Disconnected hydrogens in 6rhz

[lpravda@…]

In entry 6rhz, the following hydrogens have no bonds:

/B CLA 1238 H122
/B CLA 1238 H13
/B CLA 1238 H203

In the PDB form of the entry, they are bonded to the nearby carbon. I don't know if this is an issue with ChimeraX mmCIF reader or with the mmCIF entry itself...

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
not really a protaonation issue. probably a source code formatting issue?

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6rhz fromDatabase pdbe_updated

Summary of feedback from opening 6rhz fetched from pdbe_updated  
---  
note |  
  
  
| Summary of feedback from opening
/Users/lpravda/Downloads/ChimeraX/pdbe_updated/6rhz.cif  
  
---  
  
  
  
  
warning | Atom H1 is not in the residue template for MET #1 in chain J  
  
  
  
  
  
6rhz title:  
Structure of a minimal photosystem I from a green alga [more info...]  
  
Chain information for 6rhz #1  
---  
Chain | Description  
1 | Chlorophyll a-b binding protein, chloroplastic  
2 | Chlorophyll a-b binding protein, Lhca2  
3 | Chlorophyll a-b binding protein, chloroplastic  
4 | Chlorophyll a-b binding protein, Lhca4  
A | Photosystem I P700 chlorophyll a apoprotein A1  
B | Photosystem I P700 chlorophyll a apoprotein A2  
C | Photosystem I iron-sulfur center  
D | Photosystem I reaction center subunit II, PsaD  
E | Photosystem I reaction center subunit IV, PsaE  
F | Photosystem I reaction center subunit III, PsaF  
J | Photosystem I reaction center subunit IX  
  
Non-standard residues in 6rhz #1  
---  
BCR — β-carotene  
CHL — chlorophyll B  
CL0 — chlorophyll A isomer  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol, lutein)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)  
  
  

Invalid "hbond" argument: Expected true or false (or 1 or 0)  

> addh hbond true

Summary of feedback from adding hydrogens to 6rhz #1  
---  
warning | Unknown hybridization for atom (S4) of residue type SF4; not adding
hydrogens to it  
notes | Termini for 6rhz (#1) chain 1 determined from SEQRES records  
Termini for 6rhz (#1) chain 2 determined from SEQRES records  
Termini for 6rhz (#1) chain 3 determined from SEQRES records  
Termini for 6rhz (#1) chain 4 determined from SEQRES records  
Termini for 6rhz (#1) chain A determined from SEQRES records  
6 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 GLN 32, /2 ASP 63, /3 TYR
73, /4 ASP 123, /A VAL 13, /B PHE 6, /C ALA 2, /D PRO 69, /E GLU 65, /F ASP
78, /J MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /1 VAL 228, /2 ILE 270, /3 THR
282, /4 PHE 333, /A GLY 751, /B GLY 735, /C TYR 81, /D PRO 209, /E LYS 128, /F
SER 240, /J SER 40  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /1 VAL 228  
Missing OXT added to C-terminal residue /2 ILE 270  
Missing OXT added to C-terminal residue /3 THR 282  
Missing OXT added to C-terminal residue /4 PHE 333  
Missing OXT added to C-terminal residue /C TYR 81  
4 messages similar to the above omitted  
2001 hydrogen bonds  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 171, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 748, in add_hydrogens  
_attach_hydrogens(a, altloc_hpos_info, bonding_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 893, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 855, in add_altloc_hyds  
pos, bonding_info, alt_loc)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 881, in new_hydrogen  
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 1003, in _h_name  
while find_atom("%s%s" % (h_name, to_h36(h_num, h_digits))):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 943, in to_h36  
decimal_limit = eval('9' * max_digits)  
File "<string>", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 943, in to_h36  
decimal_limit = eval('9' * max_digits)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Reported by Lucas Pravda