![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Last modified 3 months ago
#18239 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x0000000209bf9f00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.segment._segment (total: 63)
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"procLaunch" : "2025-07-17 08:54:25.7260 +0200",
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"procExitAbsTime" : 36528142095765,
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 283073,
"sleepWakeUUID" : "FC13EE64-4579-4306-9DC7-998490E4CC80",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":45906},
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/tRNA_coding.cxs
Opened cryosparc_P346_J194_003_volume_map.mrc as #1.1.1.1, grid size
384,384,384, pixel 1.19, shown at level 0.293, step 1, values float32
Log from Wed Jul 16 16:56:30 2025 Startup Messages
---
warning | Registration file '/Users/roan.groh/Library/Application Support/ChimeraX/registration' has expired
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 6sgc
Summary of feedback from opening 6sgc fetched from pdb
---
notes | Fetching compressed mmCIF 6sgc from http://files.rcsb.org/download/6sgc.cif
Fetching CCD 12A from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/12A/12A.cif
Fetching CCD 2MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/2MU/2MU.cif
Fetching CCD 70U from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/70U/70U.cif
Fetching CCD H2U from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/H2U/H2U.cif
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc #1
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #1
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide atoms
> show cartoons
> hide atoms
[Repeated 1 time(s)]
> hide cartoons
> select #1/XX,23
1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected
> show sel cartoons
> save sel
Cannot determine format for 'sel'
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J194_003_volume_map.mrc
Opened cryosparc_P346_J194_003_volume_map.mrc as #2, grid size 384,384,384,
pixel 1.19, shown at level 0.252, step 2, values float32
> select add #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select subtract #1
Nothing selected
> select add #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> show sel cartoons
[Repeated 1 time(s)]
> set bgColor white
> lighting simple
> lighting soft
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.026961,0.87835,-0.47725,123.11,0.33104,-0.45833,-0.82483,567.07,-0.94323,-0.13575,-0.30313,637.8
> view matrix models
> #1,-0.56288,0.56327,-0.6049,398.21,-0.26259,-0.81579,-0.51529,734.29,-0.78372,-0.13121,0.6071,344.19
> view matrix models
> #1,-0.97792,-0.20882,-0.0084945,560.96,0.1812,-0.86744,0.46338,366.38,-0.10413,0.45161,0.88612,-72.908
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.97792,-0.20882,-0.0084945,601.58,0.1812,-0.86744,0.46338,344.47,-0.10413,0.45161,0.88612,-74.691
> view matrix models
> #1,-0.97792,-0.20882,-0.0084945,562.3,0.1812,-0.86744,0.46338,314.21,-0.10413,0.45161,0.88612,-118.43
> fitmap #1 inMap #2
Fit molecule 6sgc (#1) to map cryosparc_P346_J194_003_volume_map.mrc (#2)
using 218966 atoms
average map value = 0.1316, steps = 488
shifted from previous position = 34.8
rotated from previous position = 8.48 degrees
atoms outside contour = 183320, contour level = 0.25215
Position of 6sgc (#1) relative to cryosparc_P346_J194_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98066463 -0.14575461 -0.13058515 590.89285007
0.06111114 -0.86200261 0.50320664 304.88092255
-0.18590942 0.48549674 0.85424270 -82.49763079
Axis -0.08242257 0.25748142 0.96276157
Axis point 283.02756345 179.88973883 0.00000000
Rotation angle (degrees) 173.83260911
Shift along axis -49.62728285
> select subtract #1
Nothing selected
Window position QRect(1985,1064 575x259) outside any known screen, using
primary screen
> volume #2 step 1
> volume #2 level 0.2106
> select add #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select subtract #1
Nothing selected
> select add #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> hide sel cartoons
> select #1/XX,23
1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected
> show sel cartoons
> select add #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select subtract #1
Nothing selected
> color #2 #b2b2b27d models
> color #2 #b2b2b2b7 models
> color #2 #009193ff models
> color #2 #009193a3 models
> color #2 #00919380 models
> ui mousemode right translate
> ui mousemode right zoom
> volume #2 level 0.2487
> clipper associate #2 toModel #1
Opened cryosparc_P346_J194_003_volume_map.mrc as #1.1.1.1, grid size
384,384,384, pixel 1.19, shown at level 0.312, step 1, values float32
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc
---
Chain | Description | UniProt
1.2/23 1.2/33 | tRNA (Lys3) |
1.2/54 | 28S ribosomal RNA |
1.2/74 | 5S ribosomal RNA |
1.2/84 | 5.8S ribosomal RNA |
1.2/A1 | 18S ribosomal RNA |
1.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
1.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217
1.2/B1 | uS2 |
1.2/B2 | uL3 | G1TL06_RABIT 2-403
1.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
1.2/C2 | uL4 |
1.2/D1 | uS5 |
1.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
1.2/E1 | uS5 | G1TNM3_RABIT 1-243
1.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
1.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
1.2/F2 | uL30 | G1TUB1_RABIT 1-247
1.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
1.2/G2 | eL8 |
1.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
1.2/H2 | uL6 | G1TX33_RABIT 1-192
1.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
1.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
1.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
1.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
1.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
1.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
1.2/L2 | eL13 |
1.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
1.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
1.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
1.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
1.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
1.2/O2 | uL13 |
1.2/P1 | uS11 |
1.2/P2 | uL22 | G1TVT6_RABIT 1-184
1.2/Q1 | uS19 | G1U0Q2_RABIT 1-145
1.2/Q2 | eL18 |
1.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
1.2/R2 | eL19 |
1.2/S1 | eS17 | G1TU13_RABIT 1-135
1.2/S2 | eL20 |
1.2/T1 | eS13 | G1TPG3_RABIT 1-152
1.2/T2 | eL21 | G1SHQ2_RABIT 1-160
1.2/U1 | eS19 | G1TN62_RABIT 1-145
1.2/U2 | eL22 |
1.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
1.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
1.2/W1 | eS21 |
1.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
1.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
1.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
1.2/XX | poly-lysine nascent chain |
1.2/Y1 | uS12 |
1.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
1.2/Z1 | eS24 |
1.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
1.2/a1 | eS25 | G1TDB3_RABIT 1-125
1.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
1.2/b1 | eS26 |
1.2/b2 | eL29 |
1.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
1.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
1.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
1.2/d2 | eL31 | G1SHG0_RABIT 1-125
1.2/e1 | uS14 | G1U7M4_RABIT 1-56
1.2/e2 | eL32 | G1U437_RABIT 1-135
1.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
1.2/f2 | eL33 | G1SF08_RABIT 1-110
1.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
1.2/g2 | eL34 | G1U945_RABIT 1-116
1.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
1.2/h2 | uL29 | G1SIT5_RABIT 1-123
1.2/i1 | polyA mRNA |
1.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
1.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
1.2/k2 | eL38 | G1U001_RABIT 1-70
1.2/l2 | eL39 | G1TTN1_RABIT 1-51
1.2/m2 | eL40 |
1.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
1.2/o2 | eL42 | G1U344_RABIT 1-106
1.2/p2 | eL43 | G1SY53_RABIT 1-92
1.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
1.2/s2 | uL10 |
1.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #1.2
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> vop #1 st volume #1 st vop #1 style surface
> transparency #1 50
> volume #1.1.1.1 level 0.1719
> hide atoms
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> select #1/XX,23
1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected
> show #!1.2 models
> open 6sgc
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc #2
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #2
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> select add #1.2
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select add #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 10 models
selected
> select add #2
437932 atoms, 469824 bonds, 11698 pseudobonds, 35902 residues, 14 models
selected
> select subtract #1
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.30353,0.95259,-0.020974,-94.412,0.20733,-0.087513,-0.97435,532.35,-0.92999,0.29139,-0.22406,488.97
> view matrix models
> #2,-0.9081,0.082743,-0.41051,570.36,-0.30149,-0.80952,0.50377,460.01,-0.29063,0.58124,0.76007,-28.529
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.9081,0.082743,-0.41051,597.68,-0.30149,-0.80952,0.50377,438.49,-0.29063,0.58124,0.76007,-10.954
> view matrix models
> #2,-0.9081,0.082743,-0.41051,578.02,-0.30149,-0.80952,0.50377,399.84,-0.29063,0.58124,0.76007,-54.959
Must specify one map, got 0
> close #1
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J194_003_volume_map.mrc
Opened cryosparc_P346_J194_003_volume_map.mrc as #1, grid size 384,384,384,
pixel 1.19, shown at level 0.252, step 2, values float32
> fitmap #2 inMap #1
Fit molecule 6sgc (#2) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
using 218966 atoms
average map value = 0.1873, steps = 284
shifted from previous position = 12.9
rotated from previous position = 21.1 degrees
atoms outside contour = 165465, contour level = 0.25215
Position of 6sgc (#2) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.98229801 -0.13687159 -0.12789363 585.89147373
0.03751455 -0.81264194 0.58155459 275.19570461
-0.18353003 0.56646204 0.80339124 -94.67478878
Axis -0.08217323 0.30291927 0.94946694
Axis point 281.77911784 166.78862352 0.00000000
Rotation angle (degrees) 174.73089241
Shift along axis -54.67309215
> open 6sgc
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc #3
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #3
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> select subtract #2
Nothing selected
> select add #3
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.96108,-0.064244,-0.26868,586.96,0.1585,-0.92482,-0.34581,612.84,-0.22627,-0.37494,0.89901,193.46
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.96108,-0.064244,-0.26868,608.73,0.1585,-0.92482,-0.34581,540.2,-0.22627,-0.37494,0.89901,213.61
> fitmap #3 inMap #1
Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
using 218966 atoms
average map value = 0.06041, steps = 168
shifted from previous position = 28.9
rotated from previous position = 6.05 degrees
atoms outside contour = 201607, contour level = 0.25215
Position of 6sgc (#3) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.97980063 -0.08877694 -0.17919092 591.56129031
0.14110944 -0.94185710 -0.30494807 535.96571783
-0.14169988 -0.32407384 0.93535944 137.77850284
Axis -0.08183641 -0.16041873 0.98365067
Axis point 285.53422334 296.84958914 0.00000000
Rotation angle (degrees) 173.28944637
Shift along axis 1.13571978
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.95798,0.046422,-0.28305,575.71,0.027314,-0.96757,-0.25114,557.16,-0.28552,-0.24832,0.92564,154.77
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.95798,0.046422,-0.28305,572.66,0.027314,-0.96757,-0.25114,540.9,-0.28552,-0.24832,0.92564,129.09
> fitmap #3 inMap #1
Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
using 218966 atoms
average map value = 0.0663, steps = 100
shifted from previous position = 2.69
rotated from previous position = 1.43 degrees
atoms outside contour = 199648, contour level = 0.25215
Position of 6sgc (#3) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.95684098 0.05053273 -0.28618487 574.31564589
0.03132374 -0.96109585 -0.27443323 543.89064126
-0.28891895 -0.27155334 0.91803302 137.30438044
Axis 0.14681952 0.13938622 -0.97929337
Axis point 298.80326321 280.28829116 0.00000000
Rotation angle (degrees) 179.43805844
Shift along axis 25.67033918
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view matrix models
> #3,-0.95684,0.050533,-0.28618,590.35,0.031324,-0.9611,-0.27443,581.63,-0.28892,-0.27155,0.91803,167.76
> view matrix models
> #3,-0.95684,0.050533,-0.28618,569.34,0.031324,-0.9611,-0.27443,545.91,-0.28892,-0.27155,0.91803,122.47
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.98737,-0.085662,-0.13329,574.09,0.10658,-0.98156,-0.1587,500.82,-0.11723,-0.1709,0.97829,33.411
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.98737,-0.085662,-0.13329,573.07,0.10658,-0.98156,-0.1587,508.71,-0.11723,-0.1709,0.97829,49.178
> fitmap #3 inMap #1
Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
using 218966 atoms
average map value = 0.1316, steps = 724
shifted from previous position = 3.53
rotated from previous position = 39.4 degrees
atoms outside contour = 183320, contour level = 0.25215
Position of 6sgc (#3) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.98066245 -0.14578975 -0.13056231 590.90929382
0.06115674 -0.86200822 0.50319150 304.88736380
-0.18590595 0.48547624 0.85425511 -82.50217123
Axis -0.08241564 0.25747188 0.96276471
Axis point 283.03227912 179.89992220 0.00000000
Rotation angle (degrees) 173.83021276
Shift along axis -49.63042116
> show #!2 models
> matchmaker #3 to #1
No 'to' model specified
> matchmaker #3 to #2
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6sgc, chain 54 (#2) with 6sgc, chain 54 (#3), sequence alignment
score = 21821.5
RMSD between 3603 pruned atom pairs is 0.000 angstroms; (across all 3603
pairs: 0.000)
> clipper associate #1 toModel #2
Opened cryosparc_P346_J194_003_volume_map.mrc as #1.1.1.1, grid size
384,384,384, pixel 1.19, shown at level 0.326, step 1, values float32
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc
---
Chain | Description | UniProt
1.2/23 1.2/33 | tRNA (Lys3) |
1.2/54 | 28S ribosomal RNA |
1.2/74 | 5S ribosomal RNA |
1.2/84 | 5.8S ribosomal RNA |
1.2/A1 | 18S ribosomal RNA |
1.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
1.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217
1.2/B1 | uS2 |
1.2/B2 | uL3 | G1TL06_RABIT 2-403
1.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
1.2/C2 | uL4 |
1.2/D1 | uS5 |
1.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
1.2/E1 | uS5 | G1TNM3_RABIT 1-243
1.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
1.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
1.2/F2 | uL30 | G1TUB1_RABIT 1-247
1.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
1.2/G2 | eL8 |
1.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
1.2/H2 | uL6 | G1TX33_RABIT 1-192
1.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
1.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
1.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
1.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
1.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
1.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
1.2/L2 | eL13 |
1.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
1.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
1.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
1.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
1.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
1.2/O2 | uL13 |
1.2/P1 | uS11 |
1.2/P2 | uL22 | G1TVT6_RABIT 1-184
1.2/Q1 | uS19 | G1U0Q2_RABIT 1-145
1.2/Q2 | eL18 |
1.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
1.2/R2 | eL19 |
1.2/S1 | eS17 | G1TU13_RABIT 1-135
1.2/S2 | eL20 |
1.2/T1 | eS13 | G1TPG3_RABIT 1-152
1.2/T2 | eL21 | G1SHQ2_RABIT 1-160
1.2/U1 | eS19 | G1TN62_RABIT 1-145
1.2/U2 | eL22 |
1.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
1.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
1.2/W1 | eS21 |
1.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
1.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
1.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
1.2/XX | poly-lysine nascent chain |
1.2/Y1 | uS12 |
1.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
1.2/Z1 | eS24 |
1.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
1.2/a1 | eS25 | G1TDB3_RABIT 1-125
1.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
1.2/b1 | eS26 |
1.2/b2 | eL29 |
1.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
1.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
1.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
1.2/d2 | eL31 | G1SHG0_RABIT 1-125
1.2/e1 | uS14 | G1U7M4_RABIT 1-56
1.2/e2 | eL32 | G1U437_RABIT 1-135
1.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
1.2/f2 | eL33 | G1SF08_RABIT 1-110
1.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
1.2/g2 | eL34 | G1U945_RABIT 1-116
1.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
1.2/h2 | uL29 | G1SIT5_RABIT 1-123
1.2/i1 | polyA mRNA |
1.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
1.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
1.2/k2 | eL38 | G1U001_RABIT 1-70
1.2/l2 | eL39 | G1TTN1_RABIT 1-51
1.2/m2 | eL40 |
1.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
1.2/o2 | eL42 | G1U344_RABIT 1-106
1.2/p2 | eL43 | G1SY53_RABIT 1-92
1.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
1.2/s2 | uL10 |
1.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #1.2
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide sel atoms
> hide sel cartoons
> select #1/XX,23
1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected
> select #3/XX,23
1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected
> show sel cartoons
> vop #1 style surface
> transparency #1 50
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,629.65,0.037515,-0.81264,0.58155,222.2,-0.18353,0.56646,0.80339,-63.905
> select add #3
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select subtract #3
Nothing selected
> ui mousemode right translate
> ui mousemode right zoom
> select #3/23
1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected
> view sel
> select #3/xx
Nothing selected
> view sel
No objects specified.
