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Opened 19 months ago
Closed 19 months ago
#14925 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: macOS-14.3-arm64-arm-64bit
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.
While adding H to symmetric copies
Fatal Python error: Segmentation fault
Current thread 0x00000001d9595c40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/chem_group/support.py", line 40 in call_c_plus_plus
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/chem_group/chem_group.py", line 233 in find_group
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 770 in _find_acceptors
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 498 in find_hbonds
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 259 in add_hydrogens
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 184 in hbond_add_hydrogens
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mmcif.mmcif_write (total: 58)
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}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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
> /Users/abhinabadas/Desktop/KI3FK_phenix/PDBTools_5/ISOLDE/Unflipped_ASU_KI3FK-
> COOT.pdb
Chain information for Unflipped_ASU_KI3FK-COOT.pdb #1
---
Chain | Description
A B C | No description available
> sym #1 h,1.237,89.594,20 copies=True newModel True
Expected a keyword
> sym #1 h,1.237,89.594,20 copies true newModel true
Made 20 copies for Unflipped_ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> addH
Unknown command: addH
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#1) chain
A; guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#1) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#1) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#1/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #1/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #1/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#1/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #1/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #1/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.1) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.1) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.1) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.1/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.1/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.1/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.1/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.1/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.1/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.2) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.2) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.2) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.2/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.2/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.2/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.2/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.2/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.2/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.3) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.3) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.3) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.3/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.3/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.3/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.3/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.3/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.3/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.4) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.4) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.4) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.4/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.4/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.4/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.4/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.4/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.4/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.5) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.5) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.5) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.5/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.5/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.5/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.5/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.5/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.5/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.6) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.6) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.6) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.6/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.6/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.6/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.6/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.6/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.6/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.7) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.7) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.7) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.7/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.7/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.7/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.7/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.7/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.7/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.8) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.8) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.8) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.8/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.8/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.8/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.8/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.8/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.8/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.9) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.9) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.9) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.9/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.9/B ACE 0, Unflipped_ASU_KI3FK-
COOT.pdb #2.9/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.9/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.9/B LYN 6, Unflipped_ASU_KI3FK-
COOT.pdb #2.9/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.10) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.10) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.10) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.10/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.10/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.10/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.10/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.10/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.10/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.11) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.11) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.11) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.11/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.11/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.11/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.11/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.11/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.11/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.12) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.12) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.12) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.12/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.12/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.12/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.12/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.12/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