id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3001	Session save slow with molecular surfaces	goddard@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-03-31)
Description
Saving a session with a molecular surface is incredibly slow, 52 seconds for a 60,000 atom structure.  Without the molecular surface it takes 1 second.  Session file size is 160 Mbytes with surface, 1.5 Mbytes without surface.

Log:
UCSF ChimeraX version: 0.93 (2020-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1aon format mmCIF fromDatabase pdb

1aon title:  
Crystal structure of the asymmetric chaperonin complex groel/groes/(adp)7
[more info...]  
  
Chain information for 1aon #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | GROEL  
O P Q R S T U | groel/groes complex  
  
Non-standard residues in 1aon #1  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
  
  
Change tracker changes 4.410743713378906e-05  
atomic get changes 0.0010480880737304688  
atomic clear changes 1.71661376953125e-05  
atomic check changes 0.0023050308227539062  

> surface

> hide atoms

Change tracker changes 0.011063098907470703  
atomic get changes 0.01232004165649414  
atomic clear changes 0.010286092758178711  
atomic check changes 0.02386307716369629  

> time save test.cxs

> save test.cxs

command time 52.76 seconds  
draw time 0.03965 seconds  

> surface close

> show atoms

Change tracker changes 0.011584043502807617  
atomic get changes 0.013190031051635742  
atomic clear changes 0.01009678840637207  
atomic check changes 0.027158021926879883  

> time save test2.cxs

> save test2.cxs

command time 1.157 seconds  

> select

58870 atoms, 59290 bonds, 27 pseudobonds, 2 models selected  
Change tracker changes 0.024118900299072266  
atomic get changes 0.025615930557250977  
atomic clear changes 0.022425174713134766  
atomic check changes 0.0494842529296875  
draw time 33.74 seconds  




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	enhancement	closed	normal		Sessions		fixed						all	ChimeraX