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Opened 9 months ago
Closed 9 months ago
#16686 closed defect (duplicate)
Matrix is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
this error pops up when i past the following list of commands: "cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
open "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
open "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
open "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
open "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
volume flip #* axis y
open "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
#### open "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
volume #8 level 0.02292 step 4
volume #5,6,7 level 0.1 step 1
set bg white
graphics silhouettes t width 3
lighting depthCue f
hide #5,6,7,8
hide #9". it doent not pop up when i just past the commands line by line, so it might be some hidden character in my text editor. does really bother me too much.
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> vop flip axis y
> volume flip axis y
Missing or invalid "volumes" argument: invalid density maps specifier
> vop #* flip axis y
> volume #* flipNormals axis y
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> vop #1 flip axis y
> volume #1 flipNormals axis y
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume flip #1 axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #4, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> close #4
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #4, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> volume #8 level 0.427
> volume #8 level 0.02778
> hide #!8 models
> volume #7 level 0.07085
> hide #!7 models
> hide #!6 models
> hide #!5 models
> set bgColor white
> show #!5 models
> volume #5 level 0.1243
> show #!8 models
> volume #8 style mesh
> volume #8 step 4
> volume #5 level 0.1765
> volume #5 color #ff2600
> volume #5 level 0.19
> volume #5 level 0.18
> volume #5 level 0.07108
> volume #5 level 0.1608
> volume #5 level 0.18
> volume #5 level 0.08028
> volume #5 level 0.18
> show #!6 models
> volume #6 level 0.18
> volume #6 level 0.1225
> volume #6 color #0433ff
> volume #6 level 0.1184
> hide #!6 models
> show #!7 models
> volume #7 level 0.1106
> volume #7 color #ededed
> volume #7 color #4f8f00
> volume #7 level 0.104
> volume #6 level 0.1093
> show #!5 models
> hide #!6 models
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_PSI_ISIA_MDpaper/data/7umh.cif"
7umh.cif title:
Energetic robustness to large scale structural dynamics in a photosynthetic
supercomplex [more info...]
Chain information for 7umh.cif #9
---
Chain | Description | UniProt
A H a | Photosystem I P700 chlorophyll a apoprotein A1 | PSAA_SYNY3 1-751
B G b | Photosystem I P700 chlorophyll a apoprotein A2 | PSAB_SYNY3 1-731
C N c | Photosystem I iron-sulfur center | PSAC_SYNY3 1-81
D P d | Photosystem I reaction center subunit II | PSAD_SYNY3 1-141
E O e | Photosystem I reaction center subunit IV | PSAE_SYNY3 1-74
F Q f | Photosystem I reaction center subunit III | PSAF_SYNY3 -21-143
I R i | Photosystem I reaction center subunit VIII | PSAI_SYNY3 1-40
J S j | Photosystem I reaction center subunit IX | PSAJ_SYNY3 1-40
K T k | Photosystem I reaction center subunit PsaK 1 | PSAK1_SYNY3 -1-84
L U l | Photosystem I reaction center subunit XI | PSAL_SYNY3 1-157
M V m | Photosystem I reaction center subunit XII | PSAM_SYNY3 1-31
W X Y Z g h n o p q r s t u v w x y | Iron stress-induced chlorophyll-binding protein | ISIA_SYNY3 1-342
Non-standard residues in 7umh.cif #9
---
BCR — β-carotene
CA — calcium ion
CL0 — chlorophyll A isomer
CLA — chlorophyll A
ECH — beta,beta-caroten-4-one (echinenone)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LMU — dodecyl-α-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
> volume #5 level 0.08412
> select add #9
140516 atoms, 145848 bonds, 2511 pseudobonds, 14006 residues, 2 models
selected
> ui mousemode right "rotate selected models"
> hide sel atoms
> show sel cartoons
Computing secondary structure
> view matrix models
> #9,0.49432,-0.12016,0.86093,-43.401,-0.18429,0.9534,0.23888,0.081789,-0.84952,-0.27674,0.44914,351.15
> view matrix models
> #9,0.17244,0.2131,0.96169,-67.736,-0.27894,0.94692,-0.15981,102.87,-0.9447,-0.24069,0.22273,409.72
> view matrix models
> #9,0.017751,0.18369,0.98282,-33.111,-0.26444,0.94884,-0.17256,102.01,-0.96424,-0.25683,0.065418,449.45
> view matrix models
> #9,0.034018,0.10029,0.99438,-20.976,-0.27072,0.95868,-0.087433,83.829,-0.96206,-0.26622,0.059764,452.16
> ui tool show "Fit in Map"
> fitmap #9 inMap #5
Fit molecule 7umh.cif (#9) to map cryosparc_P12_J162_006_volume_map.mrc y flip
(#5) using 140516 atoms
average map value = 0.06217, steps = 172
shifted from previous position = 14
rotated from previous position = 5.53 degrees
atoms outside contour = 114985, contour level = 0.084118
Position of 7umh.cif (#9) relative to cryosparc_P12_J162_006_volume_map.mrc y
flip (#5) coordinates:
Matrix rotation and translation
0.01475667 0.00763461 0.99986197 6.96886961
-0.25092361 0.96799986 -0.00368802 71.41186245
-0.96789441 -0.25083456 0.01620016 465.27162126
Axis -0.12357329 0.98387832 -0.12927913
Axis point 244.90083051 0.00000000 233.20723933
Rotation angle (degrees) 90.02988868
Shift along axis 9.24950593
> save "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"
Chain information for 7umh_docked_J162_flipped.pdb #10
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h n o p q r s t u v w x y | No description available
> close #9
> close #10
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"
Chain information for 7umh_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h n o p q r s t u v w x y | No description available
> hide #!8 models
> hide #!9 models
> show #!9 models
> hide atoms
> show cartoons
> select /g,Z,Y,X,W,y
22449 atoms, 23417 bonds, 426 pseudobonds, 2147 residues, 2 models selected
> view matrix models
> #9,0.99663,-0.068917,-0.044377,25.838,0.069216,0.99759,0.0052272,-15.52,0.04391,-0.0082812,0.999,-7.393
> view matrix models
> #9,0.9901,-0.13975,-0.013096,36.545,0.14001,0.9899,0.022085,-32.688,0.0098775,-0.0237,0.99967,3.2967
> view matrix models
> #9,0.94877,-0.1662,0.26871,-9.0726,0.24247,-0.1623,-0.95649,415.85,0.20258,0.97264,-0.11369,-24.471
> view matrix models
> #9,0.95822,-0.096802,0.26915,-26.895,0.25266,-0.15457,-0.95513,411.61,0.13406,0.98323,-0.12366,-9.9301
> view matrix models
> #9,0.96931,-0.008812,0.24567,-44.141,0.19914,-0.55779,-0.80574,482.25,0.14413,0.82993,-0.53892,111.73
> view matrix models
> #9,0.99526,-0.078815,0.056911,6.62,0.0033171,-0.55754,-0.83014,529.71,0.097158,0.8264,-0.55464,126.05
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.99526,-0.078815,0.056911,6.2844,0.0033171,-0.55754,-0.83014,522.34,0.097158,0.8264,-0.55464,130.99
> view matrix models
> #9,0.99526,-0.078815,0.056911,10.408,0.0033171,-0.55754,-0.83014,521.92,0.097158,0.8264,-0.55464,130.76
> fitmap #9 inMap #5
Fit molecule 7umh_docked_J162_flipped.pdb (#9) to map
cryosparc_P12_J162_006_volume_map.mrc y flip (#5) using 140516 atoms
average map value = 0.06222, steps = 184
shifted from previous position = 6.28
rotated from previous position = 5.66 degrees
atoms outside contour = 114853, contour level = 0.084118
Position of 7umh_docked_J162_flipped.pdb (#9) relative to
cryosparc_P12_J162_006_volume_map.mrc y flip (#5) coordinates:
Matrix rotation and translation
0.99958280 -0.01992303 0.02091151 0.08034984
0.00821963 -0.49785256 -0.86722273 513.83082799
0.02768855 0.86703281 -0.49748110 120.55967771
Axis 0.99986073 -0.00390721 0.01622526
Axis point 0.00000000 222.00967612 209.05030722
Rotation angle (degrees) 119.85953886
Shift along axis 0.02880414
> select /g,Z,Y,X,W,y,h
26076 atoms, 27204 bonds, 495 pseudobonds, 2497 residues, 2 models selected
> select /r,q,p,o,n,x,w,s,u,t,v
41274 atoms, 43050 bonds, 784 pseudobonds, 3941 residues, 2 models selected
> delete /r,q,p,o,n,x,w,s,u,t,v
> save "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
> close #7
> close #9
> close #8
> close
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #4, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #7, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #8
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> hide atoms
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!4 models
> hide #!5 models
> show #!7 models
> volume #7 level 0.02292
> volume #7 step 4
> show #!8 models
> show target a
> volume #7 style mesh
> close #7
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> volume #7 level 0.02292 step 4
> hide #!7 models
> hide #!6 models
> volume #8 level 0.02292 step 4
> volume #8 style mesh
> volume #5,6,7 level 0.1 step 1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
> ui mousemode right translate
> view matrix
view matrix camera
-0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0
> hide target s
> hide #* target s
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!1 models
> show #!2 models
> show #!6 models
> show #!7 models
> hide #* target s
> hide #1,2,3,4 target s
> hide #1,2,3,4,5 target s
> hide #1,2,3,4,5,6 target s
> hide #1,2,3,4,5,6,7,8 target s
> show #!9
> show #!9 models
> hide #1 models
> hide #* models
> show /A,B,C,D,E,F,I,J,K,L,M target s
> show #9/A,B,C,D,E,F,I,J,K,L,M target s
> show #!9 models
> hide #9 target a
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> show /A,B,C,D,E,F,I,J,K,L,M target s
> transparency #1 100 target s
> save DC_AB_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /a,b,c,d,e,f,i,j,k,l,m target s
> transparency #1 100 target s
> save DC_ab_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /H,G,N,U,Q,S,V,P,O,T,R target s
> transparency #1 100 target s
> save DC_GH_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /g target s
> transparency #1 100 target s
> save DC_g_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> transparency #1 100 target s
> save DC_Z_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> transparency #1 100 target s
> save DC_1Y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /X target s
> transparency #1 100 target s
> save DC_X_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /W target s
> transparency #1 100 target s
> save DC_W_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /y target s
> transparency #1 100 target s
> save DC_y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> transparency #1 100 target s
> save DC_h_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide #* models
> show #!9 models
> hide #9 target a
> show /A,B,C,D,E,F,I,J,K,L,M target s
> transparency #9 100 target s
> save DC_AB_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /a,b,c,d,e,f,i,j,k,l,m target s
> transparency #9 100 target s
> save DC_ab_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /H,G,N,U,Q,S,V,P,O,T,R target s
> transparency #9 100 target s
> save DC_GH_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /g target s
> transparency #9 100 target s
> save DC_g_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> transparency #9 100 target s
> save DC_Z_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> transparency #9 100 target s
> save DC_1Y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /X target s
> transparency #9 100 target s
> save DC_X_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /W target s
> transparency #9 100 target s
> save DC_W_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /y target s
> transparency #9 100 target s
> save DC_y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> transparency #9 100 target s
> save DC_h_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide #* models
> show #!9 models
> hide #9 target a
> show /A,B,C,D,E,F,I,J,K,L,M target s
> transparency #9 100 target s
> save DC_1AB_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /a,b,c,d,e,f,i,j,k,l,m target s
> transparency #9 100 target s
> save DC_ab_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /H,G,N,U,Q,S,V,P,O,T,R target s
> transparency #9 100 target s
> save DC_GH_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /g target s
> transparency #9 100 target s
> save DC_g_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> transparency #9 100 target s
> save DC_Z_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> transparency #9 100 target s
> save DC_1Y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /X target s
> transparency #9 100 target s
> save DC_X_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /W target s
> transparency #9 100 target s
> save DC_W_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /y target s
> transparency #9 100 target s
> save DC_y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> transparency #9 100 target s
> save DC_h_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> show #!8 models
> hide #!9 models
> show #8 target s
> color #8 #76d6ffff models
> volume #8 level 0.2092
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide #5 target s
> hide #8
> hide #5,6,7,8
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> show /A,B,C,D,E,F,I,J,K,L,M target s
> hide #5,6,7,8,9
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> show /A,B,C,D,E,F,I,J,K,L,M target s
> transparency #9 100 target s
> save DC_1AB_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /a,b,c,d,e,f,i,j,k,l,m target s
> transparency #9 100 target s
> save DC_ab_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /H,G,N,U,Q,S,V,P,O,T,R target s
> transparency #9 100 target s
> save DC_GH_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /g target s
> transparency #9 100 target s
> save DC_g_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> transparency #9 100 target s
> save DC_Z_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> transparency #9 100 target s
> save DC_1Y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /X target s
> transparency #9 100 target s
> save DC_X_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /W target s
> transparency #9 100 target s
> save DC_W_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /y target s
> transparency #9 100 target s
> save DC_y_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> transparency #9 100 target s
> save DC_h_outline.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show #8 target s
> show #8
> color #8 #C71585
> transparency #8 90 target s
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample
> 4 transparentBackground true
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> show #8
> color #8 dodger blue
> transparency #8 80 target s
> save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample
> 4 transparentBackground true
> transparency #8 60 target s
> save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample
> 4 transparentBackground true
> ui tool show "Side View"
> view matrix
view matrix camera
-0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0
> show #8
> color #8 dodger blue
> transparency #8 50 target s
> save DC_7IsiA_mask_outline.png format png width 1200 height 1200 supersample
> 4 transparentBackground true
> show #!5 models
> show #5
> transparency #8 90 target s
> volume #5 level 0.09822
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> view matrix
view matrix camera
-0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#9.4,1,0,0,0,0,1,0,0,0,0,1,0,#9.5,1,0,0,0,0,1,0,0,0,0,1,0,#9.6,1,0,0,0,0,1,0,0,0,0,1,0,#9.7,1,0,0,0,0,1,0,0,0,0,1,0,#9.8,1,0,0,0,0,1,0,0,0,0,1,0,#9.9,1,0,0,0,0,1,0,0,0,0,1,0,#9.10,1,0,0,0,0,1,0,0,0,0,1,0,#9.11,1,0,0,0,0,1,0,0,0,0,1,0,#9.12,1,0,0,0,0,1,0,0,0,0,1,0,#9.13,1,0,0,0,0,1,0,0,0,0,1,0,#9.14,1,0,0,0,0,1,0,0,0,0,1,0,#9.15,1,0,0,0,0,1,0,0,0,0,1,0,#9.16,1,0,0,0,0,1,0,0,0,0,1,0,#9.17,1,0,0,0,0,1,0,0,0,0,1,0,#9.18,1,0,0,0,0,1,0,0,0,0,1,0,#9.19,1,0,0,0,0,1,0,0,0,0,1,0,#9.20,1,0,0,0,0,1,0,0,0,0,1,0,#9.21,1,0,0,0,0,1,0,0,0,0,1,0,#9.22,1,0,0,0,0,1,0,0,0,0,1,0,#9.23,1,0,0,0,0,1,0,0,0,0,1,0,#9.24,1,0,0,0,0,1,0,0,0,0,1,0,#9.25,1,0,0,0,0,1,0,0,0,0,1,0,#9.26,1,0,0,0,0,1,0,0,0,0,1,0,#9.27,1,0,0,0,0,1,0,0,0,0,1,0,#9.28,1,0,0,0,0,1,0,0,0,0,1,0,#9.29,1,0,0,0,0,1,0,0,0,0,1,0,#9.30,1,0,0,0,0,1,0,0,0,0,1,0,#9.31,1,0,0,0,0,1,0,0,0,0,1,0,#9.32,1,0,0,0,0,1,0,0,0,0,1,0,#9.33,1,0,0,0,0,1,0,0,0,0,1,0,#9.34,1,0,0,0,0,1,0,0,0,0,1,0,#9.35,1,0,0,0,0,1,0,0,0,0,1,0,#9.36,1,0,0,0,0,1,0,0,0,0,1,0,#9.37,1,0,0,0,0,1,0,0,0,0,1,0,#9.38,1,0,0,0,0,1,0,0,0,0,1,0,#9.39,1,0,0,0,0,1,0,0,0,0,1,0,#9.40,1,0,0,0,0,1,0,0,0,0,1,0,#9.41,1,0,0,0,0,1,0,0,0,0,1,0
