Missing bond

[kristen.browne@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202212010831 (2022-12-01 08:31:51 UTC)
Description
open pdbe_bio:2DEZ maxAssemblies 1 autoStyle false
Switch to the surface monochrome representation

Log:
UCSF ChimeraX version: 1.6.dev202212010831 (2022-12-01)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2DEZ

2dez title:  
Structure of human PYY [more info...]  
  
Chain information for 2dez  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Peptide YY |
PYY_HUMAN  
  

> close #1.2-20

> preset nih3d "surface monochrome"

Using preset: NIH3D / Surface Monochrome  
Changed 603 atom radii, 612 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2dez #1.1  
---  
notes | Termini for 2dez (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A TYR 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A NH2 37  
Chain-final residues that are not actual C termini:  
28 hydrogen bonds  
0 hydrogens added  
  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    surface #1.1 enclose #1.1 grid 0.5 sharp true
    color nih_blue

  

> close session

> open pdbe_bio:2DEZ maxAssemblies 1 autoStyle false

Summary of feedback from opening 2DEZ fetched from pdbe_bio  
---  
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.  
note | Fetching compressed 2DEZ bioassembly 1 from
https://www.ebi.ac.uk/pdbe/static/entry/download/2dez-assembly-1.cif.gz  
  
subunit 1 title:  
Structure of human PYY [more info...]  
  
Chain information for subunit 1 #1.1  
---  
Chain | Description  
A | Peptide YY  
  
Non-standard residues in subunit 1 #1.1  
---  
NH2 — (NH2)  
  
Chain information for subunit 2 #1.2  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 3 #1.3  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 4 #1.4  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 5 #1.5  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 6 #1.6  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 7 #1.7  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 8 #1.8  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 9 #1.9  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 10 #1.10  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 11 #1.11  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 12 #1.12  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 13 #1.13  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 14 #1.14  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 15 #1.15  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 16 #1.16  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 17 #1.17  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 18 #1.18  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 19 #1.19  
---  
Chain | Description  
A | Peptide YY  
  
Chain information for subunit 20 #1.20  
---  
Chain | Description  
A | Peptide YY  
  
Opened 1 biological assemblies for 2DEZ  

> close #1.2-20

> preset nih3d "surface monochrome"

Using preset: NIH3D / Surface Monochrome  
Changed 603 atom radii, 611 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to subunit 1 #1.1  
---  
notes | No usable SEQRES records for subunit 1 (#1.1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A TYR 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A TYR 36  
altloc_atom: /A NH2 37 N  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\ui\gui.py", line 1164, in <lambda>  
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\preset_mgr\cmd.py", line 50, in preset_cmd  
run_preset(session, cat, matches[0])  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\preset_mgr\cmd.py", line 71, in run_preset  
session.presets.preset_function(category, preset)()  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 60, in cb  
bi.run_provider(self.session, name, self)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\nih_presets\\__init__.py", line 22, in run_provider  
run_preset(session, name, mgr, **kw)  
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\nih_presets\presets.py", line 302, in run_preset  
mgr.execute(cmd)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 88, in execute  
run(self.session, line, log=False)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\hbond.py", line 214, in add_hydrogens  
_attach_hydrogens(atom, altloc_hpos_info, bonding_info)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\hbond.py", line 898, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 899, in add_altloc_hyds  
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 938, in new_hydrogen  
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 1035, in _h_name  
raise ValueError("All hydrogen names for %s taken!" % atom)  
ValueError: All hydrogen names for /A NH2 37 N taken!  
  
ValueError: All hydrogen names for /A NH2 37 N taken!  
  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 1035, in _h_name  
raise ValueError("All hydrogen names for %s taken!" % atom)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US

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[Eric Pettersen]

For open pdbe_bio:2DEZ maxAssemblies 1, the bond between TYR 36 (atom C) and NH2 37 (atom N) is missing.