> select #3/XX
100 atoms, 99 bonds, 16 residues, 1 model selected
> view sel
> hide #!1.2 models
> volume #1.1.1.1 level 0.09475
> volume #1.1.1.1 level 0.1824
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> style sel stick
Changed 100 atom styles
> style sel stick
Changed 100 atom styles
> hide sel atoms
> select #3/23
1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 1636 atom styles
> volume #1.1.1.1 level 0.1906
> volume #1.1.1.1 level 0.1842
> volume #1.1.1.1 level 0.2934
> save "/Users/roan.groh/Documents/OneDrive -
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/tRNA_coding.cxs"
——— End of log from Wed Jul 16 16:56:30 2025 ———
opened ChimeraX session
> open 6sgc
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc #2
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #2
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
> Refine_tRNA/cryosparc_P618_J54_003_volume_map.mrc
Opened cryosparc_P618_J54_003_volume_map.mrc as #4, grid size 384,384,384,
pixel 1.19, shown at level 0.29, step 2, values float32
> volume #4 step 1
> select add #3
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!2 models
> show #!2 models
> select add #2
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.81877,0.18205,0.5445,254.6,0.57124,0.16331,0.80438,-124.57,0.05751,0.96963,-0.23771,47.766
> view matrix models
> #2,-0.99925,0.027104,0.027539,488.09,-0.0039227,-0.78019,0.62553,342.85,0.03844,0.62496,0.77971,-129.5
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.99925,0.027104,0.027539,531.74,-0.0039227,-0.78019,0.62553,299.63,0.03844,0.62496,0.77971,-123.01
> view matrix models
> #2,-0.99925,0.027104,0.027539,500.7,-0.0039227,-0.78019,0.62553,258.34,0.03844,0.62496,0.77971,-158.51
> fitmap #2 inMap #4
Fit molecule 6sgc (#2) to map cryosparc_P618_J54_003_volume_map.mrc (#4) using
218966 atoms
average map value = 0.2332, steps = 208
shifted from previous position = 10.1
rotated from previous position = 14.2 degrees
atoms outside contour = 145921, contour level = 0.28985
Position of 6sgc (#2) relative to cryosparc_P618_J54_003_volume_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.97989020 -0.11868533 -0.16040260 588.93884983
0.00560370 -0.81992322 0.57244608 289.42161497
-0.19945877 0.56003545 0.80409980 -88.70086500
Axis -0.09483113 0.29843296 0.94970776
Axis point 284.77379625 168.71493739 0.00000000
Rotation angle (degrees) 176.24814645
Shift along axis -53.71668938
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select subtract #2
Nothing selected
> clipper associate #4 toModel #2
Opened cryosparc_P618_J54_003_volume_map.mrc as #2.1.1.1, grid size
384,384,384, pixel 1.19, shown at level 0.402, step 1, values float32
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc
---
Chain | Description | UniProt
2.2/23 2.2/33 | tRNA (Lys3) |
2.2/54 | 28S ribosomal RNA |
2.2/74 | 5S ribosomal RNA |
2.2/84 | 5.8S ribosomal RNA |
2.2/A1 | 18S ribosomal RNA |
2.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
2.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217
2.2/B1 | uS2 |
2.2/B2 | uL3 | G1TL06_RABIT 2-403
2.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
2.2/C2 | uL4 |
2.2/D1 | uS5 |
2.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
2.2/E1 | uS5 | G1TNM3_RABIT 1-243
2.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
2.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
2.2/F2 | uL30 | G1TUB1_RABIT 1-247
2.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
2.2/G2 | eL8 |
2.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
2.2/H2 | uL6 | G1TX33_RABIT 1-192
2.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
2.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
2.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
2.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
2.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
2.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
2.2/L2 | eL13 |
2.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
2.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
2.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
2.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
2.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
2.2/O2 | uL13 |
2.2/P1 | uS11 |
2.2/P2 | uL22 | G1TVT6_RABIT 1-184
2.2/Q1 | uS19 | G1U0Q2_RABIT 1-145
2.2/Q2 | eL18 |
2.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
2.2/R2 | eL19 |
2.2/S1 | eS17 | G1TU13_RABIT 1-135
2.2/S2 | eL20 |
2.2/T1 | eS13 | G1TPG3_RABIT 1-152
2.2/T2 | eL21 | G1SHQ2_RABIT 1-160
2.2/U1 | eS19 | G1TN62_RABIT 1-145
2.2/U2 | eL22 |
2.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
2.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
2.2/W1 | eS21 |
2.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
2.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
2.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
2.2/XX | poly-lysine nascent chain |
2.2/Y1 | uS12 |
2.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
2.2/Z1 | eS24 |
2.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
2.2/a1 | eS25 | G1TDB3_RABIT 1-125
2.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
2.2/b1 | eS26 |
2.2/b2 | eL29 |
2.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
2.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
2.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
2.2/d2 | eL31 | G1SHG0_RABIT 1-125
2.2/e1 | uS14 | G1U7M4_RABIT 1-56
2.2/e2 | eL32 | G1U437_RABIT 1-135
2.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
2.2/f2 | eL33 | G1SF08_RABIT 1-110
2.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
2.2/g2 | eL34 | G1U945_RABIT 1-116
2.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
2.2/h2 | uL29 | G1SIT5_RABIT 1-123
2.2/i1 | polyA mRNA |
2.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
2.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
2.2/k2 | eL38 | G1U001_RABIT 1-70
2.2/l2 | eL39 | G1TTN1_RABIT 1-51
2.2/m2 | eL40 |
2.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
2.2/o2 | eL42 | G1U344_RABIT 1-106
2.2/p2 | eL43 | G1SY53_RABIT 1-92
2.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
2.2/s2 | uL10 |
2.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #2.2
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> show #!3 models
> hide #!3 models
> vop #2 style surface
> transparency #2 50
> volume #2.1.1.1 level 0.1905
> show #!3 models
> hide #!2.2 models
> volume #2.1.1.1 level 0.3129
> hide #!1 models
> volume #2.1.1.1 level 0.2558
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select add #2.2
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select subtract #2.2
Nothing selected
> select add #3
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,587.59,0.037515,-0.81264,0.58155,274.91,-0.18353,0.56646,0.80339,-95.128
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,588.14,0.037515,-0.81264,0.58155,275.91,-0.18353,0.56646,0.80339,-92.203
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,587.24,0.037515,-0.81264,0.58155,277.52,-0.18353,0.56646,0.80339,-93.442
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,587.68,0.037515,-0.81264,0.58155,277.73,-0.18353,0.56646,0.80339,-93.749
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,587.75,0.037515,-0.81264,0.58155,277.72,-0.18353,0.56646,0.80339,-93.851
> volume #2.1.1.1 level 0.3499
> open from emdb:10181
'from' has no suffix
> open emdb:10181
Summary of feedback from opening 10181 fetched from emdb
---
notes | Fetching compressed map 10181 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10181/map/emd_10181.map.gz
Fetching map header 10181 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10181/header/emd-10181.xml
Opened emdb 10181 as #4, grid size 512,512,512, pixel 1.09, shown at level
0.05, step 2, values float32, fit PDB 6sgc
> hide #!2 models
> select subtract #3
Nothing selected
> hide #!3 models
> volume #4 step 1
> open 6sgc
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc #5
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #5
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide #!5 atoms
> show #!5 cartoons
> clipper associate #4 toModel #5
Opened emdb 10181 as #4.1.1.1, grid size 512,512,512, pixel 1.09, shown at
level 0.0864, step 1, values float32
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc
---
Chain | Description | UniProt
4.2/23 4.2/33 | tRNA (Lys3) |
4.2/54 | 28S ribosomal RNA |
4.2/74 | 5S ribosomal RNA |
4.2/84 | 5.8S ribosomal RNA |
4.2/A1 | 18S ribosomal RNA |
4.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
4.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217
4.2/B1 | uS2 |
4.2/B2 | uL3 | G1TL06_RABIT 2-403
4.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
4.2/C2 | uL4 |
4.2/D1 | uS5 |
4.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
4.2/E1 | uS5 | G1TNM3_RABIT 1-243
4.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
4.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
4.2/F2 | uL30 | G1TUB1_RABIT 1-247
4.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
4.2/G2 | eL8 |
4.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
4.2/H2 | uL6 | G1TX33_RABIT 1-192
4.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
4.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
4.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
4.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
4.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
4.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
4.2/L2 | eL13 |
4.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
4.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
4.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
4.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
4.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
4.2/O2 | uL13 |
4.2/P1 | uS11 |
4.2/P2 | uL22 | G1TVT6_RABIT 1-184
4.2/Q1 | uS19 | G1U0Q2_RABIT 1-145
4.2/Q2 | eL18 |
4.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
4.2/R2 | eL19 |
4.2/S1 | eS17 | G1TU13_RABIT 1-135
4.2/S2 | eL20 |
4.2/T1 | eS13 | G1TPG3_RABIT 1-152
4.2/T2 | eL21 | G1SHQ2_RABIT 1-160
4.2/U1 | eS19 | G1TN62_RABIT 1-145
4.2/U2 | eL22 |
4.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
4.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
4.2/W1 | eS21 |
4.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
4.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
4.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
4.2/XX | poly-lysine nascent chain |
4.2/Y1 | uS12 |
4.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
4.2/Z1 | eS24 |
4.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
4.2/a1 | eS25 | G1TDB3_RABIT 1-125
4.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
4.2/b1 | eS26 |
4.2/b2 | eL29 |
4.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
4.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
4.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
4.2/d2 | eL31 | G1SHG0_RABIT 1-125
4.2/e1 | uS14 | G1U7M4_RABIT 1-56
4.2/e2 | eL32 | G1U437_RABIT 1-135
4.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
4.2/f2 | eL33 | G1SF08_RABIT 1-110
4.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
4.2/g2 | eL34 | G1U945_RABIT 1-116
4.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
4.2/h2 | uL29 | G1SIT5_RABIT 1-123
4.2/i1 | polyA mRNA |
4.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
4.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
4.2/k2 | eL38 | G1U001_RABIT 1-70
4.2/l2 | eL39 | G1TTN1_RABIT 1-51
4.2/m2 | eL40 |
4.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
4.2/o2 | eL42 | G1U344_RABIT 1-106
4.2/p2 | eL43 | G1SY53_RABIT 1-92
4.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
4.2/s2 | uL10 |
4.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #4.2
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> vop #4 style surface
> transparency #4 50
> hide #!4.2 models
> hide #!4 models
> show #!1 models
> show #!3 models
> view #3 clip false
> show #!2 models
> hide #!1 models
> show #!1.2 models
> hide #!1.2 models
> hide #!1 models
> hide #!3 models
> volume #2.1.1.1 color #00f900
> volume #2.1.1.1 color #00f90080
> volume #2.1.1.1 color #76d6ff
> volume #2.1.1.1 color #76d6ff7e
> volume #2.1.1.1 level 0.4425
> volume #2.1.1.1 level 0.4209
> show #!1 models
> volume #1.1.1.1 color #ffd479
> volume #1.1.1.1 color #ffd47980
> hide #!2 models
> rename #2 "Germ - Data manager (6sgc)"
> rename #1 "Dehyd - Data manager (6sgc)"
> volume #1.1.1.1 level 0.3165
> open /Users/roan.groh/Downloads/cryosparc_P618_J123_003_volume_map.mrc
Opened cryosparc_P618_J123_003_volume_map.mrc as #5, grid size 384,384,384,
pixel 1.19, shown at level 0.274, step 2, values float32
> hide #!1 models
> volume #5 step 1
> open /Users/roan.groh/Downloads/cryosparc_P346_J294_005_volume_map.mrc
Opened cryosparc_P346_J294_005_volume_map.mrc as #6, grid size 384,384,384,
pixel 1.19, shown at level 0.181, step 2, values float32
> hide #!5 models
> volume #6 step 1
> show #!5 models
> hide #!6 models
> lighting full
> hide #!5 models
> show #!1 models
> show #!3 models
> volume #1.1.1.1 level 0.27
> volume #1.1.1.1 level 0.2003
> volume #2.1.1.1 level 0.4396
> volume #1.1.1.1 level 0.2502
> volume #1.1.1.1 level 0.3153
> fitmap #3/23 inMap #1.1.1.1 moveWholeMolecules false
Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc
(#1.1.1.1) using 1636 atoms
average map value = 0.221, steps = 2000
shifted from previous position = 15.6
rotated from previous position = 27.1 degrees
atoms outside contour = 1591, contour level = 0.31528
> show #!3 models
> volume #1.1.1.1 level 0.209
> show #!1 models
> select #3/23
1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,585.26,0.037515,-0.81264,0.58155,277.28,-0.18353,0.56646,0.80339,-92.021
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,585.12,0.037515,-0.81264,0.58155,277.52,-0.18353,0.56646,0.80339,-92.179
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,585.13,0.037515,-0.81264,0.58155,277.36,-0.18353,0.56646,0.80339,-91.634
> view matrix models
> #3,-0.9823,-0.13687,-0.12789,586.96,0.037515,-0.81264,0.58155,276.15,-0.18353,0.56646,0.80339,-92.288
> volume #1.1.1.1 level 0.2732
> volume #1.1.1.1 level 0.2898
> hide #!3 models
> volume #1.1.1.1 level 0.3255
> volume #1.1.1.1 level 0.3775
> show #!3 models
> volume #1.1.1.1 level 0.3157
> ui tool show "Side View"
> volume #1.1.1.1 level 0.362
> hide #!3 models
> show #!3 models
> show #3
> combine #3
> vop copy #1.1.1.1
Opened cryosparc_P346_J194_003_volume_map.mrc copy as #8, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
> hide #!4.1 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> hide #4.3 models
> hide #!1 models
> hide all
> hide #!3 models
> show #!7 models
> show #!8 models
> show #7 cartoons
>
Incomplete command: clipper
> clipper associate #8 toModel #7
Opened cryosparc_P346_J194_003_volume_map.mrc copy as #7.1.1.1, grid size
384,384,384, pixel 1.19, shown at level 0.321, step 1, values float32
> volume #7.1.1.1 style surface
> volume #7.1.1.1 color #00ffff2e
> graphics silhouettes true
> graphics silhouettes false
> hide #!7 models
> show #!7 models
> fitmap #7.2 inMap #7.1.1.1
Fit molecule copy of 6sgc (#7.2) to map cryosparc_P346_J194_003_volume_map.mrc
copy (#7.1.1.1) using 218966 atoms
average map value = 0.4603, steps = 68
shifted from previous position = 2.05
rotated from previous position = 0.26 degrees
atoms outside contour = 218565, contour level = 0.32099
Position of copy of 6sgc (#7.2) relative to
cryosparc_P346_J194_003_volume_map.mrc copy (#7.1.1.1) coordinates:
Matrix rotation and translation
0.99999709 0.00222344 -0.00093537 -0.87117785
-0.00222702 0.99999010 -0.00385125 0.52470336
0.00092680 0.00385332 0.99999215 -2.77644893
Axis 0.84755359 -0.20485167 -0.48958013
Axis point 0.00000000 655.62973529 161.86802583
Rotation angle (degrees) 0.26042055
Shift along axis 0.51343796
Must specify one map, got 0
> fitmap #7/23 inMap #7 moveWholeMolecules false
Fit molecule copy of 6sgc (#7.2) to map cryosparc_P346_J194_003_volume_map.mrc
copy (#7.1.1.1) using 1636 atoms
average map value = 0.2437, steps = 2000
shifted from previous position = 17.4
rotated from previous position = 24.6 degrees
atoms outside contour = 1604, contour level = 0.32099
> fitmap #7/i1 inMap #7 moveWholeMolecules false
Fit molecule copy of 6sgc (#7.2) to map cryosparc_P346_J194_003_volume_map.mrc
copy (#7.1.1.1) using 220 atoms
average map value = 0.4058, steps = 48
shifted from previous position = 2.11
rotated from previous position = 5.88 degrees
atoms outside contour = 155, contour level = 0.32099
> select #7/23
1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected
> view matrix models
> #7.2,1,0.0022234,-0.00093537,0.84805,-0.002227,0.99999,-0.0038512,-0.88697,0.0009268,0.0038533,0.99999,-2.4048
> undo
> view matrix models
> #7.2,1,0.0022234,-0.00093537,-0.40992,-0.002227,0.99999,-0.0038512,0.12743,0.0009268,0.0038533,0.99999,-2.6681
> view matrix models
> #7.2,1,0.0022234,-0.00093537,0.16347,-0.002227,0.99999,-0.0038512,-0.57566,0.0009268,0.0038533,0.99999,-2.4359
> undo
> hide #!7.1 models
> show #!7.1 models
> hide #!7.2 models
> volume #7.1.1.1 level 0.2887
> show #!7.2 models
> vop copy #1.1.1.1
Opened cryosparc_P346_J194_003_volume_map.mrc copy as #8, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
> combine §3
Expected a keyword
> hide #!7 models
> select ~sel & ##selected
217330 atoms, 233088 bonds, 5777 pseudobonds, 17875 residues, 4 models
selected
> combine #3
> hide #!9 models
> show #!9 models
> show #9 cartoons
> hide #!9 models
> show #!9 models
> hide #!8 models
> log metadata #9
No models had metadata
> log chains #9
Chain information for copy of 6sgc #9
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
> color #9 darkgrey
> select #9/54,74,84,A1
119522 atoms, 133395 bonds, 5630 pseudobonds, 5835 residues, 4 models selected
> color sel white
> show #!8 models
> hide #!9 models
> color zone #9 ear #9 d 6
Expected a keyword
> color zone #9 near #9 distance 6
color zone: No surfaces specified.
> color zone #8 near #9 distance 6
> color #8 white
> graphics silhouettes true
> color #8 ivory
> color #8 floral white
> select up
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> select up
218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
selected
> color #8 antique white
> color zone #8 near #9 distance
Missing "distance" keyword's argument
> color zone #8 near #9 distance 6
> lighting full
> lighting soft
> volume #8 level 0.362
> volume #8 level 0.3406
> volume #8 level 0.3121
> vop copy #8
Opened cryosparc_P346_J194_003_volume_map.mrc copy as #10, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
> color #8 #275c70
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!10 models
> show #!10 models
> select subtract #9
Nothing selected
> open 8b2l
Summary of feedback from opening 8b2l fetched from pdb
---
warning | Atom H1 is not in the residue template for UNK /l3:1
8b2l title:
Cryo-EM structure of the plant 80S ribosome [more info...]
