id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15078	Crash handling text input	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.1-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.
Fatal Python error: Segmentation fault

Current thread 0x00000001d6e59ec0 (most recent call first):
  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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group (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/rennayi/Downloads/Consurf_Outputs_1713995616/AF-C9RDV1-F1-model_v4copy.2_With_Conservation_Scores.pdb

AF-C9RDV1-F1-model_v4copy.2_With_Conservation_Scores.pdb title:  
Alphafold monomer V2.0 prediction for 4FE-4S ferredoxin iron-sulfur binding
domain protein (C9RDV1) [more info...]  
  
Chain information for AF-C9RDV1-F1-model_v4copy.2_With_Conservation_Scores.pdb
#1  
---  
Chain | Description | UniProt  
A | 4FE-4S ferredoxin iron-sulfur binding domain protein | C9RDV1_METVM 1-62  
  

> color bfactor

455 atoms, 62 residues, atom bfactor range -1.83 to 1.4  

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/AF-C9RDV1-F1-model_v4copy.2abs.pdb

AF-C9RDV1-F1-model_v4copy.2abs.pdb title:  
Alphafold monomer V2.0 prediction for 4FE-4S ferredoxin iron-sulfur binding
domain protein (C9RDV1) [more info...]  
  
Chain information for AF-C9RDV1-F1-model_v4copy.2abs.pdb #2  
---  
Chain | Description | UniProt  
A | 4FE-4S ferredoxin iron-sulfur binding domain protein | C9RDV1_METVM 1-62  
  

> hide #1 models

> color bfactor #2

455 atoms, 62 residues, atom bfactor range 0.095 to 4.01  

> ui tool show ""Render by Attribute""

> key blue-white-red :-1.83 :1.09 :4.01 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute a:bfactor #1-2 target cabs palette
> -1.826,blue:1.092,white:4.01,red

910 atoms, 124 residues, atom bfactor range -1.83 to 4.01  

> hide #2 models

> show #1 models

> show #1 surfaces

> color bfactor #!1

455 atoms, 62 residues, 1 surfaces, atom bfactor range -1.83 to 1.4  

> hide #!1 models

> show #2 models

> show #2 surfaces

> color bfactor #!2

455 atoms, 62 residues, 1 surfaces, atom bfactor range 0.095 to 4.01  

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> save c9rdv1conserv.png

> show #!1 models

> hide #!2 models

> save c9rdv1shannon.png

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view

> hide #!1 models

> close session

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/AF-C5A3R4-F1-model_v4change2-3.pdb

AF-C5A3R4-F1-model_v4change2-3.pdb title:  
Alphafold monomer V2.0 prediction for ferredoxin (C5A3R4) [more info...]  
  
Chain information for AF-C5A3R4-F1-model_v4change2-3.pdb #1  
---  
Chain | Description | UniProt  
A | ferredoxin | C5A3R4_THEGJ 1-63  
  

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/AF-A8A8X1-F1-model_v4change1-2.pdb

AF-A8A8X1-F1-model_v4change1-2.pdb title:  
Alphafold monomer V2.0 prediction for ferredoxin (A8A8X1) [more info...]  
  
Chain information for AF-A8A8X1-F1-model_v4change1-2.pdb #2  
---  
Chain | Description | UniProt  
A | ferredoxin | A8A8X1_IGNH4 1-79  
  

> color bfactor

1071 atoms, 142 residues, atom bfactor range -0.47 to 0.236  

> ui tool show ""Render by Attribute""

> key blue-white-red :-0.470 :-0.117 :0.236 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute a:bfactor #1-2 target cabs palette
> -0.47,blue:-0.117,white:0.236,red

1071 atoms, 142 residues, atom bfactor range -0.47 to 0.236  

> show surfaces

> ui tool show ""Render by Attribute""

> key blue-white-red :-0.470 :-0.117 :0.236 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute a:bfactor #!1-2 target cabs palette
> -0.47,blue:-0.117,white:0.236,red

1071 atoms, 142 residues, 2 surfaces, atom bfactor range -0.47 to 0.236  

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #2

> close

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g1rep.2.pdb
> /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g2rep.2.pdb

g1rep.2.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g1rep.2.pdb #1  
---  
Chain | Description  
A | No description available  
  
g2rep.2.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g2rep.2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> show surfaces

> ui tool show ""Render by Attribute""

> key blue-white-red :-0.510 :-0.068 :0.374 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute a:bfactor #!1-2 target cabs palette
> -0.51,blue:-0.068,white:0.374,red

1665 atoms, 224 residues, 2 surfaces, atom bfactor range -0.51 to 0.374  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker g1rep.2.pdb, chain A (#1) with g2rep.2.pdb, chain A (#2), sequence
alignment score = 74.3  
RMSD between 16 pruned atom pairs is 0.820 angstroms; (across all 63 pairs:
16.181)  
  

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> view

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g3rep.2abs.pdb
> /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g2rep.2abs.pdb
> /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g1rep.2abs.pdb

g3rep.2abs.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g3rep.2abs.pdb #4  
---  
Chain | Description  
A | No description available  
  
g2rep.2abs.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g2rep.2abs.pdb #5  
---  
Chain | Description  
A | No description available  
  
g1rep.2abs.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g1rep.2abs.pdb #6  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #5-6 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker g3rep.2abs.pdb, chain A (#4) with g2rep.2abs.pdb, chain A (#5),
sequence alignment score = 63.4  
RMSD between 36 pruned atom pairs is 0.915 angstroms; (across all 83 pairs:
18.306)  
  
Matchmaker g3rep.2abs.pdb, chain A (#4) with g1rep.2abs.pdb, chain A (#6),
sequence alignment score = 67.7  
RMSD between 50 pruned atom pairs is 1.043 angstroms; (across all 96 pairs:
19.952)  
  

> ui tool show Contacts

> contacts interModel false intraRes true ignoreHiddenModels true

1436 contacts  

> contacts interModel false intraRes true ignoreHiddenModels true

1436 contacts  

> hide #4 models

> hide #5 models

> ui tool show H-Bonds

> hbonds interModel false twoColors true reveal true

231 hydrogen bonds found  
109 strict hydrogen bonds found  

> show #!5 models

> hide #!6 models

> ui tool show H-Bonds

> hbonds interModel false twoColors true reveal true

231 hydrogen bonds found  
109 strict hydrogen bonds found  

> show #!4 models

> hide #!5 models

> ui tool show H-Bonds

> hbonds interModel false twoColors true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 g1rep.2.pdb
    	2 g2rep.2.pdb
    	4 g3rep.2abs.pdb
    	5 g2rep.2abs.pdb
    	6 g1rep.2abs.pdb
    
    231 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    g1rep.2.pdb #1/A ARG 11 N        g1rep.2.pdb #1/A GLU 63 O       no hydrogen  2.447  N/A
    g1rep.2.pdb #1/A TYR 12 OH       g1rep.2.pdb #1/A VAL 39 O       no hydrogen  2.663  N/A
    g1rep.2.pdb #1/A HIS 13 N        g1rep.2.pdb #1/A ALA 61 O       no hydrogen  2.699  N/A
    g1rep.2.pdb #1/A GLU 15 N        g1rep.2.pdb #1/A GLU 15 OE1     no hydrogen  2.536  N/A
    g1rep.2.pdb #1/A ARG 16 N        g1rep.2.pdb #1/A HIS 13 O       no hydrogen  3.031  N/A
    g1rep.2.pdb #1/A ARG 16 NH1      g1rep.2.pdb #1/A GLN 60 O       no hydrogen  3.468  N/A
    g1rep.2.pdb #1/A CYS 17 N        g1rep.2.pdb #1/A PRO 14 O       no hydrogen  3.094  N/A
    g1rep.2.pdb #1/A CYS 17 SG       g1rep.2.pdb #1/A TYR 12 OH      no hydrogen  3.383  N/A
    g1rep.2.pdb #1/A ASN 19 ND2      g1rep.2.pdb #1/A GLY 35 O       no hydrogen  3.460  N/A
    g1rep.2.pdb #1/A ILE 24 N        g1rep.2.pdb #1/A ARG 21 O       no hydrogen  2.935  N/A
    g1rep.2.pdb #1/A GLU 25 N        g1rep.2.pdb #1/A ARG 21 O       no hydrogen  3.129  N/A
    g1rep.2.pdb #1/A VAL 26 N        g1rep.2.pdb #1/A ARG 22 O       no hydrogen  2.909  N/A
    g1rep.2.pdb #1/A ALA 33 N        g1rep.2.pdb #1/A ALA 40 O       no hydrogen  2.787  N/A
    g1rep.2.pdb #1/A ALA 40 N        g1rep.2.pdb #1/A ALA 33 O       no hydrogen  2.841  N/A
    g1rep.2.pdb #1/A VAL 42 N        g1rep.2.pdb #1/A VAL 31 O       no hydrogen  2.808  N/A
    g1rep.2.pdb #1/A SER 43 N        g1rep.2.pdb #1/A VAL 31 O       no hydrogen  3.118  N/A
    g1rep.2.pdb #1/A GLU 45 N        g1rep.2.pdb #1/A GLU 45 OE1     no hydrogen  2.572  N/A
    g1rep.2.pdb #1/A ARG 46 N        g1rep.2.pdb #1/A SER 43 O       no hydrogen  3.039  N/A
    g1rep.2.pdb #1/A CYS 47 N        g1rep.2.pdb #1/A PRO 44 O       no hydrogen  2.840  N/A
    g1rep.2.pdb #1/A ARG 55 N        g1rep.2.pdb #1/A GLY 51 O       no hydrogen  3.054  N/A
    g1rep.2.pdb #1/A ARG 55 NH1      g1rep.2.pdb #1/A CYS 50 O       no hydrogen  3.448  N/A
    g1rep.2.pdb #1/A ARG 55 NH2      g1rep.2.pdb #1/A CYS 50 O       no hydrogen  3.179  N/A
    g1rep.2.pdb #1/A ASN 56 N        g1rep.2.pdb #1/A ALA 52 O       no hydrogen  3.134  N/A
    g1rep.2.pdb #1/A ASN 56 ND2      g1rep.2.pdb #1/A ALA 52 O       no hydrogen  2.960  N/A
    g1rep.2.pdb #1/A CYS 57 N        g1rep.2.pdb #1/A ALA 54 O       no hydrogen  3.213  N/A
    g1rep.2.pdb #1/A GLN 60 N        g1rep.2.pdb #1/A CYS 57 O       no hydrogen  3.303  N/A
    g1rep.2.pdb #1/A GLU 63 N        g1rep.2.pdb #1/A ARG 11 O       no hydrogen  2.595  N/A
    g1rep.2.pdb #1/A GLU 65 N        g1rep.2.pdb #1/A THR 9 O        no hydrogen  2.403  N/A
    g1rep.2.pdb #1/A ILE 75 N        g1rep.2.pdb #1/A ALA 71 O       no hydrogen  2.782  N/A
    g1rep.2.pdb #1/A GLY 76 N        g1rep.2.pdb #1/A TRP 72 O       no hydrogen  2.516  N/A
    g1rep.2.pdb #1/A ALA 77 N        g1rep.2.pdb #1/A ALA 73 O       no hydrogen  2.752  N/A
