Opened 22 months ago

Closed 22 months ago

Last modified 22 months ago

#14414 closed defect (can't reproduce)

Crash in garbage collection while rotating models

Reported by: bruno.haymele@… 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-6.1.0-5-amd64-x86_64-with-glibc2.37
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f9a51666740 (most recent call first):
  Garbage-collecting
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1487 in __init__
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2225 in process_changes
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 401 in _rotate
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 311 in mouse_drag
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 550 in _dispatch_mouse_event
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 651 in 
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/home/arfalas/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/home/arfalas/chimerax-1.7/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.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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 113)
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/arfalas/soondelete/caprok/struct/A0A6N1YHE5.pdb

A0A6N1YHE5.pdb title:  
A0A6N1YHE5 [more info...]  
  
Chain information for A0A6N1YHE5.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /home/arfalas/soondelete/caprok/struct/tmp/AF-A0A6N1YHE5-F1-model_v4.pdb

Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/tmp/AF-A0A6N1YHE5-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 722 UNP A0A6N1YHE5 A0A6N1YHE5_9BACT 1 722  
  
AF-A0A6N1YHE5-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A6N1YHE5) [more
info...]  
  
Chain information for AF-A0A6N1YHE5-F1-model_v4.pdb #2  
---  
Chain | Description  
A | carbonic anhydrase  
  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> display

> ~ribbon

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> open A0A6N1YHE5 fromDatabase alphafold

Summary of feedback from opening A0A6N1YHE5 fetched from alphafold  
---  
notes | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A0A6N1YHE5 from
https://alphafold.ebi.ac.uk/files/AF-A0A6N1YHE5-F1-model_v4.cif  
  
Chain information for AlphaFold A0A6N1YHE5 #3  
---  
Chain | Description | UniProt  
A | Carbonic anhydrase | A0A6N1YHE5_9BACT 1-722  
  
Color AlphaFold A0A6N1YHE5 by residue attribute pLDDT_score  

> open /home/arfalas/AF-A0A6N1YHE5-F1-model_v4.pdb
> /home/arfalas/AF-A0A379BC06-F1-model_v3.pdb

Summary of feedback from opening /home/arfalas/AF-A0A6N1YHE5-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 722 UNP A0A6N1YHE5 A0A6N1YHE5_9BACT 1 722  
  
Summary of feedback from opening /home/arfalas/AF-A0A379BC06-F1-model_v3.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 181 UNP A0A379BC06 A0A379BC06_PASMD 1 181  
  
AF-A0A6N1YHE5-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A6N1YHE5) [more
info...]  
  
Chain information for AF-A0A6N1YHE5-F1-model_v4.pdb #4  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A379BC06-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A379BC06) [more
info...]  
  
Chain information for AF-A0A379BC06-F1-model_v3.pdb #5  
---  
Chain | Description  
A | carbonic anhydrase  
  

> rename #2 api_AF-A0A6N1YHE5-F1-model_v4.pdb

> ~ribbon

> display

> hide #3 models

> hide #4 models

> hide #5 models

> hide #2 models

> show #2 models

> hide #1 models

> show #5 models

> hide #5 models

> show #4 models

> hide #2 models

> show #2 models

> hide #4 models

> show #4 models

> close #4

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> show #5 models

> show #2 models

> hide #2 models

> close #5

> show #3 models

> show #2 models

> hide #2 models

> show #2 models

> show #1 models

> hide #1 models

> hide #2 models

> hide #3 models

> show #1 models

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> mlp #1

Map values for surface "A0A6N1YHE5.pdb_A SES surface": minimum -27.95, mean
-14.86, maximum -2.551  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!1

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
A0A6N1YHE5.pdb #1/A MET 0  
A0A6N1YHE5.pdb #1/A LEU 1  
A0A6N1YHE5.pdb #1/A SER 2  
A0A6N1YHE5.pdb #1/A TYR 3  
A0A6N1YHE5.pdb #1/A LYS 4  
A0A6N1YHE5.pdb #1/A ALA 5  
A0A6N1YHE5.pdb #1/A ASN 6  
A0A6N1YHE5.pdb #1/A LEU 7  
A0A6N1YHE5.pdb #1/A ARG 8  
A0A6N1YHE5.pdb #1/A PHE 9  
A0A6N1YHE5.pdb #1/A ASP 10  
A0A6N1YHE5.pdb #1/A ILE 11  
A0A6N1YHE5.pdb #1/A PRO 12  
A0A6N1YHE5.pdb #1/A ALA 13  
A0A6N1YHE5.pdb #1/A SER 14  
A0A6N1YHE5.pdb #1/A LEU 15  
A0A6N1YHE5.pdb #1/A VAL 16  
A0A6N1YHE5.pdb #1/A VAL 17  
A0A6N1YHE5.pdb #1/A PHE 18  
A0A6N1YHE5.pdb #1/A LEU 19  
A0A6N1YHE5.pdb #1/A LEU 20  
A0A6N1YHE5.pdb #1/A ALA 21  
A0A6N1YHE5.pdb #1/A LEU 22  
A0A6N1YHE5.pdb #1/A PRO 23  
A0A6N1YHE5.pdb #1/A LEU 24  
A0A6N1YHE5.pdb #1/A CYS 25  
A0A6N1YHE5.pdb #1/A LEU 26  
A0A6N1YHE5.pdb #1/A VAL 28  
A0A6N1YHE5.pdb #1/A ALA 29  
A0A6N1YHE5.pdb #1/A LEU 30  
A0A6N1YHE5.pdb #1/A ALA 31  
A0A6N1YHE5.pdb #1/A SER 32  
A0A6N1YHE5.pdb #1/A ALA 34  
A0A6N1YHE5.pdb #1/A PRO 35  
A0A6N1YHE5.pdb #1/A LEU 36  
A0A6N1YHE5.pdb #1/A TYR 37  
A0A6N1YHE5.pdb #1/A ALA 38  
A0A6N1YHE5.pdb #1/A LEU 40  
A0A6N1YHE5.pdb #1/A ILE 41  
A0A6N1YHE5.pdb #1/A ALA 42  
A0A6N1YHE5.pdb #1/A VAL 44  
A0A6N1YHE5.pdb #1/A VAL 45  
A0A6N1YHE5.pdb #1/A LEU 48  
A0A6N1YHE5.pdb #1/A VAL 49  
A0A6N1YHE5.pdb #1/A VAL 50  
A0A6N1YHE5.pdb #1/A THR 51  
A0A6N1YHE5.pdb #1/A SER 52  
A0A6N1YHE5.pdb #1/A LEU 53  
A0A6N1YHE5.pdb #1/A SER 54  
A0A6N1YHE5.pdb #1/A ASP 55  
A0A6N1YHE5.pdb #1/A SER 56  
A0A6N1YHE5.pdb #1/A ALA 57  
A0A6N1YHE5.pdb #1/A LEU 58  
A0A6N1YHE5.pdb #1/A VAL 60  
A0A6N1YHE5.pdb #1/A THR 61  
A0A6N1YHE5.pdb #1/A PRO 63  
A0A6N1YHE5.pdb #1/A SER 64  
A0A6N1YHE5.pdb #1/A ALA 65  
A0A6N1YHE5.pdb #1/A LEU 67  
A0A6N1YHE5.pdb #1/A ALA 68  
A0A6N1YHE5.pdb #1/A MET 69  
A0A6N1YHE5.pdb #1/A ILE 70  
A0A6N1YHE5.pdb #1/A VAL 71  
A0A6N1YHE5.pdb #1/A PHE 72  
A0A6N1YHE5.pdb #1/A ALA 74  
A0A6N1YHE5.pdb #1/A ILE 75  
A0A6N1YHE5.pdb #1/A SER 76  
A0A6N1YHE5.pdb #1/A GLU 77  
A0A6N1YHE5.pdb #1/A LEU 78  
A0A6N1YHE5.pdb #1/A PHE 80  
A0A6N1YHE5.pdb #1/A GLU 81  
A0A6N1YHE5.pdb #1/A SER 82  
A0A6N1YHE5.pdb #1/A PHE 83  
A0A6N1YHE5.pdb #1/A LEU 84  
A0A6N1YHE5.pdb #1/A LEU 85  
A0A6N1YHE5.pdb #1/A ALA 86  
A0A6N1YHE5.pdb #1/A VAL 87  
A0A6N1YHE5.pdb #1/A ILE 88  
A0A6N1YHE5.pdb #1/A LEU 89  
A0A6N1YHE5.pdb #1/A ALA 90  
A0A6N1YHE5.pdb #1/A ILE 92  
A0A6N1YHE5.pdb #1/A ILE 93  
A0A6N1YHE5.pdb #1/A GLN 94  
A0A6N1YHE5.pdb #1/A PHE 95  
A0A6N1YHE5.pdb #1/A ILE 96  
A0A6N1YHE5.pdb #1/A MET 97  
A0A6N1YHE5.pdb #1/A LYS 99  
A0A6N1YHE5.pdb #1/A ILE 100  
A0A6N1YHE5.pdb #1/A THR 102  
A0A6N1YHE5.pdb #1/A VAL 104  
A0A6N1YHE5.pdb #1/A ILE 105  
A0A6N1YHE5.pdb #1/A TYR 107  
A0A6N1YHE5.pdb #1/A TYR 108  
A0A6N1YHE5.pdb #1/A PHE 109  
A0A6N1YHE5.pdb #1/A PRO 110  
A0A6N1YHE5.pdb #1/A SER 111  
A0A6N1YHE5.pdb #1/A ALA 112  
A0A6N1YHE5.pdb #1/A VAL 113  
A0A6N1YHE5.pdb #1/A ILE 114  
A0A6N1YHE5.pdb #1/A THR 115  
A0A6N1YHE5.pdb #1/A MET 117  
A0A6N1YHE5.pdb #1/A LEU 118  
A0A6N1YHE5.pdb #1/A SER 119  
A0A6N1YHE5.pdb #1/A ILE 121  
A0A6N1YHE5.pdb #1/A ILE 123  
A0A6N1YHE5.pdb #1/A ILE 124  
A0A6N1YHE5.pdb #1/A VAL 125  
A0A6N1YHE5.pdb #1/A PHE 126  
A0A6N1YHE5.pdb #1/A LEU 127  
A0A6N1YHE5.pdb #1/A LYS 128  
A0A6N1YHE5.pdb #1/A GLN 129  
A0A6N1YHE5.pdb #1/A ILE 130  
A0A6N1YHE5.pdb #1/A PRO 131  
A0A6N1YHE5.pdb #1/A HIS 132  
A0A6N1YHE5.pdb #1/A ALA 133  
A0A6N1YHE5.pdb #1/A ILE 134  
A0A6N1YHE5.pdb #1/A TYR 136  
A0A6N1YHE5.pdb #1/A ASP 137  
A0A6N1YHE5.pdb #1/A ARG 138  
A0A6N1YHE5.pdb #1/A ASP 139  
A0A6N1YHE5.pdb #1/A TYR 140  
A0A6N1YHE5.pdb #1/A GLU 141  
A0A6N1YHE5.pdb #1/A ASP 143  
A0A6N1YHE5.pdb #1/A ILE 144  
A0A6N1YHE5.pdb #1/A SER 145  
A0A6N1YHE5.pdb #1/A PHE 146  
A0A6N1YHE5.pdb #1/A PHE 147  
A0A6N1YHE5.pdb #1/A GLN 148  
A0A6N1YHE5.pdb #1/A SER 149  
A0A6N1YHE5.pdb #1/A ASP 150  
A0A6N1YHE5.pdb #1/A GLN 151  
A0A6N1YHE5.pdb #1/A TYR 152  
A0A6N1YHE5.pdb #1/A THR 153  
A0A6N1YHE5.pdb #1/A THR 154  
A0A6N1YHE5.pdb #1/A LEU 155  
A0A6N1YHE5.pdb #1/A THR 156  
A0A6N1YHE5.pdb #1/A GLU 157  
A0A6N1YHE5.pdb #1/A LEU 158  
A0A6N1YHE5.pdb #1/A GLN 159  
A0A6N1YHE5.pdb #1/A HIS 160  
A0A6N1YHE5.pdb #1/A MET 161  
A0A6N1YHE5.pdb #1/A LEU 162  
A0A6N1YHE5.pdb #1/A ASP 163  
A0A6N1YHE5.pdb #1/A PHE 164  
A0A6N1YHE5.pdb #1/A MET 165  
A0A6N1YHE5.pdb #1/A ALA 166  
A0A6N1YHE5.pdb #1/A PRO 167  
A0A6N1YHE5.pdb #1/A SER 168  
A0A6N1YHE5.pdb #1/A ALA 169  
A0A6N1YHE5.pdb #1/A ILE 170  
A0A6N1YHE5.pdb #1/A ILE 171  
A0A6N1YHE5.pdb #1/A ILE 172  
A0A6N1YHE5.pdb #1/A SER 173  
A0A6N1YHE5.pdb #1/A SER 174  
A0A6N1YHE5.pdb #1/A ILE 175  
A0A6N1YHE5.pdb #1/A CYS 176  
A0A6N1YHE5.pdb #1/A LEU 177  
A0A6N1YHE5.pdb #1/A LEU 178  
A0A6N1YHE5.pdb #1/A ILE 179  
A0A6N1YHE5.pdb #1/A LEU 180  
A0A6N1YHE5.pdb #1/A LEU 181  
A0A6N1YHE5.pdb #1/A LEU 182  
A0A6N1YHE5.pdb #1/A TRP 183  
A0A6N1YHE5.pdb #1/A GLU 184  
A0A6N1YHE5.pdb #1/A THR 185  
A0A6N1YHE5.pdb #1/A GLN 186  
A0A6N1YHE5.pdb #1/A TRP 187  
A0A6N1YHE5.pdb #1/A ILE 188  
A0A6N1YHE5.pdb #1/A LYS 189  
A0A6N1YHE5.pdb #1/A GLN 190  
A0A6N1YHE5.pdb #1/A TYR 191  
A0A6N1YHE5.pdb #1/A ARG 192  
A0A6N1YHE5.pdb #1/A PHE 193  
A0A6N1YHE5.pdb #1/A SER 194  
A0A6N1YHE5.pdb #1/A GLU 195  
A0A6N1YHE5.pdb #1/A SER 196  
A0A6N1YHE5.pdb #1/A LEU 197  
A0A6N1YHE5.pdb #1/A HIS 198  
A0A6N1YHE5.pdb #1/A ALA 200  
A0A6N1YHE5.pdb #1/A VAL 201  
A0A6N1YHE5.pdb #1/A VAL 202  
A0A6N1YHE5.pdb #1/A ALA 203  
A0A6N1YHE5.pdb #1/A VAL 204  
A0A6N1YHE5.pdb #1/A ILE 205  
A0A6N1YHE5.pdb #1/A VAL 206  
A0A6N1YHE5.pdb #1/A VAL 208  
A0A6N1YHE5.pdb #1/A VAL 209  
A0A6N1YHE5.pdb #1/A LEU 210  
A0A6N1YHE5.pdb #1/A ASN 211  
A0A6N1YHE5.pdb #1/A GLN 212  
A0A6N1YHE5.pdb #1/A VAL 213  
A0A6N1YHE5.pdb #1/A PHE 214  
A0A6N1YHE5.pdb #1/A ILE 215  
A0A6N1YHE5.pdb #1/A ALA 216  
A0A6N1YHE5.pdb #1/A PHE 217  
A0A6N1YHE5.pdb #1/A TYR 218  
A0A6N1YHE5.pdb #1/A PRO 219  
A0A6N1YHE5.pdb #1/A GLN 220  
A0A6N1YHE5.pdb #1/A TRP 221  
A0A6N1YHE5.pdb #1/A ALA 222  
A0A6N1YHE5.pdb #1/A LEU 223  
A0A6N1YHE5.pdb #1/A THR 224  
A0A6N1YHE5.pdb #1/A ASP 225  
A0A6N1YHE5.pdb #1/A LYS 226  
A0A6N1YHE5.pdb #1/A HIS 227  
A0A6N1YHE5.pdb #1/A LEU 228  
A0A6N1YHE5.pdb #1/A LEU 229  
A0A6N1YHE5.pdb #1/A VAL 230  
A0A6N1YHE5.pdb #1/A ILE 231  
A0A6N1YHE5.pdb #1/A PRO 232  
A0A6N1YHE5.pdb #1/A VAL 233  
A0A6N1YHE5.pdb #1/A VAL 234  
A0A6N1YHE5.pdb #1/A GLU 235  
A0A6N1YHE5.pdb #1/A THR 236  
A0A6N1YHE5.pdb #1/A LEU 237  
A0A6N1YHE5.pdb #1/A SER 238  
A0A6N1YHE5.pdb #1/A ASP 239  
A0A6N1YHE5.pdb #1/A LEU 240  
A0A6N1YHE5.pdb #1/A GLN 242  
A0A6N1YHE5.pdb #1/A VAL 243  
A0A6N1YHE5.pdb #1/A PHE 244  
A0A6N1YHE5.pdb #1/A THR 245  
A0A6N1YHE5.pdb #1/A PHE 246  
A0A6N1YHE5.pdb #1/A PRO 247  
A0A6N1YHE5.pdb #1/A ASN 248  
A0A6N1YHE5.pdb #1/A PHE 249  
A0A6N1YHE5.pdb #1/A SER 250  
A0A6N1YHE5.pdb #1/A GLN 251  
A0A6N1YHE5.pdb #1/A ILE 252  
A0A6N1YHE5.pdb #1/A ASN 253  
A0A6N1YHE5.pdb #1/A ASN 254  
A0A6N1YHE5.pdb #1/A PRO 255  
A0A6N1YHE5.pdb #1/A VAL 256  
A0A6N1YHE5.pdb #1/A ILE 257  
A0A6N1YHE5.pdb #1/A TYR 258  
A0A6N1YHE5.pdb #1/A HIS 259  
A0A6N1YHE5.pdb #1/A ILE 260  
A0A6N1YHE5.pdb #1/A ALA 261  
A0A6N1YHE5.pdb #1/A PHE 262  
A0A6N1YHE5.pdb #1/A MET 263  
A0A6N1YHE5.pdb #1/A ILE 264  
A0A6N1YHE5.pdb #1/A ALA 265  
A0A6N1YHE5.pdb #1/A ILE 266  
A0A6N1YHE5.pdb #1/A VAL 267  
A0A6N1YHE5.pdb #1/A ALA 268  
A0A6N1YHE5.pdb #1/A SER 269  
A0A6N1YHE5.pdb #1/A LEU 270  
A0A6N1YHE5.pdb #1/A GLU 271  
A0A6N1YHE5.pdb #1/A THR 272  
A0A6N1YHE5.pdb #1/A LEU 273  
A0A6N1YHE5.pdb #1/A LEU 274  
A0A6N1YHE5.pdb #1/A CYS 275  
A0A6N1YHE5.pdb #1/A VAL 276  
A0A6N1YHE5.pdb #1/A GLU 277  
A0A6N1YHE5.pdb #1/A ALA 278  
A0A6N1YHE5.pdb #1/A MET 279  
A0A6N1YHE5.pdb #1/A ASN 280  
A0A6N1YHE5.pdb #1/A LYS 281  
A0A6N1YHE5.pdb #1/A LEU 282  
A0A6N1YHE5.pdb #1/A ASP 283  
A0A6N1YHE5.pdb #1/A PRO 284  
A0A6N1YHE5.pdb #1/A TYR 285  
A0A6N1YHE5.pdb #1/A LYS 286  
A0A6N1YHE5.pdb #1/A ARG 287  
A0A6N1YHE5.pdb #1/A VAL 288  
A0A6N1YHE5.pdb #1/A THR 289  
A0A6N1YHE5.pdb #1/A SER 290  
A0A6N1YHE5.pdb #1/A ASN 291  
A0A6N1YHE5.pdb #1/A ASN 292  
A0A6N1YHE5.pdb #1/A ARG 293  
