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Opened 18 months ago
Closed 18 months ago
#15346 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-35-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070ffd9ffb640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007100b824bb80 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/ast.py", line 90 in copy
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
File "/usr/lib/ucsf-chimerax/lib/python3.11/contextlib.py", line 137 in __enter__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 679 in _choice
File "/usr/lib/ucsf-chimerax/lib/python3.11/contextlib.py", line 137 in __enter__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 113 in _as_term_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 89 in _atom_specifier_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 93 in _atom_specifier_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 206 in parse
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 192 in _parse_unquoted
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 121 in parse
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/defattr.py", line 180 in defattr
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 81 in add_standard_charges
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 34 in add_charges
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 110 in assign_charges
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
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/shortcuts/shortcuts.py", line 525 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mmcif.mmcif_write (total: 62)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> format session
No such file/path:
/home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> open /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> format session
No such file/path:
/home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> open /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> format session
opened ChimeraX session
> open /home/trung/Downloads/rebuild_sidechains.py
executed rebuild_sidechains.py
Drag select of 6763 atoms, 6900 bonds
Drag select of 6783 atoms, 6921 bonds
> show (sel-residues & sidechain) target ab
> save selection
Cannot determine format for 'selection'
> save altered_marked_labeled_aa format pdb displayedOnly true
> close session
> open /home/trung/Documents/eIF3I_project/altered_marked_labeled_aa
'/home/trung/Documents/eIF3I_project/altered_marked_labeled_aa' has no suffix
> open /home/trung/altered_marked_labeled_aa format pdb
No such file/path: /home/trung/altered_marked_labeled_aa
> open /home/trung/altered_marked_labeled_aa format pdb
No such file/path: /home/trung/altered_marked_labeled_aa
> open /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> format session
opened ChimeraX session
> save altered_marked_labeled_aa.cif format pdb displayedOnly true
> close session
> open /home/trung/Documents/eIF3I_project/altered_marked_labeled_aa.cif
mmCIF parsing error: unexpected data value near line 1
> open /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> format session
opened ChimeraX session
> save altered_marked_labeled_aa.pdb format pdb displayedOnly true
> close session
> open /home/trung/altered_marked_labeled_aa.pdb
Summary of feedback from opening /home/trung/altered_marked_labeled_aa.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU 5 6
ALA 5 11 1 6
Start residue of secondary structure not found: HELIX 2 2 ASP 5 15 GLU 5 30 1
16
Start residue of secondary structure not found: HELIX 3 3 ASN 5 33 THR 5 48 1
16
Start residue of secondary structure not found: HELIX 4 4 VAL 5 51 TYR 5 62 1
12
Start residue of secondary structure not found: HELIX 5 5 PRO 5 67 GLU 5 96 1
30
692 messages similar to the above omitted
Cannot find LINK/SSBOND residue C (1218 )
Cannot find LINK/SSBOND residue G (1862 )
Cannot find LINK/SSBOND residue G (1490 )
Cannot find LINK/SSBOND residue A (672 )
Cannot find LINK/SSBOND residue JMH (1219 )
122 messages similar to the above omitted
Chain information for altered_marked_labeled_aa.pdb #1
---
Chain | Description
7 | No description available
F | No description available
I | No description available
> show atoms
> hide cartoons
> open /home/trung/Downloads/rebuild_sidechains.py
FYI: command is replacing existing command: "rebuildsidechains"
executed rebuild_sidechains.py
> rebuildsidechains #1
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 32 N; /F PRO 231
N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I
PRO 709 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 239 N; /F PRO 231 N; /F PRO
138 N; /F PRO 130 N; /F PRO 143 N; /F PRO 32 N; /F PRO 156 N; /I PRO 709 N; /F
PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 231 N; /F PRO
138 N; /F PRO 239 N; /F PRO 143 N; /F PRO 156 N; /F PRO 32 N; /F PRO 287 N; /F
PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 231 N; /F PRO
138 N; /F PRO 239 N; /F PRO 143 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /F
PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 32 N; /F PRO 231
N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I
PRO 709 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 239 N; /F PRO 231 N; /F PRO
138 N; /F PRO 130 N; /F PRO 32 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F
PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 32 N; /F PRO 231
N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F
PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 32 N; /F PRO 231
N; /F PRO 239 N; /F PRO 138 N; /F PRO 287 N; /F PRO 143 N; /F PRO 295 N; /F
PRO 156 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 231 N; /F PRO
138 N; /F PRO 239 N; /F PRO 32 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F
PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F PRO 231 N; /F PRO
138 N; /F PRO 239 N; /F PRO 143 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /F
PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 3 N; /F PRO 143 N; /F PRO 239 N; /F PRO
138 N; /F PRO 130 N; /F PRO 156 N; /F PRO 32 N; /F PRO 287 N; /F PRO 295 N; /F
PRO 231 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 316 N; /F PRO 130 N; /F PRO 143 N; /F PRO
138 N; /F PRO 239 N; /F PRO 156 N; /F PRO 3 N; /F PRO 32 N; /F PRO 287 N; /F
PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 316 N; /F PRO 130 N; /F PRO 143 N; /F PRO
32 N; /F PRO 138 N; /F PRO 239 N; /F PRO 156 N; /F PRO 3 N; /I PRO 709 N; /F
PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 3 N; /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 32
N; /F PRO 138 N; /F PRO 239 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /I
PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 32 N; /F PRO
138 N; /F PRO 239 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N;
/F PRO 3 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 3 N; /F PRO 231 N; /F PRO 239 N; /F PRO 143 N; /F PRO 32
N; /F PRO 138 N; /F PRO 130 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F
PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 316 N; /F PRO 130 N; /F PRO 143 N; /F PRO
32 N; /F PRO 138 N; /F PRO 239 N; /F PRO 156 N; /F PRO 287 N; /F PRO 3 N; /I
PRO 709 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 143 N; /F PRO 32 N; /F PRO
138 N; /F PRO 130 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N;
/F PRO 3 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 130 N; /F PRO 143 N; /F PRO
138 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 3 N; /F
PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 130 N; /F PRO 143 N; /F PRO
138 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N; /F
PRO 3 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 130 N; /F PRO 143 N; /F PRO
138 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N; /F PRO 295 N; /F
PRO 3 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 130 N; /F PRO 143 N; /F PRO
138 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 3 N; /I
PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 130 N; /F PRO 143 N; /F PRO
138 N; /F PRO 32 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N; /I
PRO 709 N; /F PRO 3 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 287 N; /F PRO
32 N; /F PRO 156 N; /F PRO 295 N; /F PRO 3 N; /I PRO 709 N; /F PRO 316 N; /F
PRO 231 N; /F PRO 130 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 3 N; /F PRO 138 N; /F PRO 143 N; /F PRO 287 N; /F PRO 32
N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N; /I PRO 709 N; /F PRO 231 N; /F
PRO 239 N; /F PRO 130 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO
287 N; /F PRO 32 N; /F PRO 156 N; /F PRO 295 N; /F PRO 3 N; /F PRO 316 N; /I
PRO 709 N; /F PRO 130 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 138 N; /F PRO 143 N; /F PRO 287 N; /F PRO
32 N; /F PRO 156 N; /F PRO 295 N; /F PRO 3 N; /I PRO 709 N; /F PRO 231 N; /F
PRO 239 N; /F PRO 130 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 287 N; /F PRO
32 N; /F PRO 156 N; /F PRO 295 N; /I PRO 709 N; /F PRO 316 N; /F PRO 231 N; /F
PRO 3 N; /F PRO 130 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO
287 N; /F PRO 32 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N; /I PRO 709 N; /F
PRO 130 N; /F PRO 3 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N; /F PRO
156 N; /F PRO 32 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N; /I PRO 709 N; /F
PRO 3 N; /F PRO 130 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 295 N; /F PRO 287 N; /F PRO 32 N; /F PRO
156 N; /F PRO 316 N; /F PRO 3 N; /I PRO 709 N; /F PRO 231 N; /F PRO 239 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 32 N; /F PRO 143 N; /F PRO
287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N; /F PRO 3 N; /F PRO 130 N; /F
PRO 138 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 295 N; /F PRO 287 N; /F PRO 32 N; /F PRO
156 N; /F PRO 316 N; /F PRO 3 N; /I PRO 709 N; /F PRO 231 N; /F PRO 239 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 32 N; /F PRO 143 N; /F PRO
287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N; /I PRO 709 N; /F PRO 3 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 32 N; /F PRO 143 N; /F PRO
287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N; /I PRO 709 N; /F PRO 130 N;
/F PRO 138 N; /F PRO 3 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 3 N; /F PRO 143 N; /F PRO 295 N; /F PRO 287 N; /F PRO 32
N; /F PRO 156 N; /F PRO 316 N; /I PRO 709 N; /F PRO 231 N; /F PRO 239 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 32 N; /I PRO 709 N; /F PRO 287 N; /F PRO
295 N; /F PRO 156 N; /F PRO 316 N; /F PRO 231 N; /F PRO 3 N; /F PRO 239 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 32 N; /I PRO 709 N; /F PRO
287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 3 N; /F PRO 316 N; /F PRO 130 N; /F
PRO 138 N; /F PRO 143 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 32 N; /F PRO 287 N; /F PRO 295 N; /F PRO
316 N; /F PRO 156 N; /I PRO 709 N; /F PRO 231 N; /F PRO 239 N; /F PRO 3 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO
295 N; /F PRO 316 N; /F PRO 287 N; /F PRO 3 N; /F PRO 130 N; /F PRO 32 N; /F
PRO 138 N; /F PRO 143 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 295 N; /F PRO
316 N; /F PRO 287 N; /F PRO 130 N; /F PRO 3 N; /F PRO 231 N; /F PRO 138 N; /F
PRO 143 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 295 N; /F PRO
316 N; /F PRO 287 N; /F PRO 231 N; /F PRO 239 N; /F PRO 3 N; /F PRO 130 N; /F
PRO 138 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 295 N; /F PRO
316 N; /F PRO 287 N; /F PRO 130 N; /F PRO 138 N; /F PRO 231 N; /F PRO 143 N;
/F PRO 3 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /F PRO 156 N; /F PRO 3 N; /F PRO 295 N; /F PRO
316 N; /F PRO 287 N; /I PRO 709 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N;
/F PRO 143 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 295 N; /F PRO
316 N; /F PRO 287 N; /F PRO 231 N; /F PRO 239 N; /F PRO 3 N; /F PRO 130 N; /F
PRO 138 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 295 N; /F PRO
316 N; /F PRO 287 N; /F PRO 3 N; /F PRO 231 N; /F PRO 32 N; /F PRO 239 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 231 N; /F PRO
295 N; /F PRO 316 N; /I PRO 709 N; /F PRO 239 N; /F PRO 3 N; /F PRO 32 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 3 N; /F PRO
295 N; /F PRO 316 N; /I PRO 709 N; /F PRO 231 N; /F PRO 32 N; /F PRO 130 N; /F
PRO 239 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 3 N; /F PRO 287 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 239 N; /F PRO 130 N; /F PRO 138 N; /F PRO 143 N;
/F PRO 156 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 3 N; /F PRO 239 N; /F PRO 130 N; /F PRO 138 N; /F
PRO 143 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 3 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 231 N; /F PRO 130 N; /F PRO 239 N; /F PRO 138 N;
/F PRO 143 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /F PRO 287 N; /F PRO 3 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 231 N;
/F PRO 156 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 231 N; /F PRO
295 N; /F PRO 316 N; /I PRO 709 N; /F PRO 239 N; /F PRO 3 N; /F PRO 130 N; /F
PRO 138 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 231 N; /F PRO
295 N; /F PRO 316 N; /I PRO 709 N; /F PRO 239 N; /F PRO 3 N; /F PRO 32 N; /F
PRO 130 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 130 N; /F PRO 239 N; /F PRO 138 N; /F PRO 143 N;
/F PRO 3 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 239 N; /F PRO 130 N; /F PRO 138 N; /F PRO 3 N; /F
PRO 143 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 130 N; /F PRO 295 N; /F PRO
316 N; /I PRO 709 N; /F PRO 231 N; /F PRO 3 N; /F PRO 138 N; /F PRO 239 N; /F
PRO 143 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 3 N; /F PRO
295 N; /F PRO 316 N; /I PRO 709 N; /F PRO 231 N; /F PRO 239 N; /F PRO 130 N;
/F PRO 32 N; /F PRO 138 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 3 N; /F PRO 231 N; /F PRO
295 N; /F PRO 316 N; /F PRO 130 N; /F PRO 239 N; /F PRO 138 N; /F PRO 32 N; /F
PRO 143 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 287 N; /F PRO 239 N; /F PRO 231 N; /F PRO
295 N; /F PRO 316 N; /F PRO 130 N; /F PRO 3 N; /F PRO 138 N; /F PRO 143 N; /I
PRO 709 N; /F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 287 N; /F PRO 239 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /F PRO 130 N; /F PRO 32 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /I
PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 287 N; /F PRO 130 N; /F PRO 138 N; /F PRO 295 N; /F PRO
316 N; /F PRO 143 N; /F PRO 156 N; /F PRO 231 N; /F PRO 239 N; /F PRO 32 N; /I
PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 287 N; /F PRO 239 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /F PRO 130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 287 N; /F PRO 130 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /F PRO 138 N; /F PRO 143 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 287 N; /F PRO 130 N; /F PRO 231 N; /F PRO 295 N; /F PRO
316 N; /F PRO 138 N; /F PRO 143 N; /F PRO 239 N; /F PRO 156 N; /F PRO 32 N; /I
PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 32 N; /F PRO 156 N; /I PRO 709 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 138 N; /F PRO 316 N; /F PRO
231 N; /F PRO 143 N; /F PRO 239 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 287 N; /F PRO 138 N; /F PRO 143 N; /I PRO 709 N; /F PRO 156 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 231 N; /F PRO 316 N; /F PRO
239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 32 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
316 N; /F PRO 239 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 32 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 287 N; /I PRO 709 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 231 N; /F PRO 316 N; /F PRO
239 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 32 N; /I PRO 709 N; /F PRO 156 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
316 N; /F PRO 143 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 32 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 156 N; /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO
316 N; /F PRO 130 N; /F PRO 287 N; /F PRO 138 N; /F PRO 143 N; /F PRO 32 N; /I
PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
287 N; /F PRO 130 N; /F PRO 138 N; /I PRO 709 N; /F PRO 143 N; /F PRO 156 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
316 N; /F PRO 156 N; /F PRO 231 N; /F PRO 239 N; /I PRO 709 N; /F PRO 32 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /I PRO 709 N; /F PRO 32 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
316 N; /F PRO 239 N; /F PRO 143 N; /I PRO 709 N; /F PRO 156 N; /F PRO 32 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N;
/F PRO 32 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 32 N; /F
PRO 287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 239 N; /F PRO 231 N; /F PRO 316 N; /F PRO
130 N; /F PRO 138 N; /F PRO 143 N; /F PRO 287 N; /F PRO 156 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 143 N; /F PRO 138 N; /F PRO 130 N; /F PRO
231 N; /F PRO 156 N; /F PRO 239 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 239 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 239 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 143 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 138 N; /F PRO 143 N; /F PRO 295 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 138 N; /F PRO 143 N; /F PRO 295 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 143 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 138 N; /F PRO 295 N; /F PRO 143 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 143 N; /F PRO 138 N; /F PRO 130 N; /F PRO