Chain information for 8b2l #11
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
Non-standard residues in 8b2l #11
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
> select add #11
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> show sel cartoons
> show sel atoms
> show sel cartoons
> hide #!8 models
> show #!8 models
> hide #!10 models
> hide #!7.1 models
> hide #!7.2 models
> hide #7.3 models
> hide sel atoms
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.60126,-0.076592,-0.79537,252.21,0.71674,-0.38832,0.57922,-33.46,-0.35322,-0.91834,-0.17859,457.44
> hide #!8 models
> view matrix models
> #11,0.056689,-0.99181,0.11448,338.95,-0.96828,-0.026667,0.24845,323.63,-0.24336,-0.12493,-0.96186,456.85
> show #!8 models
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.056689,-0.99181,0.11448,399.17,-0.96828,-0.026667,0.24845,320.3,-0.24336,-0.12493,-0.96186,453.26
> fitmap #11 inMap #8
Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
(#8) using 361205 atoms
average map value = 0.06739, steps = 240
shifted from previous position = 39.7
rotated from previous position = 4.86 degrees
atoms outside contour = 330015, contour level = 0.3121
Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
(#8) coordinates:
Matrix rotation and translation
0.06022402 -0.99764011 0.03297469 417.16316133
-0.97223587 -0.05114300 0.22834591 352.74769363
-0.22612061 -0.04581109 -0.97302151 469.44404474
Axis -0.72514653 0.68530827 0.06719433
Axis point 0.00000000 404.49814120 229.53471827
Rotation angle (degrees) 169.10349249
Shift along axis -29.21952756
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.051847,-0.98827,-0.14366,452.05,-0.99743,-0.058364,0.041531,395.9,-0.049428,0.14113,-0.98876,404.64
> view matrix models
> #11,0.0016974,-0.99619,0.087193,418.5,-0.96519,-0.024437,-0.2604,442.84,0.26154,-0.083715,-0.96156,371.58
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.0016974,-0.99619,0.087193,404.44,-0.96519,-0.024437,-0.2604,459.37,0.26154,-0.083715,-0.96156,387.72
> fitmap #11 inMap #8
Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
(#8) using 361205 atoms
average map value = 0.1799, steps = 372
shifted from previous position = 9.02
rotated from previous position = 25.5 degrees
atoms outside contour = 272505, contour level = 0.3121
Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
(#8) coordinates:
Matrix rotation and translation
-0.23335507 -0.95789171 -0.16729893 500.38333037
-0.81858975 0.28637810 -0.49789401 417.93470463
0.52483928 0.02076310 -0.85094810 295.49305506
Axis 0.59203979 -0.79006603 0.15901122
Axis point 363.94927998 0.00000000 261.72253033
Rotation angle (degrees) 154.02202909
Shift along axis 13.03753919
> log metadata #11
Metadata for 8b2l #11
---
Title | Cryo-EM structure of the plant 80S ribosome
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y
Non-standard residues | B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
Sources (natural) | Nicotiana tabacum (common tobacco)
Nicotiana tabacum
CryoEM Map | EMDB 15806 — open map
Experimental method | Electron microscopy
Resolution | 2.20Å
> log chains #11
Chain information for 8b2l #11
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
> select #8/A3,B3,C3
Nothing selected
> select #11/A3,B3,C3
116098 atoms, 121178 bonds, 4063 pseudobonds, 7254 residues, 4 models selected
> select #11/A3,B3,C3,h1
170652 atoms, 177684 bonds, 6097 pseudobonds, 11038 residues, 4 models
selected
> color sel #6F92A0
> select add #11
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> select subtract #11
Nothing selected
> select add #11
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> color sel #275C70
> select #11/A3,B3,C3,h1
170652 atoms, 177684 bonds, 6097 pseudobonds, 11038 residues, 4 models
selected
> color sel #6F92A0
> color sel #B7C9CF
> color zone #8 near #11 distance 6
> hide #!11 models
> view matrix models
> #11,-0.23336,-0.95789,-0.1673,514.07,-0.81859,0.28638,-0.49789,398.8,0.52484,0.020763,-0.85095,303.2
> ui mousemode right zoom
> color zone #8 near #11 distance 6.5
> show #!11 models
> undo
> show #!11 models
> color zone #8 near #11 distance 6.5
> color zone #8 near #11 distance 10
> color zone #10 near #11 distance 10
> show #!10 models
> hide #!8 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> view #10 clip false
> show #!8 models
> hide #!10 models
> color zone #10 near #11 distance 6
> color zone #8 near #11 distance 6
> color zone #8 near #11 distance 10
> color zone #8 near #11 distance 6
> hide #!11 models
> view #8 clip false
> volume #8 level 0.2836
> volume #8 level 0.2622
> show #!9 models
> hide #!9 models
> show #!11 models
> log metadata #11
Metadata for 8b2l #11
---
Title | Cryo-EM structure of the plant 80S ribosome
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y
Non-standard residues | B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
Sources (natural) | Nicotiana tabacum (common tobacco)
Nicotiana tabacum
CryoEM Map | EMDB 15806 — open map
Experimental method | Electron microscopy
Resolution | 2.20Å
> log chains #11
Chain information for 8b2l #11
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
> select #10/i2,W2
Nothing selected
> select #11/i2,W2
4923 atoms, 5289 bonds, 154 pseudobonds, 172 residues, 2 models selected
> color sel red
> fitmap #11/i2,W2 inMap #8
Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
(#8) using 4923 atoms
average map value = 0.1344, steps = 180
shifted from previous position = 15.6
rotated from previous position = 16.9 degrees
atoms outside contour = 4146, contour level = 0.26224
Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
(#8) coordinates:
Matrix rotation and translation
-0.12860039 -0.94295209 -0.30708850 501.64792121
-0.66615166 0.31153354 -0.67763476 409.30420991
0.73464546 0.11742342 -0.66821241 202.11741168
Axis 0.59360052 -0.77777179 0.20666271
Axis point 358.16523541 0.00000000 276.25974704
Rotation angle (degrees) 137.95675880
Shift along axis 21.20332999
> undo
> fitmap #11 inMap #8
Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
(#8) using 361205 atoms
average map value = 0.1342, steps = 2000
shifted from previous position = 5.68
rotated from previous position = 13.2 degrees
atoms outside contour = 281306, contour level = 0.26224
Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
(#8) coordinates:
Matrix rotation and translation
-0.27913453 -0.92113472 -0.27128358 523.17175455
-0.75920050 0.38468328 -0.52500802 389.74495037
0.58796136 0.05941076 -0.80670431 266.33210522
Axis 0.55569039 -0.81700686 0.15397399
Axis point 348.17040360 0.00000000 259.58545552
Rotation angle (degrees) 148.27456620
Shift along axis 13.30543373
> select #11/i2,W2
4923 atoms, 5289 bonds, 154 pseudobonds, 172 residues, 2 models selected
> color sel red
> color zone #8 near #11 distance 6
> hide #!11 models
> volume #8 level 0.2373
> volume #8 level 0.21
> volume #8 level 0.2
> volume #8 level 0.22
> volume #8 level 0.23
> open /Users/roan.groh/Downloads/cryosparc_P346_J178_006_volume_map.mrc
Opened cryosparc_P346_J178_006_volume_map.mrc as #12, grid size 384,384,384,
pixel 1.19, shown at level 0.177, step 2, values float32
> hide #!8 models
> select add #11
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> volume #10 level 0.3228
> volume #12 step 1
> volume #12 level 0.1391
> open
> /Users/roan.groh/Downloads/cryosparc_P346_J179_class_01_00143_volume.mrc
Opened cryosparc_P346_J179_class_01_00143_volume.mrc as #13, grid size
160,160,160, pixel 2.85, shown at level 0.733, step 1, values float32
> hide #!12 models
> volume #13 level 0.2886
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P347_2023_Seedling/Seedling_Precessing/J179_3D_Classes/cryosparc_P347_J179_class_02_00023_volume.mrc
Opened cryosparc_P347_J179_class_02_00023_volume.mrc as #14, grid size
96,96,96, pixel 4.76, shown at level 1.07, step 1, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P347_2023_Seedling/Seedling_Precessing/J179_3D_Classes/cryosparc_P347_J179_class_03_00023_volume.mrc
Opened cryosparc_P347_J179_class_03_00023_volume.mrc as #15, grid size
96,96,96, pixel 4.76, shown at level 1.11, step 1, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P347_2023_Seedling/Seedling_Precessing/J179_3D_Classes/cryosparc_P347_J179_class_04_00023_volume.mrc
Opened cryosparc_P347_J179_class_04_00023_volume.mrc as #16, grid size
96,96,96, pixel 4.76, shown at level 1.07, step 1, values float32
> volume #14 level 0.5403
> volume #15 level 0.5556
> volume #16 level 0.4912
> hide #!14 models
> hide #!16 models
> hide #!13 models
> show #!13 models
> show #!11 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> select subtract #11
Nothing selected
> open
> /Users/roan.groh/Downloads/cryosparc_P346_J307_class_04_00021_volume.mrc
Opened cryosparc_P346_J307_class_04_00021_volume.mrc as #17, grid size
160,160,160, pixel 2.85, shown at level 0.768, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P346_J307_class_03_00021_volume.mrc
Opened cryosparc_P346_J307_class_03_00021_volume.mrc as #18, grid size
160,160,160, pixel 2.85, shown at level 0.813, step 1, values float32
> volume #18 level 0.4537
> volume #17 level 0.5378
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J193_004_volume_map.mrc
Opened cryosparc_P346_J193_004_volume_map.mrc as #19, grid size 384,384,384,
pixel 1.19, shown at level 0.232, step 2, values float32
> hide #!17 models
> volume #19 step 1
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!17 models
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J194_003_volume_map.mrc
Opened cryosparc_P346_J194_003_volume_map.mrc as #20, grid size 384,384,384,
pixel 1.19, shown at level 0.252, step 2, values float32
> hide #!17 models
> hide #!20 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J132_004_volume_map.mrc
Opened cryosparc_P618_J132_004_volume_map.mrc as #21, grid size 384,384,384,
pixel 1.19, shown at level 0.25, step 2, values float32
> volume #21 step 1
> volume #21 level 0.2683
> hide #!21 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J303_004_volume_map.mrc
Opened cryosparc_P346_J303_004_volume_map.mrc as #22, grid size 384,384,384,
pixel 1.19, shown at level 0.226, step 2, values float32
> volume #22 step 1
> show #!21 models
> fitmap #22 inMap #21
Fit map cryosparc_P346_J303_004_volume_map.mrc in map
cryosparc_P618_J132_004_volume_map.mrc using 565890 points
correlation = 0.964, correlation about mean = 0.8482, overlap = 1.185e+05
steps = 68, shift = 0.907, angle = 0.718 degrees
Position of cryosparc_P346_J303_004_volume_map.mrc (#22) relative to
cryosparc_P618_J132_004_volume_map.mrc (#21) coordinates:
Matrix rotation and translation
0.99999627 -0.00182036 -0.00203511 0.38077697
0.00179533 0.99992355 -0.01223441 2.39881311
0.00205723 0.01223071 0.99992309 -3.97164844
Axis 0.97598286 -0.16325517 0.14424010
Axis point 0.00000000 318.90662639 186.16711104
Rotation angle (degrees) 0.71813988
Shift along axis -0.59285781
> show #!12 models
> hide #!21 models
> hide #!22 models
> close #12
> show #!18 models
> close #1.3#2.3#4.3#7.3#1-11,13-22#1.1-2#2.1-2#4.1-2#7.1-2
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J51-53_NU-
> Refine_empty/cryosparc_P618_J51_003_volume_map.mrc
Opened cryosparc_P618_J51_003_volume_map.mrc as #1, grid size 384,384,384,
pixel 1.19, shown at level 0.254, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J51-53_NU-
> Refine_empty/cryosparc_P618_J52_004_volume_map.mrc
Opened cryosparc_P618_J52_004_volume_map.mrc as #2, grid size 384,384,384,
pixel 1.19, shown at level 0.273, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J51-53_NU-
> Refine_empty/cryosparc_P618_J53_003_volume_map.mrc
Opened cryosparc_P618_J53_003_volume_map.mrc as #3, grid size 384,384,384,
pixel 1.19, shown at level 0.275, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> fitmap #2 inMap #1
Fit map cryosparc_P618_J52_004_volume_map.mrc in map
cryosparc_P618_J51_003_volume_map.mrc using 567130 points
correlation = 0.9217, correlation about mean = 0.7276, overlap = 1.16e+05
steps = 64, shift = 1.4, angle = 1.66 degrees
Position of cryosparc_P618_J52_004_volume_map.mrc (#2) relative to
cryosparc_P618_J51_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999197 0.00353107 -0.00189288 -0.16361357
-0.00358405 0.99957996 -0.02875854 7.11086549
0.00179053 0.02876509 0.99958460 -7.88726609
Axis 0.99043913 -0.06342073 -0.12250774
Axis point 0.00000000 276.21517511 244.00569150
Rotation angle (degrees) 1.66407218
Shift along axis 0.35322557
> fitmap #3 inMap #1
Fit map cryosparc_P618_J53_003_volume_map.mrc in map
cryosparc_P618_J51_003_volume_map.mrc using 565425 points
correlation = 0.915, correlation about mean = 0.7278, overlap = 1.122e+05
steps = 80, shift = 1.36, angle = 1.68 degrees
Position of cryosparc_P618_J53_003_volume_map.mrc (#3) relative to
cryosparc_P618_J51_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99998937 0.00398957 -0.00231164 -0.16580550
-0.00405496 0.99957087 -0.02901086 7.24709610
0.00219491 0.02901992 0.99957642 -8.03134002
Axis 0.98761026 -0.07669586 -0.13690770
Axis point 0.00000000 278.56071744 246.69042691
Rotation angle (degrees) 1.68355743
Shift along axis 0.37997882
> vop gaussian #1,2,3 sdev 1
Opened cryosparc_P618_J51_003_volume_map.mrc gaussian as #4, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
Opened cryosparc_P618_J52_004_volume_map.mrc gaussian as #5, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
Opened cryosparc_P618_J53_003_volume_map.mrc gaussian as #6, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
> open emdb:15872
Opened emdb 15872 as #7, grid size 348,348,348, pixel 1.72, shown at level
0.0016, step 2, values float32
> open emdb:15874
Opened emdb 15874 as #8, grid size 348,348,348, pixel 1.72, shown at level