A0A6N1YHE5.pdb #1/A GLU 294  
A0A6N1YHE5.pdb #1/A LEU 295  
A0A6N1YHE5.pdb #1/A ARG 296  
A0A6N1YHE5.pdb #1/A ALA 297  
A0A6N1YHE5.pdb #1/A GLN 298  
A0A6N1YHE5.pdb #1/A ILE 300  
A0A6N1YHE5.pdb #1/A ASN 302  
A0A6N1YHE5.pdb #1/A ILE 303  
A0A6N1YHE5.pdb #1/A CYS 304  
A0A6N1YHE5.pdb #1/A SER 305  
A0A6N1YHE5.pdb #1/A LEU 307  
A0A6N1YHE5.pdb #1/A LEU 308  
A0A6N1YHE5.pdb #1/A LEU 311  
A0A6N1YHE5.pdb #1/A PRO 312  
A0A6N1YHE5.pdb #1/A MET 313  
A0A6N1YHE5.pdb #1/A THR 314  
A0A6N1YHE5.pdb #1/A GLN 315  
A0A6N1YHE5.pdb #1/A LEU 316  
A0A6N1YHE5.pdb #1/A ILE 317  
A0A6N1YHE5.pdb #1/A VAL 318  
A0A6N1YHE5.pdb #1/A ARG 319  
A0A6N1YHE5.pdb #1/A SER 320  
A0A6N1YHE5.pdb #1/A SER 321  
A0A6N1YHE5.pdb #1/A ALA 322  
A0A6N1YHE5.pdb #1/A ASN 323  
A0A6N1YHE5.pdb #1/A VAL 324  
A0A6N1YHE5.pdb #1/A GLN 325  
A0A6N1YHE5.pdb #1/A SER 326  
A0A6N1YHE5.pdb #1/A SER 328  
A0A6N1YHE5.pdb #1/A ARG 329  
A0A6N1YHE5.pdb #1/A THR 330  
A0A6N1YHE5.pdb #1/A LYS 331  
A0A6N1YHE5.pdb #1/A ALA 332  
A0A6N1YHE5.pdb #1/A SER 333  
A0A6N1YHE5.pdb #1/A ALA 334  
A0A6N1YHE5.pdb #1/A PHE 335  
A0A6N1YHE5.pdb #1/A MET 336  
A0A6N1YHE5.pdb #1/A GLN 337  
A0A6N1YHE5.pdb #1/A SER 338  
A0A6N1YHE5.pdb #1/A ILE 339  
A0A6N1YHE5.pdb #1/A PHE 340  
A0A6N1YHE5.pdb #1/A LEU 341  
A0A6N1YHE5.pdb #1/A LEU 342  
A0A6N1YHE5.pdb #1/A ILE 343  
A0A6N1YHE5.pdb #1/A ALA 344  
A0A6N1YHE5.pdb #1/A VAL 345  
A0A6N1YHE5.pdb #1/A LEU 346  
A0A6N1YHE5.pdb #1/A LEU 347  
A0A6N1YHE5.pdb #1/A VAL 348  
A0A6N1YHE5.pdb #1/A PRO 349  
A0A6N1YHE5.pdb #1/A LYS 350  
A0A6N1YHE5.pdb #1/A LEU 351  
A0A6N1YHE5.pdb #1/A ILE 352  
A0A6N1YHE5.pdb #1/A ASN 353  
A0A6N1YHE5.pdb #1/A LYS 354  
A0A6N1YHE5.pdb #1/A ILE 355  
A0A6N1YHE5.pdb #1/A PRO 356  
A0A6N1YHE5.pdb #1/A LEU 357  
A0A6N1YHE5.pdb #1/A SER 358  
A0A6N1YHE5.pdb #1/A SER 359  
A0A6N1YHE5.pdb #1/A LEU 360  
A0A6N1YHE5.pdb #1/A ALA 361  
A0A6N1YHE5.pdb #1/A ALA 362  
A0A6N1YHE5.pdb #1/A VAL 363  
A0A6N1YHE5.pdb #1/A PHE 364  
A0A6N1YHE5.pdb #1/A PHE 365  
A0A6N1YHE5.pdb #1/A VAL 366  
A0A6N1YHE5.pdb #1/A VAL 367  
A0A6N1YHE5.pdb #1/A ALA 368  
A0A6N1YHE5.pdb #1/A TYR 369  
A0A6N1YHE5.pdb #1/A LYS 370  
A0A6N1YHE5.pdb #1/A MET 371  
A0A6N1YHE5.pdb #1/A ALA 372  
A0A6N1YHE5.pdb #1/A ASN 373  
A0A6N1YHE5.pdb #1/A PRO 374  
A0A6N1YHE5.pdb #1/A LYS 375  
A0A6N1YHE5.pdb #1/A ARG 376  
A0A6N1YHE5.pdb #1/A PHE 377  
A0A6N1YHE5.pdb #1/A LYS 378  
A0A6N1YHE5.pdb #1/A THR 379  
A0A6N1YHE5.pdb #1/A LEU 380  
A0A6N1YHE5.pdb #1/A TYR 381  
A0A6N1YHE5.pdb #1/A GLN 382  
A0A6N1YHE5.pdb #1/A VAL 383  
A0A6N1YHE5.pdb #1/A SER 385  
A0A6N1YHE5.pdb #1/A TYR 386  
A0A6N1YHE5.pdb #1/A HIS 387  
A0A6N1YHE5.pdb #1/A PHE 388  
A0A6N1YHE5.pdb #1/A ILE 389  
A0A6N1YHE5.pdb #1/A PRO 390  
A0A6N1YHE5.pdb #1/A PHE 391  
A0A6N1YHE5.pdb #1/A ILE 392  
A0A6N1YHE5.pdb #1/A ALA 393  
A0A6N1YHE5.pdb #1/A THR 394  
A0A6N1YHE5.pdb #1/A ILE 395  
A0A6N1YHE5.pdb #1/A ILE 396  
A0A6N1YHE5.pdb #1/A LEU 398  
A0A6N1YHE5.pdb #1/A MET 399  
A0A6N1YHE5.pdb #1/A PHE 400  
A0A6N1YHE5.pdb #1/A SER 401  
A0A6N1YHE5.pdb #1/A ASP 402  
A0A6N1YHE5.pdb #1/A MET 403  
A0A6N1YHE5.pdb #1/A LEU 404  
A0A6N1YHE5.pdb #1/A THR 405  
A0A6N1YHE5.pdb #1/A PHE 407  
A0A6N1YHE5.pdb #1/A SER 408  
A0A6N1YHE5.pdb #1/A ILE 409  
A0A6N1YHE5.pdb #1/A MET 411  
A0A6N1YHE5.pdb #1/A CYS 413  
A0A6N1YHE5.pdb #1/A ALA 414  
A0A6N1YHE5.pdb #1/A LEU 415  
A0A6N1YHE5.pdb #1/A PHE 416  
A0A6N1YHE5.pdb #1/A PHE 417  
A0A6N1YHE5.pdb #1/A ILE 418  
A0A6N1YHE5.pdb #1/A LEU 419  
A0A6N1YHE5.pdb #1/A LEU 420  
A0A6N1YHE5.pdb #1/A GLU 421  
A0A6N1YHE5.pdb #1/A ASN 422  
A0A6N1YHE5.pdb #1/A LYS 423  
A0A6N1YHE5.pdb #1/A LYS 424  
A0A6N1YHE5.pdb #1/A LEU 425  
A0A6N1YHE5.pdb #1/A PHE 427  
A0A6N1YHE5.pdb #1/A HIS 428  
A0A6N1YHE5.pdb #1/A LEU 429  
A0A6N1YHE5.pdb #1/A HIS 430  
A0A6N1YHE5.pdb #1/A GLU 431  
A0A6N1YHE5.pdb #1/A GLN 432  
A0A6N1YHE5.pdb #1/A HIS 433  
A0A6N1YHE5.pdb #1/A HIS 435  
A0A6N1YHE5.pdb #1/A ASN 436  
A0A6N1YHE5.pdb #1/A LYS 437  
A0A6N1YHE5.pdb #1/A LYS 438  
A0A6N1YHE5.pdb #1/A ILE 439  
A0A6N1YHE5.pdb #1/A ILE 440  
A0A6N1YHE5.pdb #1/A THR 441  
A0A6N1YHE5.pdb #1/A LEU 442  
A0A6N1YHE5.pdb #1/A SER 443  
A0A6N1YHE5.pdb #1/A GLU 444  
A0A6N1YHE5.pdb #1/A ASN 445  
A0A6N1YHE5.pdb #1/A VAL 446  
A0A6N1YHE5.pdb #1/A SER 447  
A0A6N1YHE5.pdb #1/A PHE 448  
A0A6N1YHE5.pdb #1/A LEU 449  
A0A6N1YHE5.pdb #1/A ASN 450  
A0A6N1YHE5.pdb #1/A LYS 451  
A0A6N1YHE5.pdb #1/A SER 452  
A0A6N1YHE5.pdb #1/A ASN 453  
A0A6N1YHE5.pdb #1/A ILE 454  
A0A6N1YHE5.pdb #1/A LEU 455  
A0A6N1YHE5.pdb #1/A HIS 456  
A0A6N1YHE5.pdb #1/A LEU 457  
A0A6N1YHE5.pdb #1/A LEU 458  
A0A6N1YHE5.pdb #1/A SER 459  
A0A6N1YHE5.pdb #1/A GLU 460  
A0A6N1YHE5.pdb #1/A LEU 461  
A0A6N1YHE5.pdb #1/A PRO 462  
A0A6N1YHE5.pdb #1/A ARG 463  
A0A6N1YHE5.pdb #1/A ASN 464  
A0A6N1YHE5.pdb #1/A ALA 465  
A0A6N1YHE5.pdb #1/A ASN 466  
A0A6N1YHE5.pdb #1/A ILE 467  
A0A6N1YHE5.pdb #1/A VAL 468  
A0A6N1YHE5.pdb #1/A ILE 469  
A0A6N1YHE5.pdb #1/A ASP 470  
A0A6N1YHE5.pdb #1/A ALA 471  
A0A6N1YHE5.pdb #1/A THR 472  
A0A6N1YHE5.pdb #1/A TYR 473  
A0A6N1YHE5.pdb #1/A VAL 474  
A0A6N1YHE5.pdb #1/A LYS 475  
A0A6N1YHE5.pdb #1/A TYR 476  
A0A6N1YHE5.pdb #1/A ILE 477  
A0A6N1YHE5.pdb #1/A ASP 478  
A0A6N1YHE5.pdb #1/A TYR 479  
A0A6N1YHE5.pdb #1/A ASP 480  
A0A6N1YHE5.pdb #1/A VAL 481  
A0A6N1YHE5.pdb #1/A TYR 482  
A0A6N1YHE5.pdb #1/A GLU 483  
A0A6N1YHE5.pdb #1/A VAL 484  
A0A6N1YHE5.pdb #1/A ILE 485  
A0A6N1YHE5.pdb #1/A GLN 486  
A0A6N1YHE5.pdb #1/A ASN 487  
A0A6N1YHE5.pdb #1/A PHE 488  
A0A6N1YHE5.pdb #1/A LYS 489  
A0A6N1YHE5.pdb #1/A ILE 490  
A0A6N1YHE5.pdb #1/A ASP 491  
A0A6N1YHE5.pdb #1/A ALA 492  
A0A6N1YHE5.pdb #1/A LYS 493  
A0A6N1YHE5.pdb #1/A ARG 494  
A0A6N1YHE5.pdb #1/A LYS 495  
A0A6N1YHE5.pdb #1/A ILE 497  
A0A6N1YHE5.pdb #1/A ASN 498  
A0A6N1YHE5.pdb #1/A LEU 499  
A0A6N1YHE5.pdb #1/A VAL 500  
A0A6N1YHE5.pdb #1/A VAL 501  
A0A6N1YHE5.pdb #1/A GLN 502  
A0A6N1YHE5.pdb #1/A ASN 503  
A0A6N1YHE5.pdb #1/A LEU 504  
A0A6N1YHE5.pdb #1/A ARG 505  
A0A6N1YHE5.pdb #1/A PHE 507  
A0A6N1YHE5.pdb #1/A PHE 509  
A0A6N1YHE5.pdb #1/A LEU 510  
A0A6N1YHE5.pdb #1/A GLN 511  
A0A6N1YHE5.pdb #1/A PRO 512  
A0A6N1YHE5.pdb #1/A VAL 513  
A0A6N1YHE5.pdb #1/A GLU 514  
A0A6N1YHE5.pdb #1/A HIS 515  
A0A6N1YHE5.pdb #1/A VAL 516  
A0A6N1YHE5.pdb #1/A LEU 517  
A0A6N1YHE5.pdb #1/A PRO 518  
A0A6N1YHE5.pdb #1/A VAL 519  
A0A6N1YHE5.pdb #1/A SER 520  
A0A6N1YHE5.pdb #1/A GLN 521  
A0A6N1YHE5.pdb #1/A GLU 522  
A0A6N1YHE5.pdb #1/A SER 523  
A0A6N1YHE5.pdb #1/A GLN 524  
A0A6N1YHE5.pdb #1/A GLN 525  
A0A6N1YHE5.pdb #1/A LEU 526  
A0A6N1YHE5.pdb #1/A LEU 527  
A0A6N1YHE5.pdb #1/A THR 528  
A0A6N1YHE5.pdb #1/A PRO 529  
A0A6N1YHE5.pdb #1/A LYS 530  
A0A6N1YHE5.pdb #1/A ASP 531  
A0A6N1YHE5.pdb #1/A VAL 532  
A0A6N1YHE5.pdb #1/A LEU 533  
A0A6N1YHE5.pdb #1/A LYS 534  
A0A6N1YHE5.pdb #1/A ILE 535  
A0A6N1YHE5.pdb #1/A LEU 536  
A0A6N1YHE5.pdb #1/A GLN 537  
A0A6N1YHE5.pdb #1/A GLU 538  
A0A6N1YHE5.pdb #1/A ASN 540  
A0A6N1YHE5.pdb #1/A ASN 541  
A0A6N1YHE5.pdb #1/A ARG 542  
A0A6N1YHE5.pdb #1/A PHE 543  
A0A6N1YHE5.pdb #1/A VAL 544  
A0A6N1YHE5.pdb #1/A ASN 545  
A0A6N1YHE5.pdb #1/A SER 546  
A0A6N1YHE5.pdb #1/A ILE 547  
A0A6N1YHE5.pdb #1/A LYS 548  
A0A6N1YHE5.pdb #1/A ASN 549  
A0A6N1YHE5.pdb #1/A LYS 550  
A0A6N1YHE5.pdb #1/A ARG 551  
A0A6N1YHE5.pdb #1/A ASN 552  
A0A6N1YHE5.pdb #1/A LEU 553  
A0A6N1YHE5.pdb #1/A LEU 554  
A0A6N1YHE5.pdb #1/A SER 555  
A0A6N1YHE5.pdb #1/A GLN 556  
A0A6N1YHE5.pdb #1/A VAL 557  
A0A6N1YHE5.pdb #1/A ASN 558  
A0A6N1YHE5.pdb #1/A GLU 559  
A0A6N1YHE5.pdb #1/A THR 560  
A0A6N1YHE5.pdb #1/A VAL 561  
A0A6N1YHE5.pdb #1/A GLU 562  
A0A6N1YHE5.pdb #1/A GLN 564  
A0A6N1YHE5.pdb #1/A PHE 565  
A0A6N1YHE5.pdb #1/A PRO 566  
A0A6N1YHE5.pdb #1/A ILE 567  
A0A6N1YHE5.pdb #1/A ALA 568  
A0A6N1YHE5.pdb #1/A ILE 569  
A0A6N1YHE5.pdb #1/A ILE 570  
A0A6N1YHE5.pdb #1/A LEU 571  
A0A6N1YHE5.pdb #1/A SER 572  
A0A6N1YHE5.pdb #1/A CYS 573  
A0A6N1YHE5.pdb #1/A ILE 574  
A0A6N1YHE5.pdb #1/A ASP 575  
A0A6N1YHE5.pdb #1/A SER 576  
A0A6N1YHE5.pdb #1/A ARG 577  
A0A6N1YHE5.pdb #1/A THR 578  
A0A6N1YHE5.pdb #1/A SER 579  
A0A6N1YHE5.pdb #1/A ALA 580  
A0A6N1YHE5.pdb #1/A GLU 581  
A0A6N1YHE5.pdb #1/A LEU 582  
A0A6N1YHE5.pdb #1/A ILE 583  
A0A6N1YHE5.pdb #1/A PHE 584  
A0A6N1YHE5.pdb #1/A ASP 585  
A0A6N1YHE5.pdb #1/A GLN 586  
A0A6N1YHE5.pdb #1/A LEU 588  
A0A6N1YHE5.pdb #1/A ASP 590  
A0A6N1YHE5.pdb #1/A VAL 591  
A0A6N1YHE5.pdb #1/A PHE 592  
A0A6N1YHE5.pdb #1/A SER 593  
A0A6N1YHE5.pdb #1/A VAL 594  
A0A6N1YHE5.pdb #1/A ARG 595  
A0A6N1YHE5.pdb #1/A VAL 596  
A0A6N1YHE5.pdb #1/A ALA 597  
A0A6N1YHE5.pdb #1/A ASN 599  
A0A6N1YHE5.pdb #1/A VAL 600  
A0A6N1YHE5.pdb #1/A VAL 601  
A0A6N1YHE5.pdb #1/A ASN 602  
A0A6N1YHE5.pdb #1/A ASP 603  
A0A6N1YHE5.pdb #1/A ASP 604  
A0A6N1YHE5.pdb #1/A ILE 605  
A0A6N1YHE5.pdb #1/A LEU 606  
A0A6N1YHE5.pdb #1/A SER 608  
A0A6N1YHE5.pdb #1/A MET 609  
A0A6N1YHE5.pdb #1/A GLU 610  
A0A6N1YHE5.pdb #1/A TYR 611  
A0A6N1YHE5.pdb #1/A ALA 612  
A0A6N1YHE5.pdb #1/A CYS 613  
A0A6N1YHE5.pdb #1/A LYS 614  
A0A6N1YHE5.pdb #1/A VAL 615  
A0A6N1YHE5.pdb #1/A ALA 616  
A0A6N1YHE5.pdb #1/A SER 618  
A0A6N1YHE5.pdb #1/A LYS 619  
A0A6N1YHE5.pdb #1/A LEU 620  
A0A6N1YHE5.pdb #1/A VAL 621  
A0A6N1YHE5.pdb #1/A VAL 622  
A0A6N1YHE5.pdb #1/A VAL 623  
A0A6N1YHE5.pdb #1/A LEU 624  
A0A6N1YHE5.pdb #1/A HIS 626  
A0A6N1YHE5.pdb #1/A THR 627  
A0A6N1YHE5.pdb #1/A HIS 628  
A0A6N1YHE5.pdb #1/A CYS 629  
A0A6N1YHE5.pdb #1/A ALA 631  
A0A6N1YHE5.pdb #1/A ILE 632  
A0A6N1YHE5.pdb #1/A LYS 633  
A0A6N1YHE5.pdb #1/A ALA 635  
A0A6N1YHE5.pdb #1/A CYS 636  
A0A6N1YHE5.pdb #1/A ALA 637  
A0A6N1YHE5.pdb #1/A ILE 639  
A0A6N1YHE5.pdb #1/A GLU 640  
A0A6N1YHE5.pdb #1/A LEU 641  
A0A6N1YHE5.pdb #1/A ASN 643  
A0A6N1YHE5.pdb #1/A LEU 644  
A0A6N1YHE5.pdb #1/A THR 645  
A0A6N1YHE5.pdb #1/A LEU 647  
A0A6N1YHE5.pdb #1/A LEU 648  
A0A6N1YHE5.pdb #1/A ASP 649  
A0A6N1YHE5.pdb #1/A LYS 650  
A0A6N1YHE5.pdb #1/A ILE 651  
A0A6N1YHE5.pdb #1/A GLN 652  
A0A6N1YHE5.pdb #1/A PRO 653  
A0A6N1YHE5.pdb #1/A ALA 654  
A0A6N1YHE5.pdb #1/A VAL 655  
A0A6N1YHE5.pdb #1/A LYS 656  
A0A6N1YHE5.pdb #1/A ALA 657  
A0A6N1YHE5.pdb #1/A VAL 658  
A0A6N1YHE5.pdb #1/A LYS 659  
A0A6N1YHE5.pdb #1/A ALA 660  
A0A6N1YHE5.pdb #1/A ASP 662  
A0A6N1YHE5.pdb #1/A PHE 663  
A0A6N1YHE5.pdb #1/A ALA 664  
A0A6N1YHE5.pdb #1/A LYS 665  
A0A6N1YHE5.pdb #1/A ASN 666  
A0A6N1YHE5.pdb #1/A SER 667  
A0A6N1YHE5.pdb #1/A LEU 668  
A0A6N1YHE5.pdb #1/A LYS 669  
A0A6N1YHE5.pdb #1/A SER 670  
A0A6N1YHE5.pdb #1/A SER 671  
A0A6N1YHE5.pdb #1/A CYS 672  
A0A6N1YHE5.pdb #1/A LEU 673  
A0A6N1YHE5.pdb #1/A GLU 674  
A0A6N1YHE5.pdb #1/A ASP 675  
A0A6N1YHE5.pdb #1/A LYS 676  
A0A6N1YHE5.pdb #1/A VAL 677  
A0A6N1YHE5.pdb #1/A ALA 678  
A0A6N1YHE5.pdb #1/A GLU 679  
A0A6N1YHE5.pdb #1/A ARG 680  
A0A6N1YHE5.pdb #1/A ASN 681  
A0A6N1YHE5.pdb #1/A VAL 682  
A0A6N1YHE5.pdb #1/A GLU 683  
A0A6N1YHE5.pdb #1/A ILE 684  
A0A6N1YHE5.pdb #1/A MET 685  
A0A6N1YHE5.pdb #1/A VAL 686  
A0A6N1YHE5.pdb #1/A GLN 687  
A0A6N1YHE5.pdb #1/A GLU 688  
A0A6N1YHE5.pdb #1/A VAL 689  
A0A6N1YHE5.pdb #1/A LYS 690  
A0A6N1YHE5.pdb #1/A GLN 691  
A0A6N1YHE5.pdb #1/A ARG 692  
A0A6N1YHE5.pdb #1/A SER 693  
A0A6N1YHE5.pdb #1/A PRO 694  
A0A6N1YHE5.pdb #1/A LEU 695  
A0A6N1YHE5.pdb #1/A LEU 696  
A0A6N1YHE5.pdb #1/A GLN 697  
A0A6N1YHE5.pdb #1/A ALA 698  
A0A6N1YHE5.pdb #1/A MET 699  
A0A6N1YHE5.pdb #1/A GLN 700  
A0A6N1YHE5.pdb #1/A ILE 701  
A0A6N1YHE5.pdb #1/A ALA 702  
A0A6N1YHE5.pdb #1/A ASP 704  
A0A6N1YHE5.pdb #1/A ILE 705  
A0A6N1YHE5.pdb #1/A ASP 706  
A0A6N1YHE5.pdb #1/A ILE 707  
A0A6N1YHE5.pdb #1/A VAL 708  
A0A6N1YHE5.pdb #1/A SER 709  
A0A6N1YHE5.pdb #1/A ALA 710  
A0A6N1YHE5.pdb #1/A MET 711  
A0A6N1YHE5.pdb #1/A TYR 712  
A0A6N1YHE5.pdb #1/A ASN 713  
A0A6N1YHE5.pdb #1/A ILE 714  
A0A6N1YHE5.pdb #1/A GLU 715  
A0A6N1YHE5.pdb #1/A THR 716  
A0A6N1YHE5.pdb #1/A LYS 718  
A0A6N1YHE5.pdb #1/A VAL 719  
A0A6N1YHE5.pdb #1/A GLU 720  
A0A6N1YHE5.pdb #1/A PHE 721  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for A0A6N1YHE5.pdb_A SES surface #1.1: minimum, -31.48, mean
-15.31, maximum 0.02  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!1

Map values for surface "A0A6N1YHE5.pdb_A SES surface": minimum -27.95, mean
-14.86, maximum -2.551  
To also show corresponding color key, enter the above mlp command and add key
true  

> close #2-3

Alignment identifier is 1/A  

> show surfaces

> close all

> open 8h96 format mmcif fromDatabase pdb

8h96 title:  
Structure of mouse SCMC core complex [more info...]  
  
Chain information for 8h96 #1  
---  
Chain | Description | UniProt  
A | NACHT, LRR and PYD domains-containing protein 5 | NALP5_MOUSE 1-1059  
B | Transducin-like enhancer protein 6 | TLE6_MOUSE 1-581  
C | Oocyte-expressed protein homolog | OOEP_MOUSE 1-164  
  

> show surfaces

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A VAL 113  
/A HIS 116  
/A TYR 117  
/A MET 209  
/A ASP 309  
/A ASP 485  
/A VAL 613  
/A VAL 614  
/A THR 615  
/A GLU 618  
/A THR 619  
/A CYS 621  
/A ASN 1059  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 8h96_A SES surface #1.2: minimum, -33.64, mean -1.60,
maximum 12.97  
Coulombic values for 8h96_B SES surface #1.3: minimum, -18.61, mean -0.88,
maximum 11.47  
Coulombic values for 8h96_C SES surface #1.4: minimum, -24.60, mean -2.15,
maximum 6.82  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close all

> open
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A540WRI1-F1-model_v4.pdb

Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A540WRI1-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 39  
DBREF XXXX A 1 141 UNP A0A540WRI1 A0A540WRI1_9DELT 1 141  
  
AF-A0A540WRI1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for nuclear transport factor 2 family
protein (A0A540WRI1) [more info...]  
  
Chain information for AF-A0A540WRI1-F1-model_v4.pdb #1  
---  
Chain | Description  
A | nuclear transport factor 2 family protein  
  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-A0A540WRI1-F1-model_v4.pdb_A SES surface #1.1:
minimum, -12.45, mean -2.76, maximum 7.73  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close all

> open
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A540WRI1-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A1M7JX82-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A0U5AYH9-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-K9RUZ0-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A840RIJ8-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A366LA26-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A081B7B5-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A7C4ZG00-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A399UN83-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A7C5WEH9-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A0S8F5L8-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A3Q9V2P9-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A0R0F016-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-K3WH40-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A6N1YHE5-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A522XIS3-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A379BC06-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-W4FGD0-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-K8CLP3-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A7U8HCL8-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A372RUN1-F1-model_v4.pdb
> /home/arfalas/soondelete/caprok/struct/reps/AF-A0A094ICH2-F1-model_v4.pdb

Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A540WRI1-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 39  
DBREF XXXX A 1 141 UNP A0A540WRI1 A0A540WRI1_9DELT 1 141  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A1M7JX82-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 168 UNP A0A1M7JX82 A0A1M7JX82_9FLAO 1 168  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A0U5AYH9-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 154 UNP A0A0U5AYH9 A0A0U5AYH9_9BACT 1 154  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A840RIJ8-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 40  
DBREF XXXX A 1 197 UNP A0A840RIJ8 A0A840RIJ8_9NEIS 1 197  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A366LA26-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 177 UNP A0A366LA26 A0A366LA26_9SPHI 1 177  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A081B7B5-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 174 UNP A0A081B7B5 A0A081B7B5_9HYPH 1 174  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A7C4ZG00-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 165 UNP A0A7C4ZG00 A0A7C4ZG00_9DEIN 1 165  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A399UN83-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 205 UNP A0A399UN83 A0A399UN83_9ACTN 1 205  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A7C5WEH9-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 210 UNP A0A7C5WEH9 A0A7C5WEH9_9PROT 1 210  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A0S8F5L8-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 475 UNP A0A0S8F5L8 A0A0S8F5L8_9GAMM 1 475  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A3Q9V2P9-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 234 UNP A0A3Q9V2P9 A0A3Q9V2P9_9MICO 1 234  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A0R0F016-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 241 UNP A0A0R0F016 A0A0R0F016_SOYBN 1 241  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A6N1YHE5-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 722 UNP A0A6N1YHE5 A0A6N1YHE5_9BACT 1 722  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A522XIS3-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 273 UNP A0A522XIS3 A0A522XIS3_9CYAN 1 273  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A379BC06-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 181 UNP A0A379BC06 A0A379BC06_PASMD 1 181  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A7U8HCL8-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 256 UNP A0A7U8HCL8 A0A7U8HCL8_BURML 1 256  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A372RUN1-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 239 UNP A0A372RUN1 A0A372RUN1_9GLOM 1 239  
  
Summary of feedback from opening
/home/arfalas/soondelete/caprok/struct/reps/AF-A0A094ICH2-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 214 UNP A0A094ICH2 A0A094ICH2_9PEZI 1 214  
  
AF-A0A540WRI1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for nuclear transport factor 2 family
protein (A0A540WRI1) [more info...]  
  
Chain information for AF-A0A540WRI1-F1-model_v4.pdb #1  
---  
Chain | Description  
A | nuclear transport factor 2 family protein  
  
AF-A0A1M7JX82-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (A0A1M7JX82)
[more info...]  
  
Chain information for AF-A0A1M7JX82-F1-model_v4.pdb #2  
---  
Chain | Description  
A | uncharacterized protein  
  
AF-A0A0U5AYH9-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (A0A0U5AYH9)
[more info...]  
  
Chain information for AF-A0A0U5AYH9-F1-model_v4.pdb #3  
---  
Chain | Description  
A | uncharacterized protein  
  
AF-K9RUZ0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbon dioxide concentrating mechanism
protein CCMM (K9RUZ0) [more info...]  
  
Chain information for AF-K9RUZ0-F1-model_v4.pdb #4  
---  
Chain | Description | UniProt  
A | carbon dioxide concentrating mechanism protein CCMM | K9RUZ0_SYNP3 1-656  
  
AF-A0A840RIJ8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase/acetyltransferase-
like protein (isoleucine patch superfamily) (A0A840RIJ8) [more info...]  
  
Chain information for AF-A0A840RIJ8-F1-model_v4.pdb #5  
---  
Chain | Description  
A | carbonic anhydrase/acetyltransferase-like protein (isoleucine patch
superfamily)  
  
AF-A0A366LA26-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for antibiotic acetyltransferase
(A0A366LA26) [more info...]  
  
Chain information for AF-A0A366LA26-F1-model_v4.pdb #6  
---  
Chain | Description  
A | antibiotic acetyltransferase  
  
AF-A0A081B7B5-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for hexapaptide repeat-containing
transferase (A0A081B7B5) [more info...]  
  
Chain information for AF-A0A081B7B5-F1-model_v4.pdb #7  
---  
Chain | Description  
A | hexapaptide repeat-containing transferase  
  
AF-A0A7C4ZG00-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (A0A7C4ZG00)
[more info...]  
  
Chain information for AF-A0A7C4ZG00-F1-model_v4.pdb #8  
---  
Chain | Description  
A | uncharacterized protein  
  
AF-A0A399UN83-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A399UN83) [more
info...]  
  
Chain information for AF-A0A399UN83-F1-model_v4.pdb #9  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A7C5WEH9-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carboxysome shell protein (A0A7C5WEH9)
[more info...]  
  
Chain information for AF-A0A7C5WEH9-F1-model_v4.pdb #10  
---  
Chain | Description  
A | carboxysome shell protein  
  
AF-A0A0S8F5L8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A0S8F5L8) [more
info...]  
  
Chain information for AF-A0A0S8F5L8-F1-model_v4.pdb #11  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A3Q9V2P9-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A3Q9V2P9) [more
info...]  
  
Chain information for AF-A0A3Q9V2P9-F1-model_v4.pdb #12  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A0R0F016-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A0R0F016) [more
info...]  
  
Chain information for AF-A0A0R0F016-F1-model_v4.pdb #13  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-K3WH40-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (K3WH40) [more
info...]  
  
Chain information for AF-K3WH40-F1-model_v4.pdb #14  
---  
Chain | Description | UniProt  
A | carbonic anhydrase | K3WH40_GLOUD 1-305  
  
AF-A0A6N1YHE5-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A6N1YHE5) [more
info...]  
  
Chain information for AF-A0A6N1YHE5-F1-model_v4.pdb #15  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A522XIS3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A522XIS3) [more
info...]  
  
Chain information for AF-A0A522XIS3-F1-model_v4.pdb #16  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A379BC06-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A379BC06) [more
info...]  
  
Chain information for AF-A0A379BC06-F1-model_v4.pdb #17  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-W4FGD0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (W4FGD0) [more
info...]  
  
Chain information for AF-W4FGD0-F1-model_v4.pdb #18  
---  
Chain | Description | UniProt  
A | carbonic anhydrase | W4FGD0_9STRA 1-176  
  
AF-K8CLP3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (K8CLP3) [more
info...]  
  
Chain information for AF-K8CLP3-F1-model_v4.pdb #19  
---  
Chain | Description | UniProt  
A | carbonic anhydrase | K8CLP3_CROSK 1-108  
  
AF-A0A7U8HCL8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A7U8HCL8) [more
info...]  
  
Chain information for AF-A0A7U8HCL8-F1-model_v4.pdb #20  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A372RUN1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for carbonic anhydrase (A0A372RUN1) [more
info...]  
  
Chain information for AF-A0A372RUN1-F1-model_v4.pdb #21  
---  
Chain | Description  
A | carbonic anhydrase  
  
AF-A0A094ICH2-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for α-carbonic anhydrase domain-containing
protein (A0A094ICH2) [more info...]  
  
Chain information for AF-A0A094ICH2-F1-model_v4.pdb #22  
---  
Chain | Description  
A | α-carbonic anhydrase domain-containing protein  
  

> tile

22 models tiled  

> show surfaces


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.2 (Core Profile) Mesa 23.3.3-1
OpenGL renderer: Mesa Intel(R) HD Graphics 4000 (IVB GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: it_IT.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=tty
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=:0
Manufacturer: LENOVO
Model: 232566G
OS: Debian GNU/Linux n/a trixie
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz
Cache Size: 4096 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       7.4Gi       3.0Gi       415Mi       5.6Gi       7.9Gi
	Swap:             0B          0B          0B

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation 3rd Gen Core processor Graphics Controller [8086:0166] (rev 09)	
	Subsystem: Lenovo 3rd Gen Core processor Graphics Controller [17aa:21fa]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-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: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (4)

comment:1 by Eric Pettersen, 22 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection while rotating models

comment:2 by Eric Pettersen, 22 months ago

Resolution: → can't reproduce
Status: accepted → closed

Hi Bruno,

Thanks for reporting this problem. It is typically difficult for us to debug garbage-collection problems, because garbage collection isn't something that ChimeraX calls directly but instead Python calls it whenever it feels it's appropriate. Nonetheless, we will try to do what we can to try to track this down and fix it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by bruno.haymele@…, 22 months ago 

On 19/01/24 22:24, ChimeraX wrote:



Thanks! To be honest, I was not expecting any feedback: I 
semi-automatically sent the report. If it could be of any help, I ended 
up accidentally rotating thirty-something tiled structures on an old [1] 
Debian machine [2] using the latest ChimeraX [3].

do not worry too much!

comment:4 by Eric Pettersen, 22 months ago

Well, every little bit of info helps, but this crash has happened to lots of people that weren't necessarily rotating models at the time, so the root cause is something else unfortunately.

--Eric

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