id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3075	Slow coloring of large molecular surfaces	goddard@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-16)
Description
Coloring large molecular surfaces by atom is extremely slow.  For ecample 6owg (180,000 atoms) takes less than 0.1 second to color atoms bypolymer but 30 seconds to color surfaces bypolymer.

The problem is that there are 240 chain surfaces in this example and it is making a C++ set of all atoms about 480 times for inclusion testing.


Log:
UCSF ChimeraX version: 0.94.dev202004160103 (2020-04-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6owg format mmCIF fromDatabase pdb

6owg title:  
Structure of a synthetic beta-carboxysome shell, T=4 [more info...]  
  
Chain information for 6owg #1  
---  
Chain | Description  
0 2 3 4 6 7 8 A A0 A1 A2 A4 A5 A6 A8 A9 AA AC AD AE AG AH AI AK AL AM AO AP AQ
AS AT AU AW AX AY B B0 B1 B2 B4 B5 B6 B8 B9 BA BC BD BE BG BH BI BK BL BM BO
BP BQ BS BT BU BW BX BY C C0 C1 C2 C4 C5 C6 C8 C9 CA CC CD CE CG CH CI CK CL
CM CO CP CQ CS CT CU CW CX CY D0 D1 D2 D4 D5 D6 D8 D9 DA DC DD DE DG DH DI DK
DL DM DO DP DQ DS DT DU DW DX DY E E0 E1 E2 E4 E5 E6 EA EC ED EE EG EH EI EK
EL EM EO EP EQ ES ET EU EW EX EY F G I J K M N O Q R S U V W Y Z a b c e f g i
j k m n o q r s u v w y z | Microcompartments protein  
1 5 9 A3 A7 AB AF AJ AN AR AV AZ B3 B7 BB BF BJ BN BR BV BZ C3 C7 CB CF CJ CN
CR CV CZ D D3 D7 DB DF DJ DN DR DV DZ E3 E7 EB EF EJ EN ER EV EZ H L P T X d h
l p t x | Ethanolamine utilization protein EutN/carboxysome structural protein
Ccml  
  
  

> surface

> time color bypolymer surface

> color bypolymer surfaces

color surf 1 8.13290524482727  
color surf 5 0.8555378913879395  
color surf 6 20.800276041030884  
color surf 3 21.676551342010498  
command time 29.83 seconds  
draw time 0.765 seconds  

> select all

178080 atoms, 180300 bonds, 1 model selected  

> time color tan atoms

> color tan atoms

command time 0.04302 seconds  
draw time 0.07911 seconds  

> time color bypolymer atoms

> color bypolymer atoms

command time 0.04849 seconds  
draw time 0.07511 seconds  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	enhancement	closed	normal		Surface		fixed						all	ChimeraX