id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2832	Chain trace creation delayed in scripts	goddard@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-05)
Description
Loading the attached script does not hide the one chain trace pseudobond as expected.  But running the commands individually does hide it.  The trouble is that the chain trace is not created until the graphics is updated.  That happens during the view command (to determine scene bounds is does a graphics update, ribbon bounds are not correct without this), and at the end of the script.


Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-02-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/thr.cxc

> open 3gws

3gws title:  
Crystal Structure of T3-Bound Thyroid Hormone Receptor [more info...]  
  
Chain information for 3gws #1  
---  
Chain | Description  
X | Thyroid hormone receptor β  
  
Non-standard residues in 3gws #1  
---  
T3 — 3,5,3'triiodothyronine (T3; thyroid hormone; liothyronine)  
  
  

> hide solvent

> label :331,346,282,t3

> hide cartoons

> hide @n,c,o

> style @ca ball

Changed 246 atom styles  

> hide pseudobonds

> set bgColor white

> graphics silhouettes true

> view

> color ligand & C green

> swapaa interactive :331 his

> swapaa interactive :346 arg

> transparency #1.4,1.5 50 target a

> size #1.4,1.5 stickRadius .1

Changed 8 bond radii  
executed thr.cxc  

> color #1.3 red

> usage style

style [objects] [atomStyle] [dashes an integer] [ringFill ringFill]  
— change atom and bond depiction  
objects: an objects specifier or nothing  
atomStyle: one of ball, sphere, or stick or nothing  
ringFill: one of off, on, thick, or thin  

> usage show

show [objects] [what] [target object type]  
— show specified objects  
objects: an objects specifier or nothing  
what: a collection of one of atoms, bonds, cartoons, models, pbonds,
pseudobonds, ribbons, or surfaces  

> usage color

color [objects] [color [what]] [target characters from 'abcfprs']
[transparency a number] [halfbond true or false]  
— color objects  
objects: an objects specifier or nothing  
color: a color or one of byatom, bychain, byelement, byhetero, bymodel,
bynucleotide, bypolymer, fromatoms, or random  
what: a collection of one of All, atoms, bonds, cartoons, labels, pseudobonds,
ribbons, rings, or surfaces  
Subcommands are:

  * color bfactor
  * color byattribute
  * color cylindrical
  * color delete
  * color electrostatic
  * color gradient
  * color height
  * color list
  * color modify
  * color name
  * color radial
  * color sample
  * color sequential
  * color show
  * color zone

  

> color #1.3 red halfbond false




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: thr.cxc

}}}

[attachment:""thr.cxc""]
"	defect	assigned	normal		Structure Analysis				Elaine Meng Eric Pettersen				all	ChimeraX