Infinite recursion drawing alignment

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow

Current thread 0x0000175c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 2170 in _layout_line
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 2221 in layout_lines
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1555 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\seq_canvas.py", line 1567 in __init__
  ...
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_6rwb.pdb
> A.pdb" "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_Mmorganii_TcdA4_6rw9.pdb
> A.pdb" "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_Pluminescens_TcdA4_6rwa.pdb
> A.pdb" "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_TcdA1_6rw6_onechain.pdb.pdb"
> "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_Xnematophila_XptA1_6rw8.pdb
> A.pdb" "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_YenTcA_pH11_complete_TcA_monomer.pdb.pdb"

Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_6rwb.pdb
A.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 5 5 ASN A 132
ASN A 136 1 5  
Start residue of secondary structure not found: HELIX 6 6 ILE A 144 LYS A 152
1 9  
Start residue of secondary structure not found: HELIX 7 7 ASP A 156 THR A 159
1 4  
Start residue of secondary structure not found: HELIX 8 8 ASP A 177 ASP A 188
1 12  
Start residue of secondary structure not found: HELIX 9 9 LEU A 193 VAL A 198
1 6  
Start residue of secondary structure not found: HELIX 10 10 VAL A 213 GLN A
216 1 4  
39 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 56 56 PHE A 1537 ASN A
1623 1 87  
Start residue of secondary structure not found: HELIX 57 57 SER A 1627 ASN A
1643 1 17  
Start residue of secondary structure not found: HELIX 58 58 ALA A 1648 THR A
1658 1 11  
Start residue of secondary structure not found: HELIX 59 59 ALA A 1674 SER A
1760 1 87  
Start residue of secondary structure not found: HELIX 60 60 LYS A 1766 GLU A
1801 1 36  
Start residue of secondary structure not found: HELIX 61 61 ALA A 1825 MET A
1842 1 18  
18 messages similar to the above omitted  
  
Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_Mmorganii_TcdA4_6rw9.pdb
A.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 6 6 GLN A 153
ASP A 157 1 5  
Start residue of secondary structure not found: HELIX 7 7 ALA A 162 THR A 178
1 17  
Start residue of secondary structure not found: HELIX 8 8 ASN A 184 LEU A 190
1 7  
Start residue of secondary structure not found: HELIX 9 9 ALA A 203 GLN A 214
1 12  
Start residue of secondary structure not found: HELIX 10 10 LEU A 219 ASP A
221 1 3  
Start residue of secondary structure not found: HELIX 11 11 PRO A 227 ALA A
238 1 12  
48 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 69 69 PHE A 1984 ASP A
2069 1 86  
Start residue of secondary structure not found: HELIX 70 70 GLU A 2076 THR A
2091 1 16  
Start residue of secondary structure not found: HELIX 71 71 GLY A 2094 MET A
2105 1 12  
Start residue of secondary structure not found: HELIX 72 72 GLY A 2121 ARG A
2208 1 88  
Start residue of secondary structure not found: HELIX 73 73 LYS A 2213 GLN A
2248 1 36  
Start residue of secondary structure not found: HELIX 74 74 GLY A 2272 ARG A
2289 1 18  
44 messages similar to the above omitted  
  
Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_Pluminescens_TcdA4_6rwa.pdb
A.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 8 8 GLN A 152
ASP A 156 1 5  
Start residue of secondary structure not found: HELIX 9 9 THR A 161 GLN A 177
1 17  
Start residue of secondary structure not found: HELIX 10 10 ASP A 183 THR A
192 1 10  
Start residue of secondary structure not found: HELIX 11 11 ASP A 203 GLN A
215 1 13  
Start residue of secondary structure not found: HELIX 12 12 GLU A 220 LYS A
224 1 5  
Start residue of secondary structure not found: HELIX 13 13 PRO A 226 LEU A
231 1 6  
53 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 78 78 PHE A 1889 ASP A
1974 1 86  
Start residue of secondary structure not found: HELIX 79 79 ALA A 1979 THR A
1995 1 17  
Start residue of secondary structure not found: HELIX 80 80 LYS A 1999 LEU A
2008 1 10  
Start residue of secondary structure not found: HELIX 81 81 ALA A 2026 ARG A
2113 1 88  
Start residue of secondary structure not found: HELIX 82 82 GLN A 2118 GLU A
2153 1 36  
Start residue of secondary structure not found: HELIX 83 83 GLY A 2169 TYR A
2171 1 3  
49 messages similar to the above omitted  
  
Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_TcdA1_6rw6_onechain.pdb.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 8 8 GLN A 152
ASP A 156 1 5  
Start residue of secondary structure not found: HELIX 9 9 THR A 161 SER A 177
1 17  
Start residue of secondary structure not found: HELIX 10 10 TYR A 182 LEU A
189 1 8  
Start residue of secondary structure not found: HELIX 11 11 ASP A 202 GLN A
214 1 13  
Start residue of secondary structure not found: HELIX 12 12 GLU A 219 ALA A
223 1 5  
Start residue of secondary structure not found: HELIX 13 13 PRO A 225 LEU A
230 1 6  
57 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 81 81 PHE A 2019 ASP A
2104 1 86  
Start residue of secondary structure not found: HELIX 82 82 ALA A 2109 GLY A
2123 1 15  
Start residue of secondary structure not found: HELIX 83 83 THR A 2125 ALA A
2138 1 14  
Start residue of secondary structure not found: HELIX 84 84 ALA A 2156 ARG A
2243 1 88  
Start residue of secondary structure not found: HELIX 85 85 GLN A 2248 GLU A
2283 1 36  
Start residue of secondary structure not found: HELIX 86 86 GLY A 2299 TYR A
2301 1 3  
67 messages similar to the above omitted  
  
Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_Xnematophila_XptA1_6rw8.pdb
A.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 9 9 GLN A 152
ASP A 156 1 5  
Start residue of secondary structure not found: HELIX 10 10 SER A 163 GLU A
177 1 15  
Start residue of secondary structure not found: HELIX 11 11 TYR A 181 LEU A
188 1 8  
Start residue of secondary structure not found: HELIX 12 12 LEU A 201 GLN A
213 1 13  
Start residue of secondary structure not found: HELIX 13 13 LYS A 215 ARG A
222 1 8  
Start residue of secondary structure not found: HELIX 14 14 THR A 224 ALA A
227 1 4  
49 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 73 73 PHE A 2035 ASP A
2120 1 86  
Start residue of secondary structure not found: HELIX 74 74 ALA A 2125 LEU A
2156 1 32  
Start residue of secondary structure not found: HELIX 75 75 ALA A 2172 SER A
2259 1 88  
Start residue of secondary structure not found: HELIX 76 76 ALA A 2264 GLU A
2299 1 36  
Start residue of secondary structure not found: HELIX 77 77 GLY A 2315 TYR A
2317 1 3  
Start residue of secondary structure not found: HELIX 78 78 ALA A 2322 LYS A
2340 1 19  
55 messages similar to the above omitted  
  
Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/knot_regions_aligned_YenTcA_pH11_complete_TcA_monomer.pdb.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 8 8 ASP A 199
TYR A 202 1 4  
Start residue of secondary structure not found: HELIX 9 9 ALA A 207 VAL A 214
1 8  
Start residue of secondary structure not found: HELIX 10 10 GLY A 217 GLN A
225 1 9  
Start residue of secondary structure not found: HELIX 11 11 VAL A 233 ILE A
236 1 4  
Start residue of secondary structure not found: HELIX 12 12 PRO A 251 SER A
262 1 12  
55 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 78 78 PHE A 2026 LYS A
2034 1 9  
Start residue of secondary structure not found: HELIX 79 79 LEU A 2040 ASP A
2055 1 16  
Start residue of secondary structure not found: HELIX 80 80 ASP A 2060 ASP A
2069 1 10  
Start residue of secondary structure not found: HELIX 81 81 ARG A 2072 GLN A
2079 1 8  
Start residue of secondary structure not found: HELIX 82 82 ILE A 2082 ASN A
2085 1 4  
Start residue of secondary structure not found: HELIX 83 83 GLN A 2097 LEU A
2109 1 13  
51 messages similar to the above omitted  
  
knot_regions_aligned_6rwb.pdb A.pdb title:  
Cryo-em structure of yersinia pseudotuberculosis tcaa-tcab [more info...]  
  
Chain information for knot_regions_aligned_6rwb.pdb A.pdb #1  
---  
Chain | Description  
A | toxin,toxin complex subunit tcab,putative toxin subunit, putative toxin
subunit,toxin,toxin complex subunit tcab,putative toxin subunit,putative toxin
subunit,toxin,toxin complex subunit tcab,putative toxin subunit,putative toxin
subunit,toxin,toxin complex subunit tcab,putative toxin subunit,putative toxin
subunit  
  
knot_regions_aligned_Mmorganii_TcdA4_6rw9.pdb A.pdb title:  
Cryo-em structure of morganella morganii TCDA4 [more info...]  
  
Chain information for knot_regions_aligned_Mmorganii_TcdA4_6rw9.pdb A.pdb #2  
---  
Chain | Description  
A | insecticidal toxin protein TCDA4  
  
knot_regions_aligned_Pluminescens_TcdA4_6rwa.pdb A.pdb title:  
Cryo-em structure of photorhabdus luminescens TCDA4 [more info...]  
  
Chain information for knot_regions_aligned_Pluminescens_TcdA4_6rwa.pdb A.pdb
#3  
---  
Chain | Description | UniProt  
A | TCDA4 | Q8GF92_PHOLU  
  
knot_regions_aligned_TcdA1_6rw6_onechain.pdb.pdb title:  
Cryo-em structure of photorhabdus luminescens TCDA1 [more info...]  
  
Chain information for knot_regions_aligned_TcdA1_6rw6_onechain.pdb.pdb #4  
---  
Chain | Description | UniProt  
A | toxin A | Q9RN43_PHOLU  
  
knot_regions_aligned_Xnematophila_XptA1_6rw8.pdb A.pdb title:  
Cryo-em structure of xenorhabdus nematophila XPTA1 [more info...]  
  
Chain information for knot_regions_aligned_Xnematophila_XptA1_6rw8.pdb A.pdb
#5  
---  
Chain | Description  
A | A component of insecticidal toxin complex (Tc)  
  
Chain information for
knot_regions_aligned_YenTcA_pH11_complete_TcA_monomer.pdb.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select :200-2000

12114 atoms, 12460 bonds, 2 pseudobonds, 1484 residues, 8 models selected  

> color (#!1-6 & sel) light gray

> select ~sel

6532 atoms, 6671 bonds, 8 pseudobonds, 813 residues, 12 models selected  

> color (#!1-6 & sel) dim gray

> select clear

> select :200-2000

12114 atoms, 12460 bonds, 2 pseudobonds, 1484 residues, 8 models selected  

> color (#!1-6 & sel) light gray

> color (#!1-6 & sel) dark gray

> select clear

> set bgColor white

> select #6

3346 atoms, 3427 bonds, 2 pseudobonds, 408 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark slate gray

> select clear

> hide #!5 models

> hide #!4 models

> show #!5 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!4 models

> hide #!5 models

> select :200-2000

12114 atoms, 12460 bonds, 2 pseudobonds, 1484 residues, 8 models selected  

> hide sel & #!4,6 cartoons

> select clear

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> select :200-2000

12114 atoms, 12460 bonds, 2 pseudobonds, 1484 residues, 8 models selected  

> hide sel cartoons

> select clear

> select :200-2500

12812 atoms, 13180 bonds, 2 pseudobonds, 1573 residues, 8 models selected  

> hide sel cartoons

> select clear

> select #1

2637 atoms, 2705 bonds, 1 pseudobond, 324 residues, 2 models selected  

> select #2

2918 atoms, 2982 bonds, 3 pseudobonds, 371 residues, 2 models selected  

> select #3

3255 atoms, 3346 bonds, 1 pseudobond, 400 residues, 2 models selected  

> select #5

3282 atoms, 3374 bonds, 1 pseudobond, 399 residues, 2 models selected  

> select #1

2637 atoms, 2705 bonds, 1 pseudobond, 324 residues, 2 models selected  

> select #2

2918 atoms, 2982 bonds, 3 pseudobonds, 371 residues, 2 models selected  

> select #1-5

15300 atoms, 15704 bonds, 8 pseudobonds, 1889 residues, 10 models selected  

> color (#!1-5 & sel) dark gray

> select clear

> ui tool show "Side View"

> save "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/comparison_figures/long_helix.jpg"
> width 1340 height 823 supersample 3

> save "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/comparison_figures/helix-
> turn-end-NTR.jpg" width 1340 height 823 supersample 3

> select clear

Drag select of 62 residues  

> select clear

Drag select of 107 residues  

> style sel stick

Changed 854 atom styles  

> show sel atoms

> select clear

> undo

> hide sel atoms

> select clear

> open "C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
> Philosophy/pH11_structure_investigations/knot_analysis/chimera_alignment_N-
> terminal_regions.fasta"

Summary of feedback from opening
C:/Users/sroch/OneDrive/Documents/Academia/Doctorate of
Philosophy/pH11_structure_investigations/knot_analysis/chimera_alignment_N-
terminal_regions.fasta  
---  
notes | Alignment identifier is chimera_alignment_N-terminal_regions.fasta  
Associated knot_regions_aligned_6rwb.pdb A.pdb chain A to
knot_regions_aligned_6rwb.pdb A.pdb, chain A/1-2030 with 0 mismatches  
Associated knot_regions_aligned_Mmorganii_TcdA4_6rw9.pdb A.pdb chain A to
knot_regions_aligned_Mmorganii_TcdA4_6rw9.pdb A.pdb, chain A/1-2469 with 0
mismatches  
Associated knot_regions_aligned_Pluminescens_TcdA4_6rwa.pdb A.pdb chain A to
knot_regions_aligned_Pluminescens_TcdA4_6rwa.pdb A.pdb, chain A/1-2381 with 0
mismatches  
Associated knot_regions_aligned_TcdA1_6rw6_onechain.pdb.pdb chain A to
knot_regions_aligned_TcdA1_6rw6_onechain.pdb.pdb, chain A/1-2516 with 0
mismatches  
Associated knot_regions_aligned_Xnematophila_XptA1_6rw8.pdb A.pdb chain A to
knot_regions_aligned_Xnematophila_XptA1_6rw8.pdb A.pdb, chain A/1-2523 with 0
mismatches  
1 messages similar to the above omitted  
Showing conservation header ("seq_conservation" residue attribute) for
alignment chimera_alignment_N-terminal_regions.fasta  
  
Opened 6 sequences from chimera_alignment_N-terminal_regions.fasta  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20TKCTO1WW
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 16,919,126,016
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-GB
Locale: ('en_AU', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1