles, 8164, 8451, 8225, 7736, 8400, 8416, 8490, 10955 of 14824 triangles,
8185, 4338 of 12240 triangles, 8376, 8183, 54 of 10712 triangles, 8367, 8069,
8109, 9975 of 11224 triangles, 8417, 14637 of 14680 triangles, 7092, 2137 of
9848 triangles, 7560, 8155, 5134 of 11284 triangles, 7958, 8443, 8475, 8229,
5194 of 10580 triangles, 7867, 8412, 7628 of 10612 triangles, 8414, 8611 of
9516 triangles, 8481, 10333 of 10400 triangles, 8494, 8295, 8293, 6343, 4619
of 7564 triangles, 8215, 8446, 8456, 8222, 7752, 8361, 8217
Deleted 51 regions
Drag select of 8347, 38047 of 43564 triangles, 8351, 418 of 49612 triangles,
8370, 9003 of 33340 triangles, 8388, 11410 of 30200 triangles, 8357, 4002 of
29708 triangles, 8399, 6 of 19024 triangles, 8394, 18059 of 23416 triangles,
8466, 2636 of 23068 triangles, 7986, 766 of 18768 triangles, 8449, 146 of
19704 triangles, 8440, 13900 of 16036 triangles, 8390, 8459 of 19460
triangles, 8396, 3287 of 18280 triangles, 8165, 8161, 4848 of 14116 triangles,
8397, 8354, 5479 of 13744 triangles, 8063, 8976 of 14512 triangles, 8447, 9269
of 13100 triangles, 8285, 12936 of 13204 triangles, 8286, 8395, 9501 of 12288
triangles, 7663, 8463, 8477, 8369, 8339, 8097, 7299 of 8584 triangles, 8272,
454 of 9864 triangles
> select subtract #13.2
28 models selected
> select subtract #13.29
27 models selected
Deleted 27 regions
> select #13.146
1 model selected
Deleted 1 regions
> select #13.112
1 model selected
> select #13.91
1 model selected
> select add #13.112
2 models selected
> select add #13.137
3 models selected
> select add #13.173
4 models selected
> select add #13.5
5 models selected
> select add #13.149
6 models selected
> select add #13.36
7 models selected
> select add #13.53
8 models selected
> select add #13.22
9 models selected
> select add #13.78
10 models selected
> select add #13.56
11 models selected
> select add #13.39
12 models selected
> select add #13.77
13 models selected
> select add #13.147
14 models selected
> select subtract #13.147
13 models selected
> select add #13.199
14 models selected
> select add #13.68
15 models selected
> select add #13.135
16 models selected
> select add #13.19
17 models selected
> select add #13.61
18 models selected
> select add #13.96
19 models selected
> select add #13.136
20 models selected
> select subtract #13.91
19 models selected
> select subtract #13.112
18 models selected
> select subtract #13.137
17 models selected
> select add #13.137
18 models selected
Deleted 18 regions
> select add #13.91
1 model selected
> select add #13.112
2 models selected
> select add #13.30
3 models selected
> select add #13.6
4 models selected
> select add #13.31
5 models selected
> select add #13.66
6 models selected
> select add #13.130
7 models selected
> select add #13.160
8 models selected
> select add #13.45
9 models selected
> select add #13.72
10 models selected
> select add #13.46
11 models selected
> select add #13.18
12 models selected
> select add #13.23
13 models selected
> select add #13.191
14 models selected
> select add #13.115
15 models selected
> select add #13.187
16 models selected
> select add #13.14
17 models selected
> select subtract #13.14
16 models selected
> select add #13.106
17 models selected
> select add #13.184
18 models selected
> select add #13.67
19 models selected
> select add #13.90
20 models selected
> select add #13.52
21 models selected
> select add #13.129
22 models selected
> select add #13.35
23 models selected
> select add #13.95
24 models selected
> select add #13.74
25 models selected
> select add #13.65
26 models selected
> select add #13.47
27 models selected
> select add #13.24
28 models selected
> select add #13.41
29 models selected
> select subtract #13.41
28 models selected
Deleted 28 regions
> select add #13.159
1 model selected
> select add #13.14
2 models selected
> select add #13.41
3 models selected
> select subtract #13.14
2 models selected
> select add #13.14
3 models selected
Deleted 3 regions
> select add #13.139
1 model selected
> select add #13.175
2 models selected
> select add #13.40
3 models selected
> select add #13.16
4 models selected
> select add #13.142
5 models selected
Deleted 5 regions
> select add #13.165
1 model selected
> select add #13.197
2 models selected
Deleted 2 regions
> select add #13.2
1 model selected
> select add #13.111
2 models selected
Deleted 2 regions
> select add #13.51
