Add Charges: hydrogen bonded to atom that should not have hydrogens

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-13.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202302110040 (2023-02-11 00:40:33 UTC)
Description
coulombic failed on 7y5e (after about 10 minutes) with "Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /1L UNK 46 HO bonded to atom that should not have hydrogens (/1L UNK 46 O)"


Log:
UCSF ChimeraX version: 1.6.dev202302110040 (2023-02-11)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7y5e

Summary of feedback from opening 7y5e fetched from pdb  
---  
warnings | Atom C14 has no neighbors to form bonds with according to residue
template for CLA /AN:801  
Atom C14 has no neighbors to form bonds with according to residue template for
CLA /A2:802  
note | Fetching compressed mmCIF 7y5e from
http://files.rcsb.org/download/7y5e.cif  
  
7y5e title:  
In situ single-PBS-PSII-PSI-LHCs megacomplex. [more info...]  
  
Chain information for 7y5e #1  
---  
Chain | Description | UniProt  
12 1N | Chlorophyll a-b binding protein, chloroplastic | A0A5J4Z6J3_PORPP
49-222  
16 1L 46 4L | CNT |  
18 1C B5 B7 B9 BA BB BF BI BK BP CB CD CQ D5 D7 D9 DA DB DF DI DJ DK DM DP ED
EQ F5 F7 F9 FA FB FF FI FJ FK FM FP GB GD GQ H5 H7 H9 HA HB HF HI HJ HK HM HP
IB ID IQ J5 J7 J9 JA JF JI JJ JK JM JP KD KQ L5 L7 L9 LA LB LF LI LJ LK LM LP
MB MD MQ N7 NA NB NF NJ NK NM NP O5 O9 OB OD OI OQ P1 P4 P7 PA PB PE PF PG PH
PJ PK PM PO PP Q5 Q9 QB QD QI QQ R1 R4 R7 RA RB RE RF RG RH RJ RK RM RO RP S5
S9 SB SD SI SQ T1 T4 T7 TA TE TF TG TH TJ TK TM TO TP U5 U9 UD UI UQ V1 V4 V7
VA VB VE VF VG VH VJ VK VM VO VP W5 W9 WD WI WQ X7 XA XB XF XJ XK XM XP Y1 Y4
Y5 Y9 YB YD YE YG YH YI YO YQ ZB ZF ZJ ZK ZM a1 a4 aB aE aG aH aO bB bF bK c1
c4 cE cG cH cJ cM cO dB dF dK e1 e4 eB eE eG eH eJ eM eO fF fK g1 g4 gB gE gG
gH gJ gM gO hF hK i1 i4 iE iG iH iJ iM iO jF jK k1 k4 kE kG kH kJ kM kO lF lK
m1 m4 mE mG mH mJ mM mO nF nK pF pK q8 qC rF rK s8 sC tF tK u8 uC vF vK w8 wC
y8 yC | B-phycoerythrin beta chain | PHEB_PORPP 1-177  
22 2N | Chlorophyll a-b binding protein of LHCII type III, chloroplastic |
P93450_PORPP 37-202  
23 Z3 | Lrc4 | A0A5J4YTV6_PORPP 20-178  
32 3N | Chlorophyll a-b binding protein, chloroplastic | A0A5J4YYC4_PORPP
42-210  
33 a3 | LRC5 | A0A5J4Z2M2_PORPP 10-297  
42 4N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4ZAY0_PORPP 37-208  
43 b3 | FAS1 domain-containing protein | A0A5J4ZA95_PORPP 6-258  
52 5N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YSS5_PORPP 39-212  
53 Y3 | LPP2 | A0A5J4Z365_PORPP -104-57 -100-61  
62 6N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YN76_PORPP 47-215  
63 73 | Phycobiliprotein ApcE | A0A343KPB8_PORPP 1-879  
72 7N | Fucoxanthin-chlorophyll a-c binding protein, chloroplastic |
A0A5J4YKR2_PORPP 38-201  
82 8N | RedCAP | A0A5J4YP51_PORPP 34-213  
A1 A4 AD AE AG AH AO AQ Y7 YA | R-phycoerythrin gamma chain, chloroplastic |
A0A5J4YX19_PORPP 9-298  
A2 AN | PsaA | W0S1N1_PORPP 1-752  
A3 C3 E3 G3 J3 K3 N3 P3 R3 T3 c3 e3 g3 i3 l3 m3 p3 r3 t3 v3 | Allophycocyanin
alpha subunit | W0RYM0_PORPP 1-161  
A5 A7 A9 AA AF AI AK AP BD BQ C5 C7 C9 CA CF CI CJ CK CM CP DD DQ E5 E7 E9 EA
EF EI EJ EK EM EP FD FQ G5 G7 G9 GA GF GI GJ GK GM GP HD HQ I5 I7 I9 IA IF II
IJ IK IM IP JB JD JQ K5 K7 K9 KA KF KI KJ KK KM KP LD LQ M7 MA MF MJ MK MM MP
N5 N9 ND NI NQ O1 O4 O7 OA OE OF OG OH OJ OK OM OO OP P5 P9 PD PI PQ Q1 Q4 Q7
QA QE QF QG QH QJ QK QM QO QP R5 R9 RD RI RQ S1 S4 S7 SA SE SF SG SH SJ SK SM
SO SP T5 T9 TB TD TI TQ U1 U4 U7 UA UE UF UG UH UJ UK UM UO UP V5 V9 VD VI VQ
W1 W4 W7 WA WE WF WG WH WJ WK WM WO WP X5 X9 XD XI XQ YF YJ YK YM Z1 Z4 ZE ZG
ZH ZO aF aJ aK aM b1 b4 bE bG bH bO cF cK d1 d4 dE dG dH dJ dM dO eF eK f1 f4
fE fG fH fJ fM fO gF gK h1 h4 hE hG hH hJ hM hO iF iK j1 j4 jE jG jH jJ jM jO
kF kK l1 l4 lE lG lH lJ lM lO mF mK oF oK p8 pC qF qK r8 rC sF sK t8 tC uF uK
v8 vC x8 xC z8 zC | Phycoerythrin alpha subunit | E2IH77_PORPP 1-164  
A6 AL a6 aL | Photosystem II protein D1 | W0RZ08_PORPP 1-360  
A8 AC a8 aC | LRH |  
AB EB | Linker4 | A0A5J4YXP2_PORPP 287-424  
AJ AM wF wK xF xK | R-phycoerythrin gamma chain, chloroplastic |
