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Opened 18 months ago
Closed 18 months ago
#15006 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-28-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007700d67fc640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000077015b422740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 58)
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig2B.cxs
Opened 412_26NT_1.mrc as #2, grid size 152,152,152, pixel 1.14, shown at level
0.159, step 1, values float32
Opened 412_26NT_1.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Log from Tue Apr 16 15:30:53 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/PIWIL2/Figures/fig2b.cxs
Opened 412_26NT_1.mrc as #2, grid size 152,152,152, pixel 1.14, shown at level
0.123, step 1, values float32
Opened 412_26NT_1.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Log from Tue Apr 16 13:33:16 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig2B.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened RT_MILI_26nt_2.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 11 as #3.12, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 12 as #3.13, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
Log from Mon Mar 11 21:26:02 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
Opened RT_MILI_26nt_2.mrc as #1, grid size 152,152,152, pixel 1.14, shown at
level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 11 as #3.12, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 12 as #3.13, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Log from Thu Mar 7 13:21:52 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Log from Fri Jan 26 21:22:59 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs format session
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Log from Tue Jan 23 13:37:14 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig1B.cxs
Error opening map "/home/dell/shen_data/PIWI/STUCTURES/Figures/Fig1B.cxs":
File Fig1B.cxs, format mrc
MRC header value nsymbt (912209460) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
Log from Fri Jan 19 14:22:42 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/dell/shen_data/PIWI/STUCTURES/22ntMUT/RealSpaceRefine_1/1207
> MILImut 22nt-coot-1_real_space_refined_001.pdb"
Chain information for 1207 MILImut 22nt-coot-1_real_space_refined_001.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /home/dell/shen_data/PIWI/STUCTURES/22ntMUT/cryosparc_P88_J81_003_volume_map_sharp.mrc
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc as #2, grid size
152,152,152, pixel 1.14, shown at level 0.116, step 1, values float32
> set bgColor white
> volume #2 level 0.1452
> surface dust #2 size 11.4
> select #1
6971 atoms, 7220 bonds, 793 residues, 1 model selected
> show sel surfaces
> fitmap #1 inMap #2
Fit molecule 1207 MILImut 22nt-coot-1_real_space_refined_001.pdb (#1) to map
cryosparc_P88_J81_003_volume_map_sharp.mrc (#2) using 6971 atoms
average map value = 0.2701, steps = 44
shifted from previous position = 0.0248
rotated from previous position = 0.0244 degrees
atoms outside contour = 1625, contour level = 0.14522
Position of 1207 MILImut 22nt-coot-1_real_space_refined_001.pdb (#1) relative
to cryosparc_P88_J81_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999991 -0.00028128 -0.00030614 0.04951058
0.00028125 0.99999996 -0.00009097 0.00766025
0.00030616 0.00009088 0.99999995 -0.02836280
Axis 0.21366021 -0.71940215 0.66091592
Axis point 63.14145020 0.00000000 171.25407833
Rotation angle (degrees) 0.02438302
Shift along axis -0.01367779
> hide sel surfaces
> select clear
> color bychain
> color zone #2 near #1 distance 6.84
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.14
> volume splitbyzone #2
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
> hide #!1 models
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> volume #2 level 0.1822
> hide #!2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> close #3
> show #!1 models
> show #!2 models
> hide #!2 models
> select /a:723-971
1994 atoms, 2055 bonds, 249 residues, 1 model selected
> color (#!1 & sel) lime
> select /a:238-309
574 atoms, 583 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:387-498
859 atoms, 876 bonds, 104 residues, 1 model selected
> color sel aquamarine
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color (#!1 & sel) light gray
> select /a:498-598
813 atoms, 825 bonds, 101 residues, 1 model selected
> color (#!1 & sel) dim gray
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.84
> volume #2 level 0.588
> volume #2 level 0.1838
> volume #2 level 0.1551
> lighting soft
> volume #2 level 0.08037
> color zone #2 near #1 distance 29.61
> volume #2 level 0.09569
> volume #2 level 0.05738
> volume #2 level 0.08995
> color zone #2 near #1 distance 4.36
> volume #2 level 0.1053
> surface dust #2 size 11.4
> hide #!2 models
> select /a:210-238
144 atoms, 145 bonds, 19 residues, 1 model selected
> color sel deep sky blue
> show #!2 models
> color zone #2 near sel & #1 distance 6.84
> select clear
> color zone #2 near #1 distance 6.84
> color zone #2 near #1 distance 5.57
> color zone #2 near #1 distance 6.12
> volume splitbyzone #2
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> surface dust #3.10 size 11.4
> surface dust #3.11 size 11.4
> surface dust #3.12 size 11.4
> hide #!3.11 models
> hide #!3.10 models
> hide #!3.12 models
> show #!3.12 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> volume #2 level 0.1344
> volume #2 level 0.1364
> close #3
> volume splitbyzone #2
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
> hide #!3.12 models
> hide #!3.11 models
> hide #!3.10 models
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> view clip false
> help size
> windowsize 1280 720
> save /home/dell/Desktop/image7.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Fig1B.cxs
> show #!1 models
> hide #!3 models
> lighting simple
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> lighting soft
[Repeated 1 time(s)]
> show #!2 models
> hide #!3 models
> show #!3 models
> hlep locate
Unknown command: hlep locate
> show #!1 models
> hide #!2 models
> hide #!3 models
> cartoon style #1 xsection oval modeHelix default
> cartoon style #1 xsection rectangle modeHelix default
> graphics silhouettes true
> lighting simple
> cartoon style #1 xsection rectangle modeHelix default
> hide atoms
> cartoon style #1 xsection oval modeHelix default
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> cartoon style #1 xsection oval modeHelix default
> cartoon style (#1 & coil) xsection oval
> cartoon style #1 xsection barbell modeHelix default
> lighting simple
> graphics silhouettes true
> cartoon style #1 xsection oval modeHelix default
> hide atoms
> save /home/dell/Desktop/image5.png supersample 3
> show #!3 models
> hide #!1 models
> lighting soft
> save /home/dell/Desktop/image6.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Fig1B.cxs
——— End of log from Fri Jan 19 14:22:42 2024 ———
opened ChimeraX session
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
> select /b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> show #!1 models
> hide /a
> hide #1/a
> select /a
5977 atoms, 6113 bonds, 745 residues, 1 model selected
> hide sel cartoons
> select #1/b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> show sel cartoons
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 993 atom styles
> select #1/b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color (#!1 & sel) red
> select #1/c
443 atoms, 494 bonds, 21 residues, 1 model selected
> color (#!1 & sel) blue
> select clear
> select #1/b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> nucleotides sel tube/slab shape box
> select clear
> hide #!3 models
> show surfaces
> select clear
> lighting simple
> select #1/b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> hide sel surfaces
> select clear
> transparency #1 20
> transparency #1 40
> select clear
> save /home/dell/Desktop/image5.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Tue Jan 23 13:37:14 2024 ———
opened ChimeraX session
> transparency #1 60
> select /a:238-309
574 atoms, 583 bonds, 72 residues, 1 model selected
> color sel magenta
> select /a:387-498
859 atoms, 876 bonds, 104 residues, 1 model selected
> color sel dodger blue
> select clear
> nucleotides ladder
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save /home/dell/Desktop/image28.png supersample 3
> save /home/dell/Desktop/image29.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Fri Jan 26 21:22:59 2024 ———
opened ChimeraX session
> open
> /home/dell/shen_data/PIWI/STUCTURES/RT_structures/RT_MILI_26nt_2-coot-0.pdb
Chain information for RT_MILI_26nt_2-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close #3
> close #1
> open /home/dell/shen_data/PIWI/STUCTURES/RT_structures/RT_MILI_26nt_2.mrc
Opened RT_MILI_26nt_2.mrc as #1, grid size 152,152,152, pixel 1.14, shown at
level 0.108, step 1, values float32
> surface dust #1 size 11.4
> select /a:210-238
217 atoms, 218 bonds, 29 residues, 1 model selected
> color sel aquamarine
> select /a:238-309
574 atoms, 583 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color sel dark grey
> select /a:387-498
829 atoms, 845 bonds, 100 residues, 1 model selected
> color sel dodger blue
> select /a:498-598
817 atoms, 829 bonds, 101 residues, 1 model selected
> color sel dim grey
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /a:723-973
1998 atoms, 2059 bonds, 249 residues, 1 model selected
> color sel lime
> select /b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color sel red
> select /c
533 atoms, 596 bonds, 25 residues, 1 model selected
> color sel blue
> color zone #1 near sel & #2 distance 6.84
> select clear
[Repeated 1 time(s)]
> color zone #1 near #2 distance 6.84
> transparency 50
> hide cartoons
> hide atoms
> transparency 60
> transparency 50
> ui tool show "Color Zone"
Need to color zone map before it can be split
[Repeated 2 time(s)]
> color zone #1 near #2 distance 6.84
> volume splitbyzone #1
Opened RT_MILI_26nt_2.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 11 as #3.12, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 12 as #3.13, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> surface dust #3.10 size 11.4
> surface dust #3.11 size 11.4
> surface dust #3.12 size 11.4
> surface dust #3.13 size 11.4
> hide #!3.13 models
> hide #!3.12 models
> select /b,c
1083 atoms, 1209 bonds, 51 residues, 1 model selected
> show sel cartoons
> show sel atoms
> nucleotides sel stubs
> select clear
> transparency #2#3.1-11#!3 50
> select clear
> transparency #2#3.1-11#!3 60
> save /home/dell/Desktop/image9.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Thu Mar 7 13:21:52 2024 ———
opened ChimeraX session
> cartoon syle width 0.8 thick 0.8
Expected an atoms specifier or a keyword
> cartoon syle width 0.8 thick 0.8 c
Expected an atoms specifier or a keyword
> cartoon style width 0.8 thickness 0.8 c
Expected a keyword
> cartoon style width 0.8 thickness 0.8
> cartoon style #2#3.1-11#!3 xsection oval modeHelix default
> transparency #2#3.1-11#!3 50
> save /home/dell/Desktop/image7.png supersample 3
> view p1
Expected an objects specifier or a view name or a keyword
> view name p1
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Mon Mar 11 21:26:02 2024 ———
opened ChimeraX session
> close #2-3
> open
> /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb
> /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1.mrc
Summary of feedback from opening
/home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb
---
warning | Start residue of secondary structure not found: SHEET 1 A 2 THR A
220 LEU A 224 0
Chain information for 412_26NT_1-coot-8.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Opened 412_26NT_1.mrc as #2, grid size 152,152,152, pixel 1.14, shown at level
0.123, step 1, values float32
> select /a:209-238
133 atoms, 134 bonds, 18 residues, 1 model selected
> color sel aquamarine
> select /a:238-309
570 atoms, 579 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color sel dark grey
> select /a:387-500
889 atoms, 906 bonds, 108 residues, 1 model selected
> color sel dodger blue
> select /a:501-598
783 atoms, 794 bonds, 97 residues, 1 model selected
> color sel dim grey
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /a:723-973
1927 atoms, 1983 bonds, 241 residues, 1 model selected
> color sel lime
> select /b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color sel red
> select /c
533 atoms, 595 bonds, 25 residues, 1 model selected
> color sel blue
> surface dust #2 size 11.4
> color zone #2 near sel & #1 distance 6.84
> ui mousemode right select
> select clear
> color zone #2 near #1 distance 6.84
> select clear
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.14
> color zone #2 near #1 distance 7.99
> volume splitbyzone #2
Opened 412_26NT_1.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
> select clear
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> surface dust #3.10 size 11.4
> surface dust #3.11 size 11.4
> close #3.9-10
> select clear
> select /b,c
1083 atoms, 1208 bonds, 51 residues, 1 model selected
> cartoon style sel width 0.8 thickness 0.8
> select clear
> cartoon style #1,3 xsection oval modeHelix default
> select clear
> nucleotides ladder
> select clear
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> color #3 #c0bfbcff models
> hide #!3 models
> select clear
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.84
> color zone #2 near #1 distance 7.99
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.84
> volume splitbyzone #2
Opened 412_26NT_1.mrc 0 as #4.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #4.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #4.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #4.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #4.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #4.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
> surface dust #4.1 size 11.4
> surface dust #4.2 size 11.4
> surface dust #4.3 size 11.4
> surface dust #4.4 size 11.4
> surface dust #4.5 size 11.4
> surface dust #4.6 size 11.4
> surface dust #4.7 size 11.4
> hide #!4.1 models
> close #4
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show #!2 models
> color sel magenta
> color zone #2 near sel & #1 distance 6.84
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
> ，/b,c
Expected a keyword
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745，/b,c
Expected an objects specifier or a keyword
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> select add /B:26
422 atoms, 397 bonds, 48 residues, 1 model selected
> select add /C:1
445 atoms, 422 bonds, 49 residues, 1 model selected
> select up
2800 atoms, 2942 bonds, 265 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.84
> hide #!2 models
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
Drag select of 17 residues, 28 shapes
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
Drag select of 11 residues, 24 shapes
> select up
2800 atoms, 2942 bonds, 265 residues, 1 model selected
> select down
658 atoms, 375 bonds, 59 residues, 1 model selected
Drag select of 13 residues, 51 shapes
> select up
2800 atoms, 2942 bonds, 265 residues, 1 model selected
> select
> /b,c,/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
Expected an objects specifier or a keyword
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.84
> volume splitbyzone #2
Opened 412_26NT_1.mrc 0 as #4.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #4.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #4.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #4.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #4.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #4.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #4.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 8 as #4.9, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 9 as #4.10, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #4.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 11 as #4.12, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
> surface dust #4.1 size 11.4
> surface dust #4.2 size 11.4
> surface dust #4.3 size 11.4
> surface dust #4.4 size 11.4
> surface dust #4.5 size 11.4
> surface dust #4.6 size 11.4
> surface dust #4.7 size 11.4
> surface dust #4.8 size 11.4
> surface dust #4.9 size 11.4
> surface dust #4.10 size 11.4
> surface dust #4.11 size 11.4
> surface dust #4.12 size 11.4
> close #4.5-12
> close #4.1-3
> hide #!4 models
> select clear
> show surfaces
Drag select of 412_26NT_1-coot-8.pdb_B SES surface, 10619 of 86206 triangles,
412_26NT_1-coot-8.pdb_C SES surface, 7963 of 83146 triangles, 7 residues, 13
shapes
> select up
1083 atoms, 1208 bonds, 51 residues, 3 models selected
> hide sel surfaces
> select clear
> select /A:434@CA
1 atom, 1 residue, 1 model selected
Drag select of 412_26NT_1-coot-8.pdb_A SES surface, 111544 of 589802
triangles, 8 atoms, 175 residues, 7 bonds
> select up
2069 atoms, 2109 bonds, 257 residues, 2 models selected
> select up
3186 atoms, 3264 bonds, 399 residues, 2 models selected
> select up
3207 atoms, 3284 bonds, 402 residues, 2 models selected
> select up
3822 atoms, 3910 bonds, 479 residues, 2 models selected
> select up
3855 atoms, 3943 bonds, 483 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> color surf fromcartoons
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color surf bymodel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:488@CG
1 atom, 1 residue, 1 model selected
> select /a
5902 atoms, 6033 bonds, 736 residues, 1 model selected
> color surf fromcartoons
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color surf fromribbons
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel fromribbons
> select clear
> select /a:209-238
133 atoms, 134 bonds, 18 residues, 1 model selected
> color sel aquamarine
> select /a:238-309
570 atoms, 579 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color sel dark grey
> select /a:387-500
889 atoms, 906 bonds, 108 residues, 1 model selected
> color sel dodger blue
> select /a:501-598
783 atoms, 794 bonds, 97 residues, 1 model selected
> color sel dim grey
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /a:723-973
1927 atoms, 1983 bonds, 241 residues, 1 model selected
> color sel lime
> select /b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color sel red
> select /c
533 atoms, 595 bonds, 25 residues, 1 model selected
> color sel blue
> select clear
> combine #1
> nucleotides ladder
> select clear
> show (#1,5 & sidechain) target ab
> select clear
> select
> #5/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel atoms
> hide #!1 models
> undo
[Repeated 1 time(s)]
> hide #!1 models
> hide sel atoms
> select clear
> hide #!5 atoms
> select
> #5/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel atoms
> select clear
> select
> #5/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel surfaces
> color surf bymodel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel bymodel
> color sel fromcartoons
> color sel byatoms
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> select /a:209-238
266 atoms, 268 bonds, 36 residues, 2 models selected
> color sel aquamarine
> select /a:238-309
1140 atoms, 1158 bonds, 144 residues, 2 models selected
> color sel violet
> select /a:309-387
1278 atoms, 1306 bonds, 158 residues, 2 models selected
> color sel dark grey
> select /a:387-500
1778 atoms, 1812 bonds, 216 residues, 2 models selected
> color sel dodger blue
> select /a:501-598
1566 atoms, 1588 bonds, 194 residues, 2 models selected
> color sel dim grey
> select /a:598-723
1994 atoms, 2028 bonds, 252 residues, 2 models selected
> color sel gold
> select /a:723-973
3854 atoms, 3966 bonds, 482 residues, 2 models selected
> color sel lime
> select /b
1100 atoms, 1226 bonds, 52 residues, 2 models selected
> color sel red
> select /c
1066 atoms, 1190 bonds, 50 residues, 2 models selected
> color sel blue
> select clear
> show #!1 models
> hide #!5 models
> select add #1
6986 atoms, 7241 bonds, 788 residues, 1 model selected
> color sel light gray
> color (#!1 & sel) light gray
> color (#!1 & sel) dark gray
> select clear
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> select
> #1/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> hide sel surfaces
> select clear
> hide #!1 atoms
> select clear
> show #!5 models
> select clear
> transparency #1,5 50
> select clear
Drag select of 4 residues
> select up
1100 atoms, 1226 bonds, 52 residues, 3 models selected
> select /b,c
2166 atoms, 2416 bonds, 102 residues, 2 models selected
> cartoon style sel width 0.8 thickness 0.8
> select clear
> cartoon style #1,5 xsection oval modeHelix default
> select clear
> undo
Drag select of 14 residues
> select clear
Drag select of 4 residues
> select up
1100 atoms, 1226 bonds, 52 residues, 3 models selected
> color (#!1,5 & sel) red
Drag select of 4 residues
> select up
1066 atoms, 1190 bonds, 50 residues, 3 models selected
> color (#!1,5 & sel) blue
> select clear
[Repeated 1 time(s)]
> hide atoms
> select clear
> hide #5/a cartoons
> hide #1/a cartoons
> select clear
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/fig2b.cxs
> transparency #1,5 70
> hide #!1 models
> transparency #5 40
> show #!1 models
> hide #!1 models
> transparency #5 0
> show #!1 models
> save /home/dell/Desktop/image1.png supersample 3
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/fig2b.cxs
——— End of log from Tue Apr 16 13:33:16 2024 ———
opened ChimeraX session
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.1586
> select /a:209-238
266 atoms, 268 bonds, 36 residues, 2 models selected
> color sel aquamarine
> select /a:238-309
1140 atoms, 1158 bonds, 144 residues, 2 models selected
> color sel violet
> select /a:309-387
1278 atoms, 1306 bonds, 158 residues, 2 models selected
> color sel dark grey
> select /a:387-500
1778 atoms, 1812 bonds, 216 residues, 2 models selected
> color sel dodger blue
> select /a:501-598
1566 atoms, 1588 bonds, 194 residues, 2 models selected
> color sel dim grey
> select /a:598-723
1994 atoms, 2028 bonds, 252 residues, 2 models selected
> color sel gold
> select /a:723-973
3854 atoms, 3966 bonds, 482 residues, 2 models selected
> color sel lime
> select /b
1100 atoms, 1226 bonds, 52 residues, 2 models selected
> color sel red
> select /c
1066 atoms, 1190 bonds, 50 residues, 2 models selected
> color sel blue
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!1 models
> color zone #2 near sel & #1 distance 6.84
> ui mousemode right select
> select clear
> color zone #2 near #1 distance 6.84
> hide #!1 surfaces
> show #!1 cartoons
> hide #!2 models
> nucleotides #!1 ladder
Drag select of 9 residues
> select up
1083 atoms, 1208 bonds, 51 residues, 3 models selected
> show sel atoms
> nucleotides sel ladder
> select clear
> save /home/dell/Desktop/image9.png supersample 3
Drag select of 8 residues, 13 shapes
> select up
1083 atoms, 1208 bonds, 51 residues, 3 models selected
> select up
6986 atoms, 7241 bonds, 788 residues, 3 models selected
> select down
1083 atoms, 1208 bonds, 51 residues, 4 models selected
> show sel surfaces
> select clear
Drag select of 412_26NT_1-coot-8.pdb_B SES surface, 2685 of 86206 triangles,
412_26NT_1-coot-8.pdb_C SES surface, 7768 of 83146 triangles, 9 residues, 9
shapes
> select up
1195 atoms, 1323 bonds, 67 residues, 4 models selected
> select clear
Drag select of 412_26NT_1-coot-8.pdb_B SES surface, 7384 of 86206 triangles,
412_26NT_1-coot-8.pdb_C SES surface, 8453 of 83146 triangles, 6 residues, 9
shapes
> select up
1083 atoms, 1208 bonds, 51 residues, 3 models selected
> transparency (#!1 & sel) 60
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 surfaces
> show #!2 models
> lighting soft
> select /b
1100 atoms, 1226 bonds, 52 residues, 2 models selected
> color sel red
> select /c
1066 atoms, 1190 bonds, 50 residues, 2 models selected
> color sel blue
> select clear
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig2B.cxs
