AddH: z_align endpoints must be distinct

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-14)
Description
protonation issue

Log:
UCSF ChimeraX version: 0.8 (2018-12-14)  
How to cite UCSF ChimeraX  

> open 1ggr

Summary of feedback from opening 1ggr fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ggr from
http://files.rcsb.org/download/1ggr.cif  
Fetching CCD PO3 from http://ligand-expo.rcsb.org/reports/P/PO3/PO3.cif  
  
1ggr title:  
Complex of enzyme iiaglc and the histidine-containing phosphocarrier protein
HPR from escherichia coli NMR, restrained regularized mean structure [more
info...]  
  
Chain information for 1ggr  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A | PTS system, glucose-specific iia component  
1.1/B 1.2/B 1.3/B | phosphocarrier protein HPR  
  
  
FYI: command is replacing existing command: "addh"  

> addh hbond true

Termini for 1ggr (#1.1) chain B determined from SEQRES records  
Termini for 1ggr (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: 1ggr #1.1/B MET 301  
Chain-initial residues that are not actual N termini: 1ggr #1.1/A THR 19  
Chain-final residues that are actual C termini: 1ggr #1.1/B GLU 385, 1ggr
#1.1/A LYS 168  
Chain-final residues that are not actual C termini:  

Unknown hybridization for atom (P) of residue type PO3; not adding hydrogens
to it  

182 hydrogen bonds  
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py:669: RuntimeWarning: divide by zero
encountered in double_scalars  
v *= cos70_5 * bond_len / norm(v)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2585, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 155, in hbond_add_hydrogens  
in_isolation=in_isolation, **prot_schemes)  
File
"/Applications/ChimeraX.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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 741, in add_hydrogens  
bonded_pos, toward=toward, away=away, away2=away2)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 78, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 158, in tetra_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
xforms = [z_align(atom_pos, bond_pos)]  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 501, in z_align  
raise ValueError("z_align endpoints must be distinct")  
ValueError: z_align endpoints must be distinct  
  
ValueError: z_align endpoints must be distinct  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 501, in z_align  
raise ValueError("z_align endpoints must be distinct")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.9
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

The seems to be an error in the 1ggr entry. The coordinates of all the atoms of the PO3 in the first model are zero.