.12/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.13) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.13) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.13) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.13/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.13/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.13/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.13/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.13/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.13/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.14) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.14) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.14) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.14/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.14/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.14/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.14/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.14/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.14/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.15) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.15) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.15) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.15/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.15/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.15/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.15/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.15/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.15/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.16) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.16) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.16) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.16/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.16/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.16/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.16/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.16/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.16/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.17) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.17) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.17) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.17/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.17/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.17/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.17/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.17/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.17/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.18) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.18) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.18) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.18/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.18/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.18/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.18/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.18/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.18/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.19) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.19) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.19) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.19/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.19/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.19/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.19/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.19/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.19/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.20) chain A;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.20) chain B;
guessing termini instead
No usable SEQRES records for Unflipped_ASU_KI3FK-COOT.pdb (#2.20) chain C;
guessing termini instead
Chain-initial residues that are actual N termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.20/A ACE 0, Unflipped_ASU_KI3FK-COOT.pdb #2.20/B ACE 0,
Unflipped_ASU_KI3FK-COOT.pdb #2.20/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: Unflipped_ASU_KI3FK-COOT.pdb
#2.20/A LYN 6, Unflipped_ASU_KI3FK-COOT.pdb #2.20/B LYN 6,
Unflipped_ASU_KI3FK-COOT.pdb #2.20/C LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
4410 hydrogens added
> hide HC
> hbonds #2
13 hydrogen bonds found
> combine #2
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.2 to 'D'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.2 to 'E'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.2 to 'F'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.3 to 'G'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.3 to 'H'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.3 to 'I'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.4 to 'J'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.4 to 'K'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.4 to 'L'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.5 to 'M'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.5 to 'N'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.5 to 'O'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.6 to 'P'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.6 to 'Q'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.6 to 'R'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.7 to 'S'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.7 to 'T'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.7 to 'U'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.8 to 'V'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.8 to 'W'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.8 to 'X'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.9 to 'Y'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.9 to 'Z'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.9 to 'a'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.10 to 'b'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.10 to 'c'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.10 to 'd'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.11 to 'e'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.11 to 'f'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.11 to 'g'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.12 to 'h'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.12 to 'i'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.12 to 'j'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.13 to 'k'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.13 to 'l'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.13 to 'm'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.14 to 'n'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.14 to 'o'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.14 to 'p'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.15 to 'q'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.15 to 'r'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.15 to 's'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.16 to 't'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.16 to 'u'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.16 to 'v'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.17 to 'w'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.17 to 'x'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.17 to 'y'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.18 to 'z'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.18 to '1'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.18 to '2'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.19 to '3'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.19 to '4'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.19 to '5'
Remapping chain ID 'A' in Unflipped_ASU_KI3FK-COOT.pdb #2.20 to '6'
Remapping chain ID 'B' in Unflipped_ASU_KI3FK-COOT.pdb #2.20 to '7'
Remapping chain ID 'C' in Unflipped_ASU_KI3FK-COOT.pdb #2.20 to '8'
> hbonds #4
637 hydrogen bonds found
> hide #!2 models
> show backbone only
> close all
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for test_KI3FK.cif #1