A0A5J4YZM7_PORPP 11-283  
B1 B4 BE BG BH BO | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP
1-232  
B2 BN | Photosystem I P700 chlorophyll a apoprotein A2 | W0RYU6_PORPP 3-734  
B3 D3 F3 H3 I3 L3 M3 O3 Q3 S3 U3 d3 f3 h3 j3 k3 n3 o3 q3 s3 u3 w3 |
Allophycocyanin beta subunit | W0S279_PORPP 1-161  
B6 BL b6 bL | Photosystem II CP47 reaction center protein | W0RZ84_PORPP 1-509  
BJ BM yF yK | R-phycoerythrin gamma chain, chloroplastic | A0A5J4YZH3_PORPP
8-297  
C1 C4 CE CG CH CO E1 E4 EE EG EH EO G1 G4 GE GG GH GO I1 I4 IE IG IH IO K1 K4
KE KG KH KO M1 M4 ME MG MH MO | C-phycocyanin alpha subunit | W0RYI4_PORPP
1-162  
C2 CN | Photosystem I iron-sulfur center | W0S231_PORPP 1-81  
C6 CL c6 cL | Photosystem II CP43 reaction center protein | W0RYK4_PORPP 1-473  
D1 D4 DE DG DH DO F1 F4 FE FG FH FO H1 H4 HE HG HH HO J1 J4 JE JG JH JO L1 L4
LE LG LH LO N1 N4 NE NG NH NO | C-phycocyanin beta subunit | W0RZB2_PORPP
1-172  
D2 DN | Photosystem I reaction center subunit II | W0RZ23_PORPP -2-139  
D6 DL d6 dL | Photosystem II D2 protein | W0RYZ0_PORPP 2-352  
E2 EN | Photosystem I reaction center subunit IV | W0RYG1_PORPP 1-61  
E6 EL e6 eL | Cytochrome b559 subunit alpha | W0RYH5_PORPP 0-83  
F2 FN | Photosystem I reaction center subunit III | W0RZ71_PORPP 1-185  
F6 FL f6 fL | Cytochrome b559 subunit beta | W0S1X0_PORPP 2-45  
G2 GN | Cytochrome c6 | W0S1L8_PORPP 7-110  
G6 GL g6 gL | PSII_Pbs31 domain-containing protein | A0A5J4Z270_PORPP 1-213  
H6 HL h6 hL | Photosystem II reaction center protein H | W0RYU5_PORPP 1-67  
I2 IN | Photosystem I reaction center subunit VIII | W0RZ51_PORPP 1-37  
I6 IL i6 iL | Photosystem II reaction center protein I | W0RYJ5_PORPP 1-38  
J2 JN | Photosystem I reaction center subunit IX | W0RYG9_PORPP 1-42  
J6 JL j6 jL | Photosystem II reaction center protein J | W0RYQ6_PORPP 2-40  
K2 KN | Photosystem I reaction center subunit PsaK | W0RZ04_PORPP 1-70  
K6 KL k6 kL | Photosystem II reaction center protein K | W0RZ28_PORPP 1-45  
KB UB | CaRSPs1 | A0A5J4YJY8_PORPP 1-288  
L2 LN | Photosystem I reaction center subunit XI | W0S1Z0_PORPP 3-142  
L6 LL l6 lL | PsbL | W0RZ31_PORPP 0-37  
M2 MN | Photosystem I reaction center subunit XII | W0S1Z9_PORPP 1-30  
M5 M9 Z5 Z9 | R-phycoerythrin gamma chain, chloroplastic | A0A5J4YNU6_PORPP
-34-298 -33-299  
M6 ML m6 mL | PsbM | A0A5J4YYD7_PORPP -56-44  
MI ZI | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z323_PORPP 1-316  
N2 NN | Ferredoxin | W0RYF9_PORPP 1-99  
N6 NL n6 nL | Psb34 |  
O2 ON | Photosystem I subunit O | A0A5J4YUC8_PORPP 46-137  
O6 OL o6 oL | Oxygen-evolving enhancer protein | E5RPB3_PORPP -32-254  
Q6 QL q6 qL | PsbQ' | A0A5J4Z679_PORPP 1-205  
R2 RN | PsaR | A0A5J4YR43_PORPP 44-121  
R6 RL r6 rL | Photosystem II protein Y | W0S1X5_PORPP 2-34  
S6 SL | LPP1 |  
T6 TL t6 tL | Photosystem II reaction center protein T | W0RYV0_PORPP 1-31  
U6 UL u6 uL | PS II complex 12 kDa extrinsic protein | A0A5J4YLQ6_PORPP
-46-103 -46-105  
V3 x3 | Allophycocyanin gamma subunit | W0S1U6_PORPP 1-161  
V6 VL v6 vL | Cytochrome c550 | W0RYZ6_PORPP -24-137  
W3 y3 | Allophycocyanin beta 18 subunit | W0RZE2_PORPP 1-173  
W6 WL w6 wL | PsbW |  
WB cB | CaRSP2 | A0A5J4YX67_PORPP 1-327  
X1 X4 XE XG XH XO | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4YM59_PORPP 9-371  
X3 z3 | Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated,
core | A0A5J4YVZ2_PORPP 40-132  
X6 XL x6 xL | Photosystem II reaction center X protein | W0RZ76_PORPP 3-41  
Y6 YL y6 yL | Photosystem II reaction center protein Ycf12 | W0RZ91_PORPP 1-34  
YP bP | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4YMI8_PORPP -16-409  
Z2 ZN | LPS1 |  
Z6 ZL z6 zL | Photosystem II reaction center protein Z | W0RZ40_PORPP 1-62  
bJ bM | Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
| A0A5J4YX63_PORPP -28-461  
dD dQ | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z162_PORPP 5-346  
e7 eA | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z7F4_PORPP -12-290  
fB hB | FAS1 domain-containing protein | A0A5J4Z027_PORPP 0-287  
zF zK | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4YI31_PORPP 1-498  
  
