No bonds for residue UNL (unknown ligand) in 6dhf

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2019-12-24)
Description
Structure protonation

Log:
UCSF ChimeraX version: 0.92 (2019-12-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6dhf fromDatabase pdbe_updated

Summary of feedback from opening 6dhf fetched from pdbe_updated  
---  
warnings | Atom H1 is not in the residue template for MET #1 in chain L  
Atom H1 is not in the residue template for ALA #1 in chain V  
Atom H1 is not in the residue template for MET #1 in chain Z  
Atom H1 is not in the residue template for ALA #1 in chain v  
Atom H1 is not in the residue template for MET #1 in chain z  
notes | Fetching compressed mmCIF 6dhf from http://www.ebi.ac.uk/pdbe/entry-
files/download/6dhf_updated.cif  
Fetching CCD FE2 from http://ligand-expo.rcsb.org/reports/F/FE2/FE2.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD BCT from http://ligand-expo.rcsb.org/reports/B/BCT/BCT.cif  
Fetching CCD CLA from http://ligand-expo.rcsb.org/reports/C/CLA/CLA.cif  
Fetching CCD PHO from http://ligand-expo.rcsb.org/reports/P/PHO/PHO.cif  
Fetching CCD BCR from http://ligand-expo.rcsb.org/reports/B/BCR/BCR.cif  
Fetching CCD PL9 from http://ligand-expo.rcsb.org/reports/P/PL9/PL9.cif  
Fetching CCD SQD from http://ligand-expo.rcsb.org/reports/S/SQD/SQD.cif  
Fetching CCD DGD from http://ligand-expo.rcsb.org/reports/D/DGD/DGD.cif  
Fetching CCD OEX from http://ligand-expo.rcsb.org/reports/O/OEX/OEX.cif  
Fetching CCD LMG from http://ligand-expo.rcsb.org/reports/L/LMG/LMG.cif  
Fetching CCD LHG from http://ligand-expo.rcsb.org/reports/L/LHG/LHG.cif  
  
6dhf title:  
RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at
2.08 Angstrom resolution [more info...]  
  
Chain information for 6dhf #1  
---  
Chain | Description  
A a | Photosystem II protein D1 1  
B b | Photosystem II CP47 reaction center protein  
C c | Photosystem II CP43 reaction center protein  
D d | Photosystem II D2 protein  
E e | Cytochrome b559 subunit α  
F f | Cytochrome b559 subunit β  
H h | Photosystem II reaction center protein H  
I i | Photosystem II reaction center protein I  
J j | Photosystem II reaction center protein J  
K k | Photosystem II reaction center protein K  
L l | Photosystem II reaction center protein L  
M m | Photosystem II reaction center protein M  
O o | Photosystem II manganese-stabilizing polypeptide  
R r | Photosystem II protein Y  
T t | Photosystem II reaction center protein T  
U u | Photosystem II 12 kDa extrinsic protein  
V v | Cytochrome c-550  
X x | Photosystem II reaction center X protein  
Y y | Photosystem II reaction center protein Ycf12  
Z z | Photosystem II reaction center protein Z  
  
Non-standard residues in 6dhf #1  
---  
BCR — β-carotene  
BCT — bicarbonate ion  
CL — chloride ion  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE2 — Fe (II) ion  
FME — N-formylmethionine  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
UNL — unknown ligand  
  
  

> addh hbond true

Summary of feedback from adding hydrogens to 6dhf #1  
---  
warnings | Not adding hydrogens to /B SER 294 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /E LYS 84 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /H LEU 65 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /M GLN 33 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /Y LEU 22 CB because it is missing heavy-atom bond
partners  
15 messages similar to the above omitted  
Unknown hybridization for atoms (O2, O1, O3, O5) of residue type OEX; not
adding hydrogens to them  
Unknown hybridization for atoms (C16, O2, C4, C12, C8, C9, C2, C1, C6, C14,
C11, C3, C17, C10, C15, C7, O1, C13, C18, C5) of residue type UNL; not adding
hydrogens to them  
Unknown hybridization for atom (O4) of residue type LMG; not adding hydrogens
to it  
notes | Termini for 6dhf (#1) chain A determined from SEQRES records  
Termini for 6dhf (#1) chain B determined from SEQRES records  
Termini for 6dhf (#1) chain C determined from SEQRES records  
Termini for 6dhf (#1) chain D determined from SEQRES records  
Termini for 6dhf (#1) chain E determined from SEQRES records  
35 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ALA 11, /B GLY 2, /D ARG
12, /F SER 12, /H ALA 2, /I FME 1, /J GLY 5, /K LYS 10, /L MET 1, /M FME 1, /O
GLN 3, /T FME 1, /U GLU 8, /V ALA 1, /X THR 2, /Z MET 1, /R ASP 2, /a ALA 11,
/b GLY 2, /c ALA 23, /d ARG 12, /e GLY 3, /f SER 12, /h ALA 2, /i FME 1, /j
GLY 5, /k LYS 10, /m FME 1, /o GLN 3, /t FME 1, /u GLU 8, /v ALA 1, /y GLU 17,
/x THR 2, /z MET 1, /r ASP 2  
Chain-initial residues that are not actual N termini: /C GLY 32, /E THR 4, /Y
ALA 20, /l GLU 2  
Chain-final residues that are actual C termini: /A ALA 344, /B ARG 506, /C ASP
473, /D LEU 352, /E LYS 84, /F ARG 45, /H GLY 66, /I ASP 36, /J LEU 40, /K ARG
46, /L ASN 37, /M GLN 33, /O ALA 246, /T THR 30, /U LYS 104, /V TYR 137, /Y
LEU 46, /X ARG 39, /Z VAL 62, /R LEU 35, /a ALA 344, /b ARG 506, /c ASP 473,
/d LEU 352, /e LYS 84, /f ARG 45, /i ASP 36, /j LEU 40, /k ARG 46, /l ASN 37,
/o ALA 246, /t THR 30, /u LYS 104, /v TYR 137, /y LEU 46, /x ARG 39, /z VAL 62  
Chain-final residues that are not actual C termini: /h ALA 64, /m GLN 32, /r
GLN 32  
Missing OXT added to C-terminal residue /B ARG 506  
Missing OXT added to C-terminal residue /E LYS 84  
Missing OXT added to C-terminal residue /H GLY 66  
Missing OXT added to C-terminal residue /I ASP 36  
Missing OXT added to C-terminal residue /M GLN 33  
9 messages similar to the above omitted  
11101 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 2837, 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 853, 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 879, 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 1001, 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 941, 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 941, in to_h36  
decimal_limit = eval('9' * max_digits)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Apparently trying to add hydrogen to /B:620@h101 (a hydrogen!). Needs further investigation.

[Eric Pettersen]

Reported by Lukas Pravda

[Greg Couch]

Changed code to connect atoms by distance when template (CCD entry) has no bonds.