Slow surface calculation, 862 chains, 5y6p

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202010140223 (2020-10-14 02:23:41 UTC)
Description
Surface calculation on large structure 5y6p is incredibly slow even for low resolution (surf #1 res 20 grid 7).  Timing shows it is spending 145 of 153 seconds partitioning the atoms for a surface per chain, specifically 15 seconds in atoms.by_chain and 130 seconds in filtering again to get the chain atoms (unclear why) and removing solvent ligand and ions.

Log:
UCSF ChimeraX version: 1.2.dev202010140223 (2020-10-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5y6p format mmcif fromDatabase pdb

5y6p title:  
Structure of the phycobilisome from the red alga Griffithsia pacifica [more
info...]  
  
Chain information for 5y6p #1  
---  
Chain | Description  
14 R8 W5 W9 aW bW | LRC1  
24 S8 X5 X9 aX bX | LR1  
34 A2 U8 Y5 Z9 a3 aY b8 b9 bY dw dx ey ez | LR_gamma4  
44 C2 D2 T8 Y9 Z5 aZ bZ c3 c8 c9 d3 d8 d9 e8 e9 | LR_gamma5  
A1 B1 | LRC6  
A3 A4 A5 A6 A7 A9 B8 C3 C4 C5 C6 C7 C9 D8 E2 E3 E4 E5 E6 E7 E9 F8 G2 G3 G4 G5
G6 G7 G9 H8 I2 I3 I4 I5 I6 I7 I9 J8 K2 K3 K4 K5 K6 K7 K9 L8 M2 M3 M4 M5 M6 M7
M9 N8 O2 O3 O4 O5 O6 O7 O9 P8 Q2 Q3 Q4 Q5 Q6 Q7 Q9 S2 S3 S4 S5 S6 S7 S9 U2 U3
U4 U5 U6 U7 U9 W2 W3 W4 W6 W7 Y2 Y3 Y4 Y6 Y7 aA aC aE aG aI aK aM aO aQ aS aU
am ao aq as au aw ay bA bC bE bG bI bK bM bO bQ bS bU bm bt bu bv bw bx by cA
cC cD cG cI cK cS cT cU cV cW cX cZ cm ct cu cv cw cx cy dA dC dE dG dI dJ dM
dO dQ dS dU dW dZ da db dc de dg dk dm do dq ds du e2 e3 eA eC eE eG eI eK eM
eO eQ eS eU eW ea ed ef eh ej ek em eo eq es eu f6 f7 fb fe fg fh fk fl fn fp
fr ft fv fx g2 g3 g6 g7 gb gc gf gh gj gl gm go gq gs gu gw h6 h7 hA hC hE hF
hI hK hM hO hQ hS hU hW i2 i3 i6 i7 i8 iA iB j6 j7 j8 k2 k3 k6 k7 k8 l8 la lc
le lg li lk lm lo lq ls lu lw m2 m3 m4 m5 m6 m7 m8 m9 o2 o3 o4 o5 o6 o7 o9 q2
q3 q4 q5 q6 q7 q8 q9 r8 s2 s3 s4 s5 s6 s7 s8 s9 t8 u2 u3 u4 u5 u6 u7 u8 u9 v8
w2 w3 w4 w5 w6 w7 w9 x8 y2 y3 y4 y5 y9 z8 | R-phycoerythrin α chain  
A8 B3 B4 B5 B6 B7 B9 C8 D3 D4 D5 D6 D7 D9 E8 F2 F3 F4 F5 F6 F7 F9 G8 H2 H3 H4
H5 H6 H7 H9 I8 J2 J3 J4 J5 J6 J7 J9 K8 L2 L3 L4 L5 L6 L7 L9 M8 N2 N3 N4 N5 N6
N7 N9 O8 P2 P3 P4 P5 P6 P7 P9 Q8 R2 R3 R4 R5 R6 R7 R9 T2 T3 T4 T5 T6 T7 T9 V2
V3 V4 V5 V6 V7 V9 X2 X3 X4 X6 X7 Z2 Z3 Z4 Z6 Z7 a6 a7 aB aD aF aH aJ aL aN aP
aR aT aV an ap ar at av ax az b6 b7 bB bD bF bH bJ bL bN bP bR bT bV bn bo bp
bq br bs bz c6 c7 cB cE cF cH cJ cL cM cN cO cP cQ cR cY cn co cp cq cr cs cz
d6 d7 dB dD dF dH dK dL dN dP dR dT dV dX dY dd df dh di dj dl dn dp dr dt dv
e6 e7 eB eD eF eH eJ eL eN eP eR eT eV eX eb ec ee eg ei el en ep er et ev f2
f3 f8 fa fc ff fi fj fm fo fq fs fu fw fy g8 ga gd ge gg gi gk gn gp gr gt gv
gx h2 h3 h8 hB hD hG hH hJ hL hN hP hR hT hV hX iC iD iE iF iG iH j2 j3 jI jJ
jK jL jM jN jO jP kQ kR kS kT kU kV kW kX l2 l3 l6 l7 lb ld lf lh lj ll ln lp
lr lt lv lx n2 n3 n4 n5 n6 n7 n8 n9 o8 p2 p3 p4 p5 p6 p7 p8 p9 r2 r3 r4 r5 r6
r7 r9 t2 t3 t4 t5 t6 t7 t9 v2 v3 v4 v5 v6 v7 v9 w8 x2 x3 x4 x5 x6 x7 x9 y6 y7
y8 z2 z3 z4 z5 z6 z7 z9 | R-phycoerythrin β chain  
B2 b3 | LRC2  
C1 D1 | LRC4  
E1 F1 | LRC5  
G1 I1 K1 N1 P1 R1 T1 X1 Z1 b1 d1 f1 i1 k1 o1 q1 s1 u1 w1 y1 | alpha_APC  
H1 J1 L1 M1 O1 S1 U1 W1 Y1 a1 c1 e1 h1 j1 l1 n1 p1 r1 t1 v1 x1 z1 | beta_APC  
Q1 g1 | ApcF  
V1 m1 | ApcD  
V8 X8 Z8 a4 a5 aa ac ae ag ai ak b4 b5 ba bc be bg bi bk ca cc ce cg ci ck d4
d5 f4 f5 g9 i4 i5 i9 k4 k5 k9 | alpha_PC  
W8 Y8 ab ad af ah aj al bb bd bf bh bj bl c4 c5 cb cd cf ch cj cl e4 e5 f9 g4
g5 h4 h5 h9 j4 j5 j9 l4 l5 l9 | beta_PC  
a2 b2 | LCM  
a8 a9 | LRC3  
c2 d2 | LC  
dy dz | LR3  
eY eZ | LR_gamma7  
ew ex fd fz | LR2  
gy gz | LR_gamma6  
hY hZ ly lz | LR_gamma8  
ka kb | LR9  
  
Non-standard residues in 5y6p #1  
---  
CYC — phycocyanobilin  
PEB — phycoerythrobilin  
PUB — phycourobilin  
PVN — phycoviolobilin (Phycoviolobilin, bound form)  
  

> time surf #1 res 20 grid 7

> surface #1 resolution 20 gridSpacing 7

partition atoms 0.0  
atom check 0.00011110305786132812  
remove solvent 0.00019311904907226562  
chain atoms 0.013360023498535156  
loop over chains 14.823786973953247  
filter time 130.59166312217712  
make time 0.5502753257751465  
replace surfaces 145.99704599380493  
compute surfaces 146.2592101097107  
add models 151.22371006011963  
5y6p_A1 Gaussian surface contour level 0.015  
5y6p_B1 Gaussian surface contour level 0.016  
5y6p_C1 Gaussian surface contour level 0.014  
5y6p_D1 Gaussian surface contour level 0.015  
5y6p_E1 Gaussian surface contour level 0.018  
5y6p_F1 Gaussian surface contour level 0.015  
5y6p_G1 Gaussian surface contour level 0.026  
5y6p_H1 Gaussian surface contour level 0.021  
5y6p_I1 Gaussian surface contour level 0.022  
5y6p_J1 Gaussian surface contour level 0.026  
5y6p_K1 Gaussian surface contour level 0.022  
5y6p_L1 Gaussian surface contour level 0.025  
5y6p_M1 Gaussian surface contour level 0.023  
5y6p_N1 Gaussian surface contour level 0.023  
5y6p_O1 Gaussian surface contour level 0.025  
5y6p_P1 Gaussian surface contour level 0.020  
5y6p_Q1 Gaussian surface contour level 0.020  
5y6p_R1 Gaussian surface contour level 0.022  
5y6p_S1 Gaussian surface contour level 0.022  
5y6p_T1 Gaussian surface contour level 0.024  
5y6p_U1 Gaussian surface contour level 0.026  
5y6p_V1 Gaussian surface contour level 0.019  
5y6p_W1 Gaussian surface contour level 0.025  
5y6p_X1 Gaussian surface contour level 0.021  
5y6p_Y1 Gaussian surface contour level 0.026  
5y6p_Z1 Gaussian surface contour level 0.024  
5y6p_a1 Gaussian surface contour level 0.024  
5y6p_b1 Gaussian surface contour level 0.024  
5y6p_c1 Gaussian surface contour level 0.023  
5y6p_d1 Gaussian surface contour level 0.025  
5y6p_e1 Gaussian surface contour level 0.023  
5y6p_f1 Gaussian surface contour level 0.022  
5y6p_g1 Gaussian surface contour level 0.022  
5y6p_h1 Gaussian surface contour level 0.024  
5y6p_i1 Gaussian surface contour level 0.024  
5y6p_j1 Gaussian surface contour level 0.023  
5y6p_k1 Gaussian surface contour level 0.021  
5y6p_l1 Gaussian surface contour level 0.024  
5y6p_m1 Gaussian surface contour level 0.018  
5y6p_n1 Gaussian surface contour level 0.023  
5y6p_o1 Gaussian surface contour level 0.023  
5y6p_p1 Gaussian surface contour level 0.024  
5y6p_q1 Gaussian surface contour level 0.023  
5y6p_r1 Gaussian surface contour level 0.023  
5y6p_s1 Gaussian surface contour level 0.021  
5y6p_t1 Gaussian surface contour level 0.024  
5y6p_u1 Gaussian surface contour level 0.023  
5y6p_v1 Gaussian surface contour level 0.025  
5y6p_w1 Gaussian surface contour level 0.024  
5y6p_x1 Gaussian surface contour level 0.023  
5y6p_y1 Gaussian surface contour level 0.022  
5y6p_z1 Gaussian surface contour level 0.023  
5y6p_a2 Gaussian surface contour level 0.017  
5y6p_b2 Gaussian surface contour level 0.016  
5y6p_c2 Gaussian surface contour level 0.023  
5y6p_d2 Gaussian surface contour level 0.022  
5y6p_e2 Gaussian surface contour level 0.026  
5y6p_f2 Gaussian surface contour level 0.023  
5y6p_g2 Gaussian surface contour level 0.025  
5y6p_h2 Gaussian surface contour level 0.019  
5y6p_i2 Gaussian surface contour level 0.023  
5y6p_j2 Gaussian surface contour level 0.023  
5y6p_k2 Gaussian surface contour level 0.030  
5y6p_l2 Gaussian surface contour level 0.019  
5y6p_m2 Gaussian surface contour level 0.031  
5y6p_n2 Gaussian surface contour level 0.020  
5y6p_o2 Gaussian surface contour level 0.028  
5y6p_p2 Gaussian surface contour level 0.020  
5y6p_q2 Gaussian surface contour level 0.028  
5y6p_r2 Gaussian surface contour level 0.020  
5y6p_s2 Gaussian surface contour level 0.027  
5y6p_t2 Gaussian surface contour level 0.022  
5y6p_u2 Gaussian surface contour level 0.025  
5y6p_v2 Gaussian surface contour level 0.020  
5y6p_w2 Gaussian surface contour level 0.027  
5y6p_x2 Gaussian surface contour level 0.025  
5y6p_y2 Gaussian surface contour level 0.024  
5y6p_z2 Gaussian surface contour level 0.021  
5y6p_A2 Gaussian surface contour level 0.020  
5y6p_B2 Gaussian surface contour level 0.016  
5y6p_C2 Gaussian surface contour level 0.015  
5y6p_D2 Gaussian surface contour level 0.018  
5y6p_E2 Gaussian surface contour level 0.028  
5y6p_F2 Gaussian surface contour level 0.022  
5y6p_G2 Gaussian surface contour level 0.022  
5y6p_H2 Gaussian surface contour level 0.019  
5y6p_I2 Gaussian surface contour level 0.025  
5y6p_J2 Gaussian surface contour level 0.020  
5y6p_K2 Gaussian surface contour level 0.025  
5y6p_L2 Gaussian surface contour level 0.020  
5y6p_M2 Gaussian surface contour level 0.027  
5y6p_N2 Gaussian surface contour level 0.018  
5y6p_O2 Gaussian surface contour level 0.027  
5y6p_P2 Gaussian surface contour level 0.022  
5y6p_Q2 Gaussian surface contour level 0.026  
5y6p_R2 Gaussian surface contour level 0.021  
5y6p_S2 Gaussian surface contour level 0.023  
5y6p_T2 Gaussian surface contour level 0.020  
5y6p_U2 Gaussian surface contour level 0.030  
5y6p_V2 Gaussian surface contour level 0.022  
5y6p_W2 Gaussian surface contour level 0.023  
5y6p_X2 Gaussian surface contour level 0.022  
5y6p_Y2 Gaussian surface contour level 0.026  
5y6p_Z2 Gaussian surface contour level 0.019  
5y6p_A3 Gaussian surface contour level 0.026  
5y6p_B3 Gaussian surface contour level 0.022  
5y6p_C3 Gaussian surface contour level 0.023  
5y6p_D3 Gaussian surface contour level 0.023  
5y6p_E3 Gaussian surface contour level 0.027  
5y6p_F3 Gaussian surface contour level 0.024  
5y6p_G3 Gaussian surface contour level 0.025  
5y6p_H3 Gaussian surface contour level 0.020  
5y6p_I3 Gaussian surface contour level 0.025  
5y6p_J3 Gaussian surface contour level 0.021  
5y6p_K3 Gaussian surface contour level 0.027  
5y6p_L3 Gaussian surface contour level 0.021  
5y6p_M3 Gaussian surface contour level 0.029  
5y6p_N3 Gaussian surface contour level 0.022  
5y6p_O3 Gaussian surface contour level 0.024  
5y6p_P3 Gaussian surface contour level 0.022  
5y6p_Q3 Gaussian surface contour level 0.029  
5y6p_R3 Gaussian surface contour level 0.020  
5y6p_S3 Gaussian surface contour level 0.027  
5y6p_T3 Gaussian surface contour level 0.020  
5y6p_U3 Gaussian surface contour level 0.027  
5y6p_V3 Gaussian surface contour level 0.021  
5y6p_W3 Gaussian surface contour level 0.025  
5y6p_X3 Gaussian surface contour level 0.025  
5y6p_Y3 Gaussian surface contour level 0.030  
5y6p_Z3 Gaussian surface contour level 0.019  
5y6p_a3 Gaussian surface contour level 0.021  
5y6p_b3 Gaussian surface contour level 0.016  
5y6p_c3 Gaussian surface contour level 0.014  
5y6p_d3 Gaussian surface contour level 0.018  
5y6p_e3 Gaussian surface contour level 0.025  
5y6p_f3 Gaussian surface contour level 0.027  
5y6p_g3 Gaussian surface contour level 0.025  
5y6p_h3 Gaussian surface contour level 0.020  
5y6p_i3 Gaussian surface contour level 0.024  
5y6p_j3 Gaussian surface contour level 0.021  
5y6p_k3 Gaussian surface contour level 0.028  
5y6p_l3 Gaussian surface contour level 0.020  
5y6p_m3 Gaussian surface contour level 0.032  
5y6p_n3 Gaussian surface contour level 0.024  
5y6p_o3 Gaussian surface contour level 0.029  
5y6p_p3 Gaussian surface contour level 0.017  
5y6p_q3 Gaussian surface contour level 0.025  
5y6p_r3 Gaussian surface contour level 0.024  
5y6p_s3 Gaussian surface contour level 0.025  
5y6p_t3 Gaussian surface contour level 0.016  
5y6p_u3 Gaussian surface contour level 0.030  
5y6p_v3 Gaussian surface contour level 0.024  
5y6p_w3 Gaussian surface contour level 0.025  
5y6p_x3 Gaussian surface contour level 0.023  
5y6p_y3 Gaussian surface contour level 0.023  
5y6p_z3 Gaussian surface contour level 0.025  
5y6p_A4 Gaussian surface contour level 0.025  
5y6p_B4 Gaussian surface contour level 0.025  
5y6p_C4 Gaussian surface contour level 0.030  
5y6p_D4 Gaussian surface contour level 0.022  
5y6p_E4 Gaussian surface contour level 0.023  
5y6p_F4 Gaussian surface contour level 0.024  
5y6p_G4 Gaussian surface contour level 0.025  
5y6p_H4 Gaussian surface contour level 0.021  
5y6p_I4 Gaussian surface contour level 0.028  
5y6p_J4 Gaussian surface contour level 0.022  
5y6p_K4 Gaussian surface contour level 0.029  
5y6p_L4 Gaussian surface contour level 0.024  
5y6p_M4 Gaussian surface contour level 0.025  
5y6p_N4 Gaussian surface contour level 0.022  
5y6p_O4 Gaussian surface contour level 0.027  
5y6p_P4 Gaussian surface contour level 0.024  
5y6p_Q4 Gaussian surface contour level 0.026  
5y6p_R4 Gaussian surface contour level 0.021  
5y6p_S4 Gaussian surface contour level 0.027  
5y6p_T4 Gaussian surface contour level 0.023  
5y6p_U4 Gaussian surface contour level 0.025  
5y6p_V4 Gaussian surface contour level 0.022  
5y6p_W4 Gaussian surface contour level 0.024  
5y6p_X4 Gaussian surface contour level 0.022  
5y6p_Y4 Gaussian surface contour level 0.028  
5y6p_Z4 Gaussian surface contour level 0.025  
5y6p_14 Gaussian surface contour level 0.023  
5y6p_24 Gaussian surface contour level 0.019  
5y6p_34 Gaussian surface contour level 0.020  
5y6p_44 Gaussian surface contour level 0.015  
5y6p_a4 Gaussian surface contour level 0.027  
5y6p_b4 Gaussian surface contour level 0.027  
5y6p_c4 Gaussian surface contour level 0.021  
5y6p_d4 Gaussian surface contour level 0.028  
5y6p_e4 Gaussian surface contour level 0.026  
5y6p_f4 Gaussian surface contour level 0.026  
5y6p_g4 Gaussian surface contour level 0.027  
5y6p_h4 Gaussian surface contour level 0.026  
5y6p_i4 Gaussian surface contour level 0.029  
5y6p_j4 Gaussian surface contour level 0.020  
5y6p_k4 Gaussian surface contour level 0.026  
5y6p_l4 Gaussian surface contour level 0.032  
5y6p_m4 Gaussian surface contour level 0.021  
5y6p_n4 Gaussian surface contour level 0.022  
5y6p_o4 Gaussian surface contour level 0.023  
5y6p_p4 Gaussian surface contour level 0.023  
5y6p_q4 Gaussian surface contour level 0.027  
5y6p_r4 Gaussian surface contour level 0.022  
5y6p_s4 Gaussian surface contour level 0.026  
5y6p_t4 Gaussian surface contour level 0.026  
5y6p_u4 Gaussian surface contour level 0.030  
5y6p_v4 Gaussian surface contour level 0.023  
5y6p_w4 Gaussian surface contour level 0.025  
5y6p_x4 Gaussian surface contour level 0.022  
5y6p_y4 Gaussian surface contour level 0.029  
5y6p_z4 Gaussian surface contour level 0.020  
5y6p_A5 Gaussian surface contour level 0.023  
5y6p_B5 Gaussian surface contour level 0.020  
5y6p_C5 Gaussian surface contour level 0.027  
5y6p_D5 Gaussian surface contour level 0.022  
5y6p_E5 Gaussian surface contour level 0.026  
5y6p_F5 Gaussian surface contour level 0.021  
5y6p_G5 Gaussian surface contour level 0.025  
5y6p_H5 Gaussian surface contour level 0.020  
5y6p_I5 Gaussian surface contour level 0.027  
5y6p_J5 Gaussian surface contour level 0.022  
5y6p_K5 Gaussian surface contour level 0.027  
5y6p_L5 Gaussian surface contour level 0.024  
5y6p_M5 Gaussian surface contour level 0.029  
5y6p_N5 Gaussian surface contour level 0.020  
5y6p_O5 Gaussian surface contour level 0.026  
5y6p_P5 Gaussian surface contour level 0.024  
5y6p_Q5 Gaussian surface contour level 0.025  
5y6p_R5 Gaussian surface contour level 0.025  
5y6p_S5 Gaussian surface contour level 0.025  
5y6p_T5 Gaussian surface contour level 0.023  
5y6p_U5 Gaussian surface contour level 0.028  
5y6p_V5 Gaussian surface contour level 0.021  
5y6p_W5 Gaussian surface contour level 0.025  
5y6p_X5 Gaussian surface contour level 0.019  
5y6p_Y5 Gaussian surface contour level 0.020  
5y6p_Z5 Gaussian surface contour level 0.016  
5y6p_a5 Gaussian surface contour level 0.028  
5y6p_b5 Gaussian surface contour level 0.028  
5y6p_c5 Gaussian surface contour level 0.026  
5y6p_d5 Gaussian surface contour level 0.029  
5y6p_e5 Gaussian surface contour level 0.027  
5y6p_f5 Gaussian surface contour level 0.026  
5y6p_g5 Gaussian surface contour level 0.029  
5y6p_h5 Gaussian surface contour level 0.024  
5y6p_i5 Gaussian surface contour level 0.025  
5y6p_j5 Gaussian surface contour level 0.022  
5y6p_k5 Gaussian surface contour level 0.030  
5y6p_l5 Gaussian surface contour level 0.026  
5y6p_m5 Gaussian surface contour level 0.027  
5y6p_n5 Gaussian surface contour level 0.023  
5y6p_o5 Gaussian surface contour level 0.027  
5y6p_p5 Gaussian surface contour level 0.019  
5y6p_q5 Gaussian surface contour level 0.027  
5y6p_r5 Gaussian surface contour level 0.022  
5y6p_s5 Gaussian surface contour level 0.024  
5y6p_t5 Gaussian surface contour level 0.025  
5y6p_u5 Gaussian surface contour level 0.028  
5y6p_v5 Gaussian surface contour level 0.021  
5y6p_w5 Gaussian surface contour level 0.025  
5y6p_x5 Gaussian surface contour level 0.021  
5y6p_y5 Gaussian surface contour level 0.025  
5y6p_z5 Gaussian surface contour level 0.019  
5y6p_f8 Gaussian surface contour level 0.023  
5y6p_g8 Gaussian surface contour level 0.020  
5y6p_h8 Gaussian surface contour level 0.022  
5y6p_i8 Gaussian surface contour level 0.024  
5y6p_j8 Gaussian surface contour level 0.024  
5y6p_k8 Gaussian surface contour level 0.019  
5y6p_l8 Gaussian surface contour level 0.028  
5y6p_m8 Gaussian surface contour level 0.022  
5y6p_A6 Gaussian surface contour level 0.026  
5y6p_B6 Gaussian surface contour level 0.022  
5y6p_C6 Gaussian surface contour level 0.026  
5y6p_D6 Gaussian surface contour level 0.022  
5y6p_E6 Gaussian surface contour level 0.026  
5y6p_F6 Gaussian surface contour level 0.019  
5y6p_G6 Gaussian surface contour level 0.022  
5y6p_H6 Gaussian surface contour level 0.023  
5y6p_I6 Gaussian surface contour level 0.027  
5y6p_J6 Gaussian surface contour level 0.021  
5y6p_K6 Gaussian surface contour level 0.024  
5y6p_L6 Gaussian surface contour level 0.023  
5y6p_M6 Gaussian surface contour level 0.023  
5y6p_N6 Gaussian surface contour level 0.025  
5y6p_O6 Gaussian surface contour level 0.025  
5y6p_P6 Gaussian surface contour level 0.022  
5y6p_Q6 Gaussian surface contour level 0.025  
5y6p_R6 Gaussian surface contour level 0.019  
5y6p_S6 Gaussian surface contour level 0.028  
5y6p_T6 Gaussian surface contour level 0.027  
5y6p_U6 Gaussian surface contour level 0.028  
5y6p_V6 Gaussian surface contour level 0.020  
5y6p_W6 Gaussian surface contour level 0.027  
5y6p_X6 Gaussian surface contour level 0.020  
5y6p_Y6 Gaussian surface contour level 0.027  
5y6p_Z6 Gaussian surface contour level 0.020  
5y6p_a6 Gaussian surface contour level 0.022  
5y6p_b6 Gaussian surface contour level 0.019  
5y6p_c6 Gaussian surface contour level 0.023  
5y6p_d6 Gaussian surface contour level 0.023  
5y6p_e6 Gaussian surface contour level 0.023  
5y6p_f6 Gaussian surface contour level 0.028  
5y6p_g6 Gaussian surface contour level 0.029  
5y6p_h6 Gaussian surface contour level 0.021  
5y6p_i6 Gaussian surface contour level 0.023  
5y6p_j6 Gaussian surface contour level 0.027  
5y6p_k6 Gaussian surface contour level 0.020  
5y6p_l6 Gaussian surface contour level 0.022  
5y6p_m6 Gaussian surface contour level 0.025  
5y6p_n6 Gaussian surface contour level 0.026  
5y6p_o6 Gaussian surface contour level 0.028  
5y6p_p6 Gaussian surface contour level 0.019  
5y6p_q6 Gaussian surface contour level 0.025  
5y6p_r6 Gaussian surface contour level 0.021  
5y6p_s6 Gaussian surface contour level 0.025  
5y6p_t6 Gaussian surface contour level 0.023  
5y6p_u6 Gaussian surface contour level 0.029  
5y6p_v6 Gaussian surface contour level 0.020  
5y6p_w6 Gaussian surface contour level 0.020  
5y6p_x6 Gaussian surface contour level 0.020  
5y6p_y6 Gaussian surface contour level 0.022  
5y6p_z6 Gaussian surface contour level 0.020  
5y6p_n8 Gaussian surface contour level 0.019  
5y6p_o8 Gaussian surface contour level 0.023  
5y6p_p8 Gaussian surface contour level 0.022  
5y6p_q8 Gaussian surface contour level 0.025  
5y6p_r8 Gaussian surface contour level 0.027  
5y6p_s8 Gaussian surface contour level 0.025  
5y6p_t8 Gaussian surface contour level 0.024  
5y6p_u8 Gaussian surface contour level 0.024  
5y6p_A7 Gaussian surface contour level 0.028  
5y6p_B7 Gaussian surface contour level 0.020  
5y6p_C7 Gaussian surface contour level 0.029  
5y6p_D7 Gaussian surface contour level 0.022  
5y6p_E7 Gaussian surface contour level 0.027  
5y6p_F7 Gaussian surface contour level 0.024  
5y6p_G7 Gaussian surface contour level 0.025  
5y6p_H7 Gaussian surface contour level 0.019  
5y6p_I7 Gaussian surface contour level 0.025  
5y6p_J7 Gaussian surface contour level 0.020  
5y6p_K7 Gaussian surface contour level 0.026  
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5y6p_hW Gaussian surface contour level 0.024  
5y6p_hX Gaussian surface contour level 0.024  
5y6p_hY Gaussian surface contour level 0.015  
5y6p_hZ Gaussian surface contour level 0.015  
5y6p_iA Gaussian surface contour level 0.027  
5y6p_iB Gaussian surface contour level 0.025  
5y6p_iC Gaussian surface contour level 0.021  
5y6p_iD Gaussian surface contour level 0.021  
5y6p_iE Gaussian surface contour level 0.026  
5y6p_iF Gaussian surface contour level 0.030  
5y6p_iG Gaussian surface contour level 0.022  
5y6p_iH Gaussian surface contour level 0.024  
5y6p_jI Gaussian surface contour level 0.029  
5y6p_jJ Gaussian surface contour level 0.023  
5y6p_jK Gaussian surface contour level 0.029  
5y6p_jL Gaussian surface contour level 0.027  
5y6p_jM Gaussian surface contour level 0.030  
5y6p_jN Gaussian surface contour level 0.030  
5y6p_jO Gaussian surface contour level 0.030  
5y6p_jP Gaussian surface contour level 0.030  
5y6p_kQ Gaussian surface contour level 0.028  
5y6p_kR Gaussian surface contour level 0.027  
5y6p_kS Gaussian surface contour level 0.021  
5y6p_kT Gaussian surface contour level 0.030  
5y6p_kU Gaussian surface contour level 0.032  
5y6p_kV Gaussian surface contour level 0.032  
5y6p_kW Gaussian surface contour level 0.021  
5y6p_kX Gaussian surface contour level 0.022  
5y6p_ka Gaussian surface contour level 0.024  
5y6p_kb Gaussian surface contour level 0.024  
command time 153.1 seconds  
draw time 1.274 seconds  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 32 days 21:56

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.3
    ChimeraX-AtomicLibrary: 1.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202010140223
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.2
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.2
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    Send2Trash: 1.5.0
    SEQCROW: 0.18
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Tom Goddard]

Eric ran into this when converting an NIH 3D Print Exchange script.

[Tom Goddard]

Fixed.

Now "surf #1 res 20 grid 7" takes 7.5 seconds instead of 153. Problem was that surface code extracted each of the 682 chains from the full set of structure atoms with a filter operation done by numpy that is pretty slow, taking 130 seconds. I optimized it so it doesn't do that if a whole structure is being surfaced. Then another 15 seconds was being taken by Atoms.by_chain again done by numpy. I moved that to C++ so it now takes 0.2 seconds.

[Tom Goddard]

I improved Gaussian surface parallel calculation (ticket #3910) so "surf #1 res 20 grid 7" now takes 5 seconds on 5y6p and finer surfaces "surf #1 res 20" (which uses grid spacing 2) takes 23 seconds, formerly 130 seconds, using 8 threads.