Crash showing cartoons

[745324914@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x0000a200 (most recent call first):
  File "D:\software\install\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\software\install\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\software\install\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\software\install\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\software\install\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open D:/PhD/Nannochloropsis_oceanica/coot/NO1017.pdb

Summary of feedback from opening
D:/PhD/Nannochloropsis_oceanica/coot/NO1017.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CLA (802 )  
Cannot find LINK/SSBOND residue CLA (101 )  
Cannot find LINK/SSBOND residue CLA (196 )  
Cannot find LINK/SSBOND residue CLA (197 )  
Cannot find LINK/SSBOND residue CLA (607 )  
6 messages similar to the above omitted  
LINK or SSBOND record from atom to itself: C38 in residue SQD /5:628  
Cannot find LINK/SSBOND residue LMG (613 )  
  
Chain information for NO1017.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
L | No description available  
M | No description available  
R | No description available  
X | No description available  
  

> ui tool show Toolbar

> hide atoms

> show cartoons

> select ::name="SF4"

24 atoms, 54 pseudobonds, 3 residues, 2 models selected  

> show sel atoms

> open D:/PhD/Nannochloropsis_oceanica/pdb-ref/refs/7y1a.cif.gz

File reader requires uncompressed file; 'D:/PhD/Nannochloropsis_oceanica/pdb-
ref/refs/7y1a.cif.gz' is compressed  

> open D:/PhD/Nannochloropsis_oceanica/pdb-ref/refs/7y1a.cif/7y1a.cif

Summary of feedback from opening D:/PhD/Nannochloropsis_oceanica/pdb-
ref/refs/7y1a.cif/7y1a.cif  
---  
notes | Fetching CCD PEB from http://ligand-
expo.rcsb.org/reports/P/PEB/PEB.cif  
Fetching CCD MEN from http://ligand-expo.rcsb.org/reports/M/MEN/MEN.cif  
  
7y1a.cif title:  
Lateral hexamer [more info...]  
  
Chain information for 7y1a.cif #2  
---  
Chain | Description | UniProt  
1 q s u w y | B-phycoerythrin β chain | PHEB_PORPP  
A | LRH |  
a | LRH |  
p r t v x z | Phycoerythrin α subunit | E2IH77_PORPP  
  
Non-standard residues in 7y1a.cif #2  
---  
PEB — phycoerythrobilin  
  

> select #2

17782 atoms, 18083 bonds, 2314 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NO1017.pdb, chain A (#1) with 7y1a.cif, chain y (#2), sequence
alignment score = 117.1  
RMSD between 12 pruned atom pairs is 1.351 angstroms; (across all 172 pairs:
27.056)  
  

> close #2

> open D:/PhD/Nannochloropsis_oceanica/pdb-ref/refs/7y5e.cif

Summary of feedback from opening D:/PhD/Nannochloropsis_oceanica/pdb-
ref/refs/7y5e.cif  
---  
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  
  
7y5e.cif title:  
In situ single-PBS-PSII-PSI-LHCs megacomplex. [more info...]  
  
Chain information for 7y5e.cif #2  
---  
Chain | Description | UniProt  
12 1N | Chlorophyll a-b binding protein, chloroplastic | A0A5J4Z6J3_PORPP  
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 β chain | PHEB_PORPP  
22 2N | Chlorophyll a-b binding protein of LHCII type III, chloroplastic |
P93450_PORPP  
23 Z3 | Lrc4 | A0A5J4YTV6_PORPP  
32 3N | Chlorophyll a-b binding protein, chloroplastic | A0A5J4YYC4_PORPP  
33 a3 | LRC5 | A0A5J4Z2M2_PORPP  
42 4N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4ZAY0_PORPP  
43 b3 | FAS1 domain-containing protein | A0A5J4ZA95_PORPP  
52 5N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YSS5_PORPP  
53 Y3 | LPP2 | A0A5J4Z365_PORPP  
62 6N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YN76_PORPP  
63 73 | Phycobiliprotein ApcE | A0A343KPB8_PORPP  
72 7N | Fucoxanthin-chlorophyll a-c binding protein, chloroplastic |
A0A5J4YKR2_PORPP  
82 8N | RedCAP | A0A5J4YP51_PORPP  
A1 A4 AD AE AG AH AO AQ Y7 YA | R-phycoerythrin γ chain, chloroplastic |
A0A5J4YX19_PORPP  
A2 AN | PsaA | W0S1N1_PORPP  
A3 C3 E3 G3 J3 K3 N3 P3 R3 T3 c3 e3 g3 i3 l3 m3 p3 r3 t3 v3 | Allophycocyanin
α subunit | W0RYM0_PORPP  
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 α subunit | E2IH77_PORPP  
A6 AL a6 aL | Photosystem II protein D1 | W0RZ08_PORPP  
A8 AC a8 aC | LRH |  
AB EB | Linker4 | A0A5J4YXP2_PORPP  
AJ AM wF wK xF xK | R-phycoerythrin γ chain, chloroplastic | A0A5J4YZM7_PORPP  
B1 B4 BE BG BH BO | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP  
B2 BN | Photosystem I P700 chlorophyll a apoprotein A2 | W0RYU6_PORPP  
B3 D3 F3 H3 I3 L3 M3 O3 Q3 S3 U3 d3 f3 h3 j3 k3 n3 o3 q3 s3 u3 w3 |
Allophycocyanin β subunit | W0S279_PORPP  
B6 BL b6 bL | Photosystem II CP47 reaction center protein | W0RZ84_PORPP  
BJ BM yF yK | R-phycoerythrin γ chain, chloroplastic | A0A5J4YZH3_PORPP  
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 α subunit | W0RYI4_PORPP  
C2 CN | Photosystem I iron-sulfur center | W0S231_PORPP  
C6 CL c6 cL | Photosystem II CP43 reaction center protein | W0RYK4_PORPP  
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 β subunit | W0RZB2_PORPP  
D2 DN | Photosystem I reaction center subunit II | W0RZ23_PORPP  
D6 DL d6 dL | Photosystem II D2 protein | W0RYZ0_PORPP  
E2 EN | Photosystem I reaction center subunit IV | W0RYG1_PORPP  
E6 EL e6 eL | Cytochrome b559 subunit α | W0RYH5_PORPP  
F2 FN | Photosystem I reaction center subunit III | W0RZ71_PORPP  
F6 FL f6 fL | Cytochrome b559 subunit β | W0S1X0_PORPP  
G2 GN | Cytochrome c6 | W0S1L8_PORPP  
G6 GL g6 gL | PSII_Pbs31 domain-containing protein | A0A5J4Z270_PORPP  
H6 HL h6 hL | Photosystem II reaction center protein H | W0RYU5_PORPP  
I2 IN | Photosystem I reaction center subunit VIII | W0RZ51_PORPP  
I6 IL i6 iL | Photosystem II reaction center protein I | W0RYJ5_PORPP  
J2 JN | Photosystem I reaction center subunit IX | W0RYG9_PORPP  
J6 JL j6 jL | Photosystem II reaction center protein J | W0RYQ6_PORPP  
K2 KN | Photosystem I reaction center subunit PsaK | W0RZ04_PORPP  
K6 KL k6 kL | Photosystem II reaction center protein K | W0RZ28_PORPP  
KB UB | CaRSPs1 | A0A5J4YJY8_PORPP  
L2 LN | Photosystem I reaction center subunit ξ | W0S1Z0_PORPP  
L6 LL l6 lL | PsbL | W0RZ31_PORPP  
M2 MN | Photosystem I reaction center subunit XII | W0S1Z9_PORPP  
M5 M9 Z5 Z9 | R-phycoerythrin γ chain, chloroplastic | A0A5J4YNU6_PORPP  
M6 ML m6 mL | PsbM | A0A5J4YYD7_PORPP  
MI ZI | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z323_PORPP  
N2 NN | Ferredoxin | W0RYF9_PORPP  
N6 NL n6 nL | Psb34 |  
O2 ON | Photosystem I subunit O | A0A5J4YUC8_PORPP  
O6 OL o6 oL | Oxygen-evolving enhancer protein | E5RPB3_PORPP  
Q6 QL q6 qL | PsbQ' | A0A5J4Z679_PORPP  
R2 RN | PsaR | A0A5J4YR43_PORPP  
R6 RL r6 rL | Photosystem II protein Y | W0S1X5_PORPP  
S6 SL | LPP1 |  
T6 TL t6 tL | Photosystem II reaction center protein T | W0RYV0_PORPP  
U6 UL u6 uL | PS II complex 12 kDa extrinsic protein | A0A5J4YLQ6_PORPP  
V3 x3 | Allophycocyanin γ subunit | W0S1U6_PORPP  
V6 VL v6 vL | Cytochrome c550 | W0RYZ6_PORPP  
W3 y3 | Allophycocyanin β 18 subunit | W0RZE2_PORPP  
W6 WL w6 wL | PsbW |  
WB cB | CaRSP2 | A0A5J4YX67_PORPP  
X1 X4 XE XG XH XO | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4YM59_PORPP  
X3 z3 | Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated,
core | A0A5J4YVZ2_PORPP  
X6 XL x6 xL | Photosystem II reaction center X protein | W0RZ76_PORPP  
Y6 YL y6 yL | Photosystem II reaction center protein Ycf12 | W0RZ91_PORPP  
YP bP | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4YMI8_PORPP  
Z2 ZN | LPS1 |  
Z6 ZL z6 zL | Photosystem II reaction center protein Z | W0RZ40_PORPP  
bJ bM | Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
| A0A5J4YX63_PORPP  
dD dQ | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z162_PORPP  
e7 eA | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z7F4_PORPP  
fB hB | FAS1 domain-containing protein | A0A5J4Z027_PORPP  
zF zK | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4YI31_PORPP  
  
Non-standard residues in 7y5e.cif #2  
---  
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  
  

> select #2

1263707 atoms, 1289288 bonds, 2099 pseudobonds, 155789 residues, 3 models
selected  

> show sel cartoons


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 546.80
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G614JV_G614JV
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 16,779,960,320
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13980HX
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Hi Moon,

Thanks for reporting this problem. There isn't quite enough information in the report for us to reproduce the problem. Perhaps you cn upgrade to the 1.9 release candidate. There have been many, many bug fixes since the 1.3 version you are currently using, so there's an excellent chance that whatever this problem is has been fixed. Even if the problem is still there, the bug reporting mechanisms in the 1.9 version will provide us with a lot more information for tracking down the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab