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Opened 3 years ago
Last modified 2 years ago
#8446 assigned defect
Cartoon of large 7y5e is slow, takes 30 seconds first time, 4 seconds second time. — at Version 11
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Tom Goddard, Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.1-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202301231917 (2023-01-23 19:17:49 UTC)
Description
Showing cartoon of 7y5e (1.2 million atoms 150000 residues) the first time takes 35 seconds to compute, but the second timetakes 4 seconds to compute. By comparison 3j3q (2.4 million atoms, 300000 atoms) took about 9 seconds the first time the cartoon is shown. What is making the first cartoon display of 7y5e so slow? Is it computing atom types? Why?
Log:
Could not find tool "Tabbed Toolbar"
UCSF ChimeraX version: 1.6.dev202301231917 (2023-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7y5e format mmcif fromDatabase pdb
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
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
> time cartoon
> cartoon
command time 0.09195 seconds
draw time 35.93 seconds
> hide #1
> open 3j3q
3j3q title:
Atomic-level structure of the entire HIV-1 capsid [more info...]
Chain information for 3j3q #2
---
Chain | Description | UniProt
0 1 10 11 12 13 14 15 16 17 18 19 1A 1B 1C 1D 1E 1F 1G 1H 1I 1J 1K 1L 1M 1N 1O
1P 1Q 1R 1S 1T 1U 1V 1W 1X 1Y 1Z 1a 1b 1c 1d 1e 1f 1g 1h 1i 1j 1k 1l 1m 1n 1o
1p 1q 1r 1s 1t 1u 1v 1w 1x 1y 1z 2 20 21 22 23 24 25 26 27 28 29 2A 2B 2C 2D
2E 2F 2G 2H 2I 2J 2K 2L 2M 2N 2O 2P 2Q 2R 2S 2T 2U 2V 2W 2X 2Y 2Z 2a 2b 2c 2d
2e 2f 2g 2h 2i 2j 2k 2l 2m 2n 2o 2p 2q 2r 2s 2t 2u 2v 2w 2x 2y 2z 3 30 31 32
33 34 35 36 37 38 39 3A 3B 3C 3D 3E 3F 3G 3H 3I 3J 3K 3L 3M 3N 3O 3P 3Q 3R 3S
3T 3U 3V 3W 3X 3Y 3Z 3a 3b 3c 3d 3e 3f 3g 3h 3i 3j 3k 3l 3m 3n 3o 3p 3q 3r 3s
3t 3u 3v 3w 3x 3y 3z 4 40 41 42 43 44 45 46 47 48 49 4A 4B 4C 4D 4E 4F 4G 4H
4I 4J 4K 4L 4M 4N 4O 4P 4Q 4R 4S 4T 4U 4V 4W 4X 4Y 4Z 4a 4b 4c 4d 4e 4f 4g 4h
4i 4j 4k 4l 4m 4n 4o 4p 4q 4r 4s 4t 4u 4v 4w 4x 4y 4z 5 50 51 52 53 54 55 56
57 58 59 5A 5B 5C 5D 5E 5F 5G 5H 5I 5J 5K 5L 5M 5N 5O 5P 5Q 5R 5S 5T 5U 5V 5W
5X 5Y 5Z 5a 5b 5c 5d 5e 5f 5g 5h 5i 5j 5k 5l 5m 5n 5o 5p 5q 5r 5s 5t 5u 5v 5w
5x 5y 5z 6 60 61 62 63 64 65 66 67 68 69 6A 6B 6C 6D 6E 6F 6G 6H 6I 6J 6K 6L
6M 6N 6O 6P 6Q 6R 6S 6T 6U 6V 6W 6X 6Y 6Z 6a 6b 6c 6d 6e 6f 6g 6h 6i 6j 6k 6l
6m 6n 6o 6p 6q 6r 6s 6t 6u 6v 6w 6x 6y 6z 7 70 71 72 73 74 75 76 77 78 79 7A
7B 7C 7D 7E 7F 7G 7H 7I 7J 7K 7L 7M 7N 7O 7P 7Q 7R 7S 7T 7U 7V 7W 7X 7Y 7Z 7a
7b 7c 7d 7e 7f 7g 7h 7i 7j 7k 7l 7m 7n 7o 7p 7q 7r 7s 7t 7u 7v 7w 7x 7y 7z 8
80 81 82 83 84 85 86 87 88 89 8A 8B 8C 8D 8E 8F 8G 8H 8I 8J 8K 8L 8M 8N 8O 8P
8Q 8R 8S 8T 8U 8V 8W 8X 8Y 8Z 8a 8b 8c 8d 8e 8f 8g 8h 8i 8j 8k 8l 8m 8n 8o 8p
8q 8r 8s 8t 8u 8v 8w 8x 8y 8z 9 90 91 92 93 94 95 96 97 98 99 9A 9B 9C 9D 9E
9F 9G 9H 9I 9J 9K 9L 9M 9N 9O 9P 9Q 9R 9S 9T 9U 9V 9W 9X 9Y 9Z 9a 9b 9c 9d 9e
9f 9g 9h 9i 9j 9k 9l 9m 9n 9o 9p 9q 9r 9s 9t 9u 9v 9w 9x 9y 9z A B C D E F G H
I J K L M N O P Q R S T U V W X Y Z a a0 a1 a2 a3 a4 a5 a6 a7 a8 a9 aA aB aC
aD aE aF aG aH aI aJ aK aL aM aN aO aP aQ aR aS aT aU aV aW aX aY aZ aa ab ac
ad ae af ag ah ai aj ak al am an ao ap aq ar as at au av aw ax ay az b b0 b1
b2 b3 b4 b5 b6 b7 b8 b9 bA bB bC bD bE bF bG bH bI bJ bK bL bM bN bO bP bQ bR
bS bT bU bV bW bX bY bZ ba bb bc bd be bf bg bh bi bj bk bl bm bn bo bp bq br
bs bt bu bv bw bx by bz c c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 cA cB cC cD cE cF cG
cH cI cJ cK cL cM cN cO cP cQ cR cS cT cU cV cW cX cY cZ ca cb cc cd ce cf cg
ch ci cj ck cl cm cn co cp cq cr cs ct cu cv cw cx cy cz d d0 d1 d2 d3 d4 d5
d6 d7 d8 d9 dA dB dC dD dE dF dG dH dI dJ dK dL dM dN dO dP dQ dR dS dT dU dV
dW dX dY dZ da db dc dd de df dg dh di dj dk dl dm dn do dp dq dr ds dt du dv
dw dx dy dz e e0 e1 e2 e3 e4 e5 e6 e7 e8 e9 eA eB eC eD eE eF eG eH eI eJ eK
eL eM eN eO eP eQ eR eS eT eU eV eW eX eY eZ ea eb ec ed ee ef eg eh ei ej ek
el em en eo ep eq er es et eu ev ew ex ey ez f f0 f1 f2 f3 f4 f5 f6 f7 f8 f9
fA fB fC fD fE fF fG fH fI fJ fK fL fM fN fO fP fQ fR fS fT fU fV fW fX fY fZ
fa fb fc fd fe ff fg fh fi fj fk fl fm fn fo fp fq fr fs ft fu fv fw fx fy fz
g g0 g1 g2 g3 g4 g5 g6 g7 g8 g9 gA gB gC gD gE gF gG gH gI gJ gK gL gM gN gO
gP gQ gR gS gT gU gV gW gX gY gZ ga gb gc gd ge gf gg gh gi gj gk gl gm gn go
gp gq gr gs gt gu gv gw gx gy gz h h0 h1 h2 h3 h4 h5 h6 h7 h8 h9 hA hB hC hD
hE hF hG hH hI hJ hK hL hM hN hO hP hQ hR hS hT hU hV hW hX hY hZ ha hb hc hd
he hf hg hh hi hj hk hl hm hn ho hp hq hr hs ht hu hv hw hx hy hz i i0 i1 i2
i3 i4 i5 i6 i7 i8 i9 iA iB iC iD iE iF iG iH iI iJ iK iL iM iN iO iP iQ iR iS
iT iU iV iW iX iY iZ ia ib ic id ie if ig ih ii ij ik il im in io ip iq ir is
it iu iv iw ix iy iz j j0 j1 j2 j3 j4 j5 j6 j7 j8 j9 jA jB jC jD jE jF jG jH
jI jJ jK jL jM jN jO jP jQ jR jS jT jU jV jW jX jY jZ ja jb jc jd je jf jg jh
ji jj jk jl jm jn jo jp jq jr js jt ju jv jw jx jy jz k k0 k1 k2 k3 k4 k5 k6
k7 k8 k9 kA kB kC kD kE kF kG kH kI kJ kK kL kM kN kO kP kQ kR kS kT kU kV kW
kX kY kZ ka kb kc kd ke kf kg kh ki kj kk kl km kn ko kp kq kr ks kt ku kv kw
kx ky kz l l0 l1 l2 l3 l4 l5 l6 l7 l8 l9 lA lB lC lD lE lF lG lH lI lJ lK lL
lM lN lO lP lQ lR la lb lc ld le lf lg lh li lj lk ll lm ln lo lp lq lr ls lt
lu lv lw lx ly lz m n o p q r s t u v w x y z | capsid protein | Q79791_9HIV1
1-231
> time cartoon #2
> cartoon #2
command time 2.715 seconds
draw time 5.649 seconds
> hide #1 cartoons
> time cartoon #1
> cartoon #1
command time 1.288 seconds
draw time 2.514 seconds
> hide #2
> hide cartoons #2
Expected ',' or a keyword
> hide #1 cartoons
> hide #2 models
> time cartoon #1
> cartoon #1
command time 1.389 seconds
draw time 2.443 seconds
OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 499.40.2.0.0
OS Loader Version: 564.40.4~55
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 18 days, 16 hours, 40 minutes
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.5.8
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.8
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
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
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202301231917
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3.1
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: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.11
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.10
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.8
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.3
ChimeraX-PDB: 2.6.11
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
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
ChimeraX-StructMeasure: 1.1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.26
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.6
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comm: 0.1.2
contourpy: 1.0.6
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.5
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.0.0
ipykernel: 6.19.2
ipython: 8.7.0
ipython-genutils: 0.2.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 7.4.8
jupyter-core: 5.1.3
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.6.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.8
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
opt-einsum: 3.3.0
packaging: 21.3
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: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.6.2
prompt-toolkit: 3.0.36
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6: 6.4.0
PyQt6-Qt6: 6.4.1
PyQt6-sip: 13.4.0
PyQt6-WebEngine: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.1
python-dateutil: 2.8.2
pytz: 2022.7
pyzmq: 24.0.1
qtconsole: 5.4.0
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.3
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.3
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.8.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (11)
comment:1 by , 3 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cartoon of large 7y5e is slow, takes 30 seconds first time, 4 seconds second time. |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
| Cc: | added |
|---|
comment:4 by , 3 years ago
The initial depiction is spheres, so to get sphere radii it already computed atom times when the structure was first opened. So not sure what is going on to make ribbon calculation slow the first time.
