Re: [PyMOL] PyMOL-users Digest, Vol 150, Issue 13

> 
> Today's Topics:
> 
>   1. how to make selected residues blurry? (sunyeping)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 30 Nov 2018 12:14:21 +0800
> From: "sunyeping" <sun...@al...>
> To: "pymol-users" <pym...@li...>
> Subject: [PyMOL] how to make selected residues blurry?
> Message-ID:
> 	<87e...@al...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear all,
> 
> Could you please check this figure at the following link?
> https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing
> 
> The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 
> 
> I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
>    set transparency, 0.8, sele
> but it doesn't work.
> 
> Could anyone help me figure it out? With sincere thanks.
> 
> Arthur

The residues that are farther back from the viewer are increasingly transparent. 
The effect is called depth cueing, basically causing  the residues farther back to appear to get  lost in the fog. 

set depth_cue, 1  # turn on depth cueing
 
will switch the effect on. The front and back clipping planes  define  the range, although you can keep more of the front unfogged 
by additionally adjusting the  fog_start value

see https://pymolwiki.org/index.php/Depth_cue

Annemarie

____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12