Non-standard residues in 7y5e #1  
---  
3XQ — (2S)-2,3-dihydroxypropyl octadecanoate  
BCR — β-carotene  
BCT — bicarbonate ion  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CL — chloride ion  
CLA — chlorophyll A  
CYC — phycocyanobilin  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PEB — phycoerythrobilin  
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)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
PUB — phycourobilin  
SF4 — iron/sulfur cluster  
ZEX —
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol  
  

> hide atoms

> time ribbon

> ribbon

command time 0.06764 seconds  
draw time 19.84 seconds  

> time hbonds

> hbonds

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /53 PRO 15 N; /zF PRO 418 N; /bJ PRO 404 N; /zF PRO 419 N; /bJ
PRO 399 N; /bM PRO 399 N; /bM PRO 404 N; /BL ARG 476 NE; /B6 ARG 476 NE; /b6
ARG 476 NE; /bL ARG 476 NE  

114367 hydrogen bonds found  
command time 28.99 seconds  
draw time 0.1529 seconds  

> time surf

> surface

command time 31.36 seconds  
draw time 5.687 seconds  

> time color bypolymer

> color bypolymer

command time 2.195 seconds  
draw time 1.732 seconds  

> time coulomb

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /1L UNK 46 HO bonded to atom that should not have hydrogens (/1L UNK
46 O)  

> hide #!1 models

> show #!1 models




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 21 days, 23 hours, 1 minute

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
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    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.0.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.7
    ChimeraX-AtomicLibrary: 10.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
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    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
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    ChimeraX-MLP: 1.1.1
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    ChimeraX-Shell: 1.0.1
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    ChimeraX-ShowSequences: 1.0.1
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    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
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    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
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    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.27
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.1.23
    imagesize: 1.4.1
    ipykernel: 6.21.1
    ipython: 8.9.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.4
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.2.0
    jupyterlab-widgets: 3.0.5
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.0.0
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.4.2
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.3.2.post1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.0.2
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.4.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.5

[Eric Pettersen]

Need to use templates (of GLY) for UNK residue if backbone atoms present (fix: ​https://github.com/RBVI/ChimeraX/commit/62c49e2ad86dd9a6c8b4eff99ea2fda7e763e919)