    g1rep.2.pdb #1/A ALA 78 N        g1rep.2.pdb #1/A MET 74 O       no hydrogen  2.731  N/A
    g1rep.2.pdb #1/A LEU 79 N        g1rep.2.pdb #1/A ILE 75 O       no hydrogen  2.515  N/A
    g1rep.2.pdb #1/A ARG 80 N        g1rep.2.pdb #1/A GLY 76 O       no hydrogen  2.919  N/A
    g1rep.2.pdb #1/A ARG 80 N        g1rep.2.pdb #1/A ALA 77 O       no hydrogen  3.200  N/A
    g1rep.2.pdb #1/A GLY 81 N        g1rep.2.pdb #1/A ALA 78 O       no hydrogen  2.992  N/A
    g1rep.2.pdb #1/A LYS 82 NZ       g1rep.2.pdb #1/A ASN 56 OD1     no hydrogen  3.094  N/A
    g1rep.2.pdb #1/A GLY 87 N        g1rep.2.pdb #1/A MET 84 O       no hydrogen  2.603  N/A
    g1rep.2.pdb #1/A GLY 94 N        g1rep.2.pdb #1/A CYS 91 O       no hydrogen  3.383  N/A
    g1rep.2.pdb #1/A SER 95 N        g1rep.2.pdb #1/A ASP 93 OD1     no hydrogen  3.011  N/A
    g1rep.2.pdb #1/A SER 95 OG       g1rep.2.pdb #1/A ASP 93 OD1     no hydrogen  2.628  N/A
    g1rep.2.pdb #1/A SER 95 OG       g1rep.2.pdb #1/A ASP 93 OD2     no hydrogen  3.385  N/A
    g1rep.2.pdb #1/A CYS 96 SG       g1rep.2.pdb #1/A GLY 69 O       no hydrogen  2.356  N/A
    g1rep.2.pdb #1/A GLU 102 N       g1rep.2.pdb #1/A GLY 100 O      no hydrogen  2.199  N/A
    g2rep.2.pdb #2/A VAL 5 N         g2rep.2.pdb #2/A MET 1 O        no hydrogen  2.386  N/A
    g2rep.2.pdb #2/A HIS 6 N         g2rep.2.pdb #2/A CYS 2 O        no hydrogen  2.701  N/A
    g2rep.2.pdb #2/A GLY 7 N         g2rep.2.pdb #2/A MET 3 O        no hydrogen  2.894  N/A
    g2rep.2.pdb #2/A ALA 10 N        g2rep.2.pdb #2/A GLY 7 O        no hydrogen  2.751  N/A
    g2rep.2.pdb #2/A ILE 13 N        g2rep.2.pdb #2/A PRO 11 O       no hydrogen  2.922  N/A
    g2rep.2.pdb #2/A LYS 21 N        g2rep.2.pdb #2/A LYS 18 O       no hydrogen  3.210  N/A
    g2rep.2.pdb #2/A LYS 23 N        g2rep.2.pdb #2/A SER 16 O       no hydrogen  2.547  N/A
    g2rep.2.pdb #2/A ASN 25 N        g2rep.2.pdb #2/A PHE 14 O       no hydrogen  3.131  N/A
    g2rep.2.pdb #2/A LYS 35 N        g2rep.2.pdb #2/A GLY 31 O       no hydrogen  3.139  N/A
    g2rep.2.pdb #2/A VAL 36 N        g2rep.2.pdb #2/A ILE 32 O       no hydrogen  3.206  N/A
    g2rep.2.pdb #2/A ILE 43 N        g2rep.2.pdb #2/A VAL 50 O       no hydrogen  2.840  N/A
    g2rep.2.pdb #2/A VAL 45 N        g2rep.2.pdb #2/A ALA 48 O       no hydrogen  2.741  N/A
    g2rep.2.pdb #2/A ALA 48 N        g2rep.2.pdb #2/A VAL 45 O       no hydrogen  2.906  N/A
    g2rep.2.pdb #2/A PHE 49 N        g2rep.2.pdb #2/A GLN 29 OE1     no hydrogen  2.547  N/A
    g2rep.2.pdb #2/A VAL 50 N        g2rep.2.pdb #2/A ILE 43 O       no hydrogen  2.698  N/A
    g2rep.2.pdb #2/A ASP 52 N        g2rep.2.pdb #2/A ALA 41 O       no hydrogen  2.652  N/A
    g2rep.2.pdb #2/A SER 54 N        g2rep.2.pdb #2/A ASP 52 OD1     no hydrogen  2.933  N/A
    g2rep.2.pdb #2/A SER 54 OG       g2rep.2.pdb #2/A ASP 52 OD1     no hydrogen  2.583  N/A
    g2rep.2.pdb #2/A SER 54 OG       g2rep.2.pdb #2/A ASP 52 OD2     no hydrogen  3.224  N/A
    g2rep.2.pdb #2/A VAL 55 N        g2rep.2.pdb #2/A ASP 52 O       no hydrogen  3.073  N/A
    g2rep.2.pdb #2/A CYS 56 N        g2rep.2.pdb #2/A ASP 52 O       no hydrogen  3.251  N/A
    g2rep.2.pdb #2/A CYS 56 N        g2rep.2.pdb #2/A PRO 53 O       no hydrogen  3.348  N/A
    g2rep.2.pdb #2/A TYR 64 N        g2rep.2.pdb #2/A LYS 60 O       no hydrogen  3.102  N/A
    g2rep.2.pdb #2/A LEU 65 N        g2rep.2.pdb #2/A MET 61 O       no hydrogen  3.017  N/A
    g2rep.2.pdb #2/A GLY 69 N        g2rep.2.pdb #2/A CYS 66 O       no hydrogen  3.299  N/A
    g2rep.2.pdb #2/A GLU 72 N        g2rep.2.pdb #2/A GLN 86 O       no hydrogen  2.648  N/A
    g2rep.2.pdb #2/A VAL 74 N        g2rep.2.pdb #2/A VAL 84 O       no hydrogen  2.835  N/A
    g2rep.2.pdb #2/A VAL 76 N        g2rep.2.pdb #2/A ASP 82 O       no hydrogen  3.082  N/A
    g2rep.2.pdb #2/A ARG 79 NH1      g2rep.2.pdb #2/A PRO 53 O       no hydrogen  2.397  N/A
    g2rep.2.pdb #2/A VAL 84 N        g2rep.2.pdb #2/A VAL 74 O       no hydrogen  2.811  N/A
    g2rep.2.pdb #2/A GLN 86 N        g2rep.2.pdb #2/A GLU 72 O       no hydrogen  2.548  N/A
    g2rep.2.pdb #2/A LYS 87 NZ       g2rep.2.pdb #2/A PHE 49 O       no hydrogen  2.144  N/A
    g2rep.2.pdb #2/A LYS 92 N        g2rep.2.pdb #2/A ASP 89 O       no hydrogen  3.019  N/A
    g2rep.2.pdb #2/A ARG 94 N        g2rep.2.pdb #2/A CYS 91 O       no hydrogen  3.126  N/A
    g2rep.2.pdb #2/A VAL 101 N       g2rep.2.pdb #2/A PRO 98 O       no hydrogen  2.871  N/A
    g2rep.2.pdb #2/A LYS 102 N       g2rep.2.pdb #2/A PRO 98 O       no hydrogen  3.116  N/A
    g2rep.2.pdb #2/A VAL 103 N       g2rep.2.pdb #2/A ALA 99 O       no hydrogen  2.887  N/A
    g2rep.2.pdb #2/A CYS 104 N       g2rep.2.pdb #2/A CYS 100 O      no hydrogen  3.083  N/A
    g2rep.2.pdb #2/A ALA 108 N       g2rep.2.pdb #2/A LYS 105 O      no hydrogen  3.036  N/A
    g3rep.2abs.pdb #4/A VAL 2 N      g3rep.2abs.pdb #4/A THR 66 O    no hydrogen  2.783  N/A
    g3rep.2abs.pdb #4/A ARG 4 N      g3rep.2abs.pdb #4/A ARG 64 O    no hydrogen  3.227  N/A
    g3rep.2abs.pdb #4/A ARG 4 NE     g3rep.2abs.pdb #4/A VAL 67 O    no hydrogen  2.746  N/A
    g3rep.2abs.pdb #4/A ARG 4 NH1    g3rep.2abs.pdb #4/A CYS 44 O    no hydrogen  2.570  N/A
    g3rep.2abs.pdb #4/A ARG 4 NH2    g3rep.2abs.pdb #4/A GLU 41 O    no hydrogen  2.192  N/A
    g3rep.2abs.pdb #4/A ILE 6 N      g3rep.2abs.pdb #4/A GLU 62 O    no hydrogen  2.758  N/A
    g3rep.2abs.pdb #4/A LYS 8 N      g3rep.2abs.pdb #4/A SER 60 O    no hydrogen  2.744  N/A
    g3rep.2abs.pdb #4/A ASP 10 N     g3rep.2abs.pdb #4/A ALA 58 O    no hydrogen  2.643  N/A
    g3rep.2abs.pdb #4/A GLU 12 N     g3rep.2abs.pdb #4/A ASP 10 OD1  no hydrogen  3.051  N/A
    g3rep.2abs.pdb #4/A LYS 13 N     g3rep.2abs.pdb #4/A ASP 10 O    no hydrogen  2.996  N/A
    g3rep.2abs.pdb #4/A CYS 14 N     g3rep.2abs.pdb #4/A ASP 10 O    no hydrogen  3.018  N/A
    g3rep.2abs.pdb #4/A VAL 21 N     g3rep.2abs.pdb #4/A GLY 18 O    no hydrogen  3.074  N/A
    g3rep.2abs.pdb #4/A CYS 24 N     g3rep.2abs.pdb #4/A VAL 21 O    no hydrogen  3.112  N/A
    g3rep.2abs.pdb #4/A GLY 27 N     g3rep.2abs.pdb #4/A CYS 24 O    no hydrogen  3.109  N/A
    g3rep.2abs.pdb #4/A GLN 30 N     g3rep.2abs.pdb #4/A LYS 37 O    no hydrogen  2.990  N/A
    g3rep.2abs.pdb #4/A ILE 32 N     g3rep.2abs.pdb #4/A LYS 35 O    no hydrogen  2.879  N/A
    g3rep.2abs.pdb #4/A LYS 35 N     g3rep.2abs.pdb #4/A ILE 32 O    no hydrogen  3.218  N/A
    g3rep.2abs.pdb #4/A LYS 35 NZ    g3rep.2abs.pdb #4/A GLU 11 O    no hydrogen  3.148  N/A
    g3rep.2abs.pdb #4/A LYS 35 NZ    g3rep.2abs.pdb #4/A CYS 14 O    no hydrogen  2.343  N/A
    g3rep.2abs.pdb #4/A LYS 37 N     g3rep.2abs.pdb #4/A GLN 30 O    no hydrogen  2.736  N/A
    g3rep.2abs.pdb #4/A LYS 37 NZ    g3rep.2abs.pdb #4/A GLU 11 OE2  no hydrogen  1.408  N/A
    g3rep.2abs.pdb #4/A VAL 39 N     g3rep.2abs.pdb #4/A ALA 28 O    no hydrogen  2.819  N/A
    g3rep.2abs.pdb #4/A GLU 42 N     g3rep.2abs.pdb #4/A SER 40 OG   no hydrogen  3.264  N/A
    g3rep.2abs.pdb #4/A LEU 43 N     g3rep.2abs.pdb #4/A SER 40 O    no hydrogen  3.039  N/A
    g3rep.2abs.pdb #4/A CYS 44 N     g3rep.2abs.pdb #4/A GLU 41 O    no hydrogen  3.288  N/A
    g3rep.2abs.pdb #4/A MET 47 N     g3rep.2abs.pdb #4/A ASP 45 OD1  no hydrogen  3.008  N/A
    g3rep.2abs.pdb #4/A ILE 51 N     g3rep.2abs.pdb #4/A GLY 48 O    no hydrogen  3.072  N/A
    g3rep.2abs.pdb #4/A CYS 54 N     g3rep.2abs.pdb #4/A ILE 51 O    no hydrogen  3.262  N/A