comment:5 by , 3 years ago
Computing the ribbon for just one chain of 179 residues also takes over 30 seconds (time cartoon /JJ). The time is all taken in the ribbon get_polymer_spline() C++ function. Apparently something it calls does a large cached calculation for the whole structure, but I'm not sure yet what that calculation is.
comment:6 by , 3 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
The time is all taken computing secondary structure. When 7y5e is opened it does not have secondary structure assigned. That surprises me. I thought all PDB entries would have secondary structure records.
Reassigning to Eric who can close it if it is normal that a PDB model does not get secondary structure assigned from the file.
comment:7 by , 3 years ago
| Cc: | added |
|---|
This structure seems to have been deposited with no secondary structure information despite having (according to DSSP) close to 90000 helix residues and over 800 strand residues. If the secondary structure information had been present in the file then this problem would have been moot -- DSSP would not have been run. Is this something we should complain to the RCSB about?
DSSP being slow on large structures is a known issue and is on one of my lower priority to-do lists. The priority isn't high because the only place you usually run into this is using MatchMaker, which by default does not use the deposited secondary structure information. For ribbons, people typically don't look at them for these huge structure since they just look like a ball of yarn, and they're normally fast anyway because the secondary structure info is in the file.
comment:8 by , 3 years ago
I asked RCSB to fix 7y5e. The slow dssp does not seem too serious since this is a rare problem, and 30 seconds is not too long.
From: Tom Goddard Subject: Entry 7y5e missing secondary structure records Date: February 7, 2023 at 10:23:49 AM PST To: deposit-help@mail.wwpdb.org The PDB entry 7y5e has no secondary structure (alpha helix, beta sheet) records in its mmCIF file. I've never seen these missing in a PDB entry and wonder if it was a mistake. I ran into this because the missing records make it slow (30 seconds) to show cartoon depictions in ChimeraX because it has to compute the helices and sheets if the mmCIF records are missing. I am a developer of ChimeraX, and am not the depositor of 7y5e. Thanks for taking a look! Tom Goddard UC San Francisco
comment:9 by , 3 years ago
From: "Yumiko Kengaku via RT" <deposit-help@mail.wwpdb.org> Subject: Re: [pdb-deposit-help #641286] Entry 7y5e missing secondary structure records Date: February 7, 2023 at 11:48:06 PM PST To: Tom Goddard Reply-To: deposit-help@mail.wwpdb.org <URL: http://helpdesk.ebi.ac.uk/Ticket/Display.html?id=641286 > Dear Tom, Thank you for pointing out the issue. I will re-check the cif file and update with secondary structure records. Sincerely, Yumiko Kengaku The wwPDB Biocuration Staff
comment:10 by , 3 years ago
Greg Couch observed that ribbon display of 7y7a crashes ChimeraX daily on his Linux machine. That structure was deposited by the same authors as 7y5e in the same study and is twice as large, 2.5 million atoms. It does not have helix/sheet records. Greg tested just running dssp and it crashed, appears to run out of memory on his 64 GB machine. I tried ribbons on 7y7a on Windows 10 machine vive.cgl.ucsf.edu and it took about 10 minutes and was using 55 Gbytes apparently while running dssp but it did eventually complete.
These computers have 64 GB of memory while many users have 16 GB of memory and so may encounter dssp crashes when ribbons are shown for large structures in the 500-1000K atoms range.
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On my 2015 Mac, "label /62:215@o atoms attribute idatm_type" takes 0.38 seconds.