0.0032, step 2, values float32
> open emdb:15876
Opened emdb 15876 as #9, grid size 348,348,348, pixel 1.72, shown at level
0.0016, step 2, values float32
> open emdb:15877
Opened emdb 15877 as #10, grid size 348,348,348, pixel 1.72, shown at level
0.0035, step 2, values float32
> open emdb:15878
Summary of feedback from opening 15878 fetched from emdb
---
note | Fetching map header 15878 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-15878/header/emd-15878.xml
Opened emdb 15878 as #11, grid size 348,348,348, pixel 1.72, shown at level
0.0028, step 2, values float32
> select add #7
2 models selected
> select add #8
4 models selected
> select add #9
6 models selected
> select add #10
8 models selected
> select add #11
10 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#8,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#9,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#10,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#11,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#8,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#9,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#10,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#11,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61
> view matrix models
> #7,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#8,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#9,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#10,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#11,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#8,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#9,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#10,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#11,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#8,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#9,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#10,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#11,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#8,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#9,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#10,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#11,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04
> view matrix models
> #7,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#8,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#9,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#10,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#11,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17
> view matrix models
> #7,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#8,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#9,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#10,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#11,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32
> select up
22 models selected
> select down
10 models selected
> fitmap #7,8,9,10,11 inMap #4
Multiple maps for #7,8,9,10,11
> fitmap #7 inMap #4
Fit map emdb 15872 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
38975 points
correlation = 0.8713, correlation about mean = 0.511, overlap = 19.12
steps = 172, shift = 4.18, angle = 7.74 degrees
Position of emdb 15872 (#7) relative to cryosparc_P618_J51_003_volume_map.mrc
gaussian (#4) coordinates:
Matrix rotation and translation
0.15095486 0.67609126 0.72118878 -213.36408338
0.27171285 0.67307181 -0.68785644 124.03261421
-0.95046556 0.29979153 -0.08209922 450.44819691
Axis 0.49798722 0.84287369 -0.20389378
Axis point 81.43122461 0.00000000 327.11961880
Rotation angle (degrees) 97.41390561
Shift along axis -93.55234397
> fitmap #8 inMap #4
Fit map emdb 15874 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
50573 points
correlation = 0.7901, correlation about mean = 0.3651, overlap = 35.33
steps = 200, shift = 4.27, angle = 7.64 degrees
Position of emdb 15874 (#8) relative to cryosparc_P618_J51_003_volume_map.mrc
gaussian (#4) coordinates:
Matrix rotation and translation
0.15020079 0.67788455 0.71966122 -213.34327430
0.27224301 0.67141791 -0.68926174 124.63013964
-0.95043332 0.29945039 -0.08370183 450.86237576
Axis 0.49865603 0.84231061 -0.20458493
Axis point 81.05473272 0.00000000 327.27308365
Rotation angle (degrees) 97.52978432
Shift along axis -93.64727139
> fitmap #9 inMap #4
Fit map emdb 15876 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
44004 points
correlation = 0.8182, correlation about mean = 0.4956, overlap = 19.16
steps = 184, shift = 4.33, angle = 7.69 degrees
Position of emdb 15876 (#9) relative to cryosparc_P618_J51_003_volume_map.mrc
gaussian (#4) coordinates:
Matrix rotation and translation
0.15136149 0.67763961 0.71964872 -213.65395858
0.27349619 0.67090509 -0.68926498 124.40829276
-0.94988923 0.30114936 -0.08378266 450.26873802
Axis 0.49949568 0.84199810 -0.20382166
Axis point 80.75562073 0.00000000 327.05187886
Rotation angle (degrees) 97.51339860
Shift along axis -93.74220317
> fitmap #10 inMap #4
Fit map emdb 15877 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
64603 points
correlation = 0.8209, correlation about mean = 0.4433, overlap = 54.96
steps = 168, shift = 4.15, angle = 7.71 degrees
Position of emdb 15877 (#10) relative to cryosparc_P618_J51_003_volume_map.mrc
gaussian (#4) coordinates:
Matrix rotation and translation
0.14997351 0.67720895 0.72034436 -213.18207749
0.27290595 0.67192385 -0.68850613 124.19979355
-0.95027907 0.29984395 -0.08404357 450.86662304
Axis 0.49847553 0.84258090 -0.20391069
Axis point 81.25347257 0.00000000 327.08689769
Rotation angle (degrees) 97.53160719
Shift along axis -93.55420115
> fitmap #11 inMap #4
Fit map emdb 15878 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
72752 points
correlation = 0.8284, correlation about mean = 0.5131, overlap = 54.45
steps = 180, shift = 4.14, angle = 7.7 degrees
Position of emdb 15878 (#11) relative to cryosparc_P618_J51_003_volume_map.mrc
gaussian (#4) coordinates:
Matrix rotation and translation
0.14995666 0.67663978 0.72088253 -213.16999021
0.27127382 0.67298649 -0.68811315 124.23930647
-0.95074893 0.29874370 -0.08263585 451.02348959
Axis 0.49764139 0.84295205 -0.20441352
Axis point 81.56457018 0.00000000 327.30602168
Rotation angle (degrees) 97.46071355
Shift along axis -93.54973197
> rename #7 "Classic_emdb 15872"
> rename #8 "Rot-1_emdb 15874"
> rename #9 "Rot-2_emdb 15876"
> rename #10 "Translocation_emdb 15877"
> rename #11 "Post_emdb 15878"
> select subtract #7
8 models selected
> select subtract #8
6 models selected
> select subtract #9
4 models selected
> select subtract #10
2 models selected
> select subtract #11
Nothing selected
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!5 models
> hide #!6 models
> volume #7 step 1
> volume #4 level 0.1213
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> volume #8 step 1
> volume #9 step 1
> volume #10 step 1
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!4 models
> show #!5 models
> volume #5 level 0.1308
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!5 models
> hide #!7 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> ui mousemode right zoom
> show #!8 models
> hide #!4 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!6 models
> hide #!5 models
> volume #6 level 0.129
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!7 models
> show #!5 models
> vop morph #4,5,6
Map positions are not the same, cryosparc_P618_J52_004_volume_map.mrc gaussian
#5 and cryosparc_P618_J51_003_volume_map.mrc gaussian #4. Use the "volume
resample" command to make a copy of one map with the same grid as the other
map.
> hide #!5 models
> vop morph #4,6
Map positions are not the same, cryosparc_P618_J53_003_volume_map.mrc gaussian
#6 and cryosparc_P618_J51_003_volume_map.mrc gaussian #4. Use the "volume
resample" command to make a copy of one map with the same grid as the other
map.
> morph #4,6
Require at least 2 structures for morph
> morph #4 to #6
Expected a keyword
> morph #4 i #6
Expected a keyword
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> open
> /Users/roan.groh/Downloads/cryosparc_P346_J309_class_03_00033_volume.mrc
Opened cryosparc_P346_J309_class_03_00033_volume.mrc as #12, grid size
96,96,96, pixel 4.76, shown at level 1.42, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P346_J309_class_02_00033_volume.mrc
Opened cryosparc_P346_J309_class_02_00033_volume.mrc as #13, grid size
96,96,96, pixel 4.76, shown at level 1.43, step 1, values float32
> volume #12 level 0.7386
> volume #13 level 0.8024
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> fitmap #12 inMap #4
Fit map cryosparc_P346_J309_class_03_00033_volume.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 29135 points
correlation = 0.8015, correlation about mean = 0.371, overlap = 5382
steps = 88, shift = 1.25, angle = 2.64 degrees
Position of cryosparc_P346_J309_class_03_00033_volume.mrc (#12) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99920994 -0.03526362 -0.01832944 12.26451505
0.03482934 0.99911706 -0.02349520 -1.83755016
0.01914178 0.02283823 0.99955591 -10.37051771
Axis 0.50362718 -0.40729824 0.76188438
Axis point 73.30020115 360.09138746 0.00000000
Rotation angle (degrees) 2.63652104
Shift along axis -0.97596136
> fitmap #13 inMap #4
Fit map cryosparc_P346_J309_class_02_00033_volume.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 27035 points
correlation = 0.8395, correlation about mean = 0.4145, overlap = 5679
steps = 88, shift = 1.48, angle = 2.79 degrees
Position of cryosparc_P346_J309_class_02_00033_volume.mrc (#13) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99937018 -0.03014382 -0.01872407 11.03286845
0.02950256 0.99899885 -0.03362888 1.34497510
0.01971903 0.03305529 0.99925898 -13.18398277
Axis 0.68480190 -0.39478501 0.61252849
Axis point 0.00000000 379.73346370 16.34908402
Rotation angle (degrees) 2.79075805
Shift along axis -1.05121174
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!12 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> show #!8 models
> hide #!13 models
> hide #!12 models
> show #!9 models
> hide #!9 models
> vop gaussian #7,8,9,10,11 sdev 1
Opened Classic_emdb 15872 gaussian as #14, grid size 348,348,348, pixel 1.72,
shown at step 1, values float32
Opened Rot-1_emdb 15874 gaussian as #15, grid size 348,348,348, pixel 1.72,
shown at step 1, values float32
Opened Rot-2_emdb 15876 gaussian as #16, grid size 348,348,348, pixel 1.72,
shown at step 1, values float32
Opened Translocation_emdb 15877 gaussian as #17, grid size 348,348,348, pixel
1.72, shown at step 1, values float32
Opened Post_emdb 15878 gaussian as #18, grid size 348,348,348, pixel 1.72,
shown at step 1, values float32
> show #!8 models
> hide #!8 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> show #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!12 models
> show #!15 models
> show #!13 models
> hide #!13 models
> hide #!15 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!18 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!13 models
> show #!14 models
> hide #!18 models
> hide #!14 models
> show #!18 models
> hide #!18 models
> show #!13 models
> show #!11 models
> hide #!11 models
> hide #!12 models
> show #!18 models
> show #!14 models
> hide #!18 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!14 models
> color #12 #ffffb281 models
> color #12 #ffffb280 models
> color #13 #b2ffff82 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> lighting soft
> lighting full
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> show #!14 models
> hide #!18 models
> hide #!12 models
> show #!13 models
> show #!18 models
> hide #!14 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!17 models
> show #!18 models
> hide #!17 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!18 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!18 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> hide #!18 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J312_003_volume_map.mrc
Opened cryosparc_P346_J312_003_volume_map.mrc as #19, grid size 384,384,384,
pixel 1.19, shown at level 0.252, step 2, values float32
> volume #19 step 1
> hide #!19 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J311_map_sharp.mrc
Opened cryosparc_P346_J311_map_sharp.mrc as #20, grid size 384,384,384, pixel
1.19, shown at level 0.113, step 2, values float32
> volume #20 step 1
> hide #!20 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J313_003_volume_map.mrc
Opened cryosparc_P346_J313_003_volume_map.mrc as #21, grid size 384,384,384,
pixel 1.19, shown at level 0.251, step 2, values float32
> volume #21 step 1
> hide #!21 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J308_003_volume_map.mrc
Opened cryosparc_P346_J308_003_volume_map.mrc as #22, grid size 384,384,384,
pixel 1.19, shown at level 0.233, step 2, values float32
> volume #22 step 1
> show #!16 models
> show #!15 models
> hide #!16 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!16 models
> hide #!16 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J136_003_volume_map.mrc
Opened cryosparc_P618_J136_003_volume_map.mrc as #23, grid size 384,384,384,
pixel 1.19, shown at level 0.27, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J135_003_volume_map.mrc
Opened cryosparc_P618_J135_003_volume_map.mrc as #24, grid size 384,384,384,
pixel 1.19, shown at level 0.263, step 2, values float32
> hide #!22 models
> volume #23 step 1
> volume #24 step 1
> view #23 clip false
> hide #!24 models
> show #!5 models
> show #!6 models
> hide #!23 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J86_map_sharp.mrc
Opened cryosparc_P618_J86_map_sharp.mrc as #25, grid size 384,384,384, pixel
1.19, shown at level 0.0544, step 2, values float32
