Re: [PyMOL] How to make protein blur but keep ligand clear?

[Thomas H. <tho...@sc...>]

Hi Arthur,

The origin of rotation will become the focal point. So all you have to do is:

PyMOL> origin resn DUD

The blur will look better if you increase the sample size, e.g. samples=20.

Cheers,
  Thomas


> On May 15, 2019, at 9:50 AM, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Dear all,
> 
> I have a protein-ligand complex and I wish to make the protein looks blur but keep the ligand clear and sharp with pymol. I find a "focalblur" script (https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do this. However I can get the fancy effect illustrated in the examples of the wiki for this script. With the follow command:
> 
> FocalBlur aperture=2,samples=10,ray=1,width=1000,height=1000
> 
> 
> I just make the ligand rather the the protein become blur (Please see the image at https://drive.google.com/open?id=1qzXDLzVyxI85sJ8H6Zhv8pd8Cq7rA18U, and the pse file used to make this image is availabe at https://drive.google.com/open?id=1Gjrl5ePifadWEK8-AZYVXY7yX07kOLF7).
> 
> Could anyone help with this？ What does the argument "aperture" do? How to control which part become blur?   Is there better way to make the ligand blur?
> 
> Thank you very much!
> 
> Arthur
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.