---
Chain | Description
A B C | No description available
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
> sym #1 h,1.237,89.594,20 copies true newModel true
Made 20 copies for test_KI3FK.cif symmetry h,1.237,89.594,20
> close #2
> sym #1 h,1.237,89.594,20 copies true newModel true addMmcifAssembly true
Made 20 copies for test_KI3FK.cif symmetry h,1.237,89.594,20
> close #1#2
> open /Users/abhinabadas/ASU_KI3FK-COOT.pdb
Chain information for ASU_KI3FK-COOT.pdb #1
---
Chain | Description
A B C | No description available
> sym #1 h,1.237,89.594,20 copies true newModel true addMmcifAssembly true
Made 20 copies for ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> combine #2
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.2 to 'D'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.2 to 'E'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.2 to 'F'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.3 to 'G'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.3 to 'H'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.3 to 'I'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.4 to 'J'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.4 to 'K'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.4 to 'L'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.5 to 'M'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.5 to 'N'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.5 to 'O'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.6 to 'P'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.6 to 'Q'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.6 to 'R'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.7 to 'S'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.7 to 'T'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.7 to 'U'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.8 to 'V'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.8 to 'W'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.8 to 'X'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.9 to 'Y'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.9 to 'Z'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.9 to 'a'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.10 to 'b'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.10 to 'c'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.10 to 'd'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.11 to 'e'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.11 to 'f'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.11 to 'g'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.12 to 'h'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.12 to 'i'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.12 to 'j'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.13 to 'k'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.13 to 'l'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.13 to 'm'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.14 to 'n'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.14 to 'o'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.14 to 'p'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.15 to 'q'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.15 to 'r'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.15 to 's'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.16 to 't'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.16 to 'u'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.16 to 'v'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.17 to 'w'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.17 to 'x'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.17 to 'y'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.18 to 'z'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.18 to '1'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.18 to '2'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.19 to '3'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.19 to '4'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.19 to '5'
Remapping chain ID 'A' in ASU_KI3FK-COOT.pdb #2.20 to '6'
Remapping chain ID 'B' in ASU_KI3FK-COOT.pdb #2.20 to '7'
Remapping chain ID 'C' in ASU_KI3FK-COOT.pdb #2.20 to '8'
> addh #3
Summary of feedback from adding hydrogens to combination #3
---
notes | No usable SEQRES records for combination (#3) chain A; guessing
termini instead
No usable SEQRES records for combination (#3) chain B; guessing termini
instead
No usable SEQRES records for combination (#3) chain C; guessing termini
instead
No usable SEQRES records for combination (#3) chain D; guessing termini
instead
No usable SEQRES records for combination (#3) chain E; guessing termini
instead
55 messages similar to the above omitted
Chain-initial residues that are actual N termini: combination #3/A ACE 0,
combination #3/B ACE 0, combination #3/C ACE 0, combination #3/D ACE 0,
combination #3/E ACE 0, combination #3/F ACE 0, combination #3/G ACE 0,
combination #3/H ACE 0, combination #3/I ACE 0, combination #3/J ACE 0,
combination #3/K ACE 0, combination #3/L ACE 0, combination #3/M ACE 0,
combination #3/N ACE 0, combination #3/O ACE 0, combination #3/P ACE 0,
combination #3/Q ACE 0, combination #3/R ACE 0, combination #3/S ACE 0,
combination #3/T ACE 0, combination #3/U ACE 0, combination #3/V ACE 0,
combination #3/W ACE 0, combination #3/X ACE 0, combination #3/Y ACE 0,
combination #3/Z ACE 0, combination #3/a ACE 0, combination #3/b ACE 0,
combination #3/c ACE 0, combination #3/d ACE 0, combination #3/e ACE 0,
combination #3/f ACE 0, combination #3/g ACE 0, combination #3/h ACE 0,
combination #3/i ACE 0, combination #3/j ACE 0, combination #3/k ACE 0,
combination #3/l ACE 0, combination #3/m ACE 0, combination #3/n ACE 0,
combination #3/o ACE 0, combination #3/p ACE 0, combination #3/q ACE 0,
combination #3/r ACE 0, combination #3/s ACE 0, combination #3/t ACE 0,
combination #3/u ACE 0, combination #3/v ACE 0, combination #3/w ACE 0,
combination #3/x ACE 0, combination #3/y ACE 0, combination #3/z ACE 0,
combination #3/1 ACE 0, combination #3/2 ACE 0, combination #3/3 ACE 0,
combination #3/4 ACE 0, combination #3/5 ACE 0, combination #3/6 ACE 0,
combination #3/7 ACE 0, combination #3/8 ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: combination #3/A LYN 6,
combination #3/B LYN 6, combination #3/C LYN 6, combination #3/D LYN 6,
combination #3/E LYN 6, combination #3/F LYN 6, combination #3/G LYN 6,
combination #3/H LYN 6, combination #3/I LYN 6, combination #3/J LYN 6,
combination #3/K LYN 6, combination #3/L LYN 6, combination #3/M LYN 6,
combination #3/N LYN 6, combination #3/O LYN 6, combination #3/P LYN 6,
combination #3/Q LYN 6, combination #3/R LYN 6, combination #3/S LYN 6,
combination #3/T LYN 6, combination #3/U LYN 6, combination #3/V LYN 6,
combination #3/W LYN 6, combination #3/X LYN 6, combination #3/Y LYN 6,
combination #3/Z LYN 6, combination #3/a LYN 6, combination #3/b LYN 6,
combination #3/c LYN 6, combination #3/d LYN 6, combination #3/e LYN 6,
combination #3/f LYN 6, combination #3/g LYN 6, combination #3/h LYN 6,
combination #3/i LYN 6, combination #3/j LYN 6, combination #3/k LYN 6,
combination #3/l LYN 6, combination #3/m LYN 6, combination #3/n LYN 6,
combination #3/o LYN 6, combination #3/p LYN 6, combination #3/q LYN 6,
combination #3/r LYN 6, combination #3/s LYN 6, combination #3/t LYN 6,
combination #3/u LYN 6, combination #3/v LYN 6, combination #3/w LYN 6,
combination #3/x LYN 6, combination #3/y LYN 6, combination #3/z LYN 6,
combination #3/1 LYN 6, combination #3/2 LYN 6, combination #3/3 LYN 6,
combination #3/4 LYN 6, combination #3/5 LYN 6, combination #3/6 LYN 6,
combination #3/7 LYN 6, combination #3/8 LYN 6
Chain-final residues that are not actual C termini:
224 hydrogen bonds
4120 hydrogens added
> hbonds #3
686 hydrogen bonds found
> show backbone only
> close #3-4
> save /Users/abhinabadas/Desktop/test_KI3FK.cif models #1 selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warning | No mmCIF models found.