> volume #25 step 1
> open /Users/roan.groh/Downloads/cryosparc_P618_J87_map_sharp.mrc
Opened cryosparc_P618_J87_map_sharp.mrc as #26, grid size 384,384,384, pixel
1.19, shown at level 0.0564, step 2, values float32
> volume #26 step 1
> open /Users/roan.groh/Downloads/cryosparc_P618_J88_map_sharp.mrc
Opened cryosparc_P618_J88_map_sharp.mrc as #27, grid size 384,384,384, pixel
1.19, shown at level 0.0349, step 2, values float32
> volume #27 step 1
> fitmap #25 inMap #4
Fit map cryosparc_P618_J86_map_sharp.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 564176 points
correlation = 0.875, correlation about mean = 0.7311, overlap = 5.529e+04
steps = 28, shift = 0.0652, angle = 0.00553 degrees
Position of cryosparc_P618_J86_map_sharp.mrc (#25) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
1.00000000 0.00004080 -0.00000838 -0.05713261
-0.00004080 1.00000000 -0.00008708 0.04208369
0.00000837 0.00008708 1.00000000 -0.06105469
Axis 0.90212433 -0.08676510 -0.42266240
Axis point 0.00000000 843.75775233 453.93670404
Rotation angle (degrees) 0.00553082
Shift along axis -0.02938660
> fitmap #26 inMap #4
Fit map cryosparc_P618_J87_map_sharp.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 566545 points
correlation = 0.8241, correlation about mean = 0.4999, overlap = 4.618e+04
steps = 96, shift = 1.37, angle = 1.63 degrees
Position of cryosparc_P618_J87_map_sharp.mrc (#26) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99999279 0.00313949 -0.00213450 -0.02596276
-0.00319827 0.99959954 -0.02811645 6.89238144
0.00204537 0.02812307 0.99960238 -7.78464333
Axis 0.99101095 -0.07365466 -0.11167943
Axis point 0.00000000 278.89421676 242.04490105
Rotation angle (degrees) 1.62597582
Shift along axis 0.33599915
> fitmap #27 inMap #4
Fit map cryosparc_P618_J88_map_sharp.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 565831 points
correlation = 0.813, correlation about mean = 0.5465, overlap = 4.037e+04
steps = 84, shift = 1.23, angle = 1.68 degrees
Position of cryosparc_P618_J88_map_sharp.mrc (#27) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99998949 0.00396510 -0.00230253 -0.21513651
-0.00403028 0.99957038 -0.02903138 7.26879188
0.00218642 0.02904036 0.99957585 -8.07792156
Axis 0.98776267 -0.07635415 -0.13599616
Axis point 0.00000000 280.22063752 247.10089355
Rotation angle (degrees) 1.68448598
Shift along axis 0.33106002
> hide #!25 models
> hide #!26 models
> hide #!27 models
> show #!1 models
> open "/Users/roan.groh/Downloads/cryosparc_P618_J93_005_volume_map (1).mrc"
Opened cryosparc_P618_J93_005_volume_map (1).mrc as #28, grid size
384,384,384, pixel 1.19, shown at level 0.127, step 2, values float32
> open "/Users/roan.groh/Downloads/cryosparc_P618_J92_003_volume_map (1).mrc"
Opened cryosparc_P618_J92_003_volume_map (1).mrc as #29, grid size
384,384,384, pixel 1.19, shown at level 0.266, step 2, values float32
> open "/Users/roan.groh/Downloads/cryosparc_P618_J91_004_volume_map (1).mrc"
Opened cryosparc_P618_J91_004_volume_map (1).mrc as #30, grid size
384,384,384, pixel 1.19, shown at level 0.268, step 2, values float32
> open "/Users/roan.groh/Downloads/cryosparc_P618_J90_004_volume_map (1).mrc"
Opened cryosparc_P618_J90_004_volume_map (1).mrc as #31, grid size
384,384,384, pixel 1.19, shown at level 0.264, step 2, values float32
> fitmap #28 inMap #4
Fit map cryosparc_P618_J93_005_volume_map (1).mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70701 points
correlation = 0.8837, correlation about mean = 0.3608, overlap = 2460
steps = 64, shift = 1.48, angle = 0.515 degrees
Position of cryosparc_P618_J93_005_volume_map (1).mrc (#28) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99999174 0.00406012 -0.00019806 0.23269156
-0.00405840 0.99995966 0.00801275 -2.19061133
0.00023059 -0.00801188 0.99996788 1.17880203
Axis -0.89179607 -0.02385513 -0.45180825
Axis point 0.00000000 107.23586350 275.97823423
Rotation angle (degrees) 0.51477940
Shift along axis -0.68784860
> fitmap #29 inMap #4
Fit map cryosparc_P618_J92_003_volume_map (1).mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70730 points
correlation = 0.9304, correlation about mean = 0.6545, overlap = 9559
steps = 76, shift = 1.3, angle = 2.09 degrees
Position of cryosparc_P618_J92_003_volume_map (1).mrc (#29) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99966377 0.02535608 0.00542395 -6.59261686
-0.02520929 0.99935420 -0.02560621 11.27488385
-0.00606972 0.02546086 0.99965739 -5.23047046
Axis 0.70167155 0.15792516 -0.69477815
Axis point 0.00000000 189.70342087 430.66938909
Rotation angle (degrees) 2.08542989
Shift along axis 0.78875268
> fitmap #30 inMap #4
Fit map cryosparc_P618_J91_004_volume_map (1).mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70772 points
correlation = 0.9375, correlation about mean = 0.6623, overlap = 9371
steps = 68, shift = 1.24, angle = 1.87 degrees
Position of cryosparc_P618_J91_004_volume_map (1).mrc (#30) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99993362 -0.00974242 -0.00615192 3.90075157
0.00955015 0.99948773 -0.03054611 4.49253885
0.00644636 0.03048534 0.99951443 -9.23580452
Axis 0.93554619 -0.19311803 0.29573428
Axis point -0.00000000 305.71386687 142.26571544
Rotation angle (degrees) 1.86921016
Shift along axis 0.05039906
> fitmap #31 inMap #4
Fit map cryosparc_P618_J90_004_volume_map (1).mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70735 points
correlation = 0.9699, correlation about mean = 0.7573, overlap = 9299
steps = 48, shift = 0.163, angle = 0.323 degrees
Position of cryosparc_P618_J90_004_volume_map (1).mrc (#31) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99999286 -0.00325504 -0.00192154 1.20897040
0.00326303 0.99998599 0.00416766 -1.82640551
0.00190795 -0.00417391 0.99998947 0.61690219
Axis -0.74097712 -0.34017119 0.57899609
Axis point 0.00000000 135.24420588 431.94048330
Rotation angle (degrees) 0.32250610
Shift along axis 0.08265508
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!1 models
> close #28
> show #!29 models
> volume #29 step 1
> volume #30 step 1
> volume #31 step 1
> show #!30 models
> show #!31 models
> hide #!29 models
> hide #!30 models
> show #!30 models
> show #!29 models
> hide #!30 models
> hide #!31 models
> hide #!29 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> close #29-31
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
> Refine_tRNA/cryosparc_P618_J54_003_volume_map.mrc
Opened cryosparc_P618_J54_003_volume_map.mrc as #28, grid size 384,384,384,
pixel 1.19, shown at level 0.29, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
> Refine_tRNA/cryosparc_P618_J56_003_volume_map.mrc
Opened cryosparc_P618_J56_003_volume_map.mrc as #29, grid size 384,384,384,
pixel 1.19, shown at level 0.263, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
> Refine_tRNA/cryosparc_P618_J55_003_volume_map.mrc
Opened cryosparc_P618_J55_003_volume_map.mrc as #30, grid size 384,384,384,
pixel 1.19, shown at level 0.305, step 2, values float32
> hide #!3 models
> fitmap #28 inMap #4
Fit map cryosparc_P618_J54_003_volume_map.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70762 points
correlation = 0.9114, correlation about mean = 0.5594, overlap = 1.001e+04
steps = 92, shift = 1.44, angle = 1.66 degrees
Position of cryosparc_P618_J54_003_volume_map.mrc (#28) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99998746 0.00440507 -0.00238390 -0.28288346
-0.00447125 0.99958350 -0.02851031 7.27268808
0.00225732 0.02852061 0.99959066 -7.93511999
Axis 0.98492449 -0.08015398 -0.15329411
Axis point 0.00000000 279.93358189 251.99789756
Rotation angle (degrees) 1.65905498
Shift along axis 0.35485344
> fitmap #29 inMap #4
Fit map cryosparc_P618_J56_003_volume_map.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70763 points
correlation = 0.942, correlation about mean = 0.6785, overlap = 1.077e+04
steps = 44, shift = 0.0325, angle = 0.0594 degrees
Position of cryosparc_P618_J56_003_volume_map.mrc (#29) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99999967 0.00077557 0.00024116 -0.20967061
-0.00077573 0.99999949 0.00064404 0.04735992
-0.00024066 -0.00064423 0.99999976 0.18164953
Axis -0.62138303 0.23239670 -0.74824789
Axis point 59.26828730 266.06367560 0.00000000
Rotation angle (degrees) 0.05939398
Shift along axis 0.00537317
> fitmap #30 inMap #4
Fit map cryosparc_P618_J55_003_volume_map.mrc in map
cryosparc_P618_J51_003_volume_map.mrc gaussian using 70747 points
correlation = 0.9444, correlation about mean = 0.65, overlap = 1.294e+04
steps = 44, shift = 0.0701, angle = 0.0804 degrees
Position of cryosparc_P618_J55_003_volume_map.mrc (#30) relative to
cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99999930 0.00094630 0.00071295 -0.37140461
-0.00094683 0.99999927 0.00075004 0.03755462
-0.00071224 -0.00075071 0.99999946 0.26497712
Axis -0.53504974 0.50811003 -0.67494146
Axis point 18.47156924 370.46749346 0.00000000
Rotation angle (degrees) 0.08035409
Shift along axis 0.03895778
> volume #28 step 1
> volume #29 step 1
> volume #30 step 1
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!29 models
> hide #!30 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!29 models
> vop gaussian #28,29,30 sdev 1
Opened cryosparc_P618_J54_003_volume_map.mrc gaussian as #31, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
Opened cryosparc_P618_J56_003_volume_map.mrc gaussian as #32, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
Opened cryosparc_P618_J55_003_volume_map.mrc gaussian as #33, grid size
384,384,384, pixel 1.19, shown at step 1, values float32
> volume #31 level 0.1366
> volume #32 level 0.1006
> volume #32 level 0.08143
> volume #33 level 0.08398
> volume #33 level 0.05618
> close #28-33
> open /Users/roan.groh/Downloads/cryosparc_P618_J137_003_volume_map.mrc
Opened cryosparc_P618_J137_003_volume_map.mrc as #28, grid size 384,384,384,
pixel 1.19, shown at level 0.254, step 2, values float32
> volume #28 step 1
> show #!1 models
> hide #!28 models
> show #!28 models
> hide #!1 models
> hide #!28 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J314_map_sharp.mrc
Opened cryosparc_P346_J314_map_sharp.mrc as #29, grid size 384,384,384, pixel
1.19, shown at level 0.112, step 2, values float32
> volume #29 step 1
> show #!19 models
> hide #!19 models
> show #!19 models
> color #19 #ff9300ff models
> volume #29 level 0.1738
> hide #!19 models
> hide #!29 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J142_003_volume_map.mrc
Opened cryosparc_P618_J142_003_volume_map.mrc as #30, grid size 384,384,384,
pixel 1.19, shown at level 0.282, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J141_003_volume_map.mrc
Opened cryosparc_P618_J141_003_volume_map.mrc as #31, grid size 384,384,384,
pixel 1.19, shown at level 0.271, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J139_003_volume_map.mrc
Opened cryosparc_P618_J139_003_volume_map.mrc as #32, grid size 384,384,384,
pixel 1.19, shown at level 0.272, step 2, values float32
> volume #30 step 1
> volume #31 step 1
> volume #32 step 1
> hide #!31 models
> hide #!32 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!32 models
> hide #!32 models
> show #!31 models
> show #!30 models
> hide #!30 models
> hide #!31 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J133_map_sharp.mrc
Opened cryosparc_P618_J133_map_sharp.mrc as #33, grid size 384,384,384, pixel
1.19, shown at level 0.0979, step 2, values float32
> volume #33 step 1
> open /Users/roan.groh/Downloads/cryosparc_P346_J317_map_sharp.mrc
Opened cryosparc_P346_J317_map_sharp.mrc as #34, grid size 384,384,384, pixel
1.19, shown at level 0.00236, step 2, values float32
> volume #34 step 1
> volume #34 level 0.01397
> hide #!33 models
> volume #34 level 0.02848
> hide #!34 models
> open /Volumes/groups/dagdas/lab/Roan/01_Pollen-
> Project/Processing_Masks/60S_P618.mrc
Opened 60S_P618.mrc as #35, grid size 384,384,384, pixel 1.19, shown at level
0.152, step 2, values float32
> volume #35 step 1
> volume #35 level 0.0687
> volume #35 level 0.04648
> open /Users/roan.groh/Downloads/cryosparc_P346_J319_mask.mrc
Opened cryosparc_P346_J319_mask.mrc as #36, grid size 384,384,384, pixel 1.19,
shown at level 1, step 2, values float32
> volume #36 level 0.003747
> color #36 #ffb2b27f models
> color #36 #ffb2b280 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J259_004_volume_map.mrc
Opened cryosparc_P346_J259_004_volume_map.mrc as #37, grid size 384,384,384,
pixel 1.19, shown at level 0.164, step 2, values float32
> hide #!35 models
> volume #37 step 1
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_03_00065_volume.mrc
Opened cryosparc_P346_J188_class_03_00065_volume.mrc as #38, grid size
96,96,96, pixel 4.76, shown at level 1.23, step 1, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_08_00065_volume.mrc
Opened cryosparc_P346_J188_class_08_00065_volume.mrc as #39, grid size
96,96,96, pixel 4.76, shown at level 1.15, step 1, values float32
> hide #!37 models
> volume #38 level 0.3593
> volume #39 level 0.2868
> hide #!38 models
> hide #!36 models
> volume #39 level 0.2868
> ui tool show "Segment Map"
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 3 region surfaces
818 watershed regions, grouped to 3 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 3 regions, 3 surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 1 region surfaces
818 watershed regions, grouped to 1 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 1 regions, 1 surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 1 region surfaces
818 watershed regions, grouped to 1 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 1 regions, 1 surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Only showing 150 of 195 regions.
Showing 150 of 195 region surfaces
818 watershed regions, grouped to 195 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 195 regions, 150
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 33 region surfaces
818 watershed regions, grouped to 33 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 33 regions, 33
surfaces
> select #40.1
1 model selected
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 56 region surfaces
818 watershed regions, grouped to 56 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 56 regions, 56
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 59 region surfaces
818 watershed regions, grouped to 59 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 59 regions, 59
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Only showing 150 of 273 regions.
Showing 150 of 273 region surfaces
818 watershed regions, grouped to 273 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 273 regions, 150
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 122 region surfaces
818 watershed regions, grouped to 122 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 122 regions, 122
surfaces
> select #40.111
1 model selected
> select #40.113
1 model selected
> select #40.116
1 model selected
> select add #40.111
2 models selected
> select add #40.113
3 models selected
> ui mousemode right select
Drag select of 1466, 3901 of 4548 triangles, 1461, 1486, 1476, 1467, 1487,
1474, 1464, 1473, 1462, 1485, 1484, 1463, 3367 of 3376 triangles, 1478, 3757
of 3852 triangles, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 3555 of 3584
triangles, 1470, 1483, 1471, 1494, 1479, 2609 of 3336 triangles, 1482, 3086 of
3704 triangles, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475, 2931 of
2948 triangles, 1493, 1509, 1503, 2163 of 3204 triangles, 1508, 1507, 1500,
1506, 1502, 1505, 1499, 1504, 1869 of 2480 triangles, 1495, 1491, 1512, 1510,
1514, 1583 of 1676 triangles, 1513, 1511, 1460, 1455, 726 of 812 triangles,
1055, 1289, 1458, 1358, 1337, 1346, 670, 420 of 544 triangles, 1335, 1088,
1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23, 710, 67, 44, 237,
717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397, 353, 815, 117,
814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 98 of 100 triangles, 21, 143,
436, 413, 765, 396, 709, 672, 6 of 44 triangles, 817, 746, 745, 8, 713, 794,
39 cryosparc_P346_J188_class_08_00065_volume.mrc
> select #40.122
1 model selected
Drag select of 1466, 1461, 1486, 1476, 1467, 1487, 1474, 1464, 1473, 1462,
1485, 1484, 1463, 1478, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 1470, 1483,
1471, 1494, 1479, 1482, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475,
1493, 1509, 1503, 1508, 1507, 1500, 1506, 1502, 1505, 1499, 1504, 1495, 1491,
1512, 1510, 1514, 1513, 1511, 1460, 1455, 1055, 1289, 1458, 1358, 1337, 1346,
670, 1335, 1088, 1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23,
710, 67, 44, 237, 717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397,
353, 815, 117, 814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 21, 143, 436,
413, 599, 765, 575, 32 of 44 triangles, 396, 709, 672, 817, 746, 745, 8, 713,
794, 39 cryosparc_P346_J188_class_08_00065_volume.mrc
> select #40.113
1 model selected
> select #40.111
1 model selected
Drag select of 1466, 1461, 1486, 1476, 1467, 1487, 1474, 1464, 1473, 1462,
1485, 1484, 1463, 1478, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 1470, 1483,
1471, 1494, 1479, 1482, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475,
1493, 1509, 1503, 1508, 1507, 1500, 1506, 1502, 1505, 1499, 1504, 1495, 1491,
1512, 1510, 1514, 1513, 1511, 1460, 1455, 1055, 1289, 1458, 1358, 1337, 1346,
670, 1335, 1088, 1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23,
710, 67, 44, 237, 717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397,
353, 815, 117, 814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 21, 143, 436,
413, 599, 765, 575, 396, 709, 672, 817, 746, 745, 8, 713, 794, 39
cryosparc_P346_J188_class_08_00065_volume.mrc
> select #40.113
1 model selected
> ui mousemode right select
> select clear
> select #40.113
1 model selected
> select #40.111
1 model selected
> select add #40.113
2 models selected
> select add #40.116
3 models selected
> select add #40.121
4 models selected
> select add #40.119
5 models selected
> select add #40.112
6 models selected
> select add #40.118
7 models selected
> select add #40.122
8 models selected
> select add #40.120
9 models selected
> select add #40.109
10 models selected
> select add #40.110
11 models selected
> select add #40.115
12 models selected
> select add #40.114
13 models selected
> select add #40.117
14 models selected
> hide #!39 models
Drag select of 1466, 1461, 1486, 1476, 1467, 1487, 1474, 1464, 1473, 1462,
1485, 1484, 1463, 1478, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 1470, 1483,
1471, 1494, 1479, 1482, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475,
1493, 1509, 1503, 1508, 1507, 1500, 1506, 1502, 1505, 1499, 1504, 1495, 1491,
1512, 1510, 1514, 1513, 1511, 1460, 1455, 1055, 1289, 1458, 1358, 1337, 1346,
670, 1335, 1088, 1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23,
710, 67, 44, 237, 717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397,
353, 815, 117, 814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 21, 143
Saving 108 regions to mrc file...
Opened P246_60S.mrc as #41, grid size 49,59,62, pixel 4.76, shown at step 1,
values float32
Wrote P246_60S.mrc
> colume resample #41 onGrid #20
Unknown command: colume resample #41 onGrid #20
> volume resample #41 onGrid #20
Opened P246_60S.mrc resampled as #42, grid size 384,384,384, pixel 1.19, shown
at step 1, values float32
> select add #40
123 models selected
> select subtract #40
Nothing selected
> hide #!40 models
> volume #42 level 0.09094
No map chosen to save
> save /Users/roan.groh/P346_60S.mrc models #42
> save /Users/roan.groh/Desktop/P346_60S_Mask.mrc models #42
> volume #42 level 0.0132
> open "/Users/roan.groh/Downloads/Unconfirmed 38399.crdownload.mrc"
Opened Unconfirmed 38399.crdownload.mrc as #43, grid size 384,384,384, pixel
1.19, shown at level 1, step 2, values float32
> volume #43 level 0.007055
> hide #!42 models
> color #43 #ffffb27b models
> color #43 #ffffb27a models
> show #!38 models
> show #!39 models
> show #!40 models
> close #19-43
> close #12-13
> rename #14 id #12
> rename #15 id #13
> rename #16 id #14
> rename #17 id #15
> rename #18 id #16
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_03_00065_volume.mrc
Opened cryosparc_P346_J188_class_03_00065_volume.mrc as #17, grid size
96,96,96, pixel 4.76, shown at level 1.23, step 1, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_08_00065_volume.mrc
Opened cryosparc_P346_J188_class_08_00065_volume.mrc as #18, grid size
96,96,96, pixel 4.76, shown at level 1.15, step 1, values float32
> volume #17 level 0.3205
> volume #18 level 0.2658
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> close #17-18
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J143_class_00_00040_volume.mrc
Opened cryosparc_P618_J143_class_00_00040_volume.mrc as #17, grid size
96,96,96, pixel 4.76, shown at level 1.52, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J143_class_01_00040_volume.mrc
Opened cryosparc_P618_J143_class_01_00040_volume.mrc as #18, grid size
96,96,96, pixel 4.76, shown at level 1.5, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J143_class_02_00040_volume.mrc
Opened cryosparc_P618_J143_class_02_00040_volume.mrc as #19, grid size
96,96,96, pixel 4.76, shown at level 1.48, step 1, values float32
> volume #17 level 0.3237
> volume #18 level 0.393
> volume #19 level 0.2151
Drag select of 17 cryosparc_P618_J143_class_00_00040_volume.mrc , 18
cryosparc_P618_J143_class_01_00040_volume.mrc , 19
cryosparc_P618_J143_class_02_00040_volume.mrc
> ui mousemode right zoom
> select subtract #17
4 models selected
> select subtract #19
2 models selected
> select subtract #18
Nothing selected
> hide #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!17 models
> hide #!19 models
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J144_class_00_00017_volume.mrc
Opened cryosparc_P618_J144_class_00_00017_volume.mrc as #20, grid size
160,160,160, pixel 2.85, shown at level 0.84, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J144_class_07_00017_volume.mrc
Opened cryosparc_P618_J144_class_07_00017_volume.mrc as #21, grid size
160,160,160, pixel 2.85, shown at level 0.816, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J144_class_08_00017_volume.mrc
Opened cryosparc_P618_J144_class_08_00017_volume.mrc as #22, grid size
160,160,160, pixel 2.85, shown at level 0.822, step 1, values float32
> hide #!18 models
> hide #!21 models
> hide #!22 models
> volume #20 level 0.3191
> volume #21 level 0.6088
> volume #22 level 0.4996
> volume #22 level 0.3522
> hide #!22 models
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_00_00019_volume.mrc
Opened cryosparc_P618_J145_class_00_00019_volume.mrc as #23, grid size
160,160,160, pixel 2.85, shown at level 0.716, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_02_00019_volume.mrc
Opened cryosparc_P618_J145_class_02_00019_volume.mrc as #24, grid size
160,160,160, pixel 2.85, shown at level 0.808, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_06_00019_volume.mrc
Opened cryosparc_P618_J145_class_06_00019_volume.mrc as #25, grid size
160,160,160, pixel 2.85, shown at level 0.829, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_08_00019_volume.mrc
Opened cryosparc_P618_J145_class_08_00019_volume.mrc as #26, grid size
160,160,160, pixel 2.85, shown at level 0.821, step 1, values float32
> hide #!24 models
> hide #!25 models
> hide #!26 models
> volume #23 level 0.3597
> hide #!23 models
> show #!24 models
> volume #24 level 0.388
> hide #!24 models
> show #!25 models
> volume #25 level 0.4463
> volume #26 level 0.3024
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> show #!24 models
> hide #!24 models
> hide #!26 models
> show #!20 models
> hide #!25 models
> show #!21 models
> hide #!20 models
> volume #21 level 0.3818
> hide #!21 models
> show #!22 models
> show #!23 models
> hide #!23 models
> show #!20 models
> hide #!20 models
> hide #!22 models
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> volume #17 level 0.1724
> show #!18 models
> hide #!17 models
> volume #18 level 0.7042
> volume #19 level 0.8178
> hide #!19 models
> save /Users/roan.groh/Desktop/Checking-Structure_TranslationalStates.cxs
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Structure_Comparison_F2A_V2.cxs
Opened cryosparc_P346_J219_map_sharp.mrc as #1, grid size 384,384,384, pixel
1.19, shown at level 0.112, step 2, values float32
Opened cryosparc_P346_J219_map_sharp.mrc gaussian as #2, grid size
384,384,384, pixel 1.19, shown at level 0.0803, step 1, values float32
Opened cryosparc_P618_J94_map_sharp.mrc as #3, grid size 384,384,384, pixel
1.19, shown at level 0.0968, step 2, values float32
Opened cryosparc_P618_J94_map_sharp.mrc gaussian as #4, grid size 384,384,384,
pixel 1.19, shown at level 0.0803, step 1, values float32
opened ChimeraX session
> close #1-4
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Structure_Comparison_F2A_V2.cxs
Opened cryosparc_P346_J219_map_sharp.mrc as #1, grid size 384,384,384, pixel
1.19, shown at level 0.112, step 2, values float32
Opened cryosparc_P346_J219_map_sharp.mrc gaussian as #2, grid size
384,384,384, pixel 1.19, shown at level 0.0803, step 1, values float32
Opened cryosparc_P618_J94_map_sharp.mrc as #3, grid size 384,384,384, pixel
1.19, shown at level 0.0968, step 2, values float32
Opened cryosparc_P618_J94_map_sharp.mrc gaussian as #4, grid size 384,384,384,
pixel 1.19, shown at level 0.0803, step 1, values float32
opened ChimeraX session
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Dehydrated/Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc
Opened Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc as #5, grid size
384,384,384, pixel 1.19, shown at level 0.226, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Dehydrated/Consensus-J311_cryosparc_P346_J311_map_sharp.mrc
Opened Consensus-J311_cryosparc_P346_J311_map_sharp.mrc as #6, grid size
384,384,384, pixel 1.19, shown at level 0.113, step 2, values float32
> close #1-4
> rename #5 id #1
> rename #6 id #2
> volume #1 step 1
> volume #2 step 1
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Germinated/Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc
Opened Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc as #3, grid size
384,384,384, pixel 1.19, shown at level 0.25, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Germinated/Consensus-J133_cryosparc_P618_J133_map_sharp.mrc
Opened Consensus-J133_cryosparc_P618_J133_map_sharp.mrc as #4, grid size
384,384,384, pixel 1.19, shown at level 0.0979, step 2, values float32
> volume #3 step 1
> volume #4 step 1
> fitmap #2 inMap #1
Fit map Consensus-J311_cryosparc_P346_J311_map_sharp.mrc in map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc using 565618 points
correlation = 0.9447, correlation about mean = 0.8277, overlap = 1.1e+05
steps = 48, shift = 0.0154, angle = 0.0177 degrees
Position of Consensus-J311_cryosparc_P346_J311_map_sharp.mrc (#2) relative to
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999995 -0.00014916 -0.00027033 0.10006789
0.00014916 0.99999999 0.00000905 -0.02394076
0.00027033 -0.00000910 0.99999996 -0.06058140
Axis -0.02938043 -0.87518384 0.48289755
Axis point 204.06950091 0.00000000 368.90964158
Rotation angle (degrees) 0.01769778
Shift along axis -0.01124208
> fitmap #3 inMap #1
Fit map Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc in map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc using 564482 points
correlation = 0.9612, correlation about mean = 0.809, overlap = 1.225e+05
steps = 84, shift = 0.927, angle = 0.717 degrees
Position of Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc (#3)
relative to Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999672 0.00163710 0.00196767 -0.32098861
-0.00166106 0.99992372 0.01223909 -2.38932597
-0.00194749 -0.01224232 0.99992316 3.98691864
Axis -0.97882912 0.15653804 -0.13186888
Axis point 0.00000000 318.16854857 189.71425335
Rotation angle (degrees) 0.71652878
Shift along axis -0.58557789
> fitmap #4 inMap #1
Fit map Consensus-J133_cryosparc_P618_J133_map_sharp.mrc in map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc using 566625 points
correlation = 0.8877, correlation about mean = 0.6039, overlap = 8.032e+04
steps = 64, shift = 0.865, angle = 0.719 degrees
Position of Consensus-J133_cryosparc_P618_J133_map_sharp.mrc (#4) relative to
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999701 0.00135613 0.00203377 -0.35347122
-0.00138107 0.99992326 0.01231113 -2.54732653
-0.00201692 -0.01231390 0.99992215 3.92029182
Axis -0.98085704 0.16134593 -0.10902733
Axis point 0.00000000 312.72975762 202.41759885
Rotation angle (degrees) 0.71924197
Shift along axis -0.49171499
> open 8b2l
Summary of feedback from opening 8b2l fetched from pdb
---
warning | Atom H1 is not in the residue template for UNK /l3:1
8b2l title:
Cryo-EM structure of the plant 80S ribosome [more info...]
Chain information for 8b2l #5
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
Non-standard residues in 8b2l #5
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide atoms
> show cartoons
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.5994,0.19237,0.77699,-100.78,-0.66599,0.65835,0.35076,126.87,-0.44406,-0.72771,0.52273,307.1
> hide #!1 models
> view matrix models
> #5,-0.29109,-0.74227,0.60357,274.21,-0.74163,-0.22347,-0.63249,481.9,0.60436,-0.63174,-0.48544,270.15
> view matrix models
> #5,-0.43224,-0.80916,0.39802,355.15,-0.79985,0.1402,-0.58359,424.2,0.41642,-0.57061,-0.70781,342.96
> view matrix models
> #5,-0.67391,-0.73025,0.11219,448.7,-0.72053,0.61604,-0.31833,276.69,0.16335,-0.29537,-0.94132,396.09
> ui mousemode right "move picked models"
> show #!1 models
> view matrix models
> #5,-0.67391,-0.73025,0.11219,467.39,-0.72053,0.61604,-0.31833,307.24,0.16335,-0.29537,-0.94132,429.73
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.5894,-0.78166,0.20401,440.22,-0.77031,0.46771,-0.43344,364.83,0.24339,-0.41262,-0.87778,419.96
> fitmap #5 inMap #1
Fit molecule 8b2l (#5) to map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) using 361205 atoms
average map value = 0.1884, steps = 448
shifted from previous position = 31.2
rotated from previous position = 31.5 degrees
atoms outside contour = 237159, contour level = 0.22628
Position of 8b2l (#5) relative to
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.21845575 -0.96565873 -0.14064239 494.28572978
-0.83164267 0.25963155 -0.49087870 424.51433350
0.51053651 0.00972894 -0.85980103 301.94011380
Axis 0.60152754 -0.78245318 0.16103301
Axis point 368.57912383 0.00000000 262.33622588
Rotation angle (degrees) 155.41053209
Shift along axis 13.78621289
> vop copy #5
> copy #5
Unknown command: copy #5
> vop copy #5
> hide #!1 models
> select subtract #5
Nothing selected
> show #!1 models
> copy model #5
Unknown command: copy model #5
> log metadata #5
Metadata for 8b2l #5
---
Title | Cryo-EM structure of the plant 80S ribosome
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y
Non-standard residues | B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
Sources (natural) | Nicotiana tabacum (common tobacco)
Nicotiana tabacum
CryoEM Map | EMDB 15806 — open map
Experimental method | Electron microscopy
Resolution | 2.20Å
> log chains #5
Chain information for 8b2l #5
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
> color #5 #275c70
> select #9/54,74,84,A1
Nothing selected
> select #5/54,74,84,A1
4261 atoms, 4294 bonds, 266 residues, 1 model selected
> hide #!1 models
> select #5/54,74,84,A1
4261 atoms, 4294 bonds, 266 residues, 1 model selected
> select #5/A1,A3,B3,C3
120359 atoms, 125472 bonds, 4063 pseudobonds, 7520 residues, 4 models selected
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> select subtract #5
Nothing selected
> select #5/A1,A3,B3,C3,h1
174913 atoms, 181978 bonds, 6097 pseudobonds, 11304 residues, 4 models
selected
> color sel #B7C9CF
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> select subtract #5
Nothing selected
> show #!4 models
> show #!3 models
> color zone #3,4 near #5 distance 6
> color #3,4 #275c70
> color zone #3,4 near #5 distance 6
> hide #!5 models
> hide #!4 models
> volume #3 level 0.1958
> color #1,2,5 #e1b74d
> hide #!4 models
> show #!5 models
> select #5/A1,A3,B3,C3,h1
174913 atoms, 181978 bonds, 6097 pseudobonds, 11304 residues, 4 models
selected
> color sel #F5E7C4
> color zone #1,2 near #5 distance 6
> show #!1 models
> show #!2 models
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> hide #!5 models
> select subtract #5
Nothing selected
> show #!3 models
> show #!4 models
> hide #!1 models
> hide #!3 models
> volume #4 level 0.113
> ui mousemode right translate
> save "/Users/roan.groh/Documents/OneDrive -
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Structure_Comparison_F2A_V2.cxs"
> hide #!4 models
> open /Users/roan.groh/Desktop/Checking-Structure_TranslationalStates.cxs
Opened cryosparc_P618_J51_003_volume_map.mrc as #1, grid size 384,384,384,
pixel 1.19, shown at level 0.254, step 1, values float32
Opened cryosparc_P618_J52_004_volume_map.mrc as #2, grid size 384,384,384,
pixel 1.19, shown at level 0.273, step 1, values float32
Opened cryosparc_P618_J53_003_volume_map.mrc as #3, grid size 384,384,384,
pixel 1.19, shown at level 0.275, step 1, values float32
Opened cryosparc_P618_J51_003_volume_map.mrc gaussian as #4, grid size
384,384,384, pixel 1.19, shown at level 0.121, step 1, values float32
Opened cryosparc_P618_J52_004_volume_map.mrc gaussian as #5, grid size
384,384,384, pixel 1.19, shown at level 0.131, step 1, values float32
Opened cryosparc_P618_J53_003_volume_map.mrc gaussian as #6, grid size
384,384,384, pixel 1.19, shown at level 0.129, step 1, values float32
Opened Classic_emdb 15872 as #7, grid size 348,348,348, pixel 1.72, shown at
level 0.0016, step 1, values float32
Opened Rot-1_emdb 15874 as #8, grid size 348,348,348, pixel 1.72, shown at
level 0.0032, step 1, values float32
Opened Rot-2_emdb 15876 as #9, grid size 348,348,348, pixel 1.72, shown at
level 0.0016, step 1, values float32
Opened Translocation_emdb 15877 as #10, grid size 348,348,348, pixel 1.72,
shown at level 0.0035, step 1, values float32
Opened Post_emdb 15878 as #11, grid size 348,348,348, pixel 1.72, shown at
level 0.0028, step 2, values float32
Opened Classic_emdb 15872 gaussian as #12, grid size 348,348,348, pixel 1.72,
shown at level 0.00124, step 1, values float32
Opened Rot-1_emdb 15874 gaussian as #13, grid size 348,348,348, pixel 1.72,
shown at level 0.00305, step 1, values float32
Opened Rot-2_emdb 15876 gaussian as #14, grid size 348,348,348, pixel 1.72,
shown at level 0.00125, step 1, values float32
Opened Translocation_emdb 15877 gaussian as #15, grid size 348,348,348, pixel
1.72, shown at level 0.00388, step 1, values float32
Opened Post_emdb 15878 gaussian as #16, grid size 348,348,348, pixel 1.72,
shown at level 0.00347, step 1, values float32
Opened cryosparc_P618_J143_class_00_00040_volume.mrc as #17, grid size
96,96,96, pixel 4.76, shown at level 0.172, step 1, values float32
Opened cryosparc_P618_J143_class_01_00040_volume.mrc as #18, grid size
96,96,96, pixel 4.76, shown at level 0.704, step 1, values float32
Opened cryosparc_P618_J143_class_02_00040_volume.mrc as #19, grid size
96,96,96, pixel 4.76, shown at level 0.818, step 1, values float32
Opened cryosparc_P618_J144_class_00_00017_volume.mrc as #20, grid size
160,160,160, pixel 2.85, shown at level 0.319, step 1, values float32
Opened cryosparc_P618_J144_class_07_00017_volume.mrc as #21, grid size
160,160,160, pixel 2.85, shown at level 0.382, step 1, values float32
Opened cryosparc_P618_J144_class_08_00017_volume.mrc as #22, grid size
160,160,160, pixel 2.85, shown at level 0.352, step 1, values float32
Opened cryosparc_P618_J145_class_00_00019_volume.mrc as #23, grid size
160,160,160, pixel 2.85, shown at level 0.36, step 1, values float32
Opened cryosparc_P618_J145_class_02_00019_volume.mrc as #24, grid size
160,160,160, pixel 2.85, shown at level 0.388, step 1, values float32
Opened cryosparc_P618_J145_class_06_00019_volume.mrc as #25, grid size
160,160,160, pixel 2.85, shown at level 0.446, step 1, values float32
Opened cryosparc_P618_J145_class_08_00019_volume.mrc as #26, grid size
160,160,160, pixel 2.85, shown at level 0.302, step 1, values float32
opened ChimeraX session
> open /Users/roan.groh/Downloads/cryosparc_P618_J148_004_volume_map.mrc
Opened cryosparc_P618_J148_004_volume_map.mrc as #27, grid size 384,384,384,
pixel 1.19, shown at level 0.272, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J147_003_volume_map.mrc
Opened cryosparc_P618_J147_003_volume_map.mrc as #28, grid size 384,384,384,
pixel 1.19, shown at level 0.244, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J146_004_volume_map.mrc
Opened cryosparc_P618_J146_004_volume_map.mrc as #29, grid size 384,384,384,
pixel 1.19, shown at level 0.273, step 2, values float32
> volume #27 step 1
> volume #28 step 1
> volume #29 step 1
> ui mousemode right zoom
> close #27-29
> hide #!26 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J151_004_volume_map.mrc
Opened cryosparc_P618_J151_004_volume_map.mrc as #27, grid size 384,384,384,
pixel 1.19, shown at level 0.279, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J150_003_volume_map.mrc
Opened cryosparc_P618_J150_003_volume_map.mrc as #28, grid size 384,384,384,
pixel 1.19, shown at level 0.28, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J149_003_volume_map.mrc
Opened cryosparc_P618_J149_003_volume_map.mrc as #29, grid size 384,384,384,
pixel 1.19, shown at level 0.257, step 2, values float32
> volume #27 step 1
> volume #28 step 1
> volume #29 step 1
> hide #!28 models
> hide #!29 models
> show #!28 models
> hide #!27 models
> show #!29 models
> hide #!28 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J321_004_volume_map.mrc
Opened cryosparc_P346_J321_004_volume_map.mrc as #30, grid size 384,384,384,
pixel 1.19, shown at level 0.179, step 2, values float32
> hide #!29 models
> volume #30 step 1
> open /Users/roan.groh/Downloads/cryosparc_P346_J320_004_volume_map.mrc
Opened cryosparc_P346_J320_004_volume_map.mrc as #31, grid size 384,384,384,
pixel 1.19, shown at level 0.181, step 2, values float32
> hide #!30 models
> volume #31 step 1
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/roan.groh/Library/Application Support/ChimeraX/registration' has expired
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
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: MacBookPro18,3
Model Number: MKGT3D/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 25 days, 1 hour, 24 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP ENVY 27s:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
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