231 N; /F PRO 156 N; /F PRO 239 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /F PRO
287 N; /F PRO 138 N; /F PRO 295 N; /F PRO 143 N; /I PRO 709 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 239 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /F PRO
287 N; /F PRO 138 N; /F PRO 295 N; /F PRO 143 N; /I PRO 709 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO
130 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 138 N; /F PRO 287 N; /F PRO 143 N; /F PRO 295 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 239 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 138 N; /F PRO 143 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /F PRO
287 N; /F PRO 138 N; /F PRO 295 N; /F PRO 143 N; /I PRO 709 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 239 N; /I PRO
709 N; /F PRO 138 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO
130 N; /F PRO 239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 287 N; /F PRO 156 N; /I PRO 709 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 239 N; /F PRO 231 N; /F PRO 138 N; /F PRO
130 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /F PRO 130 N; /F PRO 231 N; /F PRO 138 N; /F PRO
239 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 295 N; /F PRO 138 N; /F PRO 143 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /I PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 143 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 143 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /F PRO 156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 239 N; /F PRO 138 N; /F PRO
130 N; /F PRO 156 N; /F PRO 287 N; /I PRO 709 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 143 N; /F PRO 287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /F PRO 287 N; /I PRO 709 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /F PRO 287 N; /I PRO 709 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 143 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /F PRO 287 N; /I PRO 709 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /F PRO 143 N; /F PRO 138 N; /F PRO
239 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 239 N; /F PRO 138 N; /F PRO
130 N; /I PRO 709 N; /F PRO 156 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 130 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 295 N; /F PRO 138 N; /F PRO 143 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO 239 N; /F PRO
287 N; /F PRO 295 N; /F PRO 156 N; /I PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO 239 N; /F PRO
156 N; /I PRO 709 N; /F PRO 287 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 138 N; /F PRO 143 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 138 N; /F PRO 239 N; /I PRO
709 N; /F PRO 287 N; /F PRO 156 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 143 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 143 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 295 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /F PRO 143 N; /F PRO 156 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 143 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 156 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 156 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 156 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 295 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 316 N; /F PRO 156 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 287 N; /F PRO 239 N; /I PRO
709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /I PRO 709 N; /F PRO 239 N; /F PRO
287 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 231 N; /F PRO 295 N; /F PRO 239 N; /F PRO 316 N; /F PRO
287 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /I PRO 709 N; /F PRO 295 N; /F PRO 316 N; /F PRO
287 N; /F PRO 231 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 239 N; /I PRO 709 N; /F PRO 295 N; /F PRO 316 N; /F PRO
287 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 287 N; /F PRO 295 N; /F PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 295 N; /F PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 316 N; /I PRO 709 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 709 N; /F PRO 316 N
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 709 N
> select /F:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> select /F,I,7
7932 atoms, 8138 bonds, 977 residues, 1 model selected
> style sel ball
Changed 7932 atom styles
> color sel bychain
> select /I
4746 atoms, 4877 bonds, 575 residues, 1 model selected
> color sel #26a269ff
> color sel #1c71d8ff
> color sel #62a0eaff
> color sel #b5835aff
> color sel #cdab8fff
> color sel #63452cff
> color sel #865e3cff
> color sel #986a44ff
> color sel #f66151ff
> color sel #dc8addff
> color sel #ffbe6fff
> color sel #f9f06bff
> color sel #8ff0a4ff
> color sel #99c1f1ff
> select /7
616 atoms, 628 bonds, 77 residues, 1 model selected
> color sel #cdab8fff
> select /F
2570 atoms, 2633 bonds, 325 residues, 1 model selected
> color sel #9a9996ff
> color sel #c0bfbcff
> select /F:1-39
322 atoms, 329 bonds, 39 residues, 1 model selected
> color sel cyan
> select /F:43-81
304 atoms, 312 bonds, 39 residues, 1 model selected
> color sel purple
> color sel #c061cbff
> color sel #9141acff
> color sel #c061cbff
> select /F:135-175
309 atoms, 316 bonds, 41 residues, 1 model selected
> color sel white
> select /F:221-267
361 atoms, 367 bonds, 47 residues, 1 model selected
> color sel yellow
> select /F:1-39
322 atoms, 329 bonds, 39 residues, 1 model selected
> color sel #9141acff
> color sel #c061cbff
> select /F:43-81
304 atoms, 312 bonds, 39 residues, 1 model selected
> color sel #33d17aff
> color sel #2ec27eff
> color sel #26a269ff
> color sel #8ff0a4ff
> color sel #57e389ff
> color sel #33d17aff
> color sel #2ec27eff
> select /F:135-175
309 atoms, 316 bonds, 41 residues, 1 model selected
> color sel #3584e4ff
> color sel #62a0eaff
> color sel #3584e4ff
> select /F:221-267
361 atoms, 367 bonds, 47 residues, 1 model selected
Drag select of 7 atoms, 6 bonds
> save /home/trung/Desktop/image1.png supersample 3
> ui tool show "Color Actions"
> select ~sel & ##selected
7925 atoms, 8132 bonds, 977 residues, 1 model selected
> select /F
2570 atoms, 2633 bonds, 325 residues, 1 model selected
> save /home/trung/Documents/eIF3I_project/marked_altered_WD.cxs
> color sel #dedddaff
> color sel #c0bfbcff
> select /F:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> color sel crimson
> color sel red
> color sel orange red
> color sel tomato
> color sel fire brick
> color sel crimson
> color sel orange red
> color sel red
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel chocolate
> color sel plum
> color sel pink
> color sel peach puff
> color sel light coral
> color sel red
> color sel salmon
> color sel crimson
> color sel orange red
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel orange red target acspfl
> color sel crimson target acspfl
> color sel orange red target acspfl
> color sel black target l
> color sel dark green target l
> color sel blanched almond target l
> color sel light coral target l
> color sel sky blue target l
> set bgColor light coral
> set bgColor black
> color sel light gray target l
> color sel silver target l
> color sel light gray target l
> color sel light slate gray target l
> color sel slate gray target l
> color sel white target l
> select /F:258
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel goldenrod
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue violet
> color sel medium orchid
> color sel orchid
> color sel dark violet
> color sel dark orchid
> color sel dark magenta
> color sel dark orchid
> color sel medium purple
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:248
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel cyan
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:53
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel magenta
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:268
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel black
> color sel silver
> color sel dark gray
> color sel gray
> color sel dim gray
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel light salmon
> color sel salmon
> color sel coral
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> select /F:268
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right zone
> zone /F:268
> zone label false
> zone /F:268 residueDistance 3.84 labelDistance 3.07 surfaceDistance 6.14
> zone /F:268 residueDistance 2.95 labelDistance 2.36 surfaceDistance 4.72
> zone /F:268 residueDistance 2.26 labelDistance 1.81 surfaceDistance 3.62
> zone /F:278
> zone label false
> zone clear
> zone /F:266
> zone /F:266 residueDistance 1.74 labelDistance 1.39 surfaceDistance 2.78
> zone label false
> zone clear
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
> undo
> close session
> open /home/trung/Documents/eIF3I_project/marked_altered_aa_labeled.cxs
> format session
opened ChimeraX session
> select /F:268
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> color sel navy
> color sel light slate gray
> color sel slate gray
> color sel dark slate gray
> ui mousemode right translate
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:268 lys
Using Dunbrack library
/F ARG 268: phi -111.5, psi 117.4 trans
Applying LYS rotamer (chi angles: -62.9 -178.0 -76.1 -68.7) to /F LYS 268
> select /F:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:268 arg
Using Dunbrack library
/F LYS 268: phi -111.5, psi 117.4 trans
Applying ARG rotamer (chi angles: -74.0 78.3 178.4 -85.5) to /F ARG 268
> select /F:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:11 gln
Using Dunbrack library
/F ARG 11: phi -150.2, psi -167.2 trans
Applying GLN rotamer (chi angles: -61.6 -68.6 -66.4) to /F GLN 11
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:11 arg
Using Dunbrack library
/F GLN 11: phi -150.2, psi -167.2 trans
Applying ARG rotamer (chi angles: -62.9 -70.4 -174.8 -87.3) to /F ARG 11
> select /F:258
7 atoms, 6 bonds, 1 residue, 1 model selected
> view sel
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:258 ala
Using Dunbrack library
Swapping /F THR 258 to ALA
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:258
5 atoms, 4 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:258 thr
Using Dunbrack library
/F ALA 258: phi -158.6, psi 165.4 trans
Applying THR rotamer (chi angles: -169.8) to /F THR 258
> select /F:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:233 ser
Using Dunbrack library
/F ASN 233: phi -76.1, psi -18.3 trans
Applying SER rotamer (chi angles: 67.5) to /F SER 233
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:233
6 atoms, 5 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:233 ile
Using Dunbrack library
/F SER 233: phi -76.1, psi -18.3 trans
Applying ILE rotamer (chi angles: -162.6 64.7) to /F ILE 233
> select /F:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel gold
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:233 asn
Using Dunbrack library
/F ILE 233: phi -76.1, psi -18.3 trans
Applying ASN rotamer (chi angles: 63.3 27.8) to /F ASN 233
> select /F:248
4 atoms, 3 bonds, 1 residue, 1 model selected
> view sel
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:248 asp
Using Dunbrack library
/F GLY 248: phi 164.6, psi -166.6 trans
Applying ASP rotamer (chi angles: -169.0 52.4) to /F ASP 248
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:248
