Re: [PyMOL] partially transparent structure

[DeLano S. <de...@de...>]

Janet,

Unforutnately not.  At present, cartoon_transparency must be uniform over
the entire cartoon representation.  You can split the cartoon into multiple
objects to obtain differential transparency, but as you correctly point out,
that will cause a break or gap in the cartoon.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of ko...@ge...
> Sent: Wednesday, February 13, 2008 9:38 AM
> To: pym...@li...
> Subject: [PyMOL] partially transparent structure
> 
> I would like to display a protein structure in the following way:
> 
> The first domain of the structure in red cartoons The second 
> domain of the structure in gray TRANSPARENT cartoons
> 
> I tried splitting the structure into two objects but because 
> the transition from the first domain to the second one is 
> inside the secondary structure element the element looks 
> broken after the split.
> 
> Is there any smart way of drawing partially transparent 
> structures in pymol?
> 
> Thank you in advance for your help,
> Janek Kosinski
> 
> 
> :.
> 
> 
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