AddH: More than 2 coplanar positions specified!

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-17)
Description
open 3kch; addh

Log:
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open 3kch

3kch title:  
Baranase crosslinked by glutaraldehyde [more info...]  
  
Chain information for 3kch #1  
---  
Chain | Description  
A B C | Ribonuclease  
  
Non-standard residues in 3kch #1  
---  
PTD — pentanedial  
  
3kch mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
  
  

> addh

Termini for 3kch (#1) chain A determined from SEQRES records  
Termini for 3kch (#1) chain C determined from SEQRES records  
Termini for 3kch (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A VAL 3, /C VAL 3, /B
VAL 3  
Chain-final residues that are actual C termini: /A ARG 110, /C ARG 110, /B ARG
110  
Chain-final residues that are not actual C termini:  
Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 55, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 163, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 241, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hbond.py", line 568, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[pett]

The PTD ligand covalently binds to various ARG side chains (e.g. /A:59) in a way that fundamentally changes their geometry and chemistry. They are no longer planar and the two terminal nitrogens now take 1 and 3 protons instead of 2 and 2, and therefore the templated atom types are no longer correct (it's also arguable whether this residue is really an "arginine" anymore since its character and protonation is fundamentally altered).

Would need to think about what to do here. Probably change atom typing to ignore templates if there are cross-residue side chain bonds (other than cysteine disulphide).