8 atoms, 7 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:248 gly
Using Dunbrack library
Swapping /F ASP 248 to GLY
> select /F:53
4 atoms, 3 bonds, 1 residue, 1 model selected
> view sel
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:248 arg
Using Dunbrack library
/F GLY 248: phi 164.6, psi -166.6 trans
Applying ARG rotamer (chi angles: -179.0 66.6 177.7 173.0) to /F ARG 248
> swapaa /F:248 gly
Using Dunbrack library
Swapping /F ARG 248 to GLY
> swapaa /F:53 arg
Using Dunbrack library
/F GLY 53: phi -160.7, psi 176.8 trans
Applying ARG rotamer (chi angles: -178.9 69.7 177.6 173.2) to /F ARG 53
> save /home/trung/Desktop/image1.png supersample 3
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:53 gly
Using Dunbrack library
Swapping /F ARG 53 to GLY
> swapaa /F:53 arg
Using Dunbrack library
/F GLY 53: phi -160.7, psi 176.8 trans
Applying ARG rotamer (chi angles: -178.9 69.7 177.6 173.2) to /F ARG 53
> select /F:268
11 atoms, 10 bonds, 1 residue, 1 model selected
> swapaa /F:53 gly
Using Dunbrack library
Swapping /F ARG 53 to GLY
> view sel
> save /home/trung/Desktop/image1.png supersample 3
> select /F:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> view sel
> save /home/trung/Desktop/image2.png supersample 3
> swapaa /F:148 thr
Using Dunbrack library
/F LYS 148: phi -62.2, psi 142.1 trans
Applying THR rotamer (chi angles: -60.1) to /F THR 148
> save /home/trung/Desktop/image1.png supersample 3
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /F:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> swapaa /F:148 lys
Using Dunbrack library
/F THR 148: phi -62.2, psi 142.1 trans
Applying LYS rotamer (chi angles: -67.4 -178.7 -179.6 179.2) to /F LYS 148
> select /F:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /home/trung/Desktop/image1.png supersample 3
> select /F
2570 atoms, 2633 bonds, 325 residues, 1 model selected
> view sel
> ui tool show "Side View"
> open /home/trung/Documents/eIF3I_project/8oz0.cif
8oz0.cif title:
Structure of a human 48S translation initiation complex with eIF4F and eIF4A
[more info...]
Chain information for 8oz0.cif #2
---
Chain | Description | UniProt
1 3 | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406
2 | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 196-1599
5 | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445
6 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357
7 | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320
8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352
9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25
A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382
B | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218
C | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374
D | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315
E | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
F | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN
1-144
H | Eukaryotic translation initiation factor 5 | IF5_HUMAN 1-431
I | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814
J | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913
K | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564
L | 40S ribosomal protein S7 | RS7_HUMAN 1-194
M | 40S ribosomal protein S27 | RS27_HUMAN 1-84
N | 40S ribosomal protein S21 | RS21_HUMAN 1-83
O | 40S ribosomal protein S2 | RS2_HUMAN 1-293
P | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
Q | 40S ribosomal protein SA | RSSA_HUMAN 1-295
R | 40S ribosomal protein S26 | RS26_HUMAN 1-115
S | 40S ribosomal protein S6 | RS6_HUMAN 1-249
T | 40S ribosomal protein S14 | RS14_HUMAN 1-151
U | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333
V | 40S ribosomal protein S13 | RS13_HUMAN 1-151
W | 18S rRNA |
X | 40S ribosomal protein S11 | RS11_HUMAN 1-158
Y | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
Z | 40S ribosomal protein S9 | RS9_HUMAN 1-194
a | 40S ribosomal protein S23 | RS23_HUMAN 1-143
b | 40S ribosomal protein S30 | RS30_HUMAN 75-133
c | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
d | 40S ribosomal protein S8 | RS8_HUMAN 1-208
e | 40S ribosomal protein S24 | RS24_HUMAN 1-133
f | 40S ribosomal protein S5 | RS5_HUMAN 1-204
g | 40S ribosomal protein S16 | RS16_HUMAN 1-146
h | 40S ribosomal protein S3 | RS3_HUMAN 1-243
i | 40S ribosomal protein S10 | RS10_HUMAN 1-165
j | 40S ribosomal protein S15 | RS15_HUMAN 1-145
k | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
l | 40S ribosomal protein S19 | RS19_HUMAN 1-145
m | 40S ribosomal protein S25 | RS25_HUMAN 1-125
n | Small ribosomal subunit protein uS13 | RS18_HUMAN 1-151
o | 40S ribosomal protein S29 | RS29_HUMAN 1-56
p | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156
q | 40S ribosomal protein S12 | RS12_HUMAN 1-132
s | 40S ribosomal protein S28 | RS28_HUMAN 1-69
v | 40S ribosomal protein S17 | RS17_HUMAN 1-135
w | 40S ribosomal protein S20 | RS20_HUMAN 1-119
x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548
y | tRNAiMet |
z | mRNA |
Non-standard residues in 8oz0.cif #2
---
5MC — 5-methylcytidine-5'-monophosphate
5MU — 5-methyluridine 5'-monophosphate
6MZ — N6-methyladenosine-5'-monophosphate
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)
C4J —
(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-
L-arabinitol
JMH — 3-Methylcytidine- 5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
OMC — O2'-methylycytidine-5'-monophosphate
OMG — O2'-methylguanosine-5'-monophosphate
OMU — O2'-methyluridine 5'-monophosphate
UR3 — 3-methyluridine-5'-monophoshate
ZN — zinc ion
> style sel ball
Changed 2570 atom styles
Drag select of 15633 atoms, 7295 bonds, 1 pseudobonds
> style sel ball
Changed 15633 atom styles
> view sel
Drag select of 110730 atoms, 16896 bonds, 1531 pseudobonds
> style sel ball
Changed 110730 atom styles
> view sel
Drag select of 129542 atoms, 116338 bonds, 1649 pseudobonds
> style sel ball
Changed 129542 atom styles
> select add #2
129542 atoms, 135369 bonds, 1649 pseudobonds, 14772 residues, 5 models
selected
> select subtract #2
7932 atoms, 8138 bonds, 977 residues, 1 model selected
> select add #2
129542 atoms, 135369 bonds, 1649 pseudobonds, 14772 residues, 5 models
selected
> select subtract #2
7932 atoms, 8138 bonds, 977 residues, 1 model selected
> select add #1
7932 atoms, 8138 bonds, 977 residues, 2 models selected
> select add #2
129542 atoms, 135369 bonds, 1649 pseudobonds, 14772 residues, 6 models
selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2/F
1598 atoms, 1597 bonds, 325 residues, 1 model selected
> style sel sphere
Changed 1598 atom styles
> style sel ball
Changed 1598 atom styles
> style sel stick
Changed 1598 atom styles
> select #2
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> style sel stick
Changed 121610 atom styles
> style sel sphere
Changed 121610 atom styles
> style sel sphere
Changed 121610 atom styles
> style sel ball
Changed 121610 atom styles
> select #2
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> style sel stick
Changed 121610 atom styles
> select #2/F
1598 atoms, 1597 bonds, 325 residues, 1 model selected
> hide sel atoms
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show sel cartoons
> hide sel cartoons
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> select #2/W:1248
28 atoms, 29 bonds, 1 residue, 1 model selected
> view sel
> select #1/F,I
7316 atoms, 7510 bonds, 900 residues, 1 model selected
> view sel
> hbonds sel reveal true
124 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1880 hydrogen bonds found
> swapaa #1/F:268 lys
Using Dunbrack library
altered_marked_labeled_aa.pdb #1/F ARG 268: phi -111.5, psi 117.4 trans
Applying LYS rotamer (chi angles: -62.9 -178.0 -76.1 -68.7) to
altered_marked_labeled_aa.pdb #1/F LYS 268
> hbonds sel reveal true
124 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1881 hydrogen bonds found
> swapaa #1/F:268 arg
Using Dunbrack library
altered_marked_labeled_aa.pdb #1/F LYS 268: phi -111.5, psi 117.4 trans
Applying ARG rotamer (chi angles: -74.0 78.3 178.4 -85.5) to
altered_marked_labeled_aa.pdb #1/F ARG 268
> hbonds sel reveal true
124 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1880 hydrogen bonds found
> close session
> open /home/trung/Documents/eIF3I_project/AF-Q13347-F1-model_v4.cif
Chain information for AF-Q13347-F1-model_v4.cif #1
---
Chain | Description | UniProt
A | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
Color AF-Q13347-F1-model_v4.cif by residue attribute pLDDT_score
> hide cartoons
> show atoms
> select ~sel & ##selected
Nothing selected
> select /A:53
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel magenta
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel coral
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dark magenta
> color sel dark orchid
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:248
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel cyan
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:258
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dark salmon
> color sel chartreuse
> color sel dark salmon
> color sel salmon
> color sel coral
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel sandy brown
> color sel orange
> color sel orange red
> color sel tomato
> color sel coral
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange red
> select /A:268
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel dim gray
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel crimson
> color sel fire brick
> color sel red
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save
> /home/trung/Documents/eIF3I_project/AF-Q13347-F1-model_v4_altered_aa_labeled.cif
> relModel #1
> close session
> open /home/trung/Downloads/5a5u.cif
Summary of feedback from opening /home/trung/Downloads/5a5u.cif
---
warnings | Atom CG1 is not in the residue template for UNK /A:674
Atom CD is not in the residue template for UNK /A:675
Atom CD is not in the residue template for UNK /A:676
Atom CD1 is not in the residue template for UNK /A:677
Atom CD is not in the residue template for UNK /A:678
Atom CD is not in the residue template for UNK /A:679
Atom CD is not in the residue template for UNK /A:680
Atom CD is not in the residue template for UNK /A:681
Atom CD is not in the residue template for UNK /A:682
1 messages similar to the above omitted
Atom CD1 is not in the residue template for UNK /A:684
Atom CD is not in the residue template for UNK /A:685
Atom CD is not in the residue template for UNK /A:686
Atom CD is not in the residue template for UNK /A:687
Atom CD1 is not in the residue template for UNK /A:688
Atom CD is not in the residue template for UNK /A:689
Atom OD1 is not in the residue template for UNK /A:690
Atom CD is not in the residue template for UNK /A:691
Atom CD is not in the residue template for UNK /A:692
Atom CD is not in the residue template for UNK /A:693
Atom CD is not in the residue template for UNK /A:694
Atom CG1 is not in the residue template for UNK /A:695
Atom OD1 is not in the residue template for UNK /A:696
Atom CD1 is not in the residue template for UNK /A:697
Atom CD1 is not in the residue template for UNK /A:698
Atom CD is not in the residue template for UNK /A:699
Atom CD is not in the residue template for UNK /A:700
Atom CD is not in the residue template for UNK /A:702
Atom CD is not in the residue template for UNK /A:703
Atom CD1 is not in the residue template for UNK /A:704
Atom CD is not in the residue template for UNK /A:705
Atom CG1 is not in the residue template for UNK /A:710
5a5u.cif title:
Structure of mammalian eIF3 in the context of the 43S preinitiation complex
[more info...]
Chain information for 5a5u.cif #1
---
Chain | Description | UniProt
A | EUKARYOTIC INITIATION FACTOR 3 |
B | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B | G1SZ03_RABIT 42-717
I | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I | EIF3I_YEAST 1-347
> hide cartoons
> show atoms
> color bychain
> select ~sel & ##selected
Nothing selected
> select /I:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> select /I,B,A
8124 atoms, 8323 bonds, 1009 residues, 1 model selected
> view sel
> color bfactor sel
8124 atoms, 1009 residues, atom bfactor range 0 to 103
> color sel byhetero
> color bfactor sel
8124 atoms, 1009 residues, atom bfactor range 0 to 103
> select /I:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> coulombic sel
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/trung/Downloads/5a5u.cif
Summary of feedback from opening /home/trung/Downloads/5a5u.cif
---
warnings | Atom CG1 is not in the residue template for UNK /A:674
Atom CD is not in the residue template for UNK /A:675
Atom CD is not in the residue template for UNK /A:676
Atom CD1 is not in the residue template for UNK /A:677
Atom CD is not in the residue template for UNK /A:678
Atom CD is not in the residue template for UNK /A:679
Atom CD is not in the residue template for UNK /A:680
Atom CD is not in the residue template for UNK /A:681
Atom CD is not in the residue template for UNK /A:682
1 messages similar to the above omitted
Atom CD1 is not in the residue template for UNK /A:684
Atom CD is not in the residue template for UNK /A:685
Atom CD is not in the residue template for UNK /A:686
Atom CD is not in the residue template for UNK /A:687
Atom CD1 is not in the residue template for UNK /A:688
Atom CD is not in the residue template for UNK /A:689
Atom OD1 is not in the residue template for UNK /A:690
Atom CD is not in the residue template for UNK /A:691
Atom CD is not in the residue template for UNK /A:692
Atom CD is not in the residue template for UNK /A:693
Atom CD is not in the residue template for UNK /A:694
Atom CG1 is not in the residue template for UNK /A:695
Atom OD1 is not in the residue template for UNK /A:696
Atom CD1 is not in the residue template for UNK /A:697
Atom CD1 is not in the residue template for UNK /A:698
Atom CD is not in the residue template for UNK /A:699
Atom CD is not in the residue template for UNK /A:700
Atom CD is not in the residue template for UNK /A:702
Atom CD is not in the residue template for UNK /A:703
Atom CD1 is not in the residue template for UNK /A:704
Atom CD is not in the residue template for UNK /A:705
Atom CG1 is not in the residue template for UNK /A:710
5a5u.cif title:
Structure of mammalian eIF3 in the context of the 43S preinitiation complex
[more info...]
Chain information for 5a5u.cif #1
---
Chain | Description | UniProt
A | EUKARYOTIC INITIATION FACTOR 3 |
B | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B | G1SZ03_RABIT 42-717
I | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I | EIF3I_YEAST 1-347
> show atoms
> hide cartoons
> select /I:11
11 atoms, 10 bonds, 1 residue, 1 model selected
OpenGL version: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: Quadro K4200/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 Tower 5810
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 6.5Gi 19Gi 207Mi 5.3Gi 24Gi
Swap: 15Gi 0B 15Gi
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)
Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]
Kernel driver in use: nvidia
Installed Packages:
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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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.7.1
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: 2.6.1
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: 1.5.14
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: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
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
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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-StdCommands: 1.12.4
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
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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
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comm: 0.2.1
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cxservices: 1.2.2
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Cython: 0.29.33
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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
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jedi: 0.18.2
Jinja2: 3.1.2
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jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
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line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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