> hide #!5 models
> show #!6 models
> show #6
> volume #6 level 0.09081
> volume #6 level 0.08868
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!7 models
> select ~sel & ##selected
Nothing selected
> show #7
> volume #7 level 0.09082
> volume #7 level 0.09036
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #5 level 0.1309
> volume #5 level 0.09346
> hide #!5 models
> show #!6 models
> volume #5 level 0.09822
> hide #!5 models
> volume #6 level 0.09081
> show #5,6,7
> volume #5 level 0.09822
> volume #6 level 0.08868
> volume #7 level 0.09036
> volume mask #5,6,7 surfaces #8
Opened cryosparc_P12_J162_006_volume_map.mrc y flip masked as #10, grid size
121,337,211, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip masked as #11, grid size
121,337,211, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip masked as #12, grid size
121,337,211, pixel 0.86, shown at step 1, values float32
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide #8,9
> !show #8,9
Unknown command: !show #8,9
> hide #8
> hide
> hide target s
> hide #*
> hide #* target s
> hide #10
> hide #10,11,12
> show #10
> volume #10 level 0.1042
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> color #10 grey
> save J162_masked.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide #10
> show #11
> color #11 gold
[Repeated 1 time(s)]
> volume #11 level 0.09752
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> save J163_masked.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> √
Unknown command: √
> hide #11
> show #12
> color #12 red
> volume #12 level 0.08577
> save J164_masked.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> show /Z target s
> volume #12 level 0.111
> show /Y target s
> hide /Y target s
> hide /X target s
> hide /x target s
> show /x target s
> show /X target s
> hide /X target s
> show /y target s
> hide /y target s
> show /h target s
> hide /h target s
> hide /W target s
> show /W target s
> hide /W target s
> show /g target s
> hide #!12 models
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /g target s
> color /g #045a8d target s
> transparency #9 100 target s
> save DC_g_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /g target s
> color /g #045a8d target s
> transparency #9 0 target s
> save DC_g_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> help help:user/preferences.html#startup
> lighting flat
[Repeated 1 time(s)]
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /g target s
> color /g #045a8d target s
> transparency #9 0 target s
> save DC_g_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> transparency #9 100 target s
> lighting flat
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
[Repeated 1 time(s)]
> hide target s
> show /Z target s
> color /Z #045a8d target s
> transparency #9 0 target s
> save DC_Z_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> show cartoons
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide atoms
> hide cartoons
> hide target s
> show /Y target s
> color /Y #045a8d target s
> transparency #9 75 target s
> save DC_Y_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> color /h #045a8d target s
> transparency #9 75 target s
> save DC_h_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> color /Y #045a8d target s
> transparency #9 25 target s
> save DC_Y_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> color /h #045a8d target s
> transparency #9 25 target s
> save DC_h_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /Y target s
> color /Y #045a8d target s
> transparency #9 25 target s
> save DC_Y_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> color /h #045a8d target s
> transparency #9 25 target s
> save DC_h_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/DC_h_50_color.png"
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> lighting flat
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /g target s
> color /g #045a8d target s
> transparency #9 0 target s
> save DC_g_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> color /Z #045a8d target s
> transparency #9 0 target s
> save DC_Z_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> color /Y #0570b0 target s
> transparency #9 0 target s
> save DC_Y_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> color /h #0570b0 target s
> transparency #9 0 target s
> save DC_h_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> lighting flat
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /g target s
> color /g #045a8d target s
> transparency #9 0 target s
> save DC_g_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> color /Z #045a8d target s
> transparency #9 0 target s
> save DC_Z_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> color /Y #3690c0 target s
> transparency #9 0 target s
> save DC_Y_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> color /h #3690c0 target s
> transparency #9 0 target s
> save DC_h_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> graphics silhouettes true width 3
> graphics silhouettes true width 1
> graphics silhouettes true width 2
[Repeated 1 time(s)]
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /g target s
> color /g #045a8d target s
> transparency #9 0 target s
> save DC_g_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Z target s
> color /Z #045a8d target s
> transparency #9 0 target s
> save DC_Z_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> color /Y #3690c0 target s
> transparency #9 0 target s
> save DC_Y_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /h target s
> color /h #3690c0 target s
> transparency #9 0 target s
> save DC_h_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> volume #12 level 0.09312
> volume #11 level 0.1106
> hide target s
> save DC_Z_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /Y target s
> color /Y #045a8d target s
> transparency #9 0 target s
> save DC_Y_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /X target s
> color /X #045a8d target s
> transparency #9 0 target s
> save DC_X_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide target s
> show /Y target s
> color /Y #045a8d target s
> transparency #9 0 target s
> save DC_Y_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /X target s
> color /X #045a8d target s
> transparency #9 0 target s
> save DC_X_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> volume #11 level 0.1092
> save DC_X_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> hide target s
> show /W target s
> color /W #045a8d target s
> transparency #9 0 target s
> save DC_W_full_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> volume #11 level 0.09646
> volume #11 level 0.1085
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
[Repeated 1 time(s)]
> hide target s
> show /y target s
> color /y #3690c0 target s
> transparency #9 0 target s
> save DC_y1_50_color.png format png width 1200 height 1200 supersample 4
> transparentBackground true
> volume #10 level 0.1321
> hide target s
> volume #10 level 0.1321
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #1
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> save AB.pdb format pdb models /A,B,C,D,E,F,I,J,K,L,M selectedOnly true
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb"
[Repeated 2 time(s)]
> select /A,B,C,D,E,F,I,J,K,L,M
24368 atoms, 25199 bonds, 410 pseudobonds, 2501 residues, 2 models selected
> save AB.pdb format pdb models #1
> ~select
Nothing selected
> hide #!1 models
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb"
Chain information for AB.pdb #2
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> close #2
> show #!1 models
> select /A,B,C,D,E,F,I,J,K,L,M
24368 atoms, 25199 bonds, 410 pseudobonds, 2501 residues, 2 models selected
> save AB.pdb format pdb models #1 selectedOnly true
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
Cannot find LINK/SSBOND residue ILE (282 )
70 messages similar to the above omitted
Chain information for AB.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> hide #!1 models
> close #2
> select /a,b,c,d,e,f,i,j,k,l,m
24413 atoms, 25195 bonds, 407 pseudobonds, 2550 residues, 2 models selected
> save ab1.pdb format pdb models #1 selectedOnly true
> select /H,G,N,U,Q,S,V,P,O,T,R
24385 atoms, 25200 bonds, 408 pseudobonds, 2517 residues, 2 models selected
> save GH.pdb format pdb models #1 selectedOnly true
> select /g
3777 atoms, 3938 bonds, 71 pseudobonds, 356 residues, 2 models selected
> save g.pdb format pdb models #1 selectedOnly true
> select /Z
3777 atoms, 3940 bonds, 71 pseudobonds, 359 residues, 2 models selected
> save Z.pdb format pdb models #1 selectedOnly true
> select /X
3768 atoms, 3929 bonds, 72 pseudobonds, 361 residues, 2 models selected
> save X.pdb format pdb models #1 selectedOnly true
> select /W
3684 atoms, 3845 bonds, 71 pseudobonds, 358 residues, 2 models selected
> save W.pdb format pdb models #1 selectedOnly true
> select /y
3621 atoms, 3781 bonds, 69 pseudobonds, 350 residues, 2 models selected
> save y1.pdb format pdb models #1 selectedOnly true
> select /h
3627 atoms, 3787 bonds, 69 pseudobonds, 350 residues, 2 models selected
> save h.pdb format pdb models #1 selectedOnly true
> close #1
> open /Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb
'/Users/yuvalmazor/ASU' has no suffix
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
Cannot find LINK/SSBOND residue ILE (282 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
Cannot find LINK/SSBOND residue ILE (282 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASN (17 )
Cannot find LINK/SSBOND residue ILE (282 )
Cannot find LINK/SSBOND residue GLN (316 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue ASP (56 )
Cannot find LINK/SSBOND residue ASN (17 )
96 messages similar to the above omitted
Chain information for AB.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #2
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #3
---
Chain | Description
W | No description available
Chain information for X.pdb #4
---
Chain | Description
X | No description available
Chain information for Z.pdb #5
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #6
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #7
---
Chain | Description
g | No description available
Chain information for h.pdb #8
---
Chain | Description
h | No description available
Chain information for y1.pdb #9
---
Chain | Description
y | No description available
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #1
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> select /A,B,C,D,E,F,I,J,K,L,M
24368 atoms, 25199 bonds, 410 pseudobonds, 2501 residues, 2 models selected
> save AB.pdb format pdb models #1 selectedOnly true
> select /a,b,c,d,e,f,i,j,k,l,m
24413 atoms, 25195 bonds, 407 pseudobonds, 2550 residues, 2 models selected
> save ab1.pdb format pdb models #1 selectedOnly true
> select /H,G,N,U,Q,S,V,P,O,T,R