——— End of log from Tue Apr 16 15:30:53 2024 ———
opened ChimeraX session
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/PIWIL2/Figures/fig2b.cxs
Opened 412_26NT_1.mrc as #2, grid size 152,152,152, pixel 1.14, shown at level
0.123, step 1, values float32
Opened 412_26NT_1.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Log from Tue Apr 16 13:33:16 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig2B.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened RT_MILI_26nt_2.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 11 as #3.12, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 12 as #3.13, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
Log from Mon Mar 11 21:26:02 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
Opened RT_MILI_26nt_2.mrc as #1, grid size 152,152,152, pixel 1.14, shown at
level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 11 as #3.12, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 12 as #3.13, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Log from Thu Mar 7 13:21:52 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Log from Fri Jan 26 21:22:59 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs format session
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Log from Tue Jan 23 13:37:14 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig1B.cxs
Error opening map "/home/dell/shen_data/PIWI/STUCTURES/Figures/Fig1B.cxs":
File Fig1B.cxs, format mrc
MRC header value nsymbt (912209460) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
Log from Fri Jan 19 14:22:42 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/dell/shen_data/PIWI/STUCTURES/22ntMUT/RealSpaceRefine_1/1207
> MILImut 22nt-coot-1_real_space_refined_001.pdb"
Chain information for 1207 MILImut 22nt-coot-1_real_space_refined_001.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /home/dell/shen_data/PIWI/STUCTURES/22ntMUT/cryosparc_P88_J81_003_volume_map_sharp.mrc
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc as #2, grid size
152,152,152, pixel 1.14, shown at level 0.116, step 1, values float32
> set bgColor white
> volume #2 level 0.1452
> surface dust #2 size 11.4
> select #1
6971 atoms, 7220 bonds, 793 residues, 1 model selected
> show sel surfaces
> fitmap #1 inMap #2
Fit molecule 1207 MILImut 22nt-coot-1_real_space_refined_001.pdb (#1) to map
cryosparc_P88_J81_003_volume_map_sharp.mrc (#2) using 6971 atoms
average map value = 0.2701, steps = 44
shifted from previous position = 0.0248
rotated from previous position = 0.0244 degrees
atoms outside contour = 1625, contour level = 0.14522
Position of 1207 MILImut 22nt-coot-1_real_space_refined_001.pdb (#1) relative
to cryosparc_P88_J81_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999991 -0.00028128 -0.00030614 0.04951058
0.00028125 0.99999996 -0.00009097 0.00766025
0.00030616 0.00009088 0.99999995 -0.02836280
Axis 0.21366021 -0.71940215 0.66091592
Axis point 63.14145020 0.00000000 171.25407833
Rotation angle (degrees) 0.02438302
Shift along axis -0.01367779
> hide sel surfaces
> select clear
> color bychain
> color zone #2 near #1 distance 6.84
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.14
> volume splitbyzone #2
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.145, step 1, values float32
> hide #!1 models
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> volume #2 level 0.1822
> hide #!2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> close #3
> show #!1 models
> show #!2 models
> hide #!2 models
> select /a:723-971
1994 atoms, 2055 bonds, 249 residues, 1 model selected
> color (#!1 & sel) lime
> select /a:238-309
574 atoms, 583 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:387-498
859 atoms, 876 bonds, 104 residues, 1 model selected
> color sel aquamarine
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color (#!1 & sel) light gray
> select /a:498-598
813 atoms, 825 bonds, 101 residues, 1 model selected
> color (#!1 & sel) dim gray
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.84
> volume #2 level 0.588
> volume #2 level 0.1838
> volume #2 level 0.1551
> lighting soft
> volume #2 level 0.08037
> color zone #2 near #1 distance 29.61
> volume #2 level 0.09569
> volume #2 level 0.05738
> volume #2 level 0.08995
> color zone #2 near #1 distance 4.36
> volume #2 level 0.1053
> surface dust #2 size 11.4
> hide #!2 models
> select /a:210-238
144 atoms, 145 bonds, 19 residues, 1 model selected
> color sel deep sky blue
> show #!2 models
> color zone #2 near sel & #1 distance 6.84
> select clear
> color zone #2 near #1 distance 6.84
> color zone #2 near #1 distance 5.57
> color zone #2 near #1 distance 6.12
> volume splitbyzone #2
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.105, step 1, values float32
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> surface dust #3.10 size 11.4
> surface dust #3.11 size 11.4
> surface dust #3.12 size 11.4
> hide #!3.11 models
> hide #!3.10 models
> hide #!3.12 models
> show #!3.12 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> volume #2 level 0.1344
> volume #2 level 0.1364
> close #3
> volume splitbyzone #2
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 0 as #3.1, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 1 as #3.2, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 2 as #3.3, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 3 as #3.4, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 4 as #3.5, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 5 as #3.6, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 6 as #3.7, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 7 as #3.8, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 8 as #3.9, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 9 as #3.10, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 10 as #3.11, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
Opened cryosparc_P88_J81_003_volume_map_sharp.mrc 11 as #3.12, grid size
152,152,152, pixel 1.14, shown at level 0.136, step 1, values float32
