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Opened 7 weeks ago
Closed 7 weeks ago
#18804 closed defect (fixed)
Vina output in ViewDock: KeyError: 'RMSD l.b.'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509162234 (2025-09-16 22:34:02 UTC)
Description
I have docked compounds with Vina and when opening the results file (webina_out.pdbqt), I get the following error message:
KeyError: 'RMSD l.b.'
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
After that, you can't do any analysis on the complexes (H-bonds, clashes etc). I am using this in a course, and all of my students have the same problem.
Best regards,
Käthe Dahlström
Log:
UCSF ChimeraX version: 1.11.dev202509162234 (2025-09-16)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open /Users/kadahlst/Desktop/webina_out.pdbqt
Summary of feedback from opening /Users/kadahlst/Desktop/webina_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.407 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.883
Ignored bad PDB record found on line 4
REMARK INTER: -7.535
Ignored bad PDB record found on line 5
REMARK INTRA: -0.348
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.351
166 messages similar to the above omitted
Opened webina_out.pdbqt containing 9 structures (189 atoms, 207 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 469, in table_selection_changed
self.update_model_description()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
KeyError: 'RMSD l.b.'
KeyError: 'RMSD l.b.'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> displayedOnly true
> hide #2.1 models
> show #2.2 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> show #2.3 models
> hide #2.2 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> hide #2.3 models
> show #2.4 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.1 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> displayedOnly true
> hide #2.1 models
> show #2.2 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> displayedOnly true
> hide #1 models
> show #2.1 models
> hide #2.2 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> displayedOnly true
> hide #2.1 models
> show #2.2 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> hide #2.2 models
> show #2.3 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> displayedOnly true
> hide #2.3 models
> show #2.4 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> show #2.3 models
> hide #2.4 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> displayedOnly true
> hide #2.3 models
> show #2.4 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> displayedOnly true
> show #2.2 models
> hide #2.4 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> displayedOnly true
> show #2.5 models
> hide #2.2 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> displayedOnly true
> hide #2.5 models
> show #2.6 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> displayedOnly true
> hide #2.6 models
> show #2.7 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> displayedOnly true
> hide #2.7 models
> show #2.8 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> displayedOnly true
> hide #2.8 models
> show #2.9 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
> displayedOnly true
> close #2.1
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Chain information for 5icn_B_webina_out_2.1.pdb
---
Chain | Description
2.1/B | No description available
Chain information for 5icn_B_webina_out_2.2.pdb
---
Chain | Description
3.1/B | No description available
Chain information for 5icn_B_webina_out_2.3.pdb
---
Chain | Description
4.1/B | No description available
Chain information for 5icn_B_webina_out_2.4.pdb
---
Chain | Description
5.1/B | No description available
Chain information for 5icn_B_webina_out_2.5.pdb
---
Chain | Description
6.1/B | No description available
Chain information for 5icn_B_webina_out_2.6.pdb
---
Chain | Description
7.1/B | No description available
Chain information for 5icn_B_webina_out_2.7.pdb
---
Chain | Description
8.1/B | No description available
Chain information for 5icn_B_webina_out_2.8.pdb
---
Chain | Description
9.1/B | No description available
Chain information for 5icn_B_webina_out_2.9.pdb
---
Chain | Description
10.1/B | No description available
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open /Users/kadahlst/Desktop/webina_out.pdbqt
Summary of feedback from opening /Users/kadahlst/Desktop/webina_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.407 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.883
Ignored bad PDB record found on line 4
REMARK INTER: -7.535
Ignored bad PDB record found on line 5
REMARK INTRA: -0.348
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.351
166 messages similar to the above omitted
Opened webina_out.pdbqt containing 9 structures (189 atoms, 207 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 469, in table_selection_changed
self.update_model_description()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
KeyError: 'RMSD l.b.'
KeyError: 'RMSD l.b.'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
> hide #1 models
> hide #!2 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> select add #2.1
21 atoms, 23 bonds, 1 residue, 1 model selected
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> selectedOnly true
> select subtract #2.1
Nothing selected
> hide #2.1 models
> show #2.2 models
> select add #2.2
21 atoms, 23 bonds, 1 residue, 1 model selected
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> select subtract #2.2
Nothing selected
> hide #2.2 models
> show #2.3 models
> select add #2.3
21 atoms, 23 bonds, 1 residue, 1 model selected
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> selectedOnly true
> show #2.2 models
> select add #2.2
42 atoms, 46 bonds, 2 residues, 2 models selected
> select subtract #2.3
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide #2.3 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> selectedOnly true
> show #2.4 models
> select add #2.4
42 atoms, 46 bonds, 2 residues, 2 models selected
> select subtract #2.2
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide #2.2 models
> show #2.5 models
> select add #2.5
42 atoms, 46 bonds, 2 residues, 2 models selected
> select subtract #2.4
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide #2.4 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> selectedOnly true
> hide #2.5 models
> select subtract #2.5
Nothing selected
> select add #2.6
21 atoms, 23 bonds, 1 residue, 1 model selected
> show #2.6 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> selectedOnly true
> show #2.7 models
> select add #2.7
42 atoms, 46 bonds, 2 residues, 2 models selected
> select subtract #2.6
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide #2.6 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> selectedOnly true
> hide #2.7 models
> select subtract #2.7
Nothing selected
> select add #2.8
21 atoms, 23 bonds, 1 residue, 1 model selected
> show #2.8 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> selectedOnly true
> show #2.9 models
> select add #2.9
42 atoms, 46 bonds, 2 residues, 2 models selected
> select subtract #2.8
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide #2.8 models
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
> selectedOnly true
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
22 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 VAL B 193 LYS B 200
0
Start residue of secondary structure not found: SHEET 6 6 1 ALA B 223 LEU B
228 0
Start residue of secondary structure not found: SHEET 7 7 1 ALA B 256 GLN B
260 0
Start residue of secondary structure not found: SHEET 8 8 1 MET B 295 LEU B
298 0
Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1
4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
277 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Chain information for 5icn_B_webina_out_2.4.pdb
---
Chain | Description
4.1/B | No description available
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open /Users/kadahlst/Desktop/webina_out.pdbqt
Summary of feedback from opening /Users/kadahlst/Desktop/webina_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.407 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.883
Ignored bad PDB record found on line 4
REMARK INTER: -7.535
Ignored bad PDB record found on line 5
REMARK INTRA: -0.348
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.351
166 messages similar to the above omitted
Opened webina_out.pdbqt containing 9 structures (189 atoms, 207 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 469, in table_selection_changed
self.update_model_description()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
KeyError: 'RMSD l.b.'
KeyError: 'RMSD l.b.'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
> hide #2.1 models
> hide #!2 models
> hide #1 models
> show #2.4 models
> select add #2.4
21 atoms, 23 bonds, 1 residue, 1 model selected
> save
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> selectedOnly true
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #10
---
Chain | Description
B | No description available
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
Computing secondary structure
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
> ui tool show ViewDock
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> show #1 models
> show #2 models
> ui tool show H-Bonds
> hbonds sel color #fa49f8 radius 0.1 dashes 6 intraModel false intraMol false
> intraRes false reveal true retainCurrent true log true
Atom specifier selects no atoms
> select add #2
21 atoms, 23 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fa49f8 radius 0.1 dashes 6 interModel false intraRes false
> reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 5icn_B_webina_out_2.1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select add #1
2988 atoms, 3065 bonds, 373 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fa49f8 radius 0.1 dashes 6 interModel false intraRes false
> reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5icn_B_prep.pdb
2 5icn_B_webina_out_2.1.pdb
317 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5icn_B_prep.pdb #1/B ARG 8 NH2 5icn_B_prep.pdb #1/B LEU 320 O no hydrogen 2.997 N/A
5icn_B_prep.pdb #1/B LYS 10 N 5icn_B_prep.pdb #1/B ASP 130 OD2 no hydrogen 3.036 N/A
5icn_B_prep.pdb #1/B CYS 12 N 5icn_B_prep.pdb #1/B ILE 131 O no hydrogen 2.957 N/A
5icn_B_prep.pdb #1/B CYS 12 SG 5icn_B_prep.pdb #1/B THR 129 OG1 no hydrogen 3.249 N/A
5icn_B_prep.pdb #1/B TYR 13 N 5icn_B_prep.pdb #1/B GLU 52 O no hydrogen 2.758 N/A
5icn_B_prep.pdb #1/B TYR 13 OH 5icn_B_prep.pdb #1/B HIS 39 ND1 no hydrogen 3.309 N/A
5icn_B_prep.pdb #1/B TYR 14 N 5icn_B_prep.pdb #1/B VAL 133 O no hydrogen 2.875 N/A
5icn_B_prep.pdb #1/B TYR 15 N 5icn_B_prep.pdb #1/B TYR 54 O no hydrogen 3.046 N/A
5icn_B_prep.pdb #1/B ASP 18 N 5icn_B_prep.pdb #1/B ASP 16 OD1 no hydrogen 2.986 N/A
5icn_B_prep.pdb #1/B VAL 19 N 5icn_B_prep.pdb #1/B ASP 16 O no hydrogen 2.890 N/A
5icn_B_prep.pdb #1/B ASN 21 N 5icn_B_prep.pdb #1/B ASP 18 O no hydrogen 2.834 N/A
5icn_B_prep.pdb #1/B TYR 24 OH 5icn_B_prep.pdb #1/B PHE 150 O no hydrogen 2.814 N/A
5icn_B_prep.pdb #1/B HIS 28 N 5icn_B_prep.pdb #1/B GLY 25 O no hydrogen 3.050 N/A
5icn_B_prep.pdb #1/B ARG 34 N 5icn_B_prep.pdb #1/B LYS 31 O no hydrogen 3.153 N/A
5icn_B_prep.pdb #1/B ARG 34 NH1 5icn_B_prep.pdb #1/B GLY 300 O no hydrogen 2.833 N/A
5icn_B_prep.pdb #1/B ARG 34 NH2 5icn_B_prep.pdb #1/B GLY 300 O no hydrogen 2.816 N/A
5icn_B_prep.pdb #1/B ILE 35 N 5icn_B_prep.pdb #1/B PRO 32 O no hydrogen 3.074 N/A
5icn_B_prep.pdb #1/B ARG 36 NE 5icn_B_prep.pdb #1/B TYR 333 OH no hydrogen 3.173 N/A
5icn_B_prep.pdb #1/B MET 37 N 5icn_B_prep.pdb #1/B HIS 33 O no hydrogen 3.120 N/A
5icn_B_prep.pdb #1/B THR 38 N 5icn_B_prep.pdb #1/B ARG 34 O no hydrogen 3.177 N/A
5icn_B_prep.pdb #1/B THR 38 OG1 5icn_B_prep.pdb #1/B ARG 34 O no hydrogen 2.828 N/A
5icn_B_prep.pdb #1/B HIS 39 N 5icn_B_prep.pdb #1/B ILE 35 O no hydrogen 2.835 N/A
5icn_B_prep.pdb #1/B HIS 39 ND1 5icn_B_prep.pdb #1/B TYR 13 OH no hydrogen 3.309 N/A
5icn_B_prep.pdb #1/B ASN 40 N 5icn_B_prep.pdb #1/B ARG 36 O no hydrogen 2.992 N/A
5icn_B_prep.pdb #1/B LEU 41 N 5icn_B_prep.pdb #1/B MET 37 O no hydrogen 3.082 N/A
5icn_B_prep.pdb #1/B LEU 42 N 5icn_B_prep.pdb #1/B THR 38 O no hydrogen 2.842 N/A
5icn_B_prep.pdb #1/B LEU 43 N 5icn_B_prep.pdb #1/B HIS 39 O no hydrogen 3.138 N/A
5icn_B_prep.pdb #1/B ASN 44 N 5icn_B_prep.pdb #1/B ASN 40 O no hydrogen 3.221 N/A
5icn_B_prep.pdb #1/B ASN 44 ND2 5icn_B_prep.pdb #1/B ASN 40 O no hydrogen 3.081 N/A
5icn_B_prep.pdb #1/B TYR 45 N 5icn_B_prep.pdb #1/B LEU 41 O no hydrogen 2.628 N/A
5icn_B_prep.pdb #1/B TYR 45 OH 5icn_B_prep.pdb #1/B PRO 325 O no hydrogen 2.501 N/A
5icn_B_prep.pdb #1/B TYR 45 OH 5icn_B_prep.pdb #1/B GLU 327 O no hydrogen 2.976 N/A
5icn_B_prep.pdb #1/B GLY 46 N 5icn_B_prep.pdb #1/B LEU 43 O no hydrogen 3.245 N/A
5icn_B_prep.pdb #1/B LEU 47 N 5icn_B_prep.pdb #1/B LEU 42 O no hydrogen 2.935 N/A
5icn_B_prep.pdb #1/B TYR 48 N 5icn_B_prep.pdb #1/B LEU 42 O no hydrogen 3.085 N/A
5icn_B_prep.pdb #1/B LYS 50 N 5icn_B_prep.pdb #1/B LEU 47 O no hydrogen 2.620 N/A
5icn_B_prep.pdb #1/B MET 51 N 5icn_B_prep.pdb #1/B TYR 48 O no hydrogen 3.111 N/A
5icn_B_prep.pdb #1/B GLU 52 N 5icn_B_prep.pdb #1/B VAL 11 O no hydrogen 3.020 N/A
5icn_B_prep.pdb #1/B TYR 54 N 5icn_B_prep.pdb #1/B TYR 13 O no hydrogen 2.802 N/A
5icn_B_prep.pdb #1/B ALA 59 N 5icn_B_prep.pdb #1/B GLN 111 O no hydrogen 3.258 N/A