24385 atoms, 25200 bonds, 408 pseudobonds, 2517 residues, 2 models selected
> save GH.pdb format pdb models #1 selectedOnly true
> select /g
3777 atoms, 3938 bonds, 71 pseudobonds, 356 residues, 2 models selected
> save g.pdb format pdb models #1 selectedOnly true
> select /Z
3777 atoms, 3940 bonds, 71 pseudobonds, 359 residues, 2 models selected
> save Z.pdb format pdb models #1 selectedOnly true
> select /X
3768 atoms, 3929 bonds, 72 pseudobonds, 361 residues, 2 models selected
> save X.pdb format pdb models #1 selectedOnly true
> select /Y
3822 atoms, 3984 bonds, 72 pseudobonds, 363 residues, 2 models selected
> save Y.pdb format pdb models #1 selectedOnly true
> select /W
3684 atoms, 3845 bonds, 71 pseudobonds, 358 residues, 2 models selected
> save W.pdb format pdb models #1 selectedOnly true
> select /y
3621 atoms, 3781 bonds, 69 pseudobonds, 350 residues, 2 models selected
> save y1.pdb format pdb models #1 selectedOnly true
> select /h
3627 atoms, 3787 bonds, 69 pseudobonds, 350 residues, 2 models selected
> save h.pdb format pdb models #1 selectedOnly true
> close #1
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue GLN (123 )
Cannot find LINK/SSBOND residue THR (497 )
Cannot find LINK/SSBOND residue ASP (93 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Chain information for AB.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #2
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #3
---
Chain | Description
W | No description available
Chain information for X.pdb #4
---
Chain | Description
X | No description available
Chain information for Y.pdb #5
---
Chain | Description
Y | No description available
Chain information for Z.pdb #6
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #7
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #8
---
Chain | Description
g | No description available
Chain information for h.pdb #9
---
Chain | Description
h | No description available
Chain information for y1.pdb #10
---
Chain | Description
y | No description available
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue GLN (123 )
Cannot find LINK/SSBOND residue THR (497 )
Cannot find LINK/SSBOND residue ASP (93 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Chain information for AB.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #10
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #11
---
Chain | Description
W | No description available
Chain information for X.pdb #12
---
Chain | Description
X | No description available
Chain information for Y.pdb #13
---
Chain | Description
Y | No description available
Chain information for Z.pdb #14
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #15
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #16
---
Chain | Description
g | No description available
Chain information for h.pdb #17
---
Chain | Description
h | No description available
Chain information for y1.pdb #18
---
Chain | Description
y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5,6,7,8,9
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide #5
> hide #6,7
> hide #5,6,7,8,9
> hide #5,6,7,8
> hide #9-18
[Repeated 1 time(s)]
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue GLN (123 )
Cannot find LINK/SSBOND residue THR (497 )
Cannot find LINK/SSBOND residue ASP (93 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Chain information for AB.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #10
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #11
---
Chain | Description
W | No description available
Chain information for X.pdb #12
---
Chain | Description
X | No description available
Chain information for Y.pdb #13
---
Chain | Description
Y | No description available
Chain information for Z.pdb #14
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #15
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #16
---
Chain | Description
g | No description available
Chain information for h.pdb #17
---
Chain | Description
h | No description available
Chain information for y1.pdb #18
---
Chain | Description
y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5-8
> hide #9-11
> hide #12-18
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> hide #12-18 target c
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue GLN (123 )
Cannot find LINK/SSBOND residue THR (497 )
Cannot find LINK/SSBOND residue ASP (93 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Chain information for AB.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #10
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #11
---
Chain | Description
W | No description available
Chain information for X.pdb #12
---
Chain | Description
X | No description available
Chain information for Y.pdb #13
---
Chain | Description
Y | No description available
Chain information for Z.pdb #14
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #15
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #16
---
Chain | Description
g | No description available
Chain information for h.pdb #17
---
Chain | Description
h | No description available
Chain information for y1.pdb #18
---
Chain | Description
y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5-8
> hide #9-18
> hide #9-18 target c
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue GLN (123 )
Cannot find LINK/SSBOND residue THR (497 )
Cannot find LINK/SSBOND residue ASP (93 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Chain information for AB.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #10
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #11
---
Chain | Description
W | No description available
Chain information for X.pdb #12
---
Chain | Description
X | No description available
Chain information for Y.pdb #13
---
Chain | Description
Y | No description available
Chain information for Z.pdb #14
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #15
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #16
---
Chain | Description
g | No description available
Chain information for h.pdb #17
---
Chain | Description
h | No description available
Chain information for y1.pdb #18
---
Chain | Description
y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5-8
> show #9-18 target c
> hide #9-18
> hide #9-18 target c
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/IsiADC_subunits/*.pdb"
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/AB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 95 95 GLN G 10 ALA G 13 1 4
Start residue of secondary structure not found: HELIX 96 96 ARG G 19 ALA G 26
1 8
Start residue of secondary structure not found: HELIX 97 97 PHE G 31 THR G 33
1 3
Start residue of secondary structure not found: HELIX 98 98 GLU G 39 GLN G 71
1 33
Start residue of secondary structure not found: HELIX 99 99 PHE G 74 TRP G 77
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue GLN (123 )
Cannot find LINK/SSBOND residue THR (497 )
Cannot find LINK/SSBOND residue ASP (93 )
70 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/GH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
364 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
72 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/W.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
485 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
484 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
93 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/Z.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
483 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/ab1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
368 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
Cannot find LINK/SSBOND residue CLA (1237 )
73 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/g.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
94 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/h.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
486 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/IsiADC_subunits/y1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 46 ALA A 53 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 58 GLN A 61 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU A 65 LYS A 96 1
32
Start residue of secondary structure not found: HELIX 4 4 TYR A 100 ALA A 105
1 6
Start residue of secondary structure not found: HELIX 5 5 GLN A 123 LEU A 126
1 4
487 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1012 )
Cannot find LINK/SSBOND residue CLA (1139 )
96 messages similar to the above omitted
Chain information for AB.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
Chain information for GH.pdb #10
---
Chain | Description
G | No description available
H | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Chain information for W.pdb #11
---
Chain | Description
W | No description available
Chain information for X.pdb #12
---
Chain | Description
X | No description available
Chain information for Y.pdb #13
---
Chain | Description
Y | No description available
Chain information for Z.pdb #14
---
Chain | Description
Z | No description available
Chain information for ab1.pdb #15
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
Chain information for g.pdb #16
---
Chain | Description
g | No description available
Chain information for h.pdb #17
---
Chain | Description
h | No description available
Chain information for y1.pdb #18
---
Chain | Description
y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5-8
> hide #9-18
> hide #9-18 target c
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> show /A,B,C,D,E,F,I,J,K,L,M target s
> transparency #9 100 target s
> show /A,B,C,D,E,F,I,J,K,L,M target s
> show /a,b,c,d,e,f,i,j,k,l,m target s
> transparency #9-18 100 target s
> graphics selection color black width 3
> graphics silhouettes false
> graphics selection color black width 3
> select /a,b
34889 atoms, 36186 bonds, 724 pseudobonds, 3395 residues, 4 models selected
> select /A,B
17435 atoms, 18095 bonds, 363 pseudobonds, 1686 residues, 2 models selected
> select /a,b
34889 atoms, 36186 bonds, 724 pseudobonds, 3395 residues, 4 models selected
> graphics silhouettes true
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.01
> graphics silhouettes true depthJump 0.02
> graphics silhouettes true depthJump 0.03
> graphics silhouettes true depthJump 0.04
> graphics silhouettes true depthJump 0.05
> graphics silhouettes true depthJump 0.06
> graphics silhouettes true depthJump 0.07
> show #9-18 target s
> transparency #9-18 100 target s
> graphics silhouettes true depthJump 0.01
> graphics silhouettes true depthJump 0.02
> close
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/7umh_docked_J162_flipped.pdb"
Chain information for 7umh_docked_J162_flipped.pdb #1
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h n o p q r s t u v w x y | No description available
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb" format
> swissdock
Summary of feedback from opening /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb
---
warnings | Ignored bad PDB record found on line 2
Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 6
Ignored bad PDB record found on line 8
Ignored bad PDB record found on line 10
1611 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 41 41 GLN B 10 ALA B 13
1 4
Start residue of secondary structure not found: HELIX 42 42 ARG B 19 ALA B 26
1 8
Start residue of secondary structure not found: HELIX 43 43 PHE B 31 THR B 33
1 3
Start residue of secondary structure not found: HELIX 44 44 GLU B 39 GLN B 71
1 33
Start residue of secondary structure not found: HELIX 45 45 PHE B 74 TRP B 77
1 4
456 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CYS (10 )
Cannot find LINK/SSBOND residue CLA (1221 )
Cannot find LINK/SSBOND residue CLA (1216 )
97 messages similar to the above omitted
Ignored bad PDB record found on line 3
Ignored bad PDB record found on line 6
Ignored bad PDB record found on line 9
Ignored bad PDB record found on line 12
Ignored bad PDB record found on line 15
535 messages similar to the above omitted
Chain information for PSI_IsiADC_docked_J162_flipped.pdb
---
Chain | Description
2.1/A | No description available
2.2/B 2.7/G 2.28/b | No description available
2.3/C 2.14/N 2.29/c | No description available
2.4/D 2.16/P 2.30/d | No description available
2.5/E 2.15/O 2.31/e | No description available
2.6/F 2.17/Q 2.32/f | No description available
2.8/H 2.27/a | No description available
2.9/I 2.18/R 2.35/i | No description available
2.10/J 2.19/S 2.36/j | No description available
2.11/K 2.20/T 2.37/k | No description available
2.12/L 2.21/U 2.38/l | No description available
2.13/M 2.22/V 2.39/m | No description available
2.23/W | No description available
2.24/X | No description available
2.25/Y | No description available
2.26/Z | No description available
2.33/g | No description available
2.34/h 2.40/y | No description available
Computing secondary structure
[Repeated 38 time(s)]
> viewdockx #2.1-40
No suitable models found for ViewDockX
> hide #!1 models
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5-8
> hide #9-18
> hide #9-18 target c
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5-8
> hide #9
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5,6,7,8
> hide #9
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
> view matrix camera
> -0.017413,-0.083672,-0.99634,-566.37,0.99796,0.059842,-0.022467,219.55,0.061503,-0.99469,0.082459,299.53
> close
> cd "/Users/yuvalmazor/ASU Dropbox/Yuval Mazor/1_IsiADC_paper/images"
Current working directory is: /Users/yuvalmazor/ASU Dropbox/Yuval
Mazor/1_IsiADC_paper/images
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J162_006_volume_map.mrc"
Opened cryosparc_P12_J162_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.86, shown at level 0.076, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J163_002_volume_map.mrc"
Opened cryosparc_P12_J163_002_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.86, shown at level 0.071, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_map.mrc"
Opened cryosparc_P12_J164_003_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.86, shown at level 0.0691, step 2, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/data/classificationIsiADC/cryosparc_P12_J164_003_volume_mask_refine.mrc"
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc as #4, grid size
512,512,512, pixel 0.86, shown at level 1, step 2, values float32
> volume flip #* axis y
Opened cryosparc_P12_J162_006_volume_map.mrc y flip as #5, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J163_002_volume_map.mrc y flip as #6, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_map.mrc y flip as #7, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
Opened cryosparc_P12_J164_003_volume_mask_refine.mrc y flip as #8, grid size
512,512,512, pixel 0.86, shown at step 1, values float32
> open "/Users/yuvalmazor/ASU Dropbox/Yuval
> Mazor/1_IsiADC_paper/images/PSI_IsiADC_docked_J162_flipped.pdb"
Chain information for PSI_IsiADC_docked_J162_flipped.pdb #9
---
Chain | Description
A H a | No description available
B G b | No description available
C N c | No description available
D P d | No description available
E O e | No description available
F Q f | No description available
I R i | No description available
J S j | No description available
K T k | No description available
L U l | No description available
M V m | No description available
W X Y Z g h y | No description available
> volume #8 level 0.02292 step 4
> volume #5,6,7 level 0.1 step 1
> set bgColor white
> graphics silhouettes true width 3
> lighting depthCue false
> hide #5,6,7,8
> hide #9
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 89, in flip_matrix
m = m[:,::-1,:]
~^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 7 days, 20 hours, 46 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Matrix is None |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This was fixed a month ago in the daily builds right after the ChimeraX 1.9 release. The problem is related to reading the map values to draw the flipped map when the original map has not yet been shown. That happens when you run all the commands as a script but does not happen when you run the commands by hand because when running by hand the original map is shown before you run the flip command. The daily build handles this correctly even if the original map has not been shown.
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Reported by Yuval Mazor