> close #2
> sym #1 h,1.237,89.594,20 copies true newModel true addMmcifAssembly true
Made 20 copies for ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> save /Users/abhinabadas/Desktop/test_KI3FK.cif displayedOnly true
Not saving entity_poly_seq for non-authoritative sequences
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 123, in save
mmcif_write.write_mmcif(session, path, **kw)
File "src/mmcif_write.pyx", line 160, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src/mmcif_write.pyx", line 167, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src/mmcif_write.pyx", line 899, in
chimerax.mmcif.mmcif_write.save_structure
AttributeError: 'Residue' object has no attribute 'display'
AttributeError: 'Residue' object has no attribute 'display'
File "src/mmcif_write.pyx", line 899, in
chimerax.mmcif.mmcif_write.save_structure
See log for complete Python traceback.
> close #2
> show #1 models
> show atoms
> sym #1 h,1.237,89.594,20 copies true newModel true addMmcifAssembly true
Made 20 copies for ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> select add #2
3420 atoms, 3420 bonds, 420 residues, 21 models selected
> save /Users/abhinabadas/Desktop/test_KI3FK.cif selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 279
Missing or incomplete sequence information. Inferred polymer connectivity.
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
Chain information for test_KI3FK.cif
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A
3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A 3.1/B 3.2/B 3.3/B
3.4/B 3.5/B 3.6/B 3.7/B 3.8/B 3.9/B 3.10/B 3.11/B 3.12/B 3.13/B 3.14/B 3.15/B
3.16/B 3.17/B 3.18/B 3.19/B 3.20/B 3.1/C 3.2/C 3.3/C 3.4/C 3.5/C 3.6/C 3.7/C
3.8/C 3.9/C 3.10/C 3.11/C 3.12/C 3.13/C 3.14/C 3.15/C 3.16/C 3.17/C 3.18/C
3.19/C 3.20/C | No description available
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
> close #3
> select subtract #2
Nothing selected
> select add #2
3420 atoms, 3420 bonds, 420 residues, 21 models selected
> select subtract #2
Nothing selected
> select add #2
3420 atoms, 3420 bonds, 420 residues, 21 models selected
> select subtract #2.1
3249 atoms, 3249 bonds, 399 residues, 20 models selected
> select subtract #2.2
3078 atoms, 3078 bonds, 378 residues, 19 models selected
> select subtract #2.3
2907 atoms, 2907 bonds, 357 residues, 18 models selected
> select subtract #2.4
2736 atoms, 2736 bonds, 336 residues, 17 models selected
> select subtract #2.5
2565 atoms, 2565 bonds, 315 residues, 16 models selected
> select subtract #2.6
2394 atoms, 2394 bonds, 294 residues, 15 models selected
> select subtract #2.7
2223 atoms, 2223 bonds, 273 residues, 14 models selected
> select subtract #2.8
2052 atoms, 2052 bonds, 252 residues, 13 models selected
> select subtract #2.9
1881 atoms, 1881 bonds, 231 residues, 12 models selected
> select subtract #2.10
1710 atoms, 1710 bonds, 210 residues, 11 models selected
> select subtract #2.11
1539 atoms, 1539 bonds, 189 residues, 10 models selected
> select subtract #2.12
1368 atoms, 1368 bonds, 168 residues, 9 models selected
> select subtract #2.13
1197 atoms, 1197 bonds, 147 residues, 8 models selected
> select subtract #2.14
1026 atoms, 1026 bonds, 126 residues, 7 models selected
> select subtract #2.15
855 atoms, 855 bonds, 105 residues, 6 models selected
> select subtract #2.16
684 atoms, 684 bonds, 84 residues, 5 models selected
> select subtract #2.17
513 atoms, 513 bonds, 63 residues, 4 models selected
> select subtract #2.18
342 atoms, 342 bonds, 42 residues, 3 models selected
> select subtract #2.19
171 atoms, 171 bonds, 21 residues, 2 models selected
> select subtract #2.20
1 model selected
> save /Users/abhinabadas/Desktop/test_KI3FK.cif selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warning | No mmCIF models found.
> select add #2
3420 atoms, 3420 bonds, 420 residues, 21 models selected
> select subtract #2
Nothing selected
> select add #2
3420 atoms, 3420 bonds, 420 residues, 21 models selected
> hide #!2 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1 models
> select add #1
3591 atoms, 3591 bonds, 441 residues, 22 models selected
> save /Users/abhinabadas/Desktop/test_KI3FK.cif selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' near line 680
Missing or incomplete sequence information. Inferred polymer connectivity.
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
3| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
Chain information for test_KI3FK.cif
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A
3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A 3.21/A 3.1/B 3.2/B
3.3/B 3.4/B 3.5/B 3.6/B 3.7/B 3.8/B 3.9/B 3.10/B 3.11/B 3.12/B 3.13/B 3.14/B
3.15/B 3.16/B 3.17/B 3.18/B 3.19/B 3.20/B 3.21/B 3.1/C 3.2/C 3.3/C 3.4/C 3.5/C
3.6/C 3.7/C 3.8/C 3.9/C 3.10/C 3.11/C 3.12/C 3.13/C 3.14/C 3.15/C 3.16/C
3.17/C 3.18/C 3.19/C 3.20/C 3.21/C | No description available
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
> close #3
> show #!2 models
> hide #!2 models
> select subtract #2
171 atoms, 171 bonds, 21 residues, 1 model selected
> save /Users/abhinabadas/Desktop/test_KI3FK.cif selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for test_KI3FK.cif #3
---
Chain | Description
A B C | No description available
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
3| author defined symmetry
> sym #3 assembly 1
Made 20 graphical clones for test_KI3FK.cif assembly 1
> view
> sym #3 assembly 1
Made 20 graphical clones for test_KI3FK.cif assembly 1
> view
> sym #3 assembly 2
Made 20 graphical clones for test_KI3FK.cif assembly 2
> view
> sym #3 assembly 3
Made 20 graphical clones for test_KI3FK.cif assembly 3
> view
> close #4-7
> close #3
> hide #1 models
> show #1 models
> close #2
> sym #1 h,1.237,89.594,20 copies true addMmcifAssembly true
Made 20 copies for ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> save /Users/abhinabadas/Desktop/tst_KI3FK.cif selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/tst_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/tst_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for tst_KI3FK.cif #3
---
Chain | Description
A B C | No description available
tst_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
2| author defined symmetry
3| author defined symmetry
4| author defined symmetry
> close #3#2
> clear'
Unknown command: clear'
> clear
Unknown command: clear
> close all
> open /Users/abhinabadas/ASU_KI3FK-COOT.pdb
Chain information for ASU_KI3FK-COOT.pdb #1
---
Chain | Description
A B C | No description available
> sym #1 h,1.237,89.594,20 addMmcifAssembly true
Made 20 graphical clones for ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> save /Users/abhinabadas/Desktop/test_KI3FK.cif relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/abhinabadas/Desktop/test_KI3FK.cif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for test_KI3FK.cif #2
---
Chain | Description
A B C | No description available
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
> hide #1 models
> sym #2 assembly 1
Made 20 graphical clones for test_KI3FK.cif assembly 1
> view
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> addh #3
Summary of feedback from adding hydrogens to test_KI3FK.cif assembly 1 #3
---
notes | No usable SEQRES records for test_KI3FK.cif assembly 1 (#3) chain A;
guessing termini instead
No usable SEQRES records for test_KI3FK.cif assembly 1 (#3) chain B; guessing
termini instead
No usable SEQRES records for test_KI3FK.cif assembly 1 (#3) chain C; guessing
termini instead
Chain-initial residues that are actual N termini: test_KI3FK.cif assembly 1
#3/A ACE 0, test_KI3FK.cif assembly 1 #3/B ACE 0, test_KI3FK.cif assembly 1
#3/C ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: test_KI3FK.cif assembly 1 #3/A
LYN 6, test_KI3FK.cif assembly 1 #3/B LYN 6, test_KI3FK.cif assembly 1 #3/C
LYN 6
Chain-final residues that are not actual C termini:
0 hydrogen bonds
206 hydrogens added
> hbonds #3
0 hydrogen bonds found
> combine #3
> close #3-4
> hbonds #5
0 hydrogen bonds found
> close #2-3,5
> close
> open /Users/abhinabadas/Desktop/test_KI3FK.cif format mmcif
Summary of feedback from opening /Users/abhinabadas/Desktop/test_KI3FK.cif
---
warnings | Unknown polymer entity '1' near line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for test_KI3FK.cif #1
---
Chain | Description
A B C | No description available
test_KI3FK.cif mmCIF Assemblies
---
1| author defined symmetry
> sym #1 assembly 1
Made 20 graphical clones for test_KI3FK.cif assembly 1
> view
> show #2 atoms
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select #2/A:0@C
1 atom, 1 residue, 1 model selected
> select add #2/A:1@N
2 atoms, 2 residues, 1 model selected
> open /Users/abhinabadas/ASU_KI3FK-COOT.pdb
Chain information for ASU_KI3FK-COOT.pdb #3
---
Chain | Description
A B C | No description available
> close #1-2
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> view
> select /B:0@C
1 atom, 1 residue, 1 model selected
> select add /B:1@N
2 atoms, 2 residues, 1 model selected
> ui tool show Axes/Planes/Centroids
> distance /B:0@C /B:1@N
Distance between /B ACE 0 C and LYS 1 N: 1.302Å
> select clear
> select /B:1@N
1 atom, 1 residue, 1 model selected
> select clear
> select /B:1@N
1 atom, 1 residue, 1 model selected
> select add /B:1@CA
2 atoms, 1 residue, 1 model selected
> distance /B:1@N /B:1@CA
Distance between /B LYS 1 N and CA: 1.430Å
> ~distance /B:1@N /B:1@CA
> ~distance /B:0@C /B:1@N
> select clear
> sym #1 h,1.237,89.594,20
No structures specified.
> sym #3 h,1.237,89.594,20
Made 20 graphical clones for ASU_KI3FK-COOT.pdb symmetry h,1.237,89.594,20
> close
> open
> /Users/abhinabadas/Desktop/KI3FK_phenix/PDBTools_5/ISOLDE/Flipped_ASU_KI3FK-
> COOT.pdb
Chain information for Flipped_ASU_KI3FK-COOT.pdb #1
---
Chain | Description
A B C | No description available
> open /Users/abhinabadas/Downloads/OneDrive_1_4-7-2024/FlippedASU_RSR.cif
Summary of feedback from opening
/Users/abhinabadas/Downloads/OneDrive_1_4-7-2024/FlippedASU_RSR.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 72
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for FlippedASU_RSR.cif #2
---
Chain | Description
A B C | No description available
> close #1
> sym #2 h,1.237,89.594,20
Made 20 graphical clones for FlippedASU_RSR.cif symmetry h,1.237,89.594,20
> sym #3 h,1.237,89.594,20 copies true newModel true
No structures specified.
> sym #2 h,1.237,89.594,20 copies true newModel true
Made 20 copies for FlippedASU_RSR.cif symmetry h,1.237,89.594,20
> combine #1
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.2 to 'D'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.2 to 'E'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.2 to 'F'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.3 to 'G'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.3 to 'H'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.3 to 'I'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.4 to 'J'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.4 to 'K'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.4 to 'L'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.5 to 'M'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.5 to 'N'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.5 to 'O'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.6 to 'P'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.6 to 'Q'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.6 to 'R'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.7 to 'S'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.7 to 'T'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.7 to 'U'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.8 to 'V'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.8 to 'W'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.8 to 'X'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.9 to 'Y'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.9 to 'Z'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.9 to 'a'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.10 to 'b'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.10 to 'c'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.10 to 'd'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.11 to 'e'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.11 to 'f'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.11 to 'g'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.12 to 'h'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.12 to 'i'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.12 to 'j'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.13 to 'k'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.13 to 'l'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.13 to 'm'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.14 to 'n'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.14 to 'o'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.14 to 'p'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.15 to 'q'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.15 to 'r'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.15 to 's'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.16 to 't'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.16 to 'u'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.16 to 'v'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.17 to 'w'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.17 to 'x'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.17 to 'y'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.18 to 'z'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.18 to '1'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.18 to '2'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.19 to '3'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.19 to '4'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.19 to '5'
Remapping chain ID 'A' in FlippedASU_RSR.cif #1.20 to '6'
Remapping chain ID 'B' in FlippedASU_RSR.cif #1.20 to '7'
Remapping chain ID 'C' in FlippedASU_RSR.cif #1.20 to '8'
> hide #!1 models
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> addh #3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN93LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D56)
Kernel Version: Darwin 23.3.0
Time since boot: 3 days, 23 hours, 26 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
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: 2022.12.7
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-Clipper: 0.22.4
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-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
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
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-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
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
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: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
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: 21.3
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
setuptools-scm: 7.0.5
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 , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Abhi,
--Eric