5icn_B_prep.pdb #1/B GLU 63 N 5icn_B_prep.pdb #1/B ASN 60 O no hydrogen 3.043 N/A
5icn_B_prep.pdb #1/B MET 64 N 5icn_B_prep.pdb #1/B ASN 60 O no hydrogen 3.368 N/A
5icn_B_prep.pdb #1/B THR 65 N 5icn_B_prep.pdb #1/B ALA 61 O no hydrogen 3.038 N/A
5icn_B_prep.pdb #1/B THR 65 OG1 5icn_B_prep.pdb #1/B ALA 61 O no hydrogen 2.825 N/A
5icn_B_prep.pdb #1/B THR 65 OG1 5icn_B_prep.pdb #1/B GLU 62 O no hydrogen 2.948 N/A
5icn_B_prep.pdb #1/B LYS 66 N 5icn_B_prep.pdb #1/B GLU 63 O no hydrogen 3.277 N/A
5icn_B_prep.pdb #1/B HIS 68 N 5icn_B_prep.pdb #1/B MET 64 O no hydrogen 3.068 N/A
5icn_B_prep.pdb #1/B HIS 68 ND1 5icn_B_prep.pdb #1/B MET 64 O no hydrogen 3.265 N/A
5icn_B_prep.pdb #1/B SER 69 N 5icn_B_prep.pdb #1/B LYS 144 O no hydrogen 3.374 N/A
5icn_B_prep.pdb #1/B SER 69 OG 5icn_B_prep.pdb #1/B LYS 144 O no hydrogen 3.033 N/A
5icn_B_prep.pdb #1/B SER 69 OG 5icn_B_prep.pdb #1/B SER 145 OG no hydrogen 3.057 N/A
5icn_B_prep.pdb #1/B TYR 72 N 5icn_B_prep.pdb #1/B SER 69 O no hydrogen 3.186 N/A
5icn_B_prep.pdb #1/B TYR 72 OH 5icn_B_prep.pdb #1/B TYR 152 O no hydrogen 2.846 N/A
5icn_B_prep.pdb #1/B ILE 73 N 5icn_B_prep.pdb #1/B SER 69 O no hydrogen 3.253 N/A
5icn_B_prep.pdb #1/B PHE 75 N 5icn_B_prep.pdb #1/B ASP 71 O no hydrogen 3.336 N/A
5icn_B_prep.pdb #1/B LEU 76 N 5icn_B_prep.pdb #1/B TYR 72 O no hydrogen 3.074 N/A
5icn_B_prep.pdb #1/B ARG 77 N 5icn_B_prep.pdb #1/B ILE 73 O no hydrogen 2.723 N/A
5icn_B_prep.pdb #1/B SER 78 N 5icn_B_prep.pdb #1/B LYS 74 O no hydrogen 3.017 N/A
5icn_B_prep.pdb #1/B SER 78 OG 5icn_B_prep.pdb #1/B LYS 74 O no hydrogen 2.718 N/A
5icn_B_prep.pdb #1/B ILE 79 N 5icn_B_prep.pdb #1/B PHE 75 O no hydrogen 2.751 N/A
5icn_B_prep.pdb #1/B TYR 87 N 5icn_B_prep.pdb #1/B ASN 83 O no hydrogen 3.283 N/A
5icn_B_prep.pdb #1/B SER 88 OG 5icn_B_prep.pdb #1/B MET 84 O no hydrogen 3.111 N/A
5icn_B_prep.pdb #1/B SER 88 OG 5icn_B_prep.pdb #1/B SER 85 O no hydrogen 3.043 N/A
5icn_B_prep.pdb #1/B MET 91 N 5icn_B_prep.pdb #1/B TYR 87 O no hydrogen 3.314 N/A
5icn_B_prep.pdb #1/B GLN 92 N 5icn_B_prep.pdb #1/B SER 88 O no hydrogen 3.332 N/A
5icn_B_prep.pdb #1/B PHE 94 N 5icn_B_prep.pdb #1/B GLN 90 O no hydrogen 3.194 N/A
5icn_B_prep.pdb #1/B PHE 94 N 5icn_B_prep.pdb #1/B MET 91 O no hydrogen 3.331 N/A
5icn_B_prep.pdb #1/B VAL 96 N 5icn_B_prep.pdb #1/B MET 91 O no hydrogen 3.233 N/A
5icn_B_prep.pdb #1/B LEU 106 N 5icn_B_prep.pdb #1/B PHE 103 O no hydrogen 2.986 N/A
5icn_B_prep.pdb #1/B PHE 109 N 5icn_B_prep.pdb #1/B GLY 105 O no hydrogen 2.928 N/A
5icn_B_prep.pdb #1/B CYS 110 N 5icn_B_prep.pdb #1/B LEU 106 O no hydrogen 3.099 N/A
5icn_B_prep.pdb #1/B CYS 110 SG 5icn_B_prep.pdb #1/B LEU 106 O no hydrogen 3.409 N/A
5icn_B_prep.pdb #1/B GLN 111 N 5icn_B_prep.pdb #1/B PHE 107 O no hydrogen 3.069 N/A
5icn_B_prep.pdb #1/B GLN 111 NE2 5icn_B_prep.pdb #1/B ALA 59 O no hydrogen 2.858 N/A
5icn_B_prep.pdb #1/B LEU 112 N 5icn_B_prep.pdb #1/B GLU 108 O no hydrogen 3.169 N/A
5icn_B_prep.pdb #1/B SER 113 N 5icn_B_prep.pdb #1/B PHE 109 O no hydrogen 3.129 N/A
5icn_B_prep.pdb #1/B SER 113 OG 5icn_B_prep.pdb #1/B ALA 136 O no hydrogen 3.202 N/A
5icn_B_prep.pdb #1/B THR 114 N 5icn_B_prep.pdb #1/B CYS 110 O no hydrogen 2.925 N/A
5icn_B_prep.pdb #1/B THR 114 OG1 5icn_B_prep.pdb #1/B CYS 110 O no hydrogen 2.771 N/A
5icn_B_prep.pdb #1/B GLY 115 N 5icn_B_prep.pdb #1/B GLN 111 O no hydrogen 2.811 N/A
5icn_B_prep.pdb #1/B GLY 116 N 5icn_B_prep.pdb #1/B LEU 112 O no hydrogen 3.035 N/A
5icn_B_prep.pdb #1/B SER 117 N 5icn_B_prep.pdb #1/B SER 113 O no hydrogen 3.495 N/A
5icn_B_prep.pdb #1/B SER 117 OG 5icn_B_prep.pdb #1/B SER 113 O no hydrogen 3.020 N/A
5icn_B_prep.pdb #1/B SER 117 OG 5icn_B_prep.pdb #1/B ASP 155 OD2 no hydrogen 2.486 N/A
5icn_B_prep.pdb #1/B VAL 118 N 5icn_B_prep.pdb #1/B THR 114 O no hydrogen 3.017 N/A
5icn_B_prep.pdb #1/B ALA 119 N 5icn_B_prep.pdb #1/B GLY 115 O no hydrogen 2.927 N/A
5icn_B_prep.pdb #1/B SER 120 N 5icn_B_prep.pdb #1/B GLY 116 O no hydrogen 3.206 N/A
5icn_B_prep.pdb #1/B SER 120 OG 5icn_B_prep.pdb #1/B GLY 116 O no hydrogen 2.494 N/A
5icn_B_prep.pdb #1/B SER 120 OG 5icn_B_prep.pdb #1/B SER 117 O no hydrogen 2.565 N/A
5icn_B_prep.pdb #1/B ALA 121 N 5icn_B_prep.pdb #1/B SER 117 O no hydrogen 2.960 N/A
5icn_B_prep.pdb #1/B VAL 122 N 5icn_B_prep.pdb #1/B VAL 118 O no hydrogen 2.949 N/A
5icn_B_prep.pdb #1/B LYS 123 N 5icn_B_prep.pdb #1/B ALA 119 O no hydrogen 2.953 N/A
5icn_B_prep.pdb #1/B LYS 123 NZ 5icn_B_prep.pdb #1/B TYR 54 OH no hydrogen 3.026 N/A
5icn_B_prep.pdb #1/B LEU 124 N 5icn_B_prep.pdb #1/B SER 120 O no hydrogen 2.765 N/A
5icn_B_prep.pdb #1/B ASN 125 N 5icn_B_prep.pdb #1/B ALA 121 O no hydrogen 2.799 N/A
5icn_B_prep.pdb #1/B ASN 125 ND2 5icn_B_prep.pdb #1/B GLU 162 O no hydrogen 2.750 N/A
5icn_B_prep.pdb #1/B LYS 126 N 5icn_B_prep.pdb #1/B VAL 122 O no hydrogen 2.589 N/A
5icn_B_prep.pdb #1/B GLN 127 N 5icn_B_prep.pdb #1/B LEU 124 O no hydrogen 2.992 N/A
5icn_B_prep.pdb #1/B GLN 128 N 5icn_B_prep.pdb #1/B LYS 123 O no hydrogen 3.244 N/A
5icn_B_prep.pdb #1/B THR 129 OG1 5icn_B_prep.pdb #1/B LYS 10 O no hydrogen 3.052 N/A
5icn_B_prep.pdb #1/B THR 129 OG1 5icn_B_prep.pdb #1/B ILE 131 O no hydrogen 2.586 N/A
5icn_B_prep.pdb #1/B ASP 130 N 5icn_B_prep.pdb #1/B LYS 10 O no hydrogen 3.180 N/A
5icn_B_prep.pdb #1/B ILE 131 N 5icn_B_prep.pdb #1/B LYS 10 O no hydrogen 2.970 N/A
5icn_B_prep.pdb #1/B ALA 132 N 5icn_B_prep.pdb #1/B MET 295 O no hydrogen 3.099 N/A
5icn_B_prep.pdb #1/B VAL 133 N 5icn_B_prep.pdb #1/B CYS 12 O no hydrogen 2.696 N/A
5icn_B_prep.pdb #1/B ASN 134 N 5icn_B_prep.pdb #1/B MET 297 O no hydrogen 3.051 N/A
5icn_B_prep.pdb #1/B ASN 134 ND2 5icn_B_prep.pdb #1/B SER 113 O no hydrogen 3.121 N/A
5icn_B_prep.pdb #1/B ASN 134 ND2 5icn_B_prep.pdb #1/B SER 117 OG no hydrogen 2.945 N/A
5icn_B_prep.pdb #1/B GLY 137 N 5icn_B_prep.pdb #1/B ASN 134 O no hydrogen 3.197 N/A
5icn_B_prep.pdb #1/B GLY 138 N 5icn_B_prep.pdb #1/B ASP 155 OD2 no hydrogen 2.870 N/A
5icn_B_prep.pdb #1/B LEU 139 N 5icn_B_prep.pdb #1/B ASP 155 OD1 no hydrogen 2.981 N/A
5icn_B_prep.pdb #1/B HIS 140 ND1 5icn_B_prep.pdb #1/B ASP 174 OD2 no hydrogen 2.614 N/A
5icn_B_prep.pdb #1/B LYS 143 N 5icn_B_prep.pdb #1/B GLU 146 O no hydrogen 3.004 N/A
5icn_B_prep.pdb #1/B LYS 143 NZ 5icn_B_prep.pdb #1/B ASP 181 OD2 no hydrogen 3.005 N/A
5icn_B_prep.pdb #1/B SER 145 OG 5icn_B_prep.pdb #1/B SER 69 OG no hydrogen 3.057 N/A
5icn_B_prep.pdb #1/B ALA 147 N 5icn_B_prep.pdb #1/B PHE 94 O no hydrogen 3.021 N/A
5icn_B_prep.pdb #1/B SER 148 N 5icn_B_prep.pdb #1/B CYS 151 O no hydrogen 2.968 N/A
5icn_B_prep.pdb #1/B CYS 151 N 5icn_B_prep.pdb #1/B SER 148 O no hydrogen 3.022 N/A
5icn_B_prep.pdb #1/B CYS 151 SG 5icn_B_prep.pdb #1/B GLY 149 O no hydrogen 3.185 N/A
5icn_B_prep.pdb #1/B TYR 152 OH 5icn_B_prep.pdb #1/B PRO 101 O no hydrogen 2.582 N/A
5icn_B_prep.pdb #1/B ASN 154 ND2 5icn_B_prep.pdb #1/B ALA 142 O no hydrogen 3.566 N/A
5icn_B_prep.pdb #1/B VAL 157 N 5icn_B_prep.pdb #1/B ASN 154 OD1 no hydrogen 2.690 N/A
5icn_B_prep.pdb #1/B LEU 158 N 5icn_B_prep.pdb #1/B ASN 154 O no hydrogen 3.459 N/A
5icn_B_prep.pdb #1/B ALA 159 N 5icn_B_prep.pdb #1/B ASP 155 O no hydrogen 2.880 N/A
5icn_B_prep.pdb #1/B ILE 160 N 5icn_B_prep.pdb #1/B ILE 156 O no hydrogen 2.794 N/A
5icn_B_prep.pdb #1/B LEU 161 N 5icn_B_prep.pdb #1/B VAL 157 O no hydrogen 2.726 N/A
5icn_B_prep.pdb #1/B GLU 162 N 5icn_B_prep.pdb #1/B LEU 158 O no hydrogen 3.221 N/A
5icn_B_prep.pdb #1/B LEU 163 N 5icn_B_prep.pdb #1/B ALA 159 O no hydrogen 3.175 N/A
5icn_B_prep.pdb #1/B LEU 164 N 5icn_B_prep.pdb #1/B ILE 160 O no hydrogen 2.948 N/A
5icn_B_prep.pdb #1/B LYS 165 N 5icn_B_prep.pdb #1/B GLU 162 O no hydrogen 3.140 N/A
5icn_B_prep.pdb #1/B LYS 165 NZ 5icn_B_prep.pdb #1/B GLU 162 OE2 no hydrogen 2.655 N/A
5icn_B_prep.pdb #1/B TYR 166 N 5icn_B_prep.pdb #1/B LEU 163 O no hydrogen 2.914 N/A
5icn_B_prep.pdb #1/B HIS 167 N 5icn_B_prep.pdb #1/B LEU 163 O no hydrogen 2.748 N/A
5icn_B_prep.pdb #1/B ARG 169 NE 5icn_B_prep.pdb #1/B GLN 253 O no hydrogen 3.194 N/A
5icn_B_prep.pdb #1/B VAL 170 N 5icn_B_prep.pdb #1/B ARG 192 O no hydrogen 2.905 N/A
5icn_B_prep.pdb #1/B LEU 171 N 5icn_B_prep.pdb #1/B ALA 256 O no hydrogen 2.993 N/A
5icn_B_prep.pdb #1/B TYR 172 N 5icn_B_prep.pdb #1/B MET 194 O no hydrogen 2.821 N/A
5icn_B_prep.pdb #1/B TYR 172 OH 5icn_B_prep.pdb #1/B ASP 174 OD2 no hydrogen 2.482 N/A
5icn_B_prep.pdb #1/B ILE 173 N 5icn_B_prep.pdb #1/B VAL 258 O no hydrogen 2.941 N/A
5icn_B_prep.pdb #1/B ASP 174 N 5icn_B_prep.pdb #1/B VAL 196 O no hydrogen 3.007 N/A
5icn_B_prep.pdb #1/B ILE 175 N 5icn_B_prep.pdb #1/B GLN 260 O no hydrogen 3.130 N/A
5icn_B_prep.pdb #1/B ILE 177 N 5icn_B_prep.pdb #1/B ASP 264 OD1 no hydrogen 3.286 N/A
5icn_B_prep.pdb #1/B HIS 178 N 5icn_B_prep.pdb #1/B ASP 176 OD1 no hydrogen 2.776 N/A
5icn_B_prep.pdb #1/B HIS 179 ND1 5icn_B_prep.pdb #1/B THR 208 OG1 no hydrogen 3.053 N/A
5icn_B_prep.pdb #1/B HIS 179 NE2 5icn_B_prep.pdb #1/B GLU 184 OE1 no hydrogen 3.206 N/A
5icn_B_prep.pdb #1/B ASP 181 N 5icn_B_prep.pdb #1/B HIS 179 O no hydrogen 2.741 N/A
5icn_B_prep.pdb #1/B GLU 184 N 5icn_B_prep.pdb #1/B GLY 180 O no hydrogen 3.091 N/A
5icn_B_prep.pdb #1/B GLU 185 N 5icn_B_prep.pdb #1/B ASP 181 O no hydrogen 2.816 N/A
5icn_B_prep.pdb #1/B ALA 186 N 5icn_B_prep.pdb #1/B GLY 182 O no hydrogen 3.147 N/A
5icn_B_prep.pdb #1/B PHE 187 N 5icn_B_prep.pdb #1/B GLU 184 O no hydrogen 3.031 N/A
5icn_B_prep.pdb #1/B TYR 188 N 5icn_B_prep.pdb #1/B GLU 185 O no hydrogen 3.429 N/A
5icn_B_prep.pdb #1/B TYR 188 OH 5icn_B_prep.pdb #1/B ASP 213 OD1 no hydrogen 2.487 N/A
5icn_B_prep.pdb #1/B THR 190 N 5icn_B_prep.pdb #1/B PHE 187 O no hydrogen 3.271 N/A
5icn_B_prep.pdb #1/B ARG 192 N 5icn_B_prep.pdb #1/B THR 190 OG1 no hydrogen 3.141 N/A
5icn_B_prep.pdb #1/B ARG 192 NE 5icn_B_prep.pdb #1/B GLN 168 O no hydrogen 2.855 N/A
5icn_B_prep.pdb #1/B ARG 192 NH2 5icn_B_prep.pdb #1/B LEU 164 O no hydrogen 2.745 N/A
5icn_B_prep.pdb #1/B ARG 192 NH2 5icn_B_prep.pdb #1/B HIS 167 O no hydrogen 2.650 N/A
5icn_B_prep.pdb #1/B ARG 192 NH2 5icn_B_prep.pdb #1/B GLN 168 O no hydrogen 3.551 N/A
5icn_B_prep.pdb #1/B MET 194 N 5icn_B_prep.pdb #1/B VAL 170 O no hydrogen 3.224 N/A
5icn_B_prep.pdb #1/B THR 195 N 5icn_B_prep.pdb #1/B TYR 222 O no hydrogen 3.147 N/A
5icn_B_prep.pdb #1/B THR 195 OG1 5icn_B_prep.pdb #1/B GLU 184 OE1 no hydrogen 3.494 N/A
5icn_B_prep.pdb #1/B VAL 196 N 5icn_B_prep.pdb #1/B TYR 172 O no hydrogen 2.866 N/A
5icn_B_prep.pdb #1/B SER 197 N 5icn_B_prep.pdb #1/B VAL 224 O no hydrogen 3.191 N/A
5icn_B_prep.pdb #1/B SER 197 OG 5icn_B_prep.pdb #1/B HIS 199 ND1 no hydrogen 2.954 N/A
5icn_B_prep.pdb #1/B PHE 198 N 5icn_B_prep.pdb #1/B ASP 174 O no hydrogen 3.283 N/A
5icn_B_prep.pdb #1/B HIS 199 N 5icn_B_prep.pdb #1/B TYR 226 O no hydrogen 3.135 N/A
5icn_B_prep.pdb #1/B HIS 199 ND1 5icn_B_prep.pdb #1/B SER 197 OG no hydrogen 2.954 N/A
5icn_B_prep.pdb #1/B HIS 199 NE2 5icn_B_prep.pdb #1/B GLY 209 O no hydrogen 2.496 N/A
5icn_B_prep.pdb #1/B LYS 200 N 5icn_B_prep.pdb #1/B ILE 177 O no hydrogen 3.092 N/A
5icn_B_prep.pdb #1/B LYS 200 NZ 5icn_B_prep.pdb #1/B TYR 201 O no hydrogen 3.354 N/A
5icn_B_prep.pdb #1/B LYS 200 NZ 5icn_B_prep.pdb #1/B GLY 202 O no hydrogen 2.986 N/A
5icn_B_prep.pdb #1/B TYR 201 N 5icn_B_prep.pdb #1/B LEU 228 O no hydrogen 2.893 N/A
5icn_B_prep.pdb #1/B TYR 204 OH 5icn_B_prep.pdb #1/B LEU 271 O no hydrogen 2.858 N/A
5icn_B_prep.pdb #1/B THR 208 OG1 5icn_B_prep.pdb #1/B HIS 179 ND1 no hydrogen 3.053 N/A
5icn_B_prep.pdb #1/B ARG 212 N 5icn_B_prep.pdb #1/B ASP 210 OD2 no hydrogen 3.419 N/A
5icn_B_prep.pdb #1/B ASP 213 N 5icn_B_prep.pdb #1/B ASP 210 O no hydrogen 2.946 N/A
5icn_B_prep.pdb #1/B ALA 216 N 5icn_B_prep.pdb #1/B TYR 188 O no hydrogen 3.323 N/A
5icn_B_prep.pdb #1/B LYS 218 NZ 5icn_B_prep.pdb #1/B ASP 191 OD1 no hydrogen 3.550 N/A
5icn_B_prep.pdb #1/B LYS 218 NZ 5icn_B_prep.pdb #1/B ASP 191 OD2 no hydrogen 3.447 N/A
5icn_B_prep.pdb #1/B GLY 219 N 5icn_B_prep.pdb #1/B ALA 216 O no hydrogen 2.840 N/A
5icn_B_prep.pdb #1/B LYS 220 N 5icn_B_prep.pdb #1/B GLY 217 O no hydrogen 3.361 N/A
5icn_B_prep.pdb #1/B TYR 221 N 5icn_B_prep.pdb #1/B ILE 214 O no hydrogen 3.125 N/A
5icn_B_prep.pdb #1/B TYR 222 N 5icn_B_prep.pdb #1/B GLY 219 O no hydrogen 3.246 N/A
5icn_B_prep.pdb #1/B ALA 223 N 5icn_B_prep.pdb #1/B ILE 214 O no hydrogen 3.213 N/A
5icn_B_prep.pdb #1/B VAL 224 N 5icn_B_prep.pdb #1/B THR 195 O no hydrogen 2.964 N/A
5icn_B_prep.pdb #1/B ASN 225 ND2 5icn_B_prep.pdb #1/B HIS 179 NE2 no hydrogen 3.256 N/A
5icn_B_prep.pdb #1/B ASN 225 ND2 5icn_B_prep.pdb #1/B GLU 184 OE1 no hydrogen 3.398 N/A
5icn_B_prep.pdb #1/B TYR 226 N 5icn_B_prep.pdb #1/B SER 197 O no hydrogen 2.689 N/A
5icn_B_prep.pdb #1/B ARG 229 NE 5icn_B_prep.pdb #1/B GLN 353 O no hydrogen 3.110 N/A
5icn_B_prep.pdb #1/B ARG 229 NH2 5icn_B_prep.pdb #1/B GLN 353 O no hydrogen 3.078 N/A
5icn_B_prep.pdb #1/B GLY 231 N 5icn_B_prep.pdb #1/B CYS 273 O no hydrogen 3.101 N/A
5icn_B_prep.pdb #1/B SER 236 OG 5icn_B_prep.pdb #1/B ASP 233 OD2 no hydrogen 2.930 N/A
5icn_B_prep.pdb #1/B TYR 237 N 5icn_B_prep.pdb #1/B ASP 233 O no hydrogen 3.031 N/A
5icn_B_prep.pdb #1/B GLU 238 N 5icn_B_prep.pdb #1/B ASP 234 O no hydrogen 2.773 N/A
5icn_B_prep.pdb #1/B ALA 239 N 5icn_B_prep.pdb #1/B GLU 235 O no hydrogen 3.021 N/A
5icn_B_prep.pdb #1/B ILE 240 N 5icn_B_prep.pdb #1/B TYR 237 O no hydrogen 3.096 N/A
5icn_B_prep.pdb #1/B PHE 241 N 5icn_B_prep.pdb #1/B TYR 237 O no hydrogen 2.866 N/A
5icn_B_prep.pdb #1/B PHE 241 N 5icn_B_prep.pdb #1/B GLU 238 O no hydrogen 3.129 N/A
5icn_B_prep.pdb #1/B LYS 242 N 5icn_B_prep.pdb #1/B GLU 238 O no hydrogen 3.279 N/A
5icn_B_prep.pdb #1/B MET 245 N 5icn_B_prep.pdb #1/B PHE 241 O no hydrogen 2.882 N/A
5icn_B_prep.pdb #1/B SER 246 N 5icn_B_prep.pdb #1/B LYS 242 O no hydrogen 2.960 N/A
5icn_B_prep.pdb #1/B SER 246 OG 5icn_B_prep.pdb #1/B LYS 242 O no hydrogen 2.954 N/A
5icn_B_prep.pdb #1/B LYS 247 N 5icn_B_prep.pdb #1/B PRO 243 O no hydrogen 3.203 N/A
5icn_B_prep.pdb #1/B LYS 247 NZ 5icn_B_prep.pdb #1/B GLU 250 OE2 no hydrogen 3.003 N/A
5icn_B_prep.pdb #1/B VAL 248 N 5icn_B_prep.pdb #1/B VAL 244 O no hydrogen 2.849 N/A
5icn_B_prep.pdb #1/B MET 249 N 5icn_B_prep.pdb #1/B MET 245 O no hydrogen 2.837 N/A
5icn_B_prep.pdb #1/B GLU 250 N 5icn_B_prep.pdb #1/B SER 246 O no hydrogen 2.908 N/A
5icn_B_prep.pdb #1/B MET 251 N 5icn_B_prep.pdb #1/B LYS 247 O no hydrogen 2.674 N/A
5icn_B_prep.pdb #1/B PHE 252 N 5icn_B_prep.pdb #1/B VAL 248 O no hydrogen 2.696 N/A
5icn_B_prep.pdb #1/B GLN 253 N 5icn_B_prep.pdb #1/B MET 249 O no hydrogen 2.922 N/A
5icn_B_prep.pdb #1/B GLN 253 NE2 5icn_B_prep.pdb #1/B MET 249 O no hydrogen 3.692 N/A
5icn_B_prep.pdb #1/B GLN 253 NE2 5icn_B_prep.pdb #1/B GLU 250 O no hydrogen 2.778 N/A
5icn_B_prep.pdb #1/B SER 255 N 5icn_B_prep.pdb #1/B ARG 169 O no hydrogen 2.911 N/A
5icn_B_prep.pdb #1/B SER 255 OG 5icn_B_prep.pdb #1/B HIS 167 ND1 no hydrogen 3.266 N/A
5icn_B_prep.pdb #1/B SER 255 OG 5icn_B_prep.pdb #1/B ARG 169 O no hydrogen 3.447 N/A
5icn_B_prep.pdb #1/B VAL 257 N 5icn_B_prep.pdb #1/B PRO 294 O no hydrogen 2.857 N/A
5icn_B_prep.pdb #1/B VAL 258 N 5icn_B_prep.pdb #1/B LEU 171 O no hydrogen 2.910 N/A
5icn_B_prep.pdb #1/B LEU 259 N 5icn_B_prep.pdb #1/B LEU 296 O no hydrogen 3.299 N/A
5icn_B_prep.pdb #1/B GLN 260 N 5icn_B_prep.pdb #1/B ILE 173 O no hydrogen 2.720 N/A
5icn_B_prep.pdb #1/B CYS 261 N 5icn_B_prep.pdb #1/B LEU 298 O no hydrogen 2.779 N/A
5icn_B_prep.pdb #1/B CYS 261 SG 5icn_B_prep.pdb #1/B LEU 259 O no hydrogen 3.473 N/A
5icn_B_prep.pdb #1/B CYS 261 SG 5icn_B_prep.pdb #1/B LEU 298 O no hydrogen 3.537 N/A
5icn_B_prep.pdb #1/B SER 263 N 5icn_B_prep.pdb #1/B GLY 301 O no hydrogen 2.707 N/A
5icn_B_prep.pdb #1/B SER 265 OG 5icn_B_prep.pdb #1/B ILE 175 O no hydrogen 3.269 N/A
5icn_B_prep.pdb #1/B SER 265 OG 5icn_B_prep.pdb #1/B GLY 262 O no hydrogen 3.017 N/A
5icn_B_prep.pdb #1/B SER 265 OG 5icn_B_prep.pdb #1/B HIS 281 NE2 no hydrogen 3.371 N/A
5icn_B_prep.pdb #1/B SER 267 N 5icn_B_prep.pdb #1/B LEU 276 O no hydrogen 2.749 N/A
5icn_B_prep.pdb #1/B SER 267 OG 5icn_B_prep.pdb #1/B ASN 275 OD1 no hydrogen 3.053 N/A
5icn_B_prep.pdb #1/B LEU 271 N 5icn_B_prep.pdb #1/B ASP 269 OD2 no hydrogen 3.077 N/A
5icn_B_prep.pdb #1/B GLY 272 N 5icn_B_prep.pdb #1/B ASP 269 OD2 no hydrogen 3.208 N/A
5icn_B_prep.pdb #1/B CYS 273 SG 5icn_B_prep.pdb #1/B ASP 230 OD1 no hydrogen 2.858 N/A
5icn_B_prep.pdb #1/B ASN 275 N 5icn_B_prep.pdb #1/B ILE 232 O no hydrogen 3.144 N/A
5icn_B_prep.pdb #1/B ASN 275 ND2 5icn_B_prep.pdb #1/B SER 348 O no hydrogen 2.965 N/A
5icn_B_prep.pdb #1/B ASN 275 ND2 5icn_B_prep.pdb #1/B MET 350 O no hydrogen 3.555 N/A
5icn_B_prep.pdb #1/B THR 277 N 5icn_B_prep.pdb #1/B ASP 234 OD1 no hydrogen 2.814 N/A
5icn_B_prep.pdb #1/B THR 277 OG1 5icn_B_prep.pdb #1/B ASP 234 OD2 no hydrogen 2.552 N/A
5icn_B_prep.pdb #1/B GLY 280 N 5icn_B_prep.pdb #1/B THR 277 OG1 no hydrogen 2.955 N/A
5icn_B_prep.pdb #1/B HIS 281 N 5icn_B_prep.pdb #1/B THR 277 O no hydrogen 2.803 N/A
5icn_B_prep.pdb #1/B ALA 282 N 5icn_B_prep.pdb #1/B ILE 278 O no hydrogen 2.792 N/A
5icn_B_prep.pdb #1/B LYS 283 N 5icn_B_prep.pdb #1/B LYS 279 O no hydrogen 2.962 N/A
5icn_B_prep.pdb #1/B LYS 283 NZ 5icn_B_prep.pdb #1/B GLU 286 OE1 no hydrogen 3.442 N/A
5icn_B_prep.pdb #1/B CYS 284 N 5icn_B_prep.pdb #1/B HIS 281 O no hydrogen 3.307 N/A
5icn_B_prep.pdb #1/B CYS 284 SG 5icn_B_prep.pdb #1/B GLY 280 O no hydrogen 3.884 N/A
5icn_B_prep.pdb #1/B GLU 286 N 5icn_B_prep.pdb #1/B ALA 282 O no hydrogen 2.878 N/A
5icn_B_prep.pdb #1/B PHE 287 N 5icn_B_prep.pdb #1/B LYS 283 O no hydrogen 3.014 N/A
5icn_B_prep.pdb #1/B VAL 288 N 5icn_B_prep.pdb #1/B CYS 284 O no hydrogen 2.997 N/A
5icn_B_prep.pdb #1/B LYS 289 N 5icn_B_prep.pdb #1/B VAL 285 O no hydrogen 2.894 N/A
5icn_B_prep.pdb #1/B LYS 289 NZ 5icn_B_prep.pdb #1/B ASP 321 OD1 no hydrogen 2.953 N/A
5icn_B_prep.pdb #1/B SER 290 N 5icn_B_prep.pdb #1/B GLU 286 O no hydrogen 3.026 N/A
5icn_B_prep.pdb #1/B SER 290 OG 5icn_B_prep.pdb #1/B PHE 287 O no hydrogen 2.191 N/A
5icn_B_prep.pdb #1/B PHE 291 N 5icn_B_prep.pdb #1/B VAL 288 O no hydrogen 2.840 N/A
5icn_B_prep.pdb #1/B ASN 292 N 5icn_B_prep.pdb #1/B LYS 289 O no hydrogen 2.829 N/A
5icn_B_prep.pdb #1/B MET 295 N 5icn_B_prep.pdb #1/B ASP 130 O no hydrogen 2.962 N/A
5icn_B_prep.pdb #1/B LEU 296 N 5icn_B_prep.pdb #1/B VAL 257 O no hydrogen 3.076 N/A
5icn_B_prep.pdb #1/B MET 297 N 5icn_B_prep.pdb #1/B ALA 132 O no hydrogen 2.942 N/A
5icn_B_prep.pdb #1/B LEU 298 N 5icn_B_prep.pdb #1/B LEU 259 O no hydrogen 3.099 N/A
5icn_B_prep.pdb #1/B GLY 301 N 5icn_B_prep.pdb #1/B ASP 176 OD2 no hydrogen 2.964 N/A
5icn_B_prep.pdb #1/B TYR 303 N 5icn_B_prep.pdb #1/B ASP 269 OD1 no hydrogen 2.800 N/A
5icn_B_prep.pdb #1/B THR 304 N 5icn_B_prep.pdb #1/B ASP 269 OD1 no hydrogen 3.310 N/A
5icn_B_prep.pdb #1/B THR 304 OG1 5icn_B_prep.pdb #1/B GLY 268 O no hydrogen 2.579 N/A
5icn_B_prep.pdb #1/B ASN 307 N 5icn_B_prep.pdb #1/B THR 304 O no hydrogen 2.753 N/A
5icn_B_prep.pdb #1/B VAL 308 N 5icn_B_prep.pdb #1/B THR 304 O no hydrogen 3.269 N/A
5icn_B_prep.pdb #1/B ALA 309 N 5icn_B_prep.pdb #1/B ILE 305 O no hydrogen 2.803 N/A
5icn_B_prep.pdb #1/B ARG 310 N 5icn_B_prep.pdb #1/B ARG 306 O no hydrogen 3.193 N/A
5icn_B_prep.pdb #1/B ARG 310 NE 5icn_B_prep.pdb #1/B LYS 342 O no hydrogen 2.693 N/A
5icn_B_prep.pdb #1/B ARG 310 NH1 5icn_B_prep.pdb #1/B ASN 307 OD1 no hydrogen 3.106 N/A
5icn_B_prep.pdb #1/B ARG 310 NH2 5icn_B_prep.pdb #1/B LYS 342 O no hydrogen 2.891 N/A
5icn_B_prep.pdb #1/B CYS 311 N 5icn_B_prep.pdb #1/B ASN 307 O no hydrogen 2.729 N/A
5icn_B_prep.pdb #1/B CYS 311 SG 5icn_B_prep.pdb #1/B HIS 281 ND1 no hydrogen 3.137 N/A
5icn_B_prep.pdb #1/B TRP 312 N 5icn_B_prep.pdb #1/B VAL 308 O no hydrogen 3.178 N/A
5icn_B_prep.pdb #1/B TRP 312 NE1 5icn_B_prep.pdb #1/B CYS 261 O no hydrogen 2.948 N/A
5icn_B_prep.pdb #1/B THR 313 N 5icn_B_prep.pdb #1/B ALA 309 O no hydrogen 3.053 N/A
5icn_B_prep.pdb #1/B THR 313 OG1 5icn_B_prep.pdb #1/B ALA 309 O no hydrogen 2.843 N/A
5icn_B_prep.pdb #1/B TYR 314 N 5icn_B_prep.pdb #1/B ARG 310 O no hydrogen 2.863 N/A
5icn_B_prep.pdb #1/B GLU 315 N 5icn_B_prep.pdb #1/B CYS 311 O no hydrogen 2.684 N/A
5icn_B_prep.pdb #1/B THR 316 N 5icn_B_prep.pdb #1/B TRP 312 O no hydrogen 2.961 N/A
5icn_B_prep.pdb #1/B THR 316 N 5icn_B_prep.pdb #1/B THR 313 O no hydrogen 3.140 N/A
5icn_B_prep.pdb #1/B THR 316 OG1 5icn_B_prep.pdb #1/B TRP 312 O no hydrogen 2.288 N/A
5icn_B_prep.pdb #1/B ALA 317 N 5icn_B_prep.pdb #1/B THR 313 O no hydrogen 3.175 N/A
5icn_B_prep.pdb #1/B VAL 318 N 5icn_B_prep.pdb #1/B TYR 314 O no hydrogen 3.078 N/A
5icn_B_prep.pdb #1/B ALA 319 N 5icn_B_prep.pdb #1/B GLU 315 O no hydrogen 3.313 N/A
5icn_B_prep.pdb #1/B LEU 320 N 5icn_B_prep.pdb #1/B THR 316 O no hydrogen 3.206 N/A
5icn_B_prep.pdb #1/B ASP 321 N 5icn_B_prep.pdb #1/B VAL 318 O no hydrogen 3.052 N/A
5icn_B_prep.pdb #1/B THR 322 N 5icn_B_prep.pdb #1/B ALA 317 O no hydrogen 3.247 N/A
5icn_B_prep.pdb #1/B LEU 328 N 5icn_B_prep.pdb #1/B PHE 341 O no hydrogen 3.158 N/A
5icn_B_prep.pdb #1/B TYR 330 OH 5icn_B_prep.pdb #1/B GLU 335 OE2 no hydrogen 3.058 N/A
5icn_B_prep.pdb #1/B ASN 331 ND2 5icn_B_prep.pdb #1/B PRO 329 O no hydrogen 2.853 N/A
5icn_B_prep.pdb #1/B TYR 333 N 5icn_B_prep.pdb #1/B ASN 331 OD1 no hydrogen 2.878 N/A
5icn_B_prep.pdb #1/B PHE 334 N 5icn_B_prep.pdb #1/B ASN 331 O no hydrogen 2.946 N/A
5icn_B_prep.pdb #1/B TYR 336 N 5icn_B_prep.pdb #1/B TYR 333 O no hydrogen 2.776 N/A
5icn_B_prep.pdb #1/B PHE 337 N 5icn_B_prep.pdb #1/B PHE 334 O no hydrogen 3.225 N/A
5icn_B_prep.pdb #1/B GLY 338 N 5icn_B_prep.pdb #1/B TYR 336 O no hydrogen 3.087 N/A
5icn_B_prep.pdb #1/B PHE 341 N 5icn_B_prep.pdb #1/B PHE 337 O no hydrogen 3.046 N/A
5icn_B_prep.pdb #1/B LYS 342 N 5icn_B_prep.pdb #1/B ASP 340 OD2 no hydrogen 3.280 N/A
5icn_B_prep.pdb #1/B LEU 343 N 5icn_B_prep.pdb #1/B ASN 326 O no hydrogen 2.726 N/A
5icn_B_prep.pdb #1/B HIS 344 N 5icn_B_prep.pdb #1/B ASN 326 OD1 no hydrogen 3.050 N/A
5icn_B_prep.pdb #1/B SER 348 N 5icn_B_prep.pdb #1/B ASN 275 OD1 no hydrogen 2.888 N/A
5icn_B_prep.pdb #1/B MET 350 N 5icn_B_prep.pdb #1/B SER 348 OG no hydrogen 3.358 N/A
5icn_B_prep.pdb #1/B ASN 352 ND2 5icn_B_prep.pdb #1/B ASP 233 OD2 no hydrogen 2.542 N/A
5icn_B_prep.pdb #1/B GLN 353 N 5icn_B_prep.pdb #1/B ASP 230 O no hydrogen 3.173 N/A
5icn_B_prep.pdb #1/B ASN 354 N 5icn_B_prep.pdb #1/B ASN 352 OD1 no hydrogen 2.826 N/A
5icn_B_prep.pdb #1/B TYR 358 OH 5icn_B_prep.pdb #1/B PRO 227 O no hydrogen 3.042 N/A
5icn_B_prep.pdb #1/B LEU 359 N 5icn_B_prep.pdb #1/B THR 355 O no hydrogen 3.209 N/A
5icn_B_prep.pdb #1/B GLU 360 N 5icn_B_prep.pdb #1/B ASN 356 O no hydrogen 3.133 N/A
5icn_B_prep.pdb #1/B LYS 361 N 5icn_B_prep.pdb #1/B GLU 357 O no hydrogen 3.131 N/A
5icn_B_prep.pdb #1/B LYS 363 N 5icn_B_prep.pdb #1/B LEU 359 O no hydrogen 2.869 N/A
5icn_B_prep.pdb #1/B LYS 363 NZ 5icn_B_prep.pdb #1/B GLU 360 OE2 no hydrogen 2.828 N/A
5icn_B_prep.pdb #1/B GLN 364 N 5icn_B_prep.pdb #1/B GLU 360 O no hydrogen 3.127 N/A
5icn_B_prep.pdb #1/B ARG 365 N 5icn_B_prep.pdb #1/B LYS 361 O no hydrogen 3.167 N/A
5icn_B_prep.pdb #1/B LEU 366 N 5icn_B_prep.pdb #1/B ILE 362 O no hydrogen 3.013 N/A
5icn_B_prep.pdb #1/B PHE 367 N 5icn_B_prep.pdb #1/B LYS 363 O no hydrogen 2.929 N/A
5icn_B_prep.pdb #1/B GLU 368 N 5icn_B_prep.pdb #1/B GLN 364 O no hydrogen 3.027 N/A
5icn_B_prep.pdb #1/B ASN 369 N 5icn_B_prep.pdb #1/B ARG 365 O no hydrogen 3.148 N/A
5icn_B_prep.pdb #1/B LEU 370 N 5icn_B_prep.pdb #1/B LEU 366 O no hydrogen 2.785 N/A
5icn_B_prep.pdb #1/B ARG 371 N 5icn_B_prep.pdb #1/B PHE 367 O no hydrogen 3.092 N/A
5icn_B_prep.pdb #1/B MET 372 N 5icn_B_prep.pdb #1/B ASN 369 O no hydrogen 3.118 N/A
5icn_B_prep.pdb #1/B LEU 373 N 5icn_B_prep.pdb #1/B LEU 370 O no hydrogen 3.225 N/A
317 hydrogen bonds found
> undo
[Repeated 1 time(s)]
> select add #2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select subtract #2
Nothing selected
> hide #!2 models
> hide #1 target a
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/DockedCompounds/5icn_B_webina_out_2.9.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 17 GLY B 20 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO B 32 ARG B 34 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE B 35 ASN B 44 1
10
Start residue of secondary structure not found: HELIX 4 4 TYR B 48 LYS B 50 1
3
Start residue of secondary structure not found: HELIX 5 5 ALA B 61 MET B 64 1
4
26 messages similar to the above omitted
> select add #2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3
42 atoms, 46 bonds, 2 residues, 2 models selected
> select add #4
63 atoms, 69 bonds, 3 residues, 3 models selected
> select add #5
84 atoms, 92 bonds, 4 residues, 4 models selected
> select add #6
105 atoms, 115 bonds, 5 residues, 5 models selected
> select add #7
126 atoms, 138 bonds, 6 residues, 6 models selected
> select add #8
147 atoms, 161 bonds, 7 residues, 7 models selected
> select add #9
168 atoms, 184 bonds, 8 residues, 8 models selected
> select add #10
189 atoms, 207 bonds, 9 residues, 9 models selected
> select add #1
3156 atoms, 3249 bonds, 381 residues, 10 models selected
> ui tool show H-Bonds
> hbonds sel color #fa49f8 radius 0.1 dashes 6 intraModel false intraMol false
> intraRes false reveal true retainCurrent true log true
Finding intermodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5icn_B_prep.pdb
2 5icn_B_webina_out_2.1.pdb
3 5icn_B_webina_out_2.2.pdb
4 5icn_B_webina_out_2.3.pdb
5 5icn_B_webina_out_2.4.pdb
6 5icn_B_webina_out_2.5.pdb
7 5icn_B_webina_out_2.6.pdb
8 5icn_B_webina_out_2.7.pdb
9 5icn_B_webina_out_2.8.pdb
10 5icn_B_webina_out_2.9.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5icn_B_prep.pdb #1/B ASP 99 N 5icn_B_webina_out_2.4.pdb #5//chain_id='_' SUB 1 O20 no hydrogen 3.492 N/A
5icn_B_prep.pdb #1/B CYS 100 SG 5icn_B_webina_out_2.1.pdb #2//chain_id='_' SUB 1 O8 no hydrogen 3.545 N/A
5icn_B_prep.pdb #1/B GLY 149 N 5icn_B_webina_out_2.8.pdb #9//chain_id='_' SUB 1 O20 no hydrogen 3.129 N/A
5icn_B_prep.pdb #1/B PHE 205 N 5icn_B_webina_out_2.8.pdb #9//chain_id='_' SUB 1 O3 no hydrogen 3.415 N/A
5icn_B_webina_out_2.6.pdb #7//chain_id='_' SUB 1 N1 5icn_B_prep.pdb #1/B ASP 99 OD2 5icn_B_webina_out_2.6.pdb #7//chain_id='_' SUB 1 H1 3.199 2.381
5 hydrogen bonds found
> select subtract #10
3135 atoms, 3226 bonds, 380 residues, 9 models selected
> select subtract #9
3114 atoms, 3203 bonds, 379 residues, 8 models selected
> select subtract #8
3093 atoms, 3180 bonds, 378 residues, 7 models selected
> select subtract #7
3072 atoms, 3157 bonds, 377 residues, 6 models selected
> hide #11 models
> show #11 models
> close session
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module2/Exercises/Exercise2.1/5icn_B_prep.pdbqt
Chain information for 5icn_B_prep.pdb #1
---
Chain | Description
B | No description available
Computing secondary structure
Opened 5icn_B_prep.pdbqt containing 1 structures (2967 atoms, 3042 bonds)
> open /Users/kadahlst/Desktop/webina_out.pdbqt
Summary of feedback from opening /Users/kadahlst/Desktop/webina_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.407 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -7.883
Ignored bad PDB record found on line 4
REMARK INTER: -7.535
Ignored bad PDB record found on line 5
REMARK INTRA: -0.348
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.351
166 messages similar to the above omitted
Opened webina_out.pdbqt containing 9 structures (189 atoms, 207 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 469, in table_selection_changed
self.update_model_description()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
KeyError: 'RMSD l.b.'
KeyError: 'RMSD l.b.'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 543, in update_model_description
if len(column_map[title].display_value(docking_structure)) > 20:
~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15H0000SKS/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 9 days, 16 hours, 15 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.8.0
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.16
ChimeraX-AtomicLibrary: 14.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202509162234
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.3.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.12.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.4.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.4
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 8.4.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Vina output in ViewDock: KeyError: 'RMSD l.b.' |
comment:2 by , 7 weeks ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Kathe,
--Eric
Fix: https://github.com/RBVI/ChimeraX/commit/a51d3353f735ffb9213faf350f0ae50a43b7b032