AddH: More than 2 coplanar positions specified

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/katrinawarner/Documents/pre-hook-2.pdb format pdb

Chain information for pre-hook-2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/katrinawarner/Downloads/TOM1 modeling/P77_J229_enhanced.mrc"

Opened P77_J229_enhanced.mrc as #2, grid size 260,260,260, pixel 1.15, shown
at level 0.00135, step 2, values float32  

> isolde start

> set selectionWidth 4

Populating font family aliases took 649 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 43 residues in model #1 to IUPAC-IUB
standards.  
Chain information for pre-hook-2.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> clipper associate #2 toModel #1

Opened P77_J229_enhanced.mrc as #1.1.1.1, grid size 260,260,260, pixel 1.15,
shown at step 1, values float32  

> isolde sim start sel

ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to pre-hook-2.pdb #1.2  
---  
notes | No usable SEQRES records for pre-hook-2.pdb (#1.2) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ALAA 694  
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 ALA 1068  
  
Traceback (most recent call last):  
File "/Users/katrinawarner/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "/Users/katrinawarner/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 224, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 169, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 249, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 574, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File
"/private/var/folders/z1/xpmrl_t53pj8q271bbphs90m0000gn/T/AppTranslocation/173E1313-74D9-4461-9F68-3C025EBFB578/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.31
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9323)
      Kernel Version: Darwin 18.7.0
      Time since boot: 24 days 10 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


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    cftime: 1.6.0
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    ChimeraX-AddH: 2.1.11
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[Eric Pettersen]

Was asking for the trigonal planar bonding position to an atom that had more than two other atoms bonded to it. Typically a problem with the structure, so would actually need the structure in order to say anything more.