    g3rep.2abs.pdb #4/A GLY 57 N     g3rep.2abs.pdb #4/A CYS 54 O    no hydrogen  3.272  N/A
    g3rep.2abs.pdb #4/A SER 60 N     g3rep.2abs.pdb #4/A LYS 8 O     no hydrogen  2.887  N/A
    g3rep.2abs.pdb #4/A GLU 62 N     g3rep.2abs.pdb #4/A ILE 6 O     no hydrogen  2.858  N/A
    g3rep.2abs.pdb #4/A ARG 64 N     g3rep.2abs.pdb #4/A ARG 4 O     no hydrogen  3.165  N/A
    g3rep.2abs.pdb #4/A THR 66 N     g3rep.2abs.pdb #4/A VAL 2 O     no hydrogen  2.959  N/A
    g3rep.2abs.pdb #4/A THR 66 OG1   g3rep.2abs.pdb #4/A GLU 41 OE1  no hydrogen  2.074  N/A
    g3rep.2abs.pdb #4/A VAL 67 N     g3rep.2abs.pdb #4/A THR 66 OG1  no hydrogen  2.490  N/A
    g3rep.2abs.pdb #4/A ASN 70 N     g3rep.2abs.pdb #4/A GLU 42 O    no hydrogen  2.971  N/A
    g3rep.2abs.pdb #4/A LYS 73 N     g3rep.2abs.pdb #4/A ASN 70 OD1  no hydrogen  3.006  N/A
    g3rep.2abs.pdb #4/A LYS 73 NZ    g3rep.2abs.pdb #4/A GLU 42 OE1  no hydrogen  3.002  N/A
    g3rep.2abs.pdb #4/A THR 74 N     g3rep.2abs.pdb #4/A ASN 70 O    no hydrogen  3.132  N/A
    g3rep.2abs.pdb #4/A THR 74 OG1   g3rep.2abs.pdb #4/A ARG 71 O    no hydrogen  2.414  N/A
    g3rep.2abs.pdb #4/A GLU 75 N     g3rep.2abs.pdb #4/A ARG 71 O    no hydrogen  3.006  N/A
    g3rep.2abs.pdb #4/A ALA 76 N     g3rep.2abs.pdb #4/A GLU 72 O    no hydrogen  3.045  N/A
    g3rep.2abs.pdb #4/A ALA 76 N     g3rep.2abs.pdb #4/A LYS 73 O    no hydrogen  3.179  N/A
    g3rep.2abs.pdb #4/A GLN 77 N     g3rep.2abs.pdb #4/A THR 74 O    no hydrogen  3.120  N/A
    g3rep.2abs.pdb #4/A GLN 77 NE2   g3rep.2abs.pdb #4/A LYS 73 O    no hydrogen  3.696  N/A
    g3rep.2abs.pdb #4/A LYS 80 NZ    g3rep.2abs.pdb #4/A CYS 24 O    no hydrogen  3.386  N/A
    g3rep.2abs.pdb #4/A ASP 82 N     g3rep.2abs.pdb #4/A LYS 79 O    no hydrogen  3.111  N/A
    g3rep.2abs.pdb #4/A ILE 83 N     g3rep.2abs.pdb #4/A LYS 80 O    no hydrogen  2.856  N/A
    g3rep.2abs.pdb #4/A ARG 86 NH1   g3rep.2abs.pdb #4/A GLY 91 O    no hydrogen  3.163  N/A
    g3rep.2abs.pdb #4/A CYS 87 N     g3rep.2abs.pdb #4/A ALA 92 O    no hydrogen  2.830  N/A
    g3rep.2abs.pdb #4/A PHE 88 N     g3rep.2abs.pdb #4/A TRP 110 O   no hydrogen  2.484  N/A
    g3rep.2abs.pdb #4/A GLY 91 N     g3rep.2abs.pdb #4/A CYS 87 O    no hydrogen  2.980  N/A
    g3rep.2abs.pdb #4/A HIS 97 NE2   g3rep.2abs.pdb #4/A ALA 92 O    no hydrogen  3.214  N/A
    g3rep.2abs.pdb #4/A TYR 98 N     g3rep.2abs.pdb #4/A VAL 111 O   no hydrogen  2.629  N/A
    g3rep.2abs.pdb #4/A LEU 100 N    g3rep.2abs.pdb #4/A ILE 109 O   no hydrogen  2.948  N/A
    g3rep.2abs.pdb #4/A LEU 102 N    g3rep.2abs.pdb #4/A GLU 107 O   no hydrogen  3.020  N/A
    g3rep.2abs.pdb #4/A ILE 109 N    g3rep.2abs.pdb #4/A LEU 100 O   no hydrogen  3.115  N/A
    g3rep.2abs.pdb #4/A VAL 111 N    g3rep.2abs.pdb #4/A TYR 98 O    no hydrogen  2.770  N/A
    g3rep.2abs.pdb #4/A ARG 114 NH2  g3rep.2abs.pdb #4/A GLU 94 OE2  no hydrogen  1.888  N/A
    g3rep.2abs.pdb #4/A CYS 115 N    g3rep.2abs.pdb #4/A CYS 112 O   no hydrogen  3.090  N/A
    g3rep.2abs.pdb #4/A LEU 116 N    g3rep.2abs.pdb #4/A CYS 112 O   no hydrogen  2.972  N/A
    g3rep.2abs.pdb #4/A LEU 119 N    g3rep.2abs.pdb #4/A CYS 115 O   no hydrogen  3.062  N/A
    g3rep.2abs.pdb #4/A LEU 119 N    g3rep.2abs.pdb #4/A LEU 116 O   no hydrogen  3.094  N/A
    g3rep.2abs.pdb #4/A ILE 120 N    g3rep.2abs.pdb #4/A LEU 116 O   no hydrogen  2.962  N/A
    g3rep.2abs.pdb #4/A HIS 121 N    g3rep.2abs.pdb #4/A PRO 117 O   no hydrogen  2.877  N/A
    g2rep.2abs.pdb #5/A VAL 5 N      g2rep.2abs.pdb #5/A MET 1 O     no hydrogen  2.386  N/A
    g2rep.2abs.pdb #5/A HIS 6 N      g2rep.2abs.pdb #5/A CYS 2 O     no hydrogen  2.701  N/A
    g2rep.2abs.pdb #5/A GLY 7 N      g2rep.2abs.pdb #5/A MET 3 O     no hydrogen  2.894  N/A
    g2rep.2abs.pdb #5/A ALA 10 N     g2rep.2abs.pdb #5/A GLY 7 O     no hydrogen  2.751  N/A
    g2rep.2abs.pdb #5/A ILE 13 N     g2rep.2abs.pdb #5/A PRO 11 O    no hydrogen  2.922  N/A
    g2rep.2abs.pdb #5/A LYS 21 N     g2rep.2abs.pdb #5/A LYS 18 O    no hydrogen  3.210  N/A
    g2rep.2abs.pdb #5/A LYS 23 N     g2rep.2abs.pdb #5/A SER 16 O    no hydrogen  2.547  N/A
    g2rep.2abs.pdb #5/A ASN 25 N     g2rep.2abs.pdb #5/A PHE 14 O    no hydrogen  3.131  N/A
    g2rep.2abs.pdb #5/A LYS 35 N     g2rep.2abs.pdb #5/A GLY 31 O    no hydrogen  3.139  N/A
    g2rep.2abs.pdb #5/A VAL 36 N     g2rep.2abs.pdb #5/A ILE 32 O    no hydrogen  3.206  N/A
    g2rep.2abs.pdb #5/A ILE 43 N     g2rep.2abs.pdb #5/A VAL 50 O    no hydrogen  2.840  N/A
    g2rep.2abs.pdb #5/A VAL 45 N     g2rep.2abs.pdb #5/A ALA 48 O    no hydrogen  2.741  N/A
    g2rep.2abs.pdb #5/A ALA 48 N     g2rep.2abs.pdb #5/A VAL 45 O    no hydrogen  2.906  N/A
    g2rep.2abs.pdb #5/A PHE 49 N     g2rep.2abs.pdb #5/A GLN 29 OE1  no hydrogen  2.547  N/A
    g2rep.2abs.pdb #5/A VAL 50 N     g2rep.2abs.pdb #5/A ILE 43 O    no hydrogen  2.698  N/A
    g2rep.2abs.pdb #5/A ASP 52 N     g2rep.2abs.pdb #5/A ALA 41 O    no hydrogen  2.652  N/A
    g2rep.2abs.pdb #5/A SER 54 N     g2rep.2abs.pdb #5/A ASP 52 OD1  no hydrogen  2.933  N/A
    g2rep.2abs.pdb #5/A SER 54 OG    g2rep.2abs.pdb #5/A ASP 52 OD1  no hydrogen  2.583  N/A
    g2rep.2abs.pdb #5/A SER 54 OG    g2rep.2abs.pdb #5/A ASP 52 OD2  no hydrogen  3.224  N/A
    g2rep.2abs.pdb #5/A VAL 55 N     g2rep.2abs.pdb #5/A ASP 52 O    no hydrogen  3.073  N/A
    g2rep.2abs.pdb #5/A CYS 56 N     g2rep.2abs.pdb #5/A ASP 52 O    no hydrogen  3.251  N/A
    g2rep.2abs.pdb #5/A CYS 56 N     g2rep.2abs.pdb #5/A PRO 53 O    no hydrogen  3.348  N/A
    g2rep.2abs.pdb #5/A TYR 64 N     g2rep.2abs.pdb #5/A LYS 60 O    no hydrogen  3.102  N/A
    g2rep.2abs.pdb #5/A LEU 65 N     g2rep.2abs.pdb #5/A MET 61 O    no hydrogen  3.017  N/A
    g2rep.2abs.pdb #5/A GLY 69 N     g2rep.2abs.pdb #5/A CYS 66 O    no hydrogen  3.299  N/A
    g2rep.2abs.pdb #5/A GLU 72 N     g2rep.2abs.pdb #5/A GLN 86 O    no hydrogen  2.648  N/A
    g2rep.2abs.pdb #5/A VAL 74 N     g2rep.2abs.pdb #5/A VAL 84 O    no hydrogen  2.835  N/A
    g2rep.2abs.pdb #5/A VAL 76 N     g2rep.2abs.pdb #5/A ASP 82 O    no hydrogen  3.082  N/A
    g2rep.2abs.pdb #5/A ARG 79 NH1   g2rep.2abs.pdb #5/A PRO 53 O    no hydrogen  2.397  N/A
    g2rep.2abs.pdb #5/A VAL 84 N     g2rep.2abs.pdb #5/A VAL 74 O    no hydrogen  2.811  N/A
    g2rep.2abs.pdb #5/A GLN 86 N     g2rep.2abs.pdb #5/A GLU 72 O    no hydrogen  2.548  N/A
    g2rep.2abs.pdb #5/A LYS 87 NZ    g2rep.2abs.pdb #5/A PHE 49 O    no hydrogen  2.144  N/A
    g2rep.2abs.pdb #5/A LYS 92 N     g2rep.2abs.pdb #5/A ASP 89 O    no hydrogen  3.019  N/A
    g2rep.2abs.pdb #5/A ARG 94 N     g2rep.2abs.pdb #5/A CYS 91 O    no hydrogen  3.126  N/A
    g2rep.2abs.pdb #5/A VAL 101 N    g2rep.2abs.pdb #5/A PRO 98 O    no hydrogen  2.871  N/A
    g2rep.2abs.pdb #5/A LYS 102 N    g2rep.2abs.pdb #5/A PRO 98 O    no hydrogen  3.116  N/A
    g2rep.2abs.pdb #5/A VAL 103 N    g2rep.2abs.pdb #5/A ALA 99 O    no hydrogen  2.887  N/A
    g2rep.2abs.pdb #5/A CYS 104 N    g2rep.2abs.pdb #5/A CYS 100 O   no hydrogen  3.083  N/A
    g2rep.2abs.pdb #5/A ALA 108 N    g2rep.2abs.pdb #5/A LYS 105 O   no hydrogen  3.036  N/A
    g1rep.2abs.pdb #6/A ARG 11 N     g1rep.2abs.pdb #6/A GLU 63 O    no hydrogen  2.447  N/A
    g1rep.2abs.pdb #6/A TYR 12 OH    g1rep.2abs.pdb #6/A VAL 39 O    no hydrogen  2.663  N/A
    g1rep.2abs.pdb #6/A HIS 13 N     g1rep.2abs.pdb #6/A ALA 61 O    no hydrogen  2.699  N/A
    g1rep.2abs.pdb #6/A GLU 15 N     g1rep.2abs.pdb #6/A GLU 15 OE1  no hydrogen  2.536  N/A
    g1rep.2abs.pdb #6/A ARG 16 N     g1rep.2abs.pdb #6/A HIS 13 O    no hydrogen  3.031  N/A
    g1rep.2abs.pdb #6/A ARG 16 NH1   g1rep.2abs.pdb #6/A GLN 60 O    no hydrogen  3.468  N/A
    g1rep.2abs.pdb #6/A CYS 17 N     g1rep.2abs.pdb #6/A PRO 14 O    no hydrogen  3.094  N/A
    g1rep.2abs.pdb #6/A CYS 17 SG    g1rep.2abs.pdb #6/A TYR 12 OH   no hydrogen  3.383  N/A
    g1rep.2abs.pdb #6/A ASN 19 ND2   g1rep.2abs.pdb #6/A GLY 35 O    no hydrogen  3.460  N/A
    g1rep.2abs.pdb #6/A ILE 24 N     g1rep.2abs.pdb #6/A ARG 21 O    no hydrogen  2.935  N/A
    g1rep.2abs.pdb #6/A GLU 25 N     g1rep.2abs.pdb #6/A ARG 21 O    no hydrogen  3.129  N/A
    g1rep.2abs.pdb #6/A VAL 26 N     g1rep.2abs.pdb #6/A ARG 22 O    no hydrogen  2.909  N/A
    g1rep.2abs.pdb #6/A ALA 33 N     g1rep.2abs.pdb #6/A ALA 40 O    no hydrogen  2.787  N/A
    g1rep.2abs.pdb #6/A ALA 40 N     g1rep.2abs.pdb #6/A ALA 33 O    no hydrogen  2.841  N/A
    g1rep.2abs.pdb #6/A VAL 42 N     g1rep.2abs.pdb #6/A VAL 31 O    no hydrogen  2.808  N/A
    g1rep.2abs.pdb #6/A SER 43 N     g1rep.2abs.pdb #6/A VAL 31 O    no hydrogen  3.118  N/A
    g1rep.2abs.pdb #6/A GLU 45 N     g1rep.2abs.pdb #6/A GLU 45 OE1  no hydrogen  2.572  N/A
    g1rep.2abs.pdb #6/A ARG 46 N     g1rep.2abs.pdb #6/A SER 43 O    no hydrogen  3.039  N/A
    g1rep.2abs.pdb #6/A CYS 47 N     g1rep.2abs.pdb #6/A PRO 44 O    no hydrogen  2.840  N/A
    g1rep.2abs.pdb #6/A ARG 55 N     g1rep.2abs.pdb #6/A GLY 51 O    no hydrogen  3.054  N/A
    g1rep.2abs.pdb #6/A ARG 55 NH1   g1rep.2abs.pdb #6/A CYS 50 O    no hydrogen  3.448  N/A
    g1rep.2abs.pdb #6/A ARG 55 NH2   g1rep.2abs.pdb #6/A CYS 50 O    no hydrogen  3.179  N/A
    g1rep.2abs.pdb #6/A ASN 56 N     g1rep.2abs.pdb #6/A ALA 52 O    no hydrogen  3.134  N/A
    g1rep.2abs.pdb #6/A ASN 56 ND2   g1rep.2abs.pdb #6/A ALA 52 O    no hydrogen  2.960  N/A
    g1rep.2abs.pdb #6/A CYS 57 N     g1rep.2abs.pdb #6/A ALA 54 O    no hydrogen  3.213  N/A
    g1rep.2abs.pdb #6/A GLN 60 N     g1rep.2abs.pdb #6/A CYS 57 O    no hydrogen  3.303  N/A
    g1rep.2abs.pdb #6/A GLU 63 N     g1rep.2abs.pdb #6/A ARG 11 O    no hydrogen  2.595  N/A
    g1rep.2abs.pdb #6/A GLU 65 N     g1rep.2abs.pdb #6/A THR 9 O     no hydrogen  2.403  N/A
    g1rep.2abs.pdb #6/A ILE 75 N     g1rep.2abs.pdb #6/A ALA 71 O    no hydrogen  2.782  N/A
    g1rep.2abs.pdb #6/A GLY 76 N     g1rep.2abs.pdb #6/A TRP 72 O    no hydrogen  2.516  N/A
    g1rep.2abs.pdb #6/A ALA 77 N     g1rep.2abs.pdb #6/A ALA 73 O    no hydrogen  2.752  N/A
    g1rep.2abs.pdb #6/A ALA 78 N     g1rep.2abs.pdb #6/A MET 74 O    no hydrogen  2.731  N/A
    g1rep.2abs.pdb #6/A LEU 79 N     g1rep.2abs.pdb #6/A ILE 75 O    no hydrogen  2.515  N/A
    g1rep.2abs.pdb #6/A ARG 80 N     g1rep.2abs.pdb #6/A GLY 76 O    no hydrogen  2.919  N/A
    g1rep.2abs.pdb #6/A ARG 80 N     g1rep.2abs.pdb #6/A ALA 77 O    no hydrogen  3.200  N/A
    g1rep.2abs.pdb #6/A GLY 81 N     g1rep.2abs.pdb #6/A ALA 78 O    no hydrogen  2.992  N/A
    g1rep.2abs.pdb #6/A LYS 82 NZ    g1rep.2abs.pdb #6/A ASN 56 OD1  no hydrogen  3.094  N/A
    g1rep.2abs.pdb #6/A GLY 87 N     g1rep.2abs.pdb #6/A MET 84 O    no hydrogen  2.603  N/A
    g1rep.2abs.pdb #6/A GLY 94 N     g1rep.2abs.pdb #6/A CYS 91 O    no hydrogen  3.383  N/A
    g1rep.2abs.pdb #6/A SER 95 N     g1rep.2abs.pdb #6/A ASP 93 OD1  no hydrogen  3.011  N/A
    g1rep.2abs.pdb #6/A SER 95 OG    g1rep.2abs.pdb #6/A ASP 93 OD1  no hydrogen  2.628  N/A
    g1rep.2abs.pdb #6/A SER 95 OG    g1rep.2abs.pdb #6/A ASP 93 OD2  no hydrogen  3.385  N/A
    g1rep.2abs.pdb #6/A CYS 96 SG    g1rep.2abs.pdb #6/A GLY 69 O    no hydrogen  2.356  N/A
    g1rep.2abs.pdb #6/A GLU 102 N    g1rep.2abs.pdb #6/A GLY 100 O   no hydrogen  2.199  N/A
    

  
231 hydrogen bonds found  
109 strict hydrogen bonds found  

> ui tool show Contacts

> contacts interModel false intraRes true ignoreHiddenModels true

522 contacts  

> contacts interModel false intraRes true ignoreHiddenModels true

522 contacts  

> hide #!4 models

> show #!5 models

> ui tool show Contacts

> contacts interModel false intraRes true ignoreHiddenModels true

483 contacts  

> hide #!5 models

> show #!6 models

> ui tool show Contacts

> contacts interModel false intraRes true ignoreHiddenModels true

431 contacts  

> ui tool show H-Bonds

> hbonds interModel false twoColors true reveal true

231 hydrogen bonds found  
109 strict hydrogen bonds found  

> show #!5 models

> hide #!6 models

> ui tool show H-Bonds

> hbonds interModel false reveal true

231 hydrogen bonds found  

> help help:user/tools/hbonds.html

> close #6

> ui tool show H-Bonds

> hbonds interModel false reveal true

187 hydrogen bonds found  

> hbonds interModel false reveal true

187 hydrogen bonds found  

> close

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g1rep.2.pdb

g1rep.2.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g1rep.2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g2rep2.pdb

g2rep2.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g2rep2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show ""Render by Attribute""

> key blue-white-red :-0.49 :0.22 :0.93 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute a:bfactor #1-2 target cabs palette
> -0.49,blue:0.22,white:0.93,red

1660 atoms, 220 residues, atom bfactor range -0.49 to 0.93  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker g1rep.2.pdb, chain A (#1) with g2rep2.pdb, chain A (#2), sequence
alignment score = 73.4  
RMSD between 47 pruned atom pairs is 0.946 angstroms; (across all 81 pairs:
15.582)  
  

> show surfaces

> color bfactor

1660 atoms, 220 residues, 2 surfaces, atom bfactor range -0.49 to 0.93  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> style #!1 sphere

Changed 802 atom styles  

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g2rep.2dif.pdb

g2rep.2dif.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g2rep.2dif.pdb #4  
---  
Chain | Description  
A | No description available  
  

> show #4#!1 surfaces

> color bfactor #!1,4

1665 atoms, 224 residues, 2 surfaces, atom bfactor range -0.49 to 0.417  

> hide #!1 models

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> close #4

> close

> open /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g2rep.2dif.pdb
> /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g1rep.2dif.pdb
> /Users/rennayi/Library/CloudStorage/OneDrive-
> RutgersUniversity/phdthesis/data/structures/g2rep2.2dif.pdb

g2rep.2dif.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g2rep.2dif.pdb #1  
---  
Chain | Description  
A | No description available  
  
g1rep.2dif.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g1rep.2dif.pdb #2  
---  
Chain | Description  
A | No description available  
  
g2rep2.2dif.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for g2rep2.2dif.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker g2rep.2dif.pdb, chain A (#1) with g1rep.2dif.pdb, chain A (#2),
sequence alignment score = 74.3  
RMSD between 16 pruned atom pairs is 0.820 angstroms; (across all 63 pairs:
16.181)  
  
Matchmaker g2rep.2dif.pdb, chain A (#1) with g2rep2.2dif.pdb, chain A (#3),
sequence alignment score = 87.4  
RMSD between 39 pruned atom pairs is 0.786 angstroms; (across all 86 pairs:
18.098)  
  

> show surfaces

> color bfactor

2523 atoms, 334 residues, 3 surfaces, atom bfactor range -0.49 to 0.417  

> ui tool show ""Render by Attribute""

> key blue-white-red :-0.490 :-0.037 :0.417 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute a:bfactor #!1-3 target cabs palette
> -0.49,blue:-0.0365,white:0.417,red

2523 atoms, 334 residues, 3 surfaces, atom bfactor range -0.49 to 0.417  

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> view

> ui tool show ""Render by Attribute""

> key blue-white-red :-0.490 :-0.037 :0.417 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate


===== 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 M2
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 Pro
      Model Identifier: Mac14,7
      Model Number: MNEJ3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.41.12
      OS Loader Version: 10151.41.12

Software:

    System Software Overview:

      System Version: macOS 14.1 (23B74)
      Kernel Version: Darwin 23.1.0
      Time since boot: 18 days, 13 hours, 6 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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: Yes
          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-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-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

}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX