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Opened 17 months ago
Closed 17 months ago
#15230 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
Current thread 0x00007268c090f740 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/pkg_resources/_vendor/packaging/version.py", line 518 in _cmpkey
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/pkg_resources/_vendor/packaging/version.py", line 212 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 709 in find_bundle
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 201 in class_of
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 733 in restore
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
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.pdb_lib._load_libs, 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.surface._surface, 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, chimerax.mlp._mlp, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 119)
===== 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/Alpha.Pred./AF3/AF3.cxs
Log from Wed May 15 11:25:55 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
Log from Fri May 10 12:32:23 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
Log from Thu May 9 18:31:50 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/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
Log from Fri Apr 12 21:01:49 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/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
Log from Fri Apr 12 10:48:13 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/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
> format session
Log from Fri Apr 12 09:21:22 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF 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/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> color bychain
> open
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_1.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_2.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_3.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_4.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_5.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_6.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_7.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_8.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_9.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_10.pdb
Chain information for ranked_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_3.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_4.pdb #5
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_5.pdb #6
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_6.pdb #7
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_7.pdb #8
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_8.pdb #9
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_9.pdb #10
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_10.pdb #11
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #2-11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
sequence alignment score = 3986.5
RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
0.928)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
sequence alignment score = 3999.7
RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
0.359)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#4),
sequence alignment score = 3933.7
RMSD between 718 pruned atom pairs is 0.806 angstroms; (across all 763 pairs:
1.041)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#5),
sequence alignment score = 3955.3
RMSD between 708 pruned atom pairs is 0.837 angstroms; (across all 763 pairs:
1.111)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_5.pdb, chain A (#6),
sequence alignment score = 3985.9
RMSD between 752 pruned atom pairs is 0.761 angstroms; (across all 763 pairs:
0.858)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_6.pdb, chain A (#7),
sequence alignment score = 3989.5
RMSD between 709 pruned atom pairs is 0.882 angstroms; (across all 763 pairs:
1.139)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_7.pdb, chain A (#8),
sequence alignment score = 3993.1
RMSD between 761 pruned atom pairs is 0.437 angstroms; (across all 763 pairs:
0.455)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_8.pdb, chain A (#9),
sequence alignment score = 3992.5
RMSD between 756 pruned atom pairs is 0.279 angstroms; (across all 763 pairs:
0.449)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_9.pdb, chain A (#10),
sequence alignment score = 3999.7
RMSD between 762 pruned atom pairs is 0.329 angstroms; (across all 763 pairs:
0.345)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_10.pdb, chain A (#11),
sequence alignment score = 3947.5
RMSD between 745 pruned atom pairs is 0.640 angstroms; (across all 763 pairs:
0.737)
> matchmaker #2-11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
sequence alignment score = 3986.5
RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
0.928)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
sequence alignment score = 3999.7
RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
0.359)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#4),
sequence alignment score = 3933.7
RMSD between 718 pruned atom pairs is 0.806 angstroms; (across all 763 pairs:
1.041)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#5),
sequence alignment score = 3955.3
RMSD between 708 pruned atom pairs is 0.837 angstroms; (across all 763 pairs:
1.111)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_5.pdb, chain A (#6),
sequence alignment score = 3985.9
RMSD between 752 pruned atom pairs is 0.761 angstroms; (across all 763 pairs:
0.858)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_6.pdb, chain A (#7),
sequence alignment score = 3989.5
RMSD between 709 pruned atom pairs is 0.882 angstroms; (across all 763 pairs:
1.139)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_7.pdb, chain A (#8),
sequence alignment score = 3993.1
RMSD between 761 pruned atom pairs is 0.437 angstroms; (across all 763 pairs:
0.455)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_8.pdb, chain A (#9),
sequence alignment score = 3992.5
RMSD between 756 pruned atom pairs is 0.279 angstroms; (across all 763 pairs:
0.449)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_9.pdb, chain A (#10),
sequence alignment score = 3999.7
RMSD between 762 pruned atom pairs is 0.329 angstroms; (across all 763 pairs:
0.345)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_10.pdb, chain A (#11),
sequence alignment score = 3947.5
RMSD between 745 pruned atom pairs is 0.640 angstroms; (across all 763 pairs:
0.737)
> color bychain
> select /a:26,29,36,39
605 atoms, 583 bonds, 44 residues, 11 models selected
> ui mousemode right select
> select clear
> open
> /home/dell/shen_data/PIWI/PIWIL2/RT_structures/RT_MILI_26nt_2-coot-0.pdb
Chain information for RT_MILI_26nt_2-coot-0.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with RT_MILI_26nt_2-coot-0.pdb, chain A
(#12), sequence alignment score = 3243.4
RMSD between 324 pruned atom pairs is 1.118 angstroms; (across all 751 pairs:
5.211)
> matchmaker #!12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with RT_MILI_26nt_2-coot-0.pdb, chain A
(#12), sequence alignment score = 3243.4
RMSD between 324 pruned atom pairs is 1.118 angstroms; (across all 751 pairs:
5.211)
> show cartoons
> nucleotides ladder
> select clear
> color bychain
> select clear
> select /B:26,29,36,39
1033 atoms, 990 bonds, 45 residues, 12 models selected
> show sel atoms
> select clear
> hide #2-11 target m
> select #1/B:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
246 atoms, 245 bonds, 16 residues, 1 model selected
> select up
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> color sel magenta
> select clear
> select /B:98,112,107
792 atoms, 825 bonds, 33 residues, 11 models selected
> show sel & #1 atoms
> hide H
> select clear
[Repeated 1 time(s)]
> save
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
——— End of log from Fri Apr 12 09:21:22 2024 ———
opened ChimeraX session
> show #7 models
> hide #7 models
> show #7 models
> show #11 models
> hide #11 models
> close #2-11
> combine #1
> hide #2 models
> hide #!12 models
> coulombic #1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -23.31, mean
2.59, maximum 28.26
Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -15.32, mean
-0.57, maximum 12.26
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right select
> select #1/B:13@HE3
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 2 models selected
> select up
93 atoms, 93 bonds, 6 residues, 2 models selected
> select up
2603 atoms, 2640 bonds, 167 residues, 2 models selected
> hide sel surfaces
> select clear
> select #1/B:82
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
246 atoms, 245 bonds, 16 residues, 2 models selected
> select up
2603 atoms, 2640 bonds, 167 residues, 2 models selected
> color sel byhetero
> select clear
> show #2 models
> hide #!1 models
> select clear
> mlp #2
Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
mean -3.606, maximum 24.24
Map values for surface "copy of ranked_0.pdb_B SES surface": minimum -28.26,
mean -3.591, maximum 22.8
To also show corresponding color key, enter the above mlp command and add key
true
> select #2/B:75@OG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
246 atoms, 245 bonds, 16 residues, 2 models selected
> select up
2603 atoms, 2640 bonds, 167 residues, 2 models selected
> hide sel surfaces
> select clear
> select #2/B:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
246 atoms, 245 bonds, 16 residues, 2 models selected
> select up
2603 atoms, 2640 bonds, 167 residues, 2 models selected
> color sel byhetero
> select clear
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> select #2/B:94
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:92
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:388@CG2
1 atom, 1 residue, 1 model selected
> select #2/A:388@HD12
1 atom, 1 residue, 1 model selected
> select #2/B:95
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!12 models
> select #12/a
6035 atoms, 6171 bonds, 751 residues, 1 model selected
> hide sel cartoons
> select clear
> select #12/b
550 atoms, 613 bonds, 26 residues, 1 model selected
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide H
> select clear
> select #1/B:91
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> select #1/B:96
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #1/A:587@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:118
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1/B:119
34 atoms, 34 bonds, 2 residues, 2 models selected
> select add #1/B:120
50 atoms, 49 bonds, 3 residues, 2 models selected
> select add #1/A:698@O
51 atoms, 49 bonds, 4 residues, 2 models selected
> select subtract #1/A:698@O
50 atoms, 49 bonds, 3 residues, 3 models selected
> select add #1/B:121
74 atoms, 74 bonds, 4 residues, 2 models selected
> select add #1/B:122
81 atoms, 80 bonds, 5 residues, 2 models selected
> select add #1/B:123
95 atoms, 93 bonds, 6 residues, 2 models selected
> show sel atoms
> hide H
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/B:119
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #2/B:121
44 atoms, 45 bonds, 2 residues, 2 models selected
> show sel atoms
> hide H
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> graphics silhouettes true
> graphics silhouettes false
> label @@display
> label height 1.2
> hide #12.2 models
> label @@display
> label height 1.5
> select clear
> hide #2.3 models
> select #1/A:523@HB2
1 atom, 1 residue, 1 model selected
> select #1/B:106
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:105
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save /home/dell/Desktop/image5.png supersample 3
> lighting soft
> hide #!2 models
> save /home/dell/Desktop/image6.png supersample 3
> save
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
——— End of log from Fri Apr 12 10:48:13 2024 ———
opened ChimeraX session
> combine #1
> hide #3 models
> hide #!12 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #3 models
> ui mousemode right select
> select #3/B:79
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
246 atoms, 245 bonds, 16 residues, 1 model selected
> select up
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> select sel @ show sel & #3 atoms
> show (#3 & sel-residues & sidechain) target ab
> select #3/B:86
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
246 atoms, 245 bonds, 16 residues, 1 model selected
> select up
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> hide H
> select clear
> show #!1 models
> hide #!1 models
> select #3/B:86
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3/B:108
36 atoms, 34 bonds, 2 residues, 1 model selected
> select add #3/B:73
48 atoms, 45 bonds, 3 residues, 1 model selected
> select add #3/B:75
59 atoms, 55 bonds, 4 residues, 1 model selected
> select up
359 atoms, 361 bonds, 22 residues, 1 model selected
> show sel atoms
> select #3/B:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
41 atoms, 40 bonds, 3 residues, 1 model selected
> select up
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> color sel lime
> hide H
> show #!12 models
> hide #3 models
> select #12/a:716
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> show #!12 cartoons
> select #12/a:716
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> show #3 models
> hide #!12 models
> color #3 byhetero
> select clear
[Repeated 1 time(s)]
> undo
[Repeated 9 time(s)]
> select clear
> undo
[Repeated 1 time(s)]
> show #3 models
> hide #!12 models
> select #3/B:99
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
271 atoms, 274 bonds, 19 residues, 1 model selected
> show sel atoms
> hide H
> select clear
> color #3 byhetero
> select clear
Drag select of 6 atoms, 5 bonds, 5 residues
Drag select of 1 atoms, 1 bonds, 2 residues
> select clear
Drag select of 9 atoms, 7 bonds, 7 residues
> hide sel atoms
> select clear
> color #3 byhetero
> select clear
> select #3/B:35
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:32
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:39
22 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> hide H
> select clear
> select #3/B:78
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:74
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:82
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:86@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:86
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:593
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #3/B:28
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> view sel
> select #3/B:28
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:10
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:9
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/B:11
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #3/B:28
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> undo
> view sel
> select #3/B:30
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:33
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #3/B:33
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #3/B:33
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
183 atoms, 185 bonds, 10 residues, 1 model selected
> select up
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> show sel atoms
> hide H
> select clear
> ui tool show Distances
> select #3/A:611@NE2
1 atom, 1 residue, 1 model selected
> select add #3/B:32@OH
2 atoms, 2 residues, 1 model selected
> distance #3/A:611@NE2 #3/B:32@OH
Distance between copy of ranked_0.pdb #3/A GLN 611 NE2 and /B TYR 32 OH:
2.843Å
> distance style color black
[Repeated 2 time(s)]
> select #3/A:617@OD1
1 atom, 1 residue, 1 model selected
> select add #3/B:38@NH2
2 atoms, 2 residues, 1 model selected
> distance #3/A:617@OD1 #3/B:38@NH2
Distance between copy of ranked_0.pdb #3/A ASN 617 OD1 and /B ARG 38 NH2:
4.159Å
> select #3/A:614
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/B:80@OD2
1 atom, 1 residue, 1 model selected
> select add #3/A:564@NH2
2 atoms, 2 residues, 1 model selected
> distance #3/B:80@OD2 #3/A:564@NH2
Distance between copy of ranked_0.pdb #3/B ASP 80 OD2 and /A ARG 564 NH2:
2.667Å
> select clear
> select #3/B:84@NE2
1 atom, 1 residue, 1 model selected
> select #3/B:84@NE2
1 atom, 1 residue, 1 model selected
> select add #3/A:562@OH
2 atoms, 2 residues, 1 model selected
> distance #3/B:84@NE2 #3/A:562@OH
Distance between copy of ranked_0.pdb #3/B GLN 84 NE2 and /A TYR 562 OH:
3.130Å
> select #3/B:84
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/A:755@NE2
1 atom, 1 residue, 1 model selected
> select add #3/B:87@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/A:755@NE2 #3/B:87@OD1
Distance between copy of ranked_0.pdb #3/A GLN 755 NE2 and /B ASN 87 OD1:
3.235Å
> select #3/B:86
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:82
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:81
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:577@OG
1 atom, 1 residue, 1 model selected
> lighting simple
> select clear
> select #3/A:577@OG
1 atom, 1 residue, 1 model selected
> select add #3/B:73@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/A:577@OG #3/B:73@OD1
Distance between copy of ranked_0.pdb #3/A SER 577 OG and /B ASP 73 OD1:
3.929Å
> select #3/B:56@NH1
1 atom, 1 residue, 1 model selected
> select add #3/A:576@OD2
2 atoms, 2 residues, 1 model selected
> distance #3/B:56@NH1 #3/A:576@OD2
Distance between copy of ranked_0.pdb #3/B ARG 56 NH1 and /A ASP 576 OD2:
3.224Å
> select #3/B:88
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/B:81
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
[Repeated 1 time(s)]
> select add #3/A:518@OE1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select add #3/B:96@OG
2 atoms, 2 residues, 1 model selected
> distance #3/A:518@OE1 #3/B:96@OG
Distance between copy of ranked_0.pdb #3/A GLU 518 OE1 and /B SER 96 OG:
4.209Å
> select #3/B:100@SG
1 atom, 1 residue, 1 model selected
> select add #3/A:364@ND2
2 atoms, 2 residues, 1 model selected
> distance #3/B:100@SG #3/A:364@ND2
Distance between copy of ranked_0.pdb #3/B CYS 100 SG and /A ASN 364 ND2:
3.782Å
> select #3/B:103@SG
1 atom, 1 residue, 1 model selected
> select add #3/A:523@OD2
2 atoms, 2 residues, 1 model selected
> distance #3/B:103@SG #3/A:523@OD2
Distance between copy of ranked_0.pdb #3/B CYS 103 SG and /A ASP 523 OD2:
4.693Å
> select clear
> select #3/B:106@OD2
1 atom, 1 residue, 1 model selected
> select add #3/A:527@NZ
2 atoms, 2 residues, 1 model selected
> distance #3/B:106@OD2 #3/A:527@NZ
Distance between copy of ranked_0.pdb #3/B ASP 106 OD2 and /A LYS 527 NZ:
2.753Å
> select clear
> select #3/B:110@OD2
1 atom, 1 residue, 1 model selected
> select add #3/A:709@NE2
2 atoms, 2 residues, 1 model selected
> distance #3/B:110@OD2 #3/A:709@NE2
Distance between copy of ranked_0.pdb #3/B ASP 110 OD2 and /A HIS 709 NE2:
3.429Å
> select #3/A:704@ND2
1 atom, 1 residue, 1 model selected
> select add #3/B:114@OE1
2 atoms, 2 residues, 1 model selected
> distance #3/A:704@ND2 #3/B:114@OE1
Distance between copy of ranked_0.pdb #3/A ASN 704 ND2 and /B GLN 114 OE1:
3.437Å
> select #3/B:116@OG
1 atom, 1 residue, 1 model selected
> select add #3/A:704@ND2
2 atoms, 2 residues, 1 model selected
> distance #3/B:116@OG #3/A:704@ND2
Distance between copy of ranked_0.pdb #3/B SER 116 OG and /A ASN 704 ND2:
2.930Å
> select #3/B:118
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #3/B:118@N
1 atom, 1 residue, 1 model selected
> select add #3/A:704@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/B:118@N #3/A:704@OD1
Distance between copy of ranked_0.pdb #3/B PRO 118 N and /A ASN 704 OD1:
3.907Å
> select clear
> select #3/B:119
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #3/B:121
44 atoms, 45 bonds, 2 residues, 1 model selected
> color sel orange
> select clear
> select #3/A:675
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> color #3-4 byhetero
> select #3/A:620
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/A:675
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:617
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/B:120
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:702
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 33 atoms, 27 bonds, 10 residues
> hide sel atoms
> select clear
> select #3/B:111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> select #3/B:108@OD1
1 atom, 1 residue, 1 model selected
> undo
[Repeated 9 time(s)]
> select clear
> undo
[Repeated 1 time(s)]
> select #3/A:599@NZ
1 atom, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select clear
> select #3/A:599@NZ
1 atom, 1 residue, 1 model selected
> undo
[Repeated 3 time(s)]
> select #3/B:108@OD1
1 atom, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #3/B:111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> select #3/A:599@NZ
1 atom, 1 residue, 1 model selected
> select add #3/B:108@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/A:599@NZ #3/B:108@OD1
Distance between copy of ranked_0.pdb #3/A LYS 599 NZ and /B ASP 108 OD1:
2.599Å
> select #3/A:700
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 30 atoms, 25 bonds, 10 residues
> hide sel atoms
> select clear
> select #3/B:123
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:115
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:107
24 atoms, 25 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> select #3/A:712@NH1
1 atom, 1 residue, 1 model selected
> select add #3/B:105@OE2
2 atoms, 2 residues, 1 model selected
> distance #3/A:712@NH1 #3/B:105@OE2
Distance between copy of ranked_0.pdb #3/A ARG 712 NH1 and /B GLU 105 OE2:
2.704Å
> select #3/A:712@NH2
1 atom, 1 residue, 1 model selected
> select add #3/B:105@OE1
2 atoms, 2 residues, 1 model selected
> distance #3/A:712@NH2 #3/B:105@OE1
Distance between copy of ranked_0.pdb #3/A ARG 712 NH2 and /B GLU 105 OE1:
2.703Å
> select clear
[Repeated 1 time(s)]
> select #3/B:102
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #3/A:362
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:102
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:101
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:104
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:98@CA
1 atom, 1 residue, 1 model selected
> select #3/B:85
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:88
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:90
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:91
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:92
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/B:92
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> select #3/B:93
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> show #!2 models
> select #2/b
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> hide sel cartoons
> select #2/A:527@CD
1 atom, 1 residue, 1 model selected
> select #3/B:94
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> hide #!2 models
> select #3/B:98
24 atoms, 25 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> select #3/A:369
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!2 models
> select #3/B:96
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:96
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:101
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #3/B:112
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:701
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:698
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:613
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:614
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!2 models
> select #3/B:35
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!2 models
> select #3/B:53
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> select #3/B:74
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:78
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:69
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:79
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:83
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:754
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:82
16 atoms, 15 bonds, 1 residue, 1 model selected
> show #!2 models
> select #3/B:78
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #3/B:81
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:53@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:53
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:622@HA
1 atom, 1 residue, 1 model selected
> select #3/B:52
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:68
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 33 atoms, 27 bonds, 7 residues
> hide sel atoms
> select clear
> select #3/B:8
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:9
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:28
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:12
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:10
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:13
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:31
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel orange
> select #2/A:625@HE2
1 atom, 1 residue, 1 model selected
> select #3/B:30
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:25
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:33
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:18
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 34 atoms, 30 bonds, 6 residues
> hide sel atoms
> select clear
> select #3/B:14
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:15
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:57
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:67
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 3 atoms, 2 bonds, 2 residues
> hide sel atoms
Drag select of 5 atoms, 6 bonds
> select #3/B:66
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:71
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:51
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:59
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:61
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:59
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:59
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:60
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:11
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 29 atoms, 23 bonds, 9 residues
> hide sel atoms
> select clear
> select #3/B:64
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:49
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 9 atoms, 8 bonds, 7 residues
> hide sel atoms
> select clear
> select #3/B:55
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!2 models
> select #3/A:577@OG
1 atom, 1 residue, 1 model selected
> select add #3/B:54@ND2
2 atoms, 2 residues, 1 model selected
> distance #3/A:577@OG #3/B:54@ND2
Distance between copy of ranked_0.pdb #3/A SER 577 OG and /B ASN 54 ND2:
3.842Å
> select clear
> distance style color #241f31
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select clear
> select #3/A:622
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:579
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:625
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> select #3/B:26
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:28
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:29
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 17 atoms, 14 bonds, 4 residues
> hide sel atoms
> select clear
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> select #1/b
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> show #!1 models
> hide sel cartoons
> select clear
> select #1/b
2603 atoms, 2640 bonds, 167 residues, 1 model selected
> hide sel atoms
> select clear
> hide #!2 models
> select #3/B:112
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> open
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_1.pdb
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_2.pdb
Chain information for ranked_1.pdb #5
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_2.pdb #6
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #5-6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#5),
sequence alignment score = 3986.5
RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
0.928)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#6),
sequence alignment score = 3999.7
RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
0.359)
> matchmaker #5-6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#5),
sequence alignment score = 3986.5
RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
0.928)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#6),
sequence alignment score = 3999.7
RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
0.359)
> select #6/B:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #5/B:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #6/B:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> hide #5 models
> hide #6 models
> view clip false
Drag select of 90 atoms, 79 bonds, 19 residues
> hide sel atoms
> select clear
Drag select of 54 atoms, 44 bonds, 13 residues
> hide sel atoms
> select clear
> select #3/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:77
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:622@CB
1 atom, 1 residue, 1 model selected
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> select #3/B:103
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> select #2/A:635@CA
1 atom, 1 residue, 1 model selected
> select #3/b:26,29,36,39,98,107,112
164 atoms, 163 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel yellow
> undo
> hide H
> select clear
> hide #!2 models
> select #3/b:26,29,36,39,98,107,112
164 atoms, 163 bonds, 7 residues, 1 model selected
> select clear
> show #!12 models
> select /a:813
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
No displayed objects specified.
> select /a:813
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
No displayed objects specified.
> hide #!4 models
> hide #3 models
> show sel cartoons
> select clear
> show #!12 cartoons
> select /a:813
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> show #3 models
> hide #!12 models
> show #!2 models
> save
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
> color #1 white
> hide #3 models
> show #3 models
> hide #!2 models
> select #3/A:524
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:713
19 atoms, 18 bonds, 1 residue, 1 model selected
> show #!4 models
> select #3/A:716
22 atoms, 21 bonds, 1 residue, 1 model selected
> show #!2 models
> view clip false
> select #3/b:26,29,36,39,98,107,112
164 atoms, 163 bonds, 7 residues, 1 model selected
> hide #!2 models
> show #!2 models
> open
> /home/dell/shen_data/PIWI/GTSF1_Predictions/EFPIWI_EMGTSF1/Galaxy41-[EfPIWI_EmGTSF1_pdb]/ranked_0.pdb
Chain information for ranked_0.pdb #7
---
Chain | Description
A | No description available
B | No description available
> close #7
> open
> /home/dell/shen_data/PIWI/GTSF1_Predictions/EFPIWI_EMGTSF1/Galaxy41-[EfPIWI_EmGTSF1_pdb]/AF_EFPIWI_EMGTSF1_0.pdb
Chain information for AF_EFPIWI_EMGTSF1_0.pdb #7
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF_EFPIWI_EMGTSF1_0.pdb, chain A
(#7), sequence alignment score = 2323.4
RMSD between 645 pruned atom pairs is 0.925 angstroms; (across all 757 pairs:
1.863)
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF_EFPIWI_EMGTSF1_0.pdb, chain A
(#7), sequence alignment score = 2323.4
RMSD between 645 pruned atom pairs is 0.925 angstroms; (across all 757 pairs:
1.863)
> hide #!2 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> close #5-6
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!1 models
> hide #!1 models
> show #3 models
> select #3/B:26
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #7/B:21
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #7/B:22
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> delete #7/H
> delete #7/HG
> select #7/B:22@HG2
1 atom, 1 residue, 1 model selected
> delete #7/B:HG
> delete #7/B:@HG
Missing or invalid "atoms" argument: only initial part "#7/B" of atom
specifier valid
> select clear
> select #7/B:22
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide H
> select #3/A:711
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #7/B:25
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> view sel
> select #7/B:28
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #7/B:29
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #7/B:28
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #7/B:27
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #7/B:28
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:32
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:35
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> select #7/B:52
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:582
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:583
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> select #7/A:617
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:586
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:570
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:568
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:76
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:77
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7/B:72
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:69
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> hide #3 models
> select #7/A:571
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:572
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:571
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #3 models
> select #7/A:594
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:760
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:597
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:598
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:560
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #3 models
> hide H
> select clear
> show #3 models
> select #7/A:566
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #7/A:565
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:563
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:102
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:105
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:529
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:531
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:721
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:718
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7/A:717
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:718
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:714
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:712
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #7/A:711
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:113
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:113
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #7/B:109
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:532
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:110
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:114
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:115
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #7/B:114
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide H
> select clear
Drag select of 3 residues
> select up
2300 atoms, 2326 bonds, 153 residues, 1 model selected
> select up
4491 atoms, 4538 bonds, 282 residues, 1 model selected
> select up
16932 atoms, 17114 bonds, 1050 residues, 1 model selected
> select down
4491 atoms, 4538 bonds, 282 residues, 1 model selected
> color sel cyan
> select clear
> color #3-4,7 byhetero
> select clear
> select #7/A:605
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #7/B:110@OE1
1 atom, 1 residue, 1 model selected
> select add #7/A:605@NH1
2 atoms, 2 residues, 1 model selected
> distance #7/B:110@OE1 #7/A:605@NH1
Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B GLU 110 OE1 and /A ARG 605 NH1:
2.642Å
> select clear
> select #3/B:109
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 12 atoms, 10 bonds, 4 residues
> select clear
Drag select of 12 atoms, 10 bonds, 2 residues
> hide sel atoms
> select clear
> hide #3 models
> select #7/A:529@OE1
1 atom, 1 residue, 1 model selected
> select add #7/B:105@OG
2 atoms, 2 residues, 1 model selected
> distance #7/A:529@OE1 #7/B:105@OG
Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A GLU 529 OE1 and /B SER 105 OG:
2.572Å
> select #7/B:109
24 atoms, 25 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> show #3 models
> select #7/B:100
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> select clear
> select #3/B:94
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:93
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 14 atoms, 10 bonds, 12 residues
> hide sel atoms
> select clear
> hide #3 models
> select #7/A:590
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #7/A:586
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7/B:73
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #7/B:76
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:570
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:568
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:560
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #3 models
> select #7/B:97
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #7/B:98
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #3 models
> select #7/B:97
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #7/B:97
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:96
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:98
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #7/B:98@N
1 atom, 1 residue, 1 model selected
> select add #7/A:566@NH2
2 atoms, 2 residues, 1 model selected
> distance #7/B:98@N #7/A:566@NH2
Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B THR 98 N and /A ARG 566 NH2:
3.813Å
> select clear
> select #7/B:96
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/B:97
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #3 models
> select #7/A:396
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7/A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:373
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:97
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:99
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide H
> hide #3 models
> show #3 models
> select #7/A:374
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 2 atoms, 2 bonds, 3 residues
> select #7/A:374
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:366
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7/B:96
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> select #3/B:95
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/B:79@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7/B:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #3 models
> select #7/A:571
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #7/B:72@NH2
1 atom, 1 residue, 1 model selected
> select add #7/A:583@OE1
2 atoms, 2 residues, 1 model selected
> distance #7/B:72@NH2 #7/A:583@OE1
Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B ARG 72 NH2 and /A GLU 583 OE1:
2.750Å
> select clear
> distance style color #241f31
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select #7/B:69
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7/B:49
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> select #7/A:575
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #7/A:575@OE1
1 atom, 1 residue, 1 model selected
> select add #7/B:52@NH1
2 atoms, 2 residues, 1 model selected
> distance #7/A:575@OE1 #7/B:52@NH1
Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A GLU 575 OE1 and /B ARG 52 NH1:
2.707Å
> select #7/A:582
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #3 models
> select #3/A:569@SD
1 atom, 1 residue, 1 model selected
> select add #3/B:56@NH2
2 atoms, 2 residues, 1 model selected
> select #3/A:569
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7/A:582
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide H
> select #3/A:545
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> undo
> show sel atoms
> hide sel atoms
> select clear
Drag select of 7 atoms, 5 bonds, 7 residues
> select clear
[Repeated 1 time(s)]Drag select of 2 atoms, 2 residues, 1 bonds
> select #7/A:563
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:557
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:518
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #7/A:524
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Drag select of 12 atoms, 14 bonds, 4 residues
> hide sel atoms
> select clear
Drag select of 2 atoms, 2 residues
> hide sel atoms
> select clear
[Repeated 1 time(s)]Drag select of 5 atoms, 4 bonds, 10 residues
> hide sel atoms
> select clear
Drag select of 3 atoms, 2 bonds, 2 residues
> select #7/A:721
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:721
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A:716
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/A:706
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #3 models
> select #7/B:112
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/B:112@OE2
1 atom, 1 residue, 1 model selected
> select add #7/A:711@NZ
2 atoms, 2 residues, 1 model selected
> distance #7/B:112@OE2 #7/A:711@NZ
Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B GLU 112 OE2 and /A LYS 711 NZ:
2.846Å
> select clear
> select #7/A:710
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #7/A:710
19 atoms, 18 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> combine #7
> hide #7 models
> view clip false
> coulombic #5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for copy of AF_EFPIWI_EMGTSF1_0.pdb_A SES surface #5.1:
minimum, -14.15, mean 2.15, maximum 20.16
Coulombic values for copy of AF_EFPIWI_EMGTSF1_0.pdb_B SES surface #5.2:
minimum, -15.77, mean 0.23, maximum 14.05
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of copy of AF_EFPIWI_EMGTSF1_0.pdb_B SES surface, 9709 of 545966
triangles, 5 residues
[deleted to fit within ticket limits]
> show #3.1 models
> hide #3.1 models
> select /a:26
89 atoms, 87 bonds, 5 residues, 5 models selected
> view sel
> select /a:26
89 atoms, 87 bonds, 5 residues, 5 models selected
> view sel
> show #3.1 models
> hide #!3 models
> show #5.3 models
> view sel
> select clear
> save /home/dell/Desktop/image7.png supersample 3
> save /home/dell/Desktop/image8.png supersample 3
> select #5/A:572
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> close #5.3
> label @@display
> label height 1.2
> select clear
> save /home/dell/Desktop/image9.png supersample 3
> save /home/dell/Desktop/image10.png supersample 3
> hide #!5 models
> show #!3 models
> save /home/dell/Desktop/image11.png supersample 3
> save /home/dell/Desktop/image12.png supersample 3
> select #3/B:111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel lime
> select clear
> hide #5.3 models
> hide #3.1 models
> close #3.1
> select #3/B:107
24 atoms, 25 bonds, 1 residue, 1 model selected
> select add #3/B:98
48 atoms, 50 bonds, 2 residues, 1 model selected
> select add #3/B:119
68 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/B:121
92 atoms, 95 bonds, 4 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label height 1.2
> save /home/dell/Desktop/image13.png supersample 3
> show #!5 models
> hide #!3 models
> close #5.3
> select #5/B:100@CA
1 atom, 1 residue, 1 model selected
> select add #5/B:109
25 atoms, 25 bonds, 2 residues, 2 models selected
> label (#!5 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 1.2
> select clear
> save /home/dell/Desktop/image14.png supersample 3
> graphics silhouettes true
> show #!3 models
> hide #5.3 models
> show #5.3 models
> hide #!5 models
> open /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_LZQ.pdb
Chain information for AF_LZQ.pdb #6
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF_LZQ.pdb, chain A (#6), sequence
alignment score = 3969.7
RMSD between 756 pruned atom pairs is 0.696 angstroms; (across all 763 pairs:
0.724)
> view clip false
> ui tool show Log
> save
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
——— End of log from Fri Apr 12 21:01:49 2024 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> close #2
> show #!5 models
> hide #!5 models
> open
> /home/dell/shen_data/Alpha.Pred./AF3/fold_2024_05_09_2zn_2mg_model_0.cif
Chain information for fold_2024_05_09_2zn_2mg_model_0.cif #2
---
Chain | Description
A | .
B | .
G | .
H | .
> ui tool show Matchmaker
> matchmaker #!5 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RT_MILI_26nt_2-coot-0.pdb, chain A (#12) with copy of
AF_EFPIWI_EMGTSF1_0.pdb, chain A (#5), sequence alignment score = 1683.8
RMSD between 345 pruned atom pairs is 1.267 angstroms; (across all 745 pairs:
5.311)
> matchmaker #2 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RT_MILI_26nt_2-coot-0.pdb, chain A (#12) with
fold_2024_05_09_2zn_2mg_model_0.cif, chain A (#2), sequence alignment score =
3250
RMSD between 350 pruned atom pairs is 1.105 angstroms; (across all 751 pairs:
5.938)
> matchmaker #2 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RT_MILI_26nt_2-coot-0.pdb, chain A (#12) with
fold_2024_05_09_2zn_2mg_model_0.cif, chain A (#2), sequence alignment score =
3250
RMSD between 350 pruned atom pairs is 1.105 angstroms; (across all 751 pairs:
5.938)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> close #6
> ui mousemode right select
> select #2/A:564
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/B:84
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:562
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:584
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:588
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:587
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> select #3/A:580
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right distance
> distance #2/B:84@NE2 #2/A:562@OH
Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/B GLN 84 NE2 and /A
TYR 562 OH: 4.915Å
> show #4.1 models
> ui mousemode right select
> select #2/B:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:755
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:83
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/B:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> distance #2/A:755@NE2 #2/B:83@OD1
Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/A GLN 755 NE2 and /B
ASN 83 OD1: 4.282Å
> ui mousemode right select
> select #2/B:86
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:87
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/B:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:87@ND2
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #2/A:755@NE2 #2/B:87@ND2
Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/A GLN 755 NE2 and /B
ASN 87 ND2: 4.819Å
> ui mousemode right select
> select #2/A:754
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:756
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:86
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide #!3 models
> select #2/A:754
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:88
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #2/B:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!3 models
> select #2/B:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:623
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:577
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:53
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:54
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!3 models
> ui mousemode right distance
> distance #2/B:54@ND2 #2/B:73@OD2
Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/B ASN 54 ND2 and ASP
73 OD2: 2.824Å
> distance #2/A:564@NH2 #2/B:80@OD2
Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/A ARG 564 NH2 and /B
ASP 80 OD2: 2.210Å
> show #!3 models
> ui mousemode right select
> select #3/B:77
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/B:76
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:88
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/B:88
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:584
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:588
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:587@NZ
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #2/B:84@OE1 #2/A:587@NZ
Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/B GLN 84 OE1 and /A
LYS 587 NZ: 5.090Å
> ~distance #2/B:84@OE1 #2/A:587@NZ
> ~distance #2/B:84@NE2 #2/A:562@OH
> ~distance #2/A:755@NE2 #2/B:87@ND2
> ui mousemode right select
> select #3/A:754
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:755
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save
> /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
> ui mousemode right distance
> ~distance #2/A:755@NE2 #2/B:83@OD1
> ui mousemode right zoom
> view clip false
> show #!12 models
> hide #!12 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> open
> /home/dell/shen_data/PIWI/PIWIL2/mismatch/fold_2024_05_09_ter_8nt_model_0.cif
Chain information for fold_2024_05_09_ter_8nt_model_0.cif #6
---
Chain | Description
A | .
D | .
E | .
> ui tool show Matchmaker
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with
fold_2024_05_09_ter_8nt_model_0.cif, chain A (#6), sequence alignment score =
3931.3
RMSD between 515 pruned atom pairs is 0.856 angstroms; (across all 763 pairs:
2.912)
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with
fold_2024_05_09_ter_8nt_model_0.cif, chain A (#6), sequence alignment score =
3931.3
RMSD between 515 pruned atom pairs is 0.856 angstroms; (across all 763 pairs:
2.912)
> hide #!3 models
> show #2 models
> hide #2 models
> show #2 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!12 models
> hide #!12 models
> show #!3 models
> hide #6 models
> ui mousemode right select
> select #3/A:365
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:367
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:366
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:365
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:521
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:522
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> select clear
> select #3/A:388
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:388
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:368
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:369
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:521
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:520
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:518
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:519
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 14 atoms, 7 residues, 15 bonds
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> label @@display
> select #2/A:522
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/A:521
4 atoms, 3 bonds, 1 residue, 1 model selected
> ~label sel residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ui mousemode right select
Drag select of 3 atoms, 8 residues, 2 bonds
> select clear
Drag select of 5 atoms, 4 residues, 4 bonds
> hide sel atoms
> select clear
> ui tool show "Side View"
> select clear
> save /home/dell/Desktop/image1.png supersample 3
> select #3/A:525
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> select #2/A:712
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:709
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:107
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:525
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #2/A:713
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:526
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select ~sel & ##selected
8570 atoms, 8871 bonds, 2 pseudobonds, 985 residues, 2 models selected
> hide H
> select clear
> select #2/B:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> rename #2 2zn_2mg_model_0.cif
> rename #6 ter_8nt_model_0.cif
> show #!5 models
> hide #!5 models
> close #5
> close #7
> close #12
> hide #!3 models
Drag select of 29 atoms, 11 residues, 30 bonds
> select clear
> select #2/B:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/B:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 4 residues
> select up
70 atoms, 73 bonds, 7 residues, 1 model selected
> select up
1337 atoms, 1374 bonds, 167 residues, 1 model selected
> select up
8578 atoms, 8878 bonds, 986 residues, 1 model selected
> select up
45389 atoms, 46262 bonds, 21 pseudobonds, 3645 residues, 5 models selected
> select down
8578 atoms, 8878 bonds, 986 residues, 3 models selected
> select down
1337 atoms, 1374 bonds, 167 residues, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> show target m
> hide #!1 models
> hide #!6 models
> hide #!3 models
> view #3 clip false
> close #3.1
> close #2.1
> show #3 models
> select #2/B:98
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:367
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:716
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> mlp sel
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
Drag select of 71 residues, 1 shapes
> select up
935 atoms, 308 bonds, 72 residues, 3 models selected
> select up
2213 atoms, 2296 bonds, 160 residues, 3 models selected
> select up
19061 atoms, 19404 bonds, 1552 residues, 3 models selected
> select up
23554 atoms, 24030 bonds, 1916 residues, 3 models selected
> select down
19061 atoms, 19404 bonds, 1552 residues, 3 models selected
> mlp sel
Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
mean -3.606, maximum 24.24
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!2-3 & sel) 50
> select #2/A:716@CD
1 atom, 1 residue, 1 model selected
Drag select of copy of ranked_0.pdb_A SES surface, 37220 of 833356 triangles,
2zn_2mg_model_0.cif_A SES surface, 22056 of 657748 triangles, 58 atoms, 126
residues, 49 bonds, 1 pseudobonds, 14 shapes
> close #2.1
> close #3.1
> mlp sel
Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
mean -3.606, maximum 24.24
Map values for surface "copy of ranked_0.pdb_B SES surface": minimum -28.26,
mean -3.591, maximum 22.8
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
Map values for surface "2zn_2mg_model_0.cif_B SES surface": minimum -28.54,
mean -4.628, maximum 23.24
To also show corresponding color key, enter the above mlp command and add key
true
> select #3/B:105@CG
1 atom, 1 residue, 1 model selected
> select #3/B:105@HB2
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> select up
271 atoms, 274 bonds, 19 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select #3/B:107@HD1
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 2 models selected
> surface hidePatches (#!3 & sel)
> select #2/B:105@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
134 atoms, 137 bonds, 17 residues, 2 models selected
> select up
1337 atoms, 1374 bonds, 167 residues, 2 models selected
> hide sel surfaces
> select #2/A:526
8 atoms, 7 bonds, 1 residue, 1 model selected
> mlp sel
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> select #3/A:709@O
1 atom, 1 residue, 1 model selected
> view sel
> select clear
> hide #!2-3 surfaces
> close #2.1-2
> close #3.1-2
> select clear
> select #3/B:107
24 atoms, 25 bonds, 1 residue, 1 model selected
> view sel
> hide #3 models
Drag select of 51 atoms, 22 residues, 47 bonds
> select add #2/B:110
198 atoms, 54 bonds, 24 residues, 1 model selected
> select subtract #2/B:111
194 atoms, 51 bonds, 23 residues, 1 model selected
> select add #2/B:111
202 atoms, 58 bonds, 24 residues, 1 model selected
> select subtract #2/B:108
194 atoms, 58 bonds, 23 residues, 1 model selected
> select add #2/B:108
202 atoms, 65 bonds, 24 residues, 1 model selected
> select subtract #2/B:104
194 atoms, 65 bonds, 23 residues, 1 model selected
> select subtract #2/B:105
185 atoms, 60 bonds, 22 residues, 1 model selected
> select subtract #2/B:106
177 atoms, 60 bonds, 21 residues, 1 model selected
> select subtract #2/B:107
163 atoms, 48 bonds, 20 residues, 1 model selected
> select subtract #2/B:108
155 atoms, 41 bonds, 19 residues, 1 model selected
> select subtract #2/B:109
146 atoms, 41 bonds, 18 residues, 1 model selected
> select subtract #2/B:110
138 atoms, 34 bonds, 17 residues, 1 model selected
> select subtract #2/B:111
130 atoms, 27 bonds, 16 residues, 1 model selected
> mlp sel
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> close #2.1
> show sel surfaces
> mlp sel
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> close #2.1
Drag select of 52 atoms, 25 residues, 48 bonds
> label @@display
> select clear
> select #2/A:525
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:526
15 atoms, 14 bonds, 2 residues, 1 model selected
> color sel red
> color sel byhetero
> select clear
> select #2/A:709
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> select clear
Drag select of 49 atoms, 22 residues, 46 bonds
> select clear
Drag select of 4 residues
> select up
204 atoms, 211 bonds, 24 residues, 1 model selected
> select clear
Drag select of 49 atoms, 30 residues, 47 bonds
> mlp sel
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
Map values for surface "2zn_2mg_model_0.cif_B SES surface": minimum -28.54,
mean -4.628, maximum 23.24
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select #2/B:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
134 atoms, 137 bonds, 17 residues, 2 models selected
> select up
1337 atoms, 1374 bonds, 167 residues, 2 models selected
> hide sel surfaces
> select clear
Drag select of 2zn_2mg_model_0.cif_A SES surface, 1092 of 657748 triangles, 20
atoms, 24 residues, 18 bonds
> show sel surfaces
> select #2/B:98@CA
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select up
134 atoms, 137 bonds, 17 residues, 2 models selected
> select up
1337 atoms, 1374 bonds, 167 residues, 2 models selected
> hide sel surfaces
> transparency (#!2 & sel) 50
> select clear
> transparency #2,4 50
> hide #2.3 models
> hide #2.2 models
> show #2.2 models
> close #2.3
> transparency #2,4 70
> select #2/A:526@CD1
1 atom, 1 residue, 1 model selected
> select #2/B:107
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
[Repeated 1 time(s)]
> ui mousemode right "move label"
> color #2.1 black models
> ui mousemode right select
> select clear
> save /home/dell/Desktop/image2.png supersample 3
> hide #!2 surfaces
> select clear
> save /home/dell/Desktop/image3.png supersample 3
> view sel
> select clear
> ui mousemode right "move label"
> ui mousemode right distance
> distance #2/A:364@ND2 #2/B:100@SG
Distance between 2zn_2mg_model_0.cif #2/A ASN 364 ND2 and /B CYS 100 SG:
3.349Å
> color #2.1 black models
> save /home/dell/Desktop/image4.png supersample 3
> open
> /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb
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 #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2zn_2mg_model_0.cif, chain A (#2) with 412_26NT_1-coot-8.pdb, chain
A (#5), sequence alignment score = 3383.2
RMSD between 418 pruned atom pairs is 1.088 angstroms; (across all 736 pairs:
4.016)
> matchmaker #!5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2zn_2mg_model_0.cif, chain A (#2) with 412_26NT_1-coot-8.pdb, chain
A (#5), sequence alignment score = 3383.2
RMSD between 418 pruned atom pairs is 1.088 angstroms; (across all 736 pairs:
4.016)
> ui mousemode right select
> select #5/A:596
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:920
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:917
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:734
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:733
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:921
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> label @@display
> select clear
> hide #!2 models
> ui mousemode right "move label"
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save /home/dell/Desktop/image5.png supersample 3
> open
> /home/dell/shen_data/PIWI/PIWIL2/mismatch/fold_2024_05_09_efpiwi_emgtsf1_model_0.cif
Chain information for fold_2024_05_09_efpiwi_emgtsf1_model_0.cif #7
---
Chain | Description
A | .
B | .
G | .
H | .
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with
fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7), sequence alignment
score = 2301.1
RMSD between 470 pruned atom pairs is 1.001 angstroms; (across all 757 pairs:
5.493)
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with
fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7), sequence alignment
score = 2301.1
RMSD between 470 pruned atom pairs is 1.001 angstroms; (across all 757 pairs:
5.493)
> show #!2 models
> hide #!5 models
> set bgColor white
> ui mousemode right select
> select #7/B:109
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:531
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #7/A:532
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select #7/A:714
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #7/A:717
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> select #7/A:718
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:530
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:524
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> hide #!2 models
> label @@display
> open "/home/dell/shen_data/PIWI/PIWIL2/PIWI_structures_published/7yfq
> EfPIWI(N959K) 2024.pdb"
7yfq EfPIWI(N959K) 2024.pdb title:
Cryo-em structure of the efpiwi (N959K)-piRNA-target ternary complex [more
info...]
Chain information for 7yfq EfPIWI(N959K) 2024.pdb #8
---
Chain | Description | UniProt
A | PIWI | D5MRY8_9METZ 220-987
B | PIRNA |
C | RNA (5'-R(*up*CP*CP*ap*up*GP*up*up*GP*ap*up*GP*GP*up*ap*A)- 3')
|
Non-standard residues in 7yfq EfPIWI(N959K) 2024.pdb #8
---
MG — magnesium ion
OMU — O2'-methyluridine 5'-monophosphate
> ui tool show Matchmaker
> matchmaker #!8 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7) with 7yfq
EfPIWI(N959K) 2024.pdb, chain A (#8), sequence alignment score = 3604.5
RMSD between 469 pruned atom pairs is 0.891 angstroms; (across all 733 pairs:
3.573)
> matchmaker #!8 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7) with 7yfq
EfPIWI(N959K) 2024.pdb, chain A (#8), sequence alignment score = 3604.5
RMSD between 469 pruned atom pairs is 0.891 angstroms; (across all 733 pairs:
3.573)
> select #8/A:936
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #8/A:937
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add #8/A:749
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #8/A:750
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #8/A:751
42 atoms, 38 bonds, 5 residues, 1 model selected
> select subtract #8/A:749
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #8/A:933
44 atoms, 41 bonds, 5 residues, 1 model selected
> show sel atoms
> select add #8/A:749
52 atoms, 48 bonds, 6 residues, 1 model selected
> show sel atoms
> label @@display
> hide #!7 models
> select clear
> show #!7 models
> show #!2 models
> save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
> rename #7 efpiwi_emgtsf1_AF3_model_0.cif
> select #8/A:615
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/A:591
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:592
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/A:591
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:526
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> label @@display
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!2 models
> show #!7 models
> select #7/A:372
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> color sel byhetero
> select clear
> select #8/A:593
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:590
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:363
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:592
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:593
9 atoms, 8 bonds, 1 residue, 1 model selected
> rename #2 2zn_2mg_AF3_model_0.cif
> rename #1 AF2_MILI_GTSF1
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> close #1
> save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
——— End of log from Thu May 9 18:31:50 2024 ———
opened ChimeraX session
> open
> /home/dell/shen_data/Alpha.Pred./AF3/fold_2024_05_09_26nt_2/fold_af3_hili_209_t718s_model_0.cif
Chain information for fold_af3_hili_209_t718s_model_0.cif #1
---
Chain | Description
A | .
> open /home/dell/shen_data/Alpha.Pred./AF3/fold_hili_210_l718t_model_0.cif
Chain information for fold_hili_210_l718t_model_0.cif #9
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #1,9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_af3_hili_209_t718s_model_0.cif, chain A (#1), sequence alignment score =
3854.7
RMSD between 509 pruned atom pairs is 0.757 angstroms; (across all 763 pairs:
3.449)
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_hili_210_l718t_model_0.cif, chain A (#9), sequence alignment score = 3844
RMSD between 552 pruned atom pairs is 0.811 angstroms; (across all 763 pairs:
3.187)
> matchmaker #1,9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_af3_hili_209_t718s_model_0.cif, chain A (#1), sequence alignment score =
3854.7
RMSD between 509 pruned atom pairs is 0.757 angstroms; (across all 763 pairs:
3.449)
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_hili_210_l718t_model_0.cif, chain A (#9), sequence alignment score = 3844
RMSD between 552 pruned atom pairs is 0.811 angstroms; (across all 763 pairs:
3.187)
> view clip false
> show #!5 models
> hide #!7 models
> hide #!8 models
> hide #9 models
> hide #4.1 models
> hide #!3 models
> rename #1 fold_af3_hili_209_l718s_model_0.cif
> rename #1 id #10
> show #9 models
> nucleotides #9-10#!5 ladder
> close #6.1
> close #7.1
> close #2.1
> close #3.1
> close #5.2
> select /a:718
59 atoms, 51 bonds, 8 residues, 8 models selected
> select #5/a:718
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> hide #!4 models
> select #5/a:716
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> ui mousemode right select
> select #10/A:508
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:508
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right label
> label delete residues
> label #5/A:716
> label #10/A:508
> label #9/A:508
> ui mousemode right "move label"
> save /home/dell/Desktop/image1.png supersample 3
> view clip false
> save /home/dell/Desktop/image2.png supersample 3
> show #!2 models
> hide #!5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!2 models
> save /home/dell/Desktop/image3.png supersample 3
> ui mousemode right select
> select #9/A:418
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:415
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:418
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:419
5 atoms, 4 bonds, 1 residue, 1 model selected
> save /home/dell/Desktop/image4.png supersample 3
> show sel atoms
> save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
——— End of log from Fri May 10 12:32:23 2024 ———
opened ChimeraX session
> open /home/dell/shen_data/Alpha.Pred./AF3/fold_mili_18nt_gtsf1_model_0.cif
> /home/dell/shen_data/Alpha.Pred./AF3/fold_mili_20nt_gtsf1_model_0.cif
Chain information for fold_mili_18nt_gtsf1_model_0.cif #1
---
Chain | Description
A | .
B | .
G | .
H | .
Chain information for fold_mili_20nt_gtsf1_model_0.cif #11
---
Chain | Description
A | .
B | .
G | .
H | .
> ui tool show Matchmaker
> matchmaker #1,11 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_mili_18nt_gtsf1_model_0.cif, chain A (#1), sequence alignment score =
3996.7
RMSD between 752 pruned atom pairs is 0.550 angstroms; (across all 763 pairs:
0.658)
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_mili_20nt_gtsf1_model_0.cif, chain A (#11), sequence alignment score =
4006.9
RMSD between 701 pruned atom pairs is 0.626 angstroms; (across all 763 pairs:
1.257)
> matchmaker #1,11 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_mili_18nt_gtsf1_model_0.cif, chain A (#1), sequence alignment score =
3996.7
RMSD between 752 pruned atom pairs is 0.550 angstroms; (across all 763 pairs:
0.658)
Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
fold_mili_20nt_gtsf1_model_0.cif, chain A (#11), sequence alignment score =
4006.9
RMSD between 701 pruned atom pairs is 0.626 angstroms; (across all 763 pairs:
1.257)
> select /a:1-209
14846 atoms, 15119 bonds, 1672 residues, 8 models selected
> hide #!9 models
> hide #!10 models
> hide sel & #1,11 cartoons
> delete atoms (#1,11 & sel)
> delete bonds (#1,11 & sel)
> show #!2 models
> ui mousemode right select
> select clear
> show #!5 models
> save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
——— End of log from Wed May 15 11:25:55 2024 ———
opened ChimeraX session
> close #1
> close #11
> show #3 models
> hide #3 models
> show #3 models
> show #7 models
> hide #!5 models
> hide #3 models
> hide #!2 models
> show #!2 models
> ui mousemode right select
> select #7/B:79
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
87 atoms, 86 bonds, 11 residues, 1 model selected
> select up
2263 atoms, 2310 bonds, 282 residues, 1 model selected
> color sel lime
> color sel byhetero
> select clear
> hide #7 models
> show #3 models
> show #!4 models
> cartoon style #2-3#!4 xsection oval modeHelix default
> select clear
> select add #2
8578 atoms, 8878 bonds, 3 pseudobonds, 986 residues, 2 models selected
> select clear
> select #2/A:738
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:86
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/B:87
14 atoms, 13 bonds, 1 residue, 1 model selected
> view sel
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right distance
> distance #2/A:755@NE2 #2/B:83@ND2
Distance between 2zn_2mg_AF3_model_0.cif #2/A GLN 755 NE2 and /B ASN 83 ND2:
4.220Å
> show #4.1 models
> distance #2/A:755@NE2 #2/B:83@OD1
Distance between 2zn_2mg_AF3_model_0.cif #2/A GLN 755 NE2 and /B ASN 83 OD1:
4.282Å
> ~distance #2/A:755@NE2 #2/B:83@ND2
> ~distance #2/A:755@NE2 #2/B:83@OD1
> ui mousemode right select
> select #2/B:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/A:588
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:81
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:78
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/B:77
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/B:81
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:587
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:77
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:566
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:567
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:565
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance style radius 0.06
[Repeated 2 time(s)]
> select clear
> hide #!2 models
> show #!2 models
> ui mousemode right distance
> hide #3 models
> show #3 models
> distance #2/A:577@OG #2/B:73@OD1
Distance between 2zn_2mg_AF3_model_0.cif #2/A SER 577 OG and /B ASP 73 OD1:
6.068Å
> ui mousemode right swapaa
> swapaa mousemode #2/B:73 ASN
> swapaa mousemode #2/B:73 GLN
> swapaa mousemode #2/B:73 CYS
[Repeated 2 time(s)]
> swapaa mousemode #2/B:73 GLN
> ui mousemode right "bond rotation"
> ui mousemode right swapaa
> swapaa mousemode #2/B:73 GLU
> ui mousemode right "bond rotation"
> undo
> show #3 models
> ui mousemode right select
> select #2/A:577@OG
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #2/B:73@OE1 #2/A:577@OG
Distance between 2zn_2mg_AF3_model_0.cif #2/B GLU 73 OE1 and /A SER 577 OG:
4.457Å
> distance #2/A:577@OG #3/B:54@ND2
Distance between 2zn_2mg_AF3_model_0.cif #2/A SER 577 OG and copy of
ranked_0.pdb #3/B ASN 54 ND2: 4.930Å
> ui mousemode right select
> select clear
> select #3/B:94
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/B:93
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/B:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:365
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/A:557
14 atoms, 13 bonds, 1 residue, 1 model selected
Drag select of 10 residues
> show sel atoms
> hide H
> select clear
> select #2/A:523
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #2/A:523@OD1 #2/B:100@SG
Distance between 2zn_2mg_AF3_model_0.cif #2/A ASP 523 OD1 and /B CYS 100 SG:
3.987Å
> ui mousemode right select
> select clear
> select #2/A:365
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 69 atoms, 52 residues, 61 bonds, 3 pseudobonds
> mlp sel
Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
mean -3.606, maximum 24.24
Map values for surface "copy of ranked_0.pdb_B SES surface": minimum -28.26,
mean -3.591, maximum 22.8
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
Map values for surface "2zn_2mg_AF3_model_0.cif_B SES surface": minimum
-28.54, mean -4.617, maximum 23.24
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!2-3 & sel) 50
> hide sel surfaces
> select clear
Drag select of 2 atoms, 2 residues
> select up
324 atoms, 328 bonds, 28 residues, 4 models selected
Drag select of 2 residues, 1 atoms
> hide sel atoms
> select clear
Drag select of 2 residues, 1 atoms
> hide sel atoms
> select clear
Drag select of 18 atoms, 10 residues, 15 bonds
> hide sel atoms
> select clear
> select #3/A:557
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:559
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Drag select of 2 residues, 1 atoms
> hide sel atoms
> select clear
Drag select of 1 atoms, 6 residues
> hide sel atoms
> select clear
> select #3/B:94
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/B:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> hide #!3 models
> ui mousemode right distance
> distance #2/A:709@NE2 #2/B:110@OD2
Distance between 2zn_2mg_AF3_model_0.cif #2/A HIS 709 NE2 and /B ASP 110 OD2:
3.315Å
> distance #2/B:105@OE2 #2/B:107@NE1
Distance between 2zn_2mg_AF3_model_0.cif #2/B GLU 105 OE2 and TRP 107 NE1:
2.993Å
> distance #2/A:712@NH1 #2/B:105@OE2
Distance between 2zn_2mg_AF3_model_0.cif #2/A ARG 712 NH1 and /B GLU 105 OE2:
2.807Å
> ui mousemode right select
> select #2/B:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> view clip false
> nucleotides sel ladder
> select clear
> nucleotides #!2 ladder
> show #!3 models
> select #2/B:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> select #2/B:29
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/B:33
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/B:23
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select clear
> show #!5 models
> hide #!5 models
> select #2/H:7
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
556 atoms, 621 bonds, 26 residues, 1 model selected
> color sel blue
> select #2/G:22
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
549 atoms, 612 bonds, 26 residues, 1 model selected
> color sel red
> select clear
> select #3/B:39
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #2/B:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!3 models
> select clear
> select #2/G:15
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/G:14
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/G:16
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/H:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/H:7
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> ui mousemode right distance
> distance #2/B:26@NH1 #2/H:7@OP1
Distance between 2zn_2mg_AF3_model_0.cif #2/B ARG 26 NH1 and /H A 7 OP1:
2.881Å
> ui mousemode right select
> select clear
> select #2/H:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> ui mousemode right distance
> distance #2/B:26@NH2 #2/H:6@O3'
Distance between 2zn_2mg_AF3_model_0.cif #2/B ARG 26 NH2 and /H A 6 O3':
2.455Å
> ui mousemode right select
> select clear
> ui mousemode right label
> ui mousemode right distance
> distance #2/B:29@NH2 #2/G:16@OP2
Distance between 2zn_2mg_AF3_model_0.cif #2/B ARG 29 NH2 and /G A 16 OP2:
2.795Å
> ui mousemode right select
> select #2/B:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!3 models
> hide #!3 models
> show sel atoms
> select #2/A:611
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> ~distance #3/A:611@NE2 #3/B:32@OH
> distance #2/B:32@OH #2/A:611@NE2
Distance between 2zn_2mg_AF3_model_0.cif #2/B TYR 32 OH and /A GLN 611 NE2:
3.160Å
> ui mousemode right select
> show #!3 models
> hide #!3 models
> select #2/H:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/H:4
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> ui mousemode right distance
> ui mousemode right select
> select #2/D:1@ZN
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #2/B:36@NZ #2/H:4@OP1
Distance between 2zn_2mg_AF3_model_0.cif #2/B LYS 36 NZ and /H C 4 OP1: 2.535Å
> distance #2/H:5@OP1 #2/B:33@ND1
Distance between 2zn_2mg_AF3_model_0.cif #2/H C 5 OP1 and /B HIS 33 ND1:
2.754Å
> distance style radius 0.06
> view #3 clip false
> close #9-10
> show #7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> close #8
> close #6
> hide #7 models
> show #!3 models
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> transparency sel 80 cartoons
> lighting full
> ui mousemode right select
> select clear
> graphics silhouettes false
> select clear
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
> select /b,c
7289 atoms, 7533 bonds, 1 pseudobond, 669 residues, 5 models selected
> cartoon style sel width 0.8 thickness 0.8
> select #2/G:4
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/H:25
42 atoms, 45 bonds, 2 residues, 1 model selected
> select up
1105 atoms, 1233 bonds, 52 residues, 1 model selected
> select up
8579 atoms, 8879 bonds, 986 residues, 1 model selected
> select down
1105 atoms, 1233 bonds, 52 residues, 3 models selected
> cartoon style sel width 0.8 thickness 0.8
> select clear
> select #3/B:121
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:676
24 atoms, 25 bonds, 1 residue, 1 model selected
> undo
> show sel atoms
> select clear
> hide H
> select clear
> lighting shadows false
> select clear
> hide #!3 models
> hide #!2 atoms
> show #!2 cartoons
Drag select of 61 residues
> select up
805 atoms, 819 bonds, 98 residues, 2 models selected
> select up
6132 atoms, 6271 bonds, 763 residues, 2 models selected
> rename #2 id #1
> rename #3 id #2
> color #1 #3584e4ff
> select clear
Drag select of 8 residues
> select up
104 atoms, 106 bonds, 13 residues, 2 models selected
> select up
1338 atoms, 1375 bonds, 167 residues, 2 models selected
> color (#!1 & sel) lime
> select clear
Drag select of 46 residues
> select #1/H:19
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
556 atoms, 621 bonds, 26 residues, 1 model selected
> color sel blue
> select #1/G:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
549 atoms, 612 bonds, 26 residues, 1 model selected
> color sel red
> select clear
Drag select of 133 residues
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> color (#!1 & sel) orange
> select clear
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> color (#!1 & sel) dark gray
> color (#!1 & sel) yellow
> select clear
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> color (#!1 & sel) byhetero
> ui tool show "Color Actions"
> color sel hot pink
> select clear
Drag select of 83 residues
> select up
937 atoms, 954 bonds, 113 residues, 2 models selected
> select up
6132 atoms, 6271 bonds, 763 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light salmon
> select clear
Drag select of 97 residues
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> ui tool show "Color Actions"
> color sel gold
> select clear
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> ui tool show "Color Actions"
> color sel sandy brown
> select clear
Drag select of 3 residues
> select up
1105 atoms, 1233 bonds, 52 residues, 1 model selected
> select clear
Drag select of 2 residues
> select up
1105 atoms, 1233 bonds, 52 residues, 1 model selected
> show sel atoms
> nucleotides sel ladder
> select clear
> view name p1
[Repeated 1 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save /home/dell/Desktop/2.png width 1872 height 1872 supersample 3
> turn y 90
> turn y 10
[Repeated 3 time(s)]
> view name p2
> save /home/dell/Desktop/3.png width 1872 height 1872 supersample 3
> view p2
> view p1
> select add #1/H:7
45 atoms, 24 bonds, 2 residues, 1 model selected
> select up
1105 atoms, 1233 bonds, 52 residues, 1 model selected
> cartoon style sel width 0.7 thickness 0.7
> select clear
> nucleotides sel ladder radius 0.3
> select #1/G:24
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/H:6
42 atoms, 45 bonds, 2 residues, 1 model selected
> select up
1105 atoms, 1233 bonds, 52 residues, 1 model selected
> nucleotides sel ladder radius 0.3
> select clear
> undo
> cartoon style sel width 0.6 thickness 0.6
> select clear
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
——— End of log from Thu May 16 14:46:31 2024 ———
opened ChimeraX session
Drag select of 61 residues
> select up
1225 atoms, 1244 bonds, 150 residues, 2 models selected
> select up
6132 atoms, 6271 bonds, 763 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
mean 1.18, maximum 16.69
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency #1,4 50
> view p2
[Repeated 1 time(s)]
> view name p2
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> hide sel & #!1 cartoons
> select clear
> transparency #1,4 0
> select clear
> select /a
30602 atoms, 31146 bonds, 3030 residues, 4 models selected
> mlp sel & #!1
Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
mean -4.508, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel & #!1
Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
mean 1.18, maximum 16.69
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> view p1
> turn y 90
> turn y 10
> turn y 20
> ui mousemode right "color key"
> key blue-white-red :min : :1
> key blue-white-red :min : :10
> key blue-white-red :- : :10
> key blue-white-red :-1 : :10
> key blue-white-red :-10 : :10
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
[Repeated 1 time(s)]
> key size 0.2000,0.05000
> key red-white-blue :10 : :-10
> key blue-white-red :-10 : :10
> key red-white-blue :10 : :-10
> key blue-white-red :-10 : :10
> key size 0.20000,0.0000
> key size 0.20000,0.00000
> key size 0.20000,0.30000
[Repeated 1 time(s)]
> key size 0.20000,0.03000
> key labelColor #bfbfbf
> key labelColor default
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 20
> view name p3
> save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
——— End of log from Thu May 16 14:53:45 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 2.4Gi 56Gi 108Mi 4.0Gi 59Gi
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 , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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