> hide #!3.12 models
> hide #!3.11 models
> hide #!3.10 models
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> view clip false
> help size
> windowsize 1280 720
> save /home/dell/Desktop/image7.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Fig1B.cxs
> show #!1 models
> hide #!3 models
> lighting simple
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> lighting soft
[Repeated 1 time(s)]
> show #!2 models
> hide #!3 models
> show #!3 models
> hlep locate
Unknown command: hlep locate
> show #!1 models
> hide #!2 models
> hide #!3 models
> cartoon style #1 xsection oval modeHelix default
> cartoon style #1 xsection rectangle modeHelix default
> graphics silhouettes true
> lighting simple
> cartoon style #1 xsection rectangle modeHelix default
> hide atoms
> cartoon style #1 xsection oval modeHelix default
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> cartoon style #1 xsection oval modeHelix default
> cartoon style (#1 & coil) xsection oval
> cartoon style #1 xsection barbell modeHelix default
> lighting simple
> graphics silhouettes true
> cartoon style #1 xsection oval modeHelix default
> hide atoms
> save /home/dell/Desktop/image5.png supersample 3
> show #!3 models
> hide #!1 models
> lighting soft
> save /home/dell/Desktop/image6.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Fig1B.cxs
——— End of log from Fri Jan 19 14:22:42 2024 ———
opened ChimeraX session
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
> select /b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> show #!1 models
> hide /a
> hide #1/a
> select /a
5977 atoms, 6113 bonds, 745 residues, 1 model selected
> hide sel cartoons
> select #1/b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> show sel cartoons
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 993 atom styles
> select #1/b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color (#!1 & sel) red
> select #1/c
443 atoms, 494 bonds, 21 residues, 1 model selected
> color (#!1 & sel) blue
> select clear
> select #1/b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> nucleotides sel tube/slab shape box
> select clear
> hide #!3 models
> show surfaces
> select clear
> lighting simple
> select #1/b,c
993 atoms, 1107 bonds, 47 residues, 1 model selected
> hide sel surfaces
> select clear
> transparency #1 20
> transparency #1 40
> select clear
> save /home/dell/Desktop/image5.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Tue Jan 23 13:37:14 2024 ———
opened ChimeraX session
> transparency #1 60
> select /a:238-309
574 atoms, 583 bonds, 72 residues, 1 model selected
> color sel magenta
> select /a:387-498
859 atoms, 876 bonds, 104 residues, 1 model selected
> color sel dodger blue
> select clear
> nucleotides ladder
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save /home/dell/Desktop/image28.png supersample 3
> save /home/dell/Desktop/image29.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Fri Jan 26 21:22:59 2024 ———
opened ChimeraX session
> open
> /home/dell/shen_data/PIWI/STUCTURES/RT_structures/RT_MILI_26nt_2-coot-0.pdb
Chain information for RT_MILI_26nt_2-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close #3
> close #1
> open /home/dell/shen_data/PIWI/STUCTURES/RT_structures/RT_MILI_26nt_2.mrc
Opened RT_MILI_26nt_2.mrc as #1, grid size 152,152,152, pixel 1.14, shown at
level 0.108, step 1, values float32
> surface dust #1 size 11.4
> select /a:210-238
217 atoms, 218 bonds, 29 residues, 1 model selected
> color sel aquamarine
> select /a:238-309
574 atoms, 583 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color sel dark grey
> select /a:387-498
829 atoms, 845 bonds, 100 residues, 1 model selected
> color sel dodger blue
> select /a:498-598
817 atoms, 829 bonds, 101 residues, 1 model selected
> color sel dim grey
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /a:723-973
1998 atoms, 2059 bonds, 249 residues, 1 model selected
> color sel lime
> select /b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color sel red
> select /c
533 atoms, 596 bonds, 25 residues, 1 model selected
> color sel blue
> color zone #1 near sel & #2 distance 6.84
> select clear
[Repeated 1 time(s)]
> color zone #1 near #2 distance 6.84
> transparency 50
> hide cartoons
> hide atoms
> transparency 60
> transparency 50
> ui tool show "Color Zone"
Need to color zone map before it can be split
[Repeated 2 time(s)]
> color zone #1 near #2 distance 6.84
> volume splitbyzone #1
Opened RT_MILI_26nt_2.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown
at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 11 as #3.12, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
Opened RT_MILI_26nt_2.mrc 12 as #3.13, grid size 152,152,152, pixel 1.14,
shown at level 0.108, step 1, values float32
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> surface dust #3.10 size 11.4
> surface dust #3.11 size 11.4
> surface dust #3.12 size 11.4
> surface dust #3.13 size 11.4
> hide #!3.13 models
> hide #!3.12 models
> select /b,c
1083 atoms, 1209 bonds, 51 residues, 1 model selected
> show sel cartoons
> show sel atoms
> nucleotides sel stubs
> select clear
> transparency #2#3.1-11#!3 50
> select clear
> transparency #2#3.1-11#!3 60
> save /home/dell/Desktop/image9.png supersample 3
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Thu Mar 7 13:21:52 2024 ———
opened ChimeraX session
> cartoon syle width 0.8 thick 0.8
Expected an atoms specifier or a keyword
> cartoon syle width 0.8 thick 0.8 c
Expected an atoms specifier or a keyword
> cartoon style width 0.8 thickness 0.8 c
Expected a keyword
> cartoon style width 0.8 thickness 0.8
> cartoon style #2#3.1-11#!3 xsection oval modeHelix default
> transparency #2#3.1-11#!3 50
> save /home/dell/Desktop/image7.png supersample 3
> view p1
Expected an objects specifier or a view name or a keyword
> view name p1
> save /home/dell/shen_data/PIWI/STUCTURES/Figures/Fig2B.cxs
——— End of log from Mon Mar 11 21:26:02 2024 ———
opened ChimeraX session
> close #2-3
> open
> /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb
> /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1.mrc
Summary of feedback from opening
/home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb
---
warning | Start residue of secondary structure not found: SHEET 1 A 2 THR A
220 LEU A 224 0
Chain information for 412_26NT_1-coot-8.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Opened 412_26NT_1.mrc as #2, grid size 152,152,152, pixel 1.14, shown at level
0.123, step 1, values float32
> select /a:209-238
133 atoms, 134 bonds, 18 residues, 1 model selected
> color sel aquamarine
> select /a:238-309
570 atoms, 579 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color sel dark grey
> select /a:387-500
889 atoms, 906 bonds, 108 residues, 1 model selected
> color sel dodger blue
> select /a:501-598
783 atoms, 794 bonds, 97 residues, 1 model selected
> color sel dim grey
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /a:723-973
1927 atoms, 1983 bonds, 241 residues, 1 model selected
> color sel lime
> select /b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color sel red
> select /c
533 atoms, 595 bonds, 25 residues, 1 model selected
> color sel blue
> surface dust #2 size 11.4
> color zone #2 near sel & #1 distance 6.84
> ui mousemode right select
> select clear
> color zone #2 near #1 distance 6.84
> select clear
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.14
> color zone #2 near #1 distance 7.99
> volume splitbyzone #2
Opened 412_26NT_1.mrc 0 as #3.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #3.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #3.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #3.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #3.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #3.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #3.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #3.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 8 as #3.9, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 9 as #3.10, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #3.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
> select clear
> surface dust #3.1 size 11.4
> surface dust #3.2 size 11.4
> surface dust #3.3 size 11.4
> surface dust #3.4 size 11.4
> surface dust #3.5 size 11.4
> surface dust #3.6 size 11.4
> surface dust #3.7 size 11.4
> surface dust #3.8 size 11.4
> surface dust #3.9 size 11.4
> surface dust #3.10 size 11.4
> surface dust #3.11 size 11.4
> close #3.9-10
> select clear
> select /b,c
1083 atoms, 1208 bonds, 51 residues, 1 model selected
> cartoon style sel width 0.8 thickness 0.8
> select clear
> cartoon style #1,3 xsection oval modeHelix default
> select clear
> nucleotides ladder
> select clear
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> color #3 #c0bfbcff models
> hide #!3 models
> select clear
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.84
> color zone #2 near #1 distance 7.99
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.84
> volume splitbyzone #2
Opened 412_26NT_1.mrc 0 as #4.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #4.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #4.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #4.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #4.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #4.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
> surface dust #4.1 size 11.4
> surface dust #4.2 size 11.4
> surface dust #4.3 size 11.4
> surface dust #4.4 size 11.4
> surface dust #4.5 size 11.4
> surface dust #4.6 size 11.4
> surface dust #4.7 size 11.4
> hide #!4.1 models
> close #4
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show #!2 models
> color sel magenta
> color zone #2 near sel & #1 distance 6.84
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
> ，/b,c
Expected a keyword
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745，/b,c
Expected an objects specifier or a keyword
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> select add /B:26
422 atoms, 397 bonds, 48 residues, 1 model selected
> select add /C:1
445 atoms, 422 bonds, 49 residues, 1 model selected
> select up
2800 atoms, 2942 bonds, 265 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.84
> hide #!2 models
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
Drag select of 17 residues, 28 shapes
> select
> /a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
Drag select of 11 residues, 24 shapes
> select up
2800 atoms, 2942 bonds, 265 residues, 1 model selected
> select down
658 atoms, 375 bonds, 59 residues, 1 model selected
Drag select of 13 residues, 51 shapes
> select up
2800 atoms, 2942 bonds, 265 residues, 1 model selected
> select
> /b,c,/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
Expected an objects specifier or a keyword
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.84
> volume splitbyzone #2
Opened 412_26NT_1.mrc 0 as #4.1, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 1 as #4.2, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 2 as #4.3, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 3 as #4.4, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 4 as #4.5, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 5 as #4.6, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 6 as #4.7, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 7 as #4.8, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 8 as #4.9, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 9 as #4.10, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 10 as #4.11, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
Opened 412_26NT_1.mrc 11 as #4.12, grid size 152,152,152, pixel 1.14, shown at
level 0.123, step 1, values float32
> surface dust #4.1 size 11.4
> surface dust #4.2 size 11.4
> surface dust #4.3 size 11.4
> surface dust #4.4 size 11.4
> surface dust #4.5 size 11.4
> surface dust #4.6 size 11.4
> surface dust #4.7 size 11.4
> surface dust #4.8 size 11.4
> surface dust #4.9 size 11.4
> surface dust #4.10 size 11.4
> surface dust #4.11 size 11.4
> surface dust #4.12 size 11.4
> close #4.5-12
> close #4.1-3
> hide #!4 models
> select clear
> show surfaces
Drag select of 412_26NT_1-coot-8.pdb_B SES surface, 10619 of 86206 triangles,
412_26NT_1-coot-8.pdb_C SES surface, 7963 of 83146 triangles, 7 residues, 13
shapes
> select up
1083 atoms, 1208 bonds, 51 residues, 3 models selected
> hide sel surfaces
> select clear
> select /A:434@CA
1 atom, 1 residue, 1 model selected
Drag select of 412_26NT_1-coot-8.pdb_A SES surface, 111544 of 589802
triangles, 8 atoms, 175 residues, 7 bonds
> select up
2069 atoms, 2109 bonds, 257 residues, 2 models selected
> select up
3186 atoms, 3264 bonds, 399 residues, 2 models selected
> select up
3207 atoms, 3284 bonds, 402 residues, 2 models selected
> select up
3822 atoms, 3910 bonds, 479 residues, 2 models selected
> select up
3855 atoms, 3943 bonds, 483 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> color surf fromcartoons
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color surf bymodel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select /A:488@CG
1 atom, 1 residue, 1 model selected
> select /a
5902 atoms, 6033 bonds, 736 residues, 1 model selected
> color surf fromcartoons
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color surf fromribbons
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel fromribbons
> select clear
> select /a:209-238
133 atoms, 134 bonds, 18 residues, 1 model selected
> color sel aquamarine
> select /a:238-309
570 atoms, 579 bonds, 72 residues, 1 model selected
> color sel violet
> select /a:309-387
639 atoms, 653 bonds, 79 residues, 1 model selected
> color sel dark grey
> select /a:387-500
889 atoms, 906 bonds, 108 residues, 1 model selected
> color sel dodger blue
> select /a:501-598
783 atoms, 794 bonds, 97 residues, 1 model selected
> color sel dim grey
> select /a:598-723
997 atoms, 1014 bonds, 126 residues, 1 model selected
> color sel gold
> select /a:723-973
1927 atoms, 1983 bonds, 241 residues, 1 model selected
> color sel lime
> select /b
550 atoms, 613 bonds, 26 residues, 1 model selected
> color sel red
> select /c
533 atoms, 595 bonds, 25 residues, 1 model selected
> color sel blue
> select clear
> combine #1
> nucleotides ladder
> select clear
> show (#1,5 & sidechain) target ab
> select clear
> select
> #5/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel atoms
> hide #!1 models
> undo
[Repeated 1 time(s)]
> hide #!1 models
> hide sel atoms
> select clear
> hide #!5 atoms
> select
> #5/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel atoms
> select clear
> select
> #5/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> show sel surfaces
> color surf bymodel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel bymodel
> color sel fromcartoons
> color sel byatoms
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> select /a:209-238
266 atoms, 268 bonds, 36 residues, 2 models selected
> color sel aquamarine
> select /a:238-309
1140 atoms, 1158 bonds, 144 residues, 2 models selected
> color sel violet
> select /a:309-387
1278 atoms, 1306 bonds, 158 residues, 2 models selected
> color sel dark grey
> select /a:387-500
1778 atoms, 1812 bonds, 216 residues, 2 models selected
> color sel dodger blue
> select /a:501-598
1566 atoms, 1588 bonds, 194 residues, 2 models selected
> color sel dim grey
> select /a:598-723
1994 atoms, 2028 bonds, 252 residues, 2 models selected
> color sel gold
> select /a:723-973
3854 atoms, 3966 bonds, 482 residues, 2 models selected
> color sel lime
> select /b
1100 atoms, 1226 bonds, 52 residues, 2 models selected
> color sel red
> select /c
1066 atoms, 1190 bonds, 50 residues, 2 models selected
> color sel blue
> select clear
> show #!1 models
> hide #!5 models
> select add #1
6986 atoms, 7241 bonds, 788 residues, 1 model selected
> color sel light gray
> color (#!1 & sel) light gray
> color (#!1 & sel) dark gray
> select clear
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> select
> #1/a:683,679,695,718,722,931,929,937,892,893,896,898,857,378-381,326,424,499,308,242,240,307,851-853,516,339,813-819,366,322,364,366,943,946,275,273,900,892,506,971,745
401 atoms, 375 bonds, 47 residues, 1 model selected
> hide sel surfaces
> select clear
> hide #!1 atoms
> select clear
> show #!5 models
> select clear
> transparency #1,5 50
> select clear
Drag select of 4 residues
> select up
1100 atoms, 1226 bonds, 52 residues, 3 models selected
> select /b,c
2166 atoms, 2416 bonds, 102 residues, 2 models selected
> cartoon style sel width 0.8 thickness 0.8
> select clear
> cartoon style #1,5 xsection oval modeHelix default
> select clear
> undo
Drag select of 14 residues
> select clear
Drag select of 4 residues
> select up
1100 atoms, 1226 bonds, 52 residues, 3 models selected
> color (#!1,5 & sel) red
Drag select of 4 residues
> select up
1066 atoms, 1190 bonds, 50 residues, 3 models selected
> color (#!1,5 & sel) blue
> select clear
[Repeated 1 time(s)]
> hide atoms
> select clear
> hide #5/a cartoons
> hide #1/a cartoons
> select clear
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/fig2b.cxs
> transparency #1,5 70
> hide #!1 models
> transparency #5 40
> show #!1 models
> hide #!1 models
> transparency #5 0
> show #!1 models
> save /home/dell/Desktop/image1.png supersample 3
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/fig2b.cxs
——— End of log from Tue Apr 16 13:33:16 2024 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900K
Cache Size: 36864 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 2.8Gi 55Gi 77Mi 3.8Gi 58Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104GL [RTX A4000] [10de:24b0] (rev a1)
Subsystem: Dell GA104GL [RTX A4000] [1028:14ad]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.1
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyqtgraph: 0.13.3
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 18 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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