1 model selected
> select add #13.147
2 models selected
> select add #13.101
3 models selected
Deleted 3 regions
> select add #13.29
1 model selected
> select add #13.79
2 models selected
> select add #13.55
3 models selected
> select add #13.140
4 models selected
> select add #13.176
5 models selected
> select add #13.148
6 models selected
> select add #13.131
7 models selected
Deleted 7 regions
> select add #13.83
1 model selected
Deleted 1 regions
> select #13.70
1 model selected
> select add #13.180
2 models selected
> select add #13.162
3 models selected
> select add #13.151
4 models selected
Deleted 4 regions
> select #13.126
1 model selected
> select #13.15
1 model selected
> select #13.15
1 model selected
> select subtract #13.15
Nothing selected
> select #13.32
1 model selected
> select clear
Drag select of 8402, 8352, 8366, 8389, 8454, 8003, 8464, 8409, 8363, 8457,
8398, 8178, 8405, 8448, 7970, 8478, 8393, 8482, 8444, 8384, 8027, 8480, 8473,
8362, 8486, 8401, 8342, 8391, 8200, 8176, 8474, 8415, 8368, 8360, 8392, 8488,
8492, 8346, 8471, 8028, 8036, 8436, 8430, 8300, 8283, 8378, 8479, 8377
Grouped 48 regions
Ungrouped to 48 regions
> select #13.29
1 model selected
Ungrouped to 4 regions
> select #13.32
1 model selected
> select #13.36
1 model selected
Ungrouped to 2 regions
Ungrouped to 7 regions
> select #13.54
1 model selected
> select add #13.36
2 models selected
> select add #13.49
3 models selected
> select subtract #13.49
2 models selected
> select add #13.55
3 models selected
Deleted 3 regions
> show #!11 models
> hide #!13 models
> hide #!11 models
> show #!13 models
Drag select of 8473, 8200, 8398, 8036, 8300, 8415, 8360, 8366, 8027, 8405,
8444, 8028, 7970, 8478, 8436, 8409, 8352, 8457, 8430, 8492, 8368, 8464, 8391,
8401, 8178, 8471, 8176, 8378, 8486, 8384, 8448, 8377, 8003, 8488, 8362, 8392,
8393, 8482, 8454, 8342, 8402, 8479, 8363, 8283, 8346, 8474, 7066, 7995, 7996,
7744, 7018, 1853, 1731, 1890
Grouped 54 regions
> select clear
> show #!11 models
> transparency #13#11.1 50
> hide #!11 models
> transparency #13 0
> show #!11 models
> hide #!11 models
> select #13.1
1 model selected
Ungrouped to 54 regions
> select #13.25
1 model selected
> select add #13.24
2 models selected
> select add #13.54
3 models selected
> select add #13.39
4 models selected
> select clear
> select #13.39
1 model selected
Ungrouped to 16 regions
> select clear
> select #13.68
1 model selected
> select add #13.25
2 models selected
> select add #13.24
3 models selected
> select add #13.54
4 models selected
Deleted 4 regions
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> select #13.29
1 model selected
> show #!11 models
Deleted 1 regions
> hide #!11 models
> select #13.27
1 model selected
Ungrouped to 4 regions
> select #13.24
1 model selected
Deleted 1 regions
> select #13.25
1 model selected
Deleted 1 regions
> select #13.48
1 model selected
> select add #13.55
2 models selected
Grouped 2 regions
Ungrouped to 2 regions
> select clear
> select #13.27
1 model selected
Ungrouped to 2 regions
Ungrouped to 9 regions
> select #13.54
1 model selected
> select add #13.27
2 models selected
> select add #13.25
3 models selected
Grouped 3 regions
> select clear
> select #13.68
1 model selected
> select #13.24
1 model selected
> select add #13.68
2 models selected
Grouped 2 regions
> select clear
> select #13.24
1 model selected
Drag select of 7996, 10854 of 10856 triangles, 8473, 8200, 8398, 8036, 8300,
8415, 8360, 12726 of 12772 triangles, 8366, 8027, 1853, 1909 of 2316
triangles, 8405, 8444, 8028, 7970, 18486 of 19756 triangles, 8478, 1890, 8436,
8409, 8352, 8457, 8430, 8464, 8283, 8178, 8471, 8176, 8378, 1731, 8486, 8384,
8448, 8377, 8488, 8362, 13270 of 14028 triangles, 8392, 8393, 11014 of 12204
triangles, 7744, 8482, 8454, 8342, 7018, 5716 of 6308 triangles, 8479, 7066,
8363, 25855 of 26092 triangles, 7995, 6457, 7464, 2520 of 4412 triangles,
7184, 7093, 3015, 2744, 2941, 7397, 2789, 7052, 7535, 7646, 7636, 6662, 7730,
7989, 2087 of 2220 triangles, 8181, 7335, 2664, 2666, 7473, 7327, 7312, 8499
Grouped 70 regions
> volume mask #13 #11 fullMap true
Missing required "surfaces" argument
> volume mask #13 surfaces #11 fullMap true
No volumes specified
> show #!11 models
> hide #!11 models
> volume mask #13 surfaces #11 fullMap true
No volumes specified
> volume mask #13 surfaces #11
No volumes specified
Saving 1 regions to mrc file...
Opened J345_MCM_channel_G4_mask.mrc as #14, grid size 121,117,122, pixel
0.826, shown at step 1, values float32
Wrote J345_MCM_channel_G4_mask.mrc
> hide #!13 models
> volume #14 level 0.1353
> vop resample #14 ongrid #11
Opened J345_MCM_channel_G4_mask.mrc resampled as #15, grid size 448,448,448,
pixel 0.826, shown at step 1, values float32
> close #14
> save "/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My
> Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-
> reaction/J345-MCM-channel-G4-mask.mrc" models #15
> hide #!15 models
> show #!1.1 models
> transparency #1.1.1 50
[Repeated 9 time(s)]
> color #1.1 #b2b2ffff models
> hide #!1.1 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.3 models
> volume #1.1 level 0.9257
> hide #!1.1 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!1.1 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.1 models
> transparency #1.5.1 50
> color #1.5 #67bce2ff models
> transparency #1.5.1 50
[Repeated 4 time(s)]
> volume #!1.5 style surface
> volume #!1.5 hide
> volume show
> volume #!3-5,7,11,15#!1.1,3-5 style surface
> volume #!3-5,7,11,15#!1.1,3-5 hide
> show #!1.5 models
> transparency #1.5.1 50
[Repeated 1 time(s)]
> color #1.5 #67bce2ff models
> color #1.5 #67bce2f2 models
> color #1.5 #67bce2ff models
[Repeated 1 time(s)]
> transparency #1.5.1 50
[Repeated 1 time(s)]
> color #1.5 #67bce2ff models
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 71 days 3:01
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
ASUS PB287Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (5)
comment:1 by , 3 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Map→Style→Transparent surface not toggling transparency |
comment:2 by , 3 years ago
| Cc: | added |
|---|
Testing shows if you have a selected hidden model and a shown volume then the map transparency toolbar button look at whether the hidden selected model is transparent or opaque, but then changes the shown map.
I don't remember how the Toolbar buttons are supposed to behave when you have a hidden model selected. Are they supposed to work on only the visible models and ignore any hidden selected model? Elaine do you know the answer to that? I vaguely recall that toolbar buttons never act on hidden models.
follow-up: 3 comment:3 by , 3 years ago
I’m sorry for wasting your time – it must have been something to do with hidden models and my own misuse of the button. I just tried again after re-opening my maps in a new session and it seems to be working perfectly.
Thank you for your quick response!
Ben
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, December 1, 2022 at 9:57 PM
To:
Cc: Benjamin Allwein <bta4001@med.cornell.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8107: Map→Style→Transparent surface not toggling transparency
#8107: Map→Style→Transparent surface not toggling transparency
----------------------------------+-------------------------
Reporter: bta4001@… | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Volume Data | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Changes (by Tom Goddard):
* cc: Elaine Meng (added)
Comment:
Testing shows if you have a selected hidden model and a shown volume then
the map transparency toolbar button look at whether the hidden selected
model is transparent or opaque, but then changes the shown map.
I don't remember how the Toolbar buttons are supposed to behave when you
have a hidden model selected. Are they supposed to work on only the
visible models and ignore any hidden selected model? Elaine do you know
the answer to that? I vaguely recall that toolbar buttons never act on
hidden models.
--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac_ChimeraX_ticket_8107-23comment-3A2&d=DwIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=Aqknn2UGJPKBnn51nd1HTZYdx5bjEusVsWNV97AoaDM&m=KcifZhoXDOYbhAnJ6p85tDY674iSWyIro3RnHIbY7L4rNtGNrgFKOkN6yb5xx0qx&s=UJVoj0zYRoMQ0SFuvy2cgYKix4itZp_oHgBU_lBc554&e= >
ChimeraX <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=Aqknn2UGJPKBnn51nd1HTZYdx5bjEusVsWNV97AoaDM&m=KcifZhoXDOYbhAnJ6p85tDY674iSWyIro3RnHIbY7L4rNtGNrgFKOkN6yb5xx0qx&s=jUXPUrNWoo1faNtiB2QenaqUis-NDdbHFOcYixxcNUY&e= >
ChimeraX Issue Tracker
follow-up: 4 comment:4 by , 3 years ago
Hi Ben, At least according to the Map Toolbar documentation, the icons are supposed to apply to displayed map models only: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/densitymaps.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
comment:5 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Made map transparency toolbar button ignore hidden models even if they are selected.
Thanks for reporting the problem!
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Reported by Ben Allwein