AddH: incorrect removal from hbond_info

[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 error

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

> open 4uub

Summary of feedback from opening 4uub fetched from pdb  
---  
notes | Fetching compressed mmCIF 4uub from
http://files.rcsb.org/download/4uub.cif  
Fetching CCD BEZ from http://ligand-expo.rcsb.org/reports/B/BEZ/BEZ.cif  
Fetching CCD EPE from http://ligand-expo.rcsb.org/reports/E/EPE/EPE.cif  
Fetching CCD DMS from http://ligand-expo.rcsb.org/reports/D/DMS/DMS.cif  
Fetching CCD SU8 from http://ligand-expo.rcsb.org/reports/S/SU8/SU8.cif  
  
FYI: command is replacing existing command: "lighting"  
4uub title:  
Crystal structure of zebrafish Sirtuin 5 in complex with 2R-butyl-
succinylated CPS1-peptide [more info...]  
  
Chain information for 4uub #1  
---  
Chain | Description  
A B | nad-dependent protein deacylase sirtuin-5, mitochondrial  
D | carbamoylphosphate synthetase I  
  
Non-standard residues in 4uub #1  
---  
BEZ — benzoic acid  
DMS — dimethyl sulfoxide  
EDO — 1,2-ethanediol (ethylene glycol)  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
NA — sodium ion  
SU8 — (2R)-2-butylbutanedioic acid ((2R)-2-butylsuccinic acid)  
ZN — zinc ion  
  
4uub mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
  
FYI: command is replacing existing command: "addh"  

> addh hbond true

Termini for 4uub (#1) chain D determined from SEQRES records  
Termini for 4uub (#1) chain A determined from SEQRES records  
Termini for 4uub (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /D BEZ 0  
Chain-initial residues that are not actual N termini: /A ASP 35, /A LYS 282,
/B SER 33, /B PHE 281  
Chain-final residues that are actual C termini: /D VAL 8, /A GLU 298, /B GLU
298  
Chain-final residues that are not actual C termini: /A GLN 279, /B ALA 277  
Missing OXT added to C-terminal residue /D VAL 8  
611 hydrogen bonds  
Adding 'H' to /A ASP 35  
Adding 'H' to /A LYS 282  
Adding 'H' to /B SER 33  
Adding 'H' to /B PHE 281  
/A GLN 279 is not terminus, removing H atom from 'C'  
/B ALA 277 is not terminus, removing H atom from 'C'  
4241 hydrogens added  
FYI: command is replacing existing command: "delete"  

> delete #1

> open 4ubb

Summary of feedback from opening 4ubb fetched from pdb  
---  
notes | Fetching compressed mmCIF 4ubb from
http://files.rcsb.org/download/4ubb.cif  
Fetching CCD DC from http://ligand-expo.rcsb.org/reports/D/DC/DC.cif  
Fetching CCD DG from http://ligand-expo.rcsb.org/reports/D/DG/DG.cif  
Fetching CCD DA from http://ligand-expo.rcsb.org/reports/D/DA/DA.cif  
Fetching CCD DT from http://ligand-expo.rcsb.org/reports/D/DT/DT.cif  
Fetching CCD 8OG from http://ligand-expo.rcsb.org/reports/8/8OG/8OG.cif  
Fetching CCD 8DG from http://ligand-expo.rcsb.org/reports/8/8DG/8DG.cif  
Fetching CCD PPV from http://ligand-expo.rcsb.org/reports/P/PPV/PPV.cif  
  
4ubb title:  
DNA polymerase β reactant complex with a templating cytosine and incoming
8-oxodGTP, 40 s [more info...]  
  
Chain information for 4ubb #1  
---  
Chain | Description  
A | DNA polymerase β  
D | 5'-D(P*GP*TP*CP*GP*G)-3'  
P | 5'-D(*GP*CP*TP*GP*ap*TP*GP*CP*GP*CP*(8OG))-3'  
T | 5'-D(*CP*CP*GP*ap*CP*CP*GP*CP*GP*CP*ap*TP*CP*ap*GP*C)-3'  
  
Non-standard residues in 4ubb #1  
---  
8DG — 8-oxo-2'-deoxyguanosine-5'-triphosphate  
CA — calcium ion  
MG — magnesium ion  
PPV — pyrophosphate  
  
  

> addh hbond true

Termini for 4ubb (#1) chain D determined from SEQRES records  
Termini for 4ubb (#1) chain T determined from SEQRES records  
Termini for 4ubb (#1) chain A determined from SEQRES records  
Termini for 4ubb (#1) chain P determined from SEQRES records  
Chain-initial residues that are actual N termini: /D DG 1, /T DC 1, /P DG 1  
Chain-initial residues that are not actual N termini: /A THR 10  
Chain-final residues that are actual C termini: /D DG 5, /T DC 16, /A GLU 335,
/P 8OG 11  
Chain-final residues that are not actual C termini:  
1116 hydrogen bonds  
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 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 443, in add_hydrogens  
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 1141, in _try_finish  
hbond_info[other].remove((not is_acc, atom))  
KeyError: <chimerax.atomic.molobject.Atom object at 0x12be45dc8>  
  
KeyError:  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 1141, in _try_finish  
hbond_info[other].remove((not is_acc, atom))  
  
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]

2izq now also exhibits his behavior (after microheterogenicity problem was fixed)

[Eric Pettersen]

Metals being noted as "acceptors